Wellcome Sanger Institute

 

2025

  • Genomics Define Malignant Transformation in Myeloma Precursor Conditions.

    Maura F, Bergsagel PL, Ziccheddu B, Kumar S, Maclachlan K, Derkach A, Garces JJ, Firestone R, Braggio E, Asmann Y et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2025;JCO2501733

    PUBMED: 41061199; DOI: 10.1200/JCO-25-01733

  • Hotspots of human mutation point to clonal expansions in spermatogonia.

    Seplyarskiy V, Moldovan MA, Koch E, Kar P, Neville MDC, Rahbari R and Sunyaev S

    Nature 2025

    PUBMED: 41062699; DOI: 10.1038/s41586-025-09579-7

  • Somatic mutation and selection at population scale.

    Lawson ARJ, Abascal F, Nicola PA, Lensing SV, Roberts AL, Kalantzis G, Baez-Ortega A, Brzozowska N, El-Sayed Moustafa JS, Vaitkute D et al.

    Nature 2025

    PUBMED: 41062696; DOI: 10.1038/s41586-025-09584-w

  • Sperm sequencing reveals extensive positive selection in the male germline.

    Neville MDC, Lawson ARJ, Sanghvi R, Abascal F, Pham MH, Cagan A, Nicola PA, Bayzetinova T, Baez-Ortega A, Roberts K et al.

    Nature 2025

    PUBMED: 41062690; DOI: 10.1038/s41586-025-09448-3

  • Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.

    Sibale LL, Lo SW, Kalata N, Nyazika TK, Mitole N, Dyster V, Kusakala A, Khwiya M, Sagawa G, Phiri JA et al.

    Nature communications 2025;16;1;8920

    PUBMED: 41057336; PMC: 12504720; DOI: 10.1038/s41467-025-63974-2

  • The Hippo terminal effector YAP boosts enterovirus replication in type 1 diabetes.

    Geravandi S, Liu H, Pahwa H, Madduri MK, Atawneh F, Miraki Feriz A, Rafizadeh S, Kruf AE, Khazaei M, Bahrami P et al.

    Nature communications 2025;16;1;8882

    PUBMED: 41053097; PMC: 12500894; DOI: 10.1038/s41467-025-64508-6

  • Mondo: Integrating Disease Terminology Across Communities.

    Vasilevsky NA, Toro S, Matentzoglu N, Flack JE, Mullen KR, Hegde H, Gehrke S, Whetzel PL, Shwetar Y, Harris NL et al.

    Genetics 2025

    PUBMED: 41052288; DOI: 10.1093/genetics/iyaf215

  • Prevalence and impact of SARS-CoV-2, influenza, respiratory syncytial virus (RSV) infection and respiratory illness on UK healthcare workers during winter 2023/24 (September 2023 to March 2024): SIREN cohort study.

    Foulkes S, Munro K, Sparkes D, Khawam J, Russell S, Dunne A, Timeyin J, Hettiarachchi N, Cairns M, Bradley DT et al.

    The Journal of infection 2025;91;4;106620

    PUBMED: 41045989; DOI: 10.1016/j.jinf.2025.106620

  • Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.

    Glendening AM, Stephens C, Vuruputoor VS, Chaganti T, Myles MN, Stern DL, Abdelalim M, Juang YP, Hogenhout SA, Mathers TC et al.

    G3 (Bethesda, Md.) 2025

    PUBMED: 41042102; DOI: 10.1093/g3journal/jkaf232

  • Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.

    Potapova TA, Kostos P, McKinney S, Borchers M, Haug J, Guarracino A, Solar SJ, Mattingly M, Anez GM, de Lima LG et al.

    Cell genomics 2025;101031

    PUBMED: 41043432; DOI: 10.1016/j.xgen.2025.101031

  • Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus.

    Freimann K, Brümmer A, Warmerdam R, Rupall TS, Hernández-Ledesma AL, Chiou J, Holzinger ER, Maranville JC, Nakic N, Ongen H et al.

    Nature communications 2025;16;1;8795

    PUBMED: 41038828; DOI: 10.1038/s41467-025-63856-7

  • Understanding the global rise of artemisinin resistance: Insights from over 100,000 Plasmodium falciparum samples.

    Balmer AJ, White NFD, Ünlü ES, Lee C, Pearson RD, Almagro-Garcia J and Ariani C

    eLife 2025;14

    PUBMED: 41037007; DOI: 10.7554/eLife.105544

  • Ghosts of symbionts past: The hidden history of the dynamic association between filarial nematodes and their Wolbachia endosymbionts.

    Vancaester E, Oldrieve GR, Reid A, Koutsovoulos G, Laetsch DR, Makepeace BL, Tanya V, Poppert S, Krücken J, Wolstenholme A and Blaxter M

    G3 (Bethesda, Md.) 2025

    PUBMED: 41030195; DOI: 10.1093/g3journal/jkaf226

  • Polygenic and developmental profiles of autism differ by age at diagnosis.

    Zhang X, Grove J, Gu Y, Buus CK, Nielsen LK, Neufeld SAS, Koko M, Malawsky DS, Wade EM, Verhoef E et al.

    Nature 2025

    PUBMED: 41034588; DOI: 10.1038/s41586-025-09542-6

  • Scaling DNA synthesis with a microchip-based massively parallel synthesis system.

    Zhang X, Jiang X, Wang Y, Chen Q, Jiang H, Zhang H, Beltran A, Yang W, Chen T, Liang C et al.

    Nature biotechnology 2025

    PUBMED: 41034496; DOI: 10.1038/s41587-025-02844-0

  • Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.

    Bogan SN, Surendran N, Hotaling S, Desvignes T, Bista I, Lins LSF, Eilertsen MH, Le François NR, Algayer T, Hamilton SL et al.

    Molecular biology and evolution 2025;42;10

    PUBMED: 41065271; DOI: 10.1093/molbev/msaf219

  • Toward Ethical Provenance Tracking: The GA4GH Model Data Access Agreement (DAA).

    Bernier A, Knoppers BM, Lawson J, McDougall R, Raven-Adams M and Rahimzadeh V

    Genetics in medicine : official journal of the American College of Medical Genetics 2025;101594

    PUBMED: 41046474; DOI: 10.1016/j.gim.2025.101594

  • A consensus blood transcriptomic framework for sepsis.

    Scicluna BP, Cano-Gamez K, Burnham KL, Davenport EE, Moore AR, Khan S, Hinds CJ, Cremer OL, Khatri P, Sweeney TE et al.

    Nature medicine 2025

    PUBMED: 41028542; DOI: 10.1038/s41591-025-03964-5

  • Systematic review and mega-analysis of the peripheral blood transcriptome in depression implicates dysregulation of lymphoid cells and histones.

    Erady C, Bethlehem R, Bullmore E and Lynall ME

    Biological psychiatry 2025

    PUBMED: 41033620; DOI: 10.1016/j.biopsych.2025.09.008

  • Transcriptomic and epigenetic mechanisms controlling cholangiocytes transdifferentiation into hepatocytes.

    Galanakis V, Gribben C, Munteanu A, Cagna M, Roos FJM, Bulgaru C, Ciortuz L, Allison M, Mohorianu I and Vallier L

    Journal of hepatology 2025

    PUBMED: 41033615; DOI: 10.1016/j.jhep.2025.09.021

  • The genome sequence of the Anthracite Bee-fly, Anthrax anthrax (Schrank, 1781).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;306

    PUBMED: 41050511; PMC: 12489455; DOI: 10.12688/wellcomeopenres.24305.2

  • The genome sequence of the Common Buzzard, Buteo buteo (Linnaeus, 1758).

    Blows E, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;130

    PUBMED: 41036236; PMC: 12481152; DOI: 10.12688/wellcomeopenres.23873.2

  • Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance.

    Cazares A, Figueroa W, Cazares D, Lima L, Turnbull JD, McGregor H, Dicks J, Alexander S, Iqbal Z and Thomson NR

    Science (New York, N.Y.) 2025;eadr1522

    PUBMED: 40997220; DOI: 10.1126/science.adr1522

  • The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution.

    Sebé-Pedrós A, Tanay A, Lawniczak MKN, Arendt D, Aerts S, Archibald J, Arnone MI, Blaxter M, Cleves P, Coelho SM et al.

    Nature 2025;645;8082;877-885

    PUBMED: 40993253; DOI: 10.1038/s41586-025-09312-4

  • GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project.

    Hung HCH, Kumar N, Dyster V, Yeats C, Metcalf B, Li Y, Hawkins PA, McGee L, Bentley SD and Lo SW

    Nature communications 2025;16;1;8345

    PUBMED: 40993121; PMC: 12460886; DOI: 10.1038/s41467-025-64018-5

  • A TGF-βR/IL-2R immunomodulatory fusion protein transforms immunosuppression into T cell activation to enhance adoptive T cell therapy.

    Su Y, Thelen A, Wirth LV, Jenkins CM, Mak SR, Chen DG, Gottardo R and Greenberg PD

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;39;e2516951122

    PUBMED: 40986340; DOI: 10.1073/pnas.2516951122

  • A small molecule stabilizer rescues the surface expression of nearly all missense variants in a GPCR.

    Mighell TL and Lehner B

    Nature structural & molecular biology 2025

    PUBMED: 40983772; DOI: 10.1038/s41594-025-01659-6

  • Zoonotic threats hidden in wildlife.

    King AC and Mellor KC

    Nature reviews. Microbiology 2025

    PUBMED: 40983728; DOI: 10.1038/s41579-025-01239-x

  • Protocol for pooled FACS-based CRISPR knockout screening in human iPSC-derived microglia.

    Washer SJ, Navarro-Guerrero E, Cowley SA, Ebner DV and Bassett AR

    STAR protocols 2025;6;4;104111

    PUBMED: 40975871; DOI: 10.1016/j.xpro.2025.104111

  • A compendium of synthetic lethal gene pairs defined by extensive combinatorial pan-cancer CRISPR screening.

    Harle V, Offord V, Gökbağ B, Fotopoulos L, Williams T, Alexander D, Mehta I, Thompson NA, Olvera-León R, Peidli S et al.

    Genome biology 2025;26;1;284

    PUBMED: 40968372; PMC: 12445041; DOI: 10.1186/s13059-025-03737-w

  • The genome sequence of the Treble Lines, Charanyca trigrammica (Hufnagel, 1766) (Lepidoptera: Noctuidae).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Acquisition Lab, Darwin Tree of Life Barcoding Collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;520

    PUBMED: 41063755; PMC: 12501593; DOI: 10.12688/wellcomeopenres.24867.1

  • Genomic diversity of the African malaria vector Anopheles funestus.

    Boddé M, Nwezeobi J, Korlević P, Makunin A, Akone-Ella O, Barasa S, Gadji M, Hart L, Kaindoa EW, Love K et al.

    Science (New York, N.Y.) 2025;389;6766;eadu3596

    PUBMED: 40966334; DOI: 10.1126/science.adu3596

  • Protocol for a human placental explant model to study acute responses to pathogens.

    Ruiz-Morales ER, Hoo R, Waller RF, Lee MCS, Fernandez-Antoran D, Kelava I and Vento-Tormo R

    STAR protocols 2025;6;4;104097

    PUBMED: 40966089; DOI: 10.1016/j.xpro.2025.104097

  • Prevalence of resistance markers of artemisinin, partner drugs, and sulfadoxine-pyrimethamine in Nanyumbu and Masasi Districts, Tanzania between 2020 and 2021.

    Mwaiswelo RO, Mmbando BP, Chacky F, Molteni F, Mohamed A, Lazaro S, Samuel B, Ariani CV, Gonçalves S, Drury E and Ngasala B

    Antimicrobial agents and chemotherapy 2025;e0175124

    PUBMED: 40938322; DOI: 10.1128/aac.01751-24

  • Effect of CVA21, an Oncolytic Virus, in combination with Pembrolizumab on immunogenicity and the tumour microenvironment in advanced NSCLC: a phase I/II trial.

    Balasubramanian A, Marceaux C, Kanwal S, Tarasova I, Batey D, Senko C, Asadi K, Yokote K, Palmer J, Christie M et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2025

    PUBMED: 40932352; DOI: 10.1158/1078-0432.CCR-25-1449

  • Synthetic lethality in cancer drug discovery: challenges and opportunities.

    Gonçalves E, Ryan CJ and Adams DJ

    Nature reviews. Drug discovery 2025

    PUBMED: 40935881; DOI: 10.1038/s41573-025-01273-7

  • The genome sequence of the Leafhopper, Cicadella viridis (Linnaeus, 1758) (Hemiptera: Cicadellidae).

    Crowley LM, McCulloch J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding Collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;502

    PUBMED: 41040649; PMC: 12485336; DOI: 10.12688/wellcomeopenres.24866.1

  • Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly.

    Wright CJ, Absolon D, Gascoigne-Pees M, Vila R, Lawniczak MKN and Blaxter M

    Current biology : CB 2025

    PUBMED: 40934916; DOI: 10.1016/j.cub.2025.08.032

  • Genomic insights into a diarrheal outbreak in Bangladesh reveal novel ETEC lineages and expansion of CS23 colonization factor.

    Rahman SIA, Jubair M, Akhtar M, Akter A, Tauheed I, Begum YA, Bhattacharjee P, Afrad MH, Khanam F, Islam MT et al.

    Microbiology spectrum 2025;e0331524

    PUBMED: 40928300; DOI: 10.1128/spectrum.03315-24

  • Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi.

    Rigby J, Wilson CN, Zuza A, Diness Y, Mkwanda C, Tonthola K, Kanjerwa O, Salifu C, Pearse O, Msefula C et al.

    PLoS neglected tropical diseases 2025;19;9;e0012413

    PUBMED: 40924746; DOI: 10.1371/journal.pntd.0012413

  • The genome sequence of the Orange Beauty, Commophila aeneana (Hübner, 1799-1800) (Lepidoptera: Tortricidae).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding Collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;489

    PUBMED: 41063756; PMC: 12501591; DOI: 10.12688/wellcomeopenres.24865.1

  • Changes in carriage and serotype diversity of Streptococcus pneumoniae and other respiratory pathobionts in the UK between pre-PCV13 (2006-10), early-PCV13 (2010-12) and late-PCV13 (2012-23) periods.

    Cleary DW, Anderson R, Jones J, Gladstone RA, Osman KL, Devine VT, Morris DE, Lister AJJ, Gomer S, Hocknell RE et al.

    Pneumonia (Nathan Qld.) 2025;17;1;20

    PUBMED: 40908474; DOI: 10.1186/s41479-025-00174-y

  • Mass azithromycin distributions: balancing childhood mortality and antimicrobial resistance - Authors' reply.

    Kalizang'oma A, Chaguza C, French N and Heyderman RS

    The Lancet. Infectious diseases 2025

    PUBMED: 40921173; DOI: 10.1016/S1473-3099(25)00532-8

  • The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life

    Blaxter M,, Lewin HA,, DiPalma F,, Challis R,, da Silva M,, Durbin R,, Formenti G,, Franz N,, Guigo R,, Harrison PW, et al.

    Frontiers in Science 2025;3;1514835

    DOI: 10.3389/fsci.2025.1514835; URL: https://doi.org/10.3389/fsci.2025.1514835

  • Cell fate specification modes shape transcriptome evolution in the highly conserved spiral cleavage.

    Liang Y, Wei J, Kang Y, Carrillo-Baltodano AM and Martín-Durán JM

    EMBO reports 2025

    PUBMED: 40908303; DOI: 10.1038/s44319-025-00569-4

  • Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data.

    Sozzoni M, Balacco J, Bellavita M, Brüniche-Olsen A, Formenti G, Jain N, Koo B, Mountcastle J, Palmada-Flores M, Trifonov V et al.

    Molecular ecology resources 2025;e70040

    PUBMED: 40905325; DOI: 10.1111/1755-0998.70040

  • Lumbar MRI and Back Pain After Failed Conservative Treatment: The RuDDS Study.

    Leonova O, Elgaeva E, Berdnikova A, Tsepilov Y and Krutko A

    Global spine journal 2025;21925682251373046

    PUBMED: 40901806; PMC: 12408541; DOI: 10.1177/21925682251373046

  • Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.

    Rahmani S, Jafree DJ, Lee PD, Tafforeau P, Brunet J, Nandanwar S, Zhou Y, Jacob J, Bellier A, Ackermann M et al.

    Npj imaging 2025;3;1;39

    PUBMED: 40903539; PMC: 12408821; DOI: 10.1038/s44303-025-00090-2

  • Sensory neurons shape local macrophage identity via TGF-β signaling.

    Kolter J, Döring CL, Sarout S, Baasch S, Steele L, Alsumati R, Lucena Silva GV, Aníbal Silva CE, Paiva IM, Mansoori Moghadam Z et al.

    Immunity 2025

    PUBMED: 40914152; DOI: 10.1016/j.immuni.2025.08.004

  • Chromosome-level genome assembly of the Tyrrhenian tree frog (Hyla sarda).

    Paris JR, Bisconti R, Chiocchio A, Abueg L, Absolon DE, Tilley T, Jain N, Balacco J, O'Toole B, Jarvis ED et al.

    Scientific data 2025;12;1;1539

    PUBMED: 40897714; PMC: 12405506; DOI: 10.1038/s41597-025-05760-9

  • AmpliconTyper - a tool for analysing ONT multiplex PCR data from environmental and other complex samples.

    Spadar A, Mahindroo J, Troman C, Owusu M, Adu-Sarkodie Y, Owusu-Dabo E, Abraham D, Benny B, Govindan K, Mohan VR et al.

    Microbial genomics 2025;11;9

    PUBMED: 40928958; DOI: 10.1099/mgen.0.001421

  • Chronic social defeat stress induces meningeal neutrophilia via type I interferon signaling in male mice.

    Kigar SL, Lynall ME, DePuyt AE, Atkinson R, Sun VH, Samuels JD, Eassa NE, Poffenberger CN, Lehmann ML, Listwak SJ et al.

    Nature communications 2025;16;1;8153

    PUBMED: 40890098; PMC: 12402070; DOI: 10.1038/s41467-025-62840-5

  • Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022.

    Cheng HR, Kuo SC, Lai JF, Wu HC, Chen FJ, Sytwu HK, Lo SW, Bentley SD and Huang YC

    Microbial genomics 2025;11;9

    PUBMED: 40924938; DOI: 10.1099/mgen.0.001498

  • Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.

    Njoroge SM, Kulohoma BW, Falzon LC, Kamanu TK, Momanyi K, Muinde P, Murungi MK, Ogendo A, Ogola J, Wambua L et al.

    Microbial genomics 2025;11;9

    PUBMED: 40996892; DOI: 10.1099/mgen.0.001515

  • Identification of severity related mutation hotspots in SARS-CoV-2 using a density-based clustering approach.

    Youn S, Jeong D, Kwon H, Han E, Kim S and Jung I

    BioData mining 2025;18;1;61

    PUBMED: 40890768; PMC: 12400602; DOI: 10.1186/s13040-025-00476-3

  • Opportunities and considerations for using artificial intelligence in bioinformatics education.

    Piccolo SR, Nathan A, Brazas MD, Kandpal M, Miró-Herrans AT, Kleinschmit AJ, McClatchy S, Mutheiwana P, Nikolic D, Gallo LI et al.

    Bioinformatics advances 2025;5;1;vbaf169

    PUBMED: 40900913; PMC: 12401575; DOI: 10.1093/bioadv/vbaf169

  • Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review.

    Sunmonu GT, Lo SW, Sheppard AE and Ogunniyi AD

    Microbial genomics 2025;11;9

    PUBMED: 40924620; DOI: 10.1099/mgen.0.001497

  • Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing.

    Baeza-Centurión P, Miñana B, Faure AJ, Thompson M, Bonnal S, Quarantani G, Clarke J, Lehner B and Valcárcel J

    Nature communications 2025;16;1;8117

    PUBMED: 40885722; PMC: 12398528; DOI: 10.1038/s41467-025-62957-7

  • Malat1 regulates female Th2 cell cytokine expression through controlling early differentiation and response to IL-2.

    Gwynne M, West KA, van Dongen S, Kourtzelis I, Coverley D, Teichmann SA, James KR, Hewitson JP and Lagos D

    Journal of immunology (Baltimore, Md. : 1950) 2025

    PUBMED: 40865984; DOI: 10.1093/jimmun/vkaf177

  • Telomere attrition becomes an instrument for clonal selection in aging hematopoiesis and leukemogenesis.

    McLoughlin MA, Cheloor Kovilakam S, Dunn WG, Gu M, Tobin J, Pershad Y, Williams N, Leongamornlert D, Dawson K, Bond L et al.

    Nature genetics 2025

    PUBMED: 40877435; DOI: 10.1038/s41588-025-02296-x

  • Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.

    Panousis NI, El Garwany O, Knights A, Rop JC, Kumasaka N, Imaz M, Boquete Vilarino L, Tsingene A, Tokolyi A, Barnett A et al.

    Nature communications 2025;16;1;7204

    PUBMED: 40866338; PMC: 12391345; DOI: 10.1038/s41467-025-61670-9

  • Naturally acquired promoter variation influences Streptococcus pneumoniae infection outcomes.

    Barton TE, Green AE, Mellor KC, McKnight AE, Bacher K, Kumar S, Newbold K, Lorenz O, Pohler E, Monshi MS et al.

    Cell host & microbe 2025

    PUBMED: 40902603; DOI: 10.1016/j.chom.2025.08.005

  • Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk.

    El Garwany O, Panousis NI, Knights A, Kumasaka N, Imaz M, Vilarino LB, Tsingene A, Tokolyi A, Martin CC, Alegbe T et al.

    Nature communications 2025;16;1;7205

    PUBMED: 40866368; PMC: 12391537; DOI: 10.1038/s41467-025-61669-2

  • Characterization of the OMP biogenesis machinery in Fusobacterium nucleatum.

    Cottom CO, Heinz E, Erramilli S, Kossiakoff A, Slade DJ and Noinaj N

    Structure (London, England : 1993) 2025

    PUBMED: 40897170; DOI: 10.1016/j.str.2025.08.008

  • Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr.

    Kurta K, Fedi MO, Baker K, Barker T, Catchpole L, Ciofi C, Cocco A, Collins J, Diedericks G, Diroma MA et al.

    Molecular ecology 2025;e70085

    PUBMED: 40856096; DOI: 10.1111/mec.70085

  • G-quadruplexes as a source of vulnerability in BRCA2-deficient granule cell progenitors and medulloblastoma.

    Keahi DL, Sanders MA, Paul MR, Webster ALH, Fang Y, Wiley TF, Shalaby S, Carroll TS, Chandrasekharappa SC, Sandoval-Garcia C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;35;e2503872122

    PUBMED: 40854122; DOI: 10.1073/pnas.2503872122

  • POT1 genetic testing in melanoma-prone families in Sweden: germline variant prevalence and tumor spectrum in identified carriers.

    Papadakis K, Portelli F, Schultz K, Olsson Sterky H, Vassilaki I, Lapins J, Sargen MR, Obolenski S, Adams DJ, Yang M et al.

    Acta oncologica (Stockholm, Sweden) 2025;64;1102-1108

    PUBMED: 40851494; DOI: 10.2340/1651-226X.2025.44048

  • Red Queen dynamics shape host immunogenetic diversity.

    Huang W

    Nature ecology & evolution 2025

    PUBMED: 40855226; DOI: 10.1038/s41559-025-02841-1

  • The genome sequence of the Nickerl's Fritillary, Melitaea aurelia Nickerl, 1850 (Lepidoptera: Nymphalidae).

    Chittaro Y, Sanchez A, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;459

    PUBMED: 41050512; PMC: 12495394; DOI: 10.12688/wellcomeopenres.24749.1

  • The genome sequence of the Oak Polypore, Buglossoporus quercinus (Schrad.) Kotl. & Pouzar.

    Wright R, Woof K, Gaya E, Royal Botanic Gardens Kew Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;456

    PUBMED: 41058758; PMC: 12498085; DOI: 10.12688/wellcomeopenres.24714.1

  • Genomic epidemiology of enteropathogenic Escherichia coli in southwestern Nigeria.

    Akinlabi OC, Dada RA, Olayinka AA, Oginni-Falajiki IO, Bejide OS, Adewole PD, Thomson NR, Aboderin AO and Okeke IN

    PLoS neglected tropical diseases 2025;19;8;e0013442

    PUBMED: 40845059; DOI: 10.1371/journal.pntd.0013442

  • Leveraging sequences missing from the human genome to diagnose cancer.

    Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Chan CSY, Patsakis M, Nayak A, Bradley R, Mahajan M, Sims J, Cintron DL et al.

    Communications medicine 2025;5;1;363

    PUBMED: 40841759; DOI: 10.1038/s43856-025-01067-3

  • TCF1 and LEF1 promote B-1a cell homeostasis and regulatory function.

    Shen Q, Wang H, Roco JA, Meng X, Bosticardo M, Hodges M, Battaglia M, Feng ZP, Talks BJ, Powell J et al.

    Nature 2025

    PUBMED: 40836098; DOI: 10.1038/s41586-025-09421-0

  • A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells.

    Jones MJK, Rai SK, Pfuderer PL, Bonfim-Melo A, Pagan JK, Clarke PR, Totañes FIG, Merrick CJ, McClelland SE and Boemo MA

    Nature communications 2025;16;1;7732

    PUBMED: 40830365; PMC: 12365011; DOI: 10.1038/s41467-025-63168-w

  • Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades.

    Picao-Osorio J, Bouleau C, Gonzalez de la Rosa PM, Stevens L, Fekonja N, Blaxter M, Braendle C and Félix MA

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;34;e2507529122

    PUBMED: 40828025; DOI: 10.1073/pnas.2507529122

  • Rapid divergence of visual systems and signalling traits to contrasting light regimes during early speciation of African crater lake cichlid fish.

    Carruthers M, Carleton KL, Linderoth T, Bridle J, Hudson AG, Malinsky M, Andrew M, Ngatunga BP, Saxon AD, Shechonge AH et al.

    Molecular biology and evolution 2025

    PUBMED: 40828888; DOI: 10.1093/molbev/msaf204

  • NANOG is repurposed after implantation to repress Sox2 and begin pluripotency extinction.

    Wong FCK, Zhang M, Thomson E, Schumacher LJ, Tsakiridis A, Ashmore J, Li T, Blin G, Karagianni E, Mullin NP et al.

    The EMBO journal 2025

    PUBMED: 40826182; DOI: 10.1038/s44318-025-00527-9

  • The genome sequence of the Pine Beauty, Panolis flammea (Denis & Schiffermüller), 1775 (Lepidoptera: Noctuidae).

    Chittaro Y, Cornet C, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;444

    PUBMED: 40969198; PMC: 12441672; DOI: 10.12688/wellcomeopenres.24674.1

  • HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.

    Golubchik T, Abeler-Dörner L, Hall M, Wymant C, Bonsall D, Macintyre-Cockett G, Thomson L, Baeten JM, Celum CL, Galiwango RM et al.

    BMC bioinformatics 2025;26;1;212

    PUBMED: 40813968; PMC: 12351810; DOI: 10.1186/s12859-025-06189-y

  • Novel Inhibitors of Plasmodium Phosphatidylinositol 4-kinase IIIβ with Low Propensity for Resistance: Life Cycle Stage Activity and In Vivo Efficacy in a Humanized Mouse Malaria Infection Model.

    Dziwornu GA, Mmonwa MM, Coertzen D, Krugmann L, Salomane N, Leshabane M, Thomas J, da Rocha S, Reader J, Masike K et al.

    Journal of medicinal chemistry 2025

    PUBMED: 40811478; DOI: 10.1021/acs.jmedchem.5c01417

  • Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variantsh.

    Lim TY, Horsfield ST, Troman CM, Bentley SD, Kwun MJ and Croucher NJ

    PLoS pathogens 2025;21;8;e1013392

    PUBMED: 40811750; DOI: 10.1371/journal.ppat.1013392

  • Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.

    Wells SB, Rainbow DB, Mark M, Szabo PA, Ergen C, Caron DP, Maceiras AR, Rahmani E, Benuck E, Valiollah Pour Amiri V et al.

    Nature immunology 2025

    PUBMED: 40804529; DOI: 10.1038/s41590-025-02241-4

  • The chromosomal genome sequence of the mollusc, Ctena decussata (O.G.Costa, 1829) and its bacterial endosymbiont Candidatus Thiodiazotropha sp. CDECU1 (Chromatiales).

    Wilkins L, Yuen B, Petersen J, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H et al.

    Wellcome open research 2025;10;435

    PUBMED: 41040656; PMC: 12485333; DOI: 10.12688/wellcomeopenres.24738.1

  • The genome sequence of Malacosoma alpicola Staudinger, 1871 (Lepidoptera: Lasiocampidae).

    Potocký P, Klečková I, Matos-Maraví P, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;420

    PUBMED: 40873553; PMC: 12378395; DOI: 10.12688/wellcomeopenres.24677.1

  • The genome sequence of Risso's dolphin, Grampus griseus (G.Cuvier, 1812) (Artiodactyla: Delphinidae).

    Davison NJ, Morin PA, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations – Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;431

    PUBMED: 41024935; PMC: 12476538; DOI: 10.12688/wellcomeopenres.24752.1

  • The genome sequence of the Common Marble, Celypha lacunana (Denis & Schiffermüller, 1775) (Lepidoptera: Tortricidae).

    Gardiner A, Broad GR, Sivess L, Holt S, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations – Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;428

    PUBMED: 41036235; PMC: 12481151; DOI: 10.12688/wellcomeopenres.24736.1

  • The genome sequence of the de Prunner's Ringlet, Erebia triaria von Prunner, 1798 (Lepidoptera: Nymphalidae).

    Chittaro Y, Vila M, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;425

    PUBMED: 40949818; PMC: 12423621; DOI: 10.12688/wellcomeopenres.24693.1

  • The genome sequence of the Dusky Grizzled Skipper, Pyrgus cacaliae (Rambur, 1839) (Lepidoptera: Hesperiidae).

    Chittaro Y, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;424

    PUBMED: 41000328; PMC: 12457891; DOI: 10.12688/wellcomeopenres.24672.1

  • The genome sequence of the Queen of Spain Fritillary, Issoria lathonia (Linnaeus, 1758) (Lepidoptera: Nymphalidae).

    Chittaro Y, Sanchez A, Cornet C, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;427

    PUBMED: 41000327; PMC: 12457893; DOI: 10.12688/wellcomeopenres.24702.1

  • The genome sequence of the Scarce Copper, Lycaena virgaureae (Linnaeus, 1758) (Lepidoptera: Lycaenidae).

    Escuer P, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;434

    PUBMED: 40949820; PMC: 12432500; DOI: 10.12688/wellcomeopenres.24748.1

  • The genome sequence of the Violet Copper, Helleia helle (Denis & Schiffermüller), 1776 (Lepidoptera: Lycaenidae).

    Escuer P, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;429

    PUBMED: 40949817; PMC: 12432499; DOI: 10.12688/wellcomeopenres.24699.1

  • ONE-STEP tagging: a versatile method for rapid site-specific integration by simultaneous reagent delivery.

    Migliori V, Bruntraeger MB, Gyulev IS, Lichou F, Burgold T, Gitterman DP, Iwama S, Trinh AL, Washer SJ, Jones CP et al.

    Nucleic acids research 2025;53;15

    PUBMED: 40823809; PMC: 12359036; DOI: 10.1093/nar/gkaf809

  • Tau uptake by human neurons depends on receptor LRP1 and kinase LRRK2.

    Evans LD, Strano A, Tuck E, Campbell A, Smith J, Hung C, Behr TS, Ghetti B, Ryskeldi-Falcon B, Karakoc E et al.

    The EMBO journal 2025

    PUBMED: 40790356; DOI: 10.1038/s44318-025-00514-0

  • Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq.

    Wang Y, Li J, Malcolm AA, Mansfield W, Clark SJ, Argelaguet R, Biggins L, Acton RJ, Andrews S, Reik W et al.

    Science advances 2025;11;32;eadu3308

    PUBMED: 40768587; PMC: 12327464; DOI: 10.1126/sciadv.adu3308

  • Genomic epidemiology of SARS-CoV-2 in Bolivia, 2020-2024.

    Pérez-Cascales E, Caballero F, Martínez-Ventura A, Ayzanoa B, Prado-Zapata M, Baldiviezo-Soliz E, Carballo-Jiménez P, Tinajeros-Guzmán F, Cuicapuza D and Tsukayama P

    Microbiology spectrum 2025;e0128025

    PUBMED: 40767570; DOI: 10.1128/spectrum.01280-25

  • Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae.

    Krishna A, Tonkin-Hill G, Morel-Journel T, Bentley S, Turner P, Blanquart F and Lehtinen S

    PLoS biology 2025;23;8;e3003300

    PUBMED: 40763153; PMC: 12324126; DOI: 10.1371/journal.pbio.3003300

  • The genome sequence of the Piedmont Ringlet, Erebia meolans von Prunner, 1798 (Lepidoptera: Nymphalidae).

    Vila M, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;408

    PUBMED: 41019573; PMC: 12475900; DOI: 10.12688/wellcomeopenres.24665.1

  • The genome sequence of the Dusky Meadow Brown, Cercyonis lycaon (Lepidoptera: Nymphalidae).

    Chittaro Y, Toro-Delgado E, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;395

    PUBMED: 40917438; PMC: 12411839; DOI: 10.12688/wellcomeopenres.24656.1

  • The genome sequence of the Map, Araschnia levana (Linnaeus, 1758) (Lepidoptera: Nymphalidae).

    Joron M, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;398

    PUBMED: 40904417; PMC: 12402765; DOI: 10.12688/wellcomeopenres.24633.1

  • The genome sequence of the Silver-washed Fritillary, Argynnis paphia (Linnaeus, 1758) (Lepidoptera: Nymphalidae).

    Chittaro Y, Sanchez A, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;399

    PUBMED: 40949819; PMC: 12426599; DOI: 10.12688/wellcomeopenres.24635.1

  • The genome sequence of Glacies alpinata (Scopoli, 1763) (Lepidoptera: Geometridae).

    Escuer P, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;392

    PUBMED: 40931743; PMC: 12417988; DOI: 10.12688/wellcomeopenres.24664.1

  • The genome sequence of the Lesser Mountain Ringlet, Erebia melampus Füssly, 1775 (Lepidoptera: Nymphalidae).

    Bouaouina S, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;394

    PUBMED: 40994706; PMC: 12455180; DOI: 10.12688/wellcomeopenres.24659.1

  • Case Report: Genetic evolution of Burkholderia pseudomallei during treatment leading to antibiotic resistance and disease relapse.

    Evans TJ, Keeratipusana C, Douangnouvong A, Phimolsarnnousith V, Sengdatka D, Chang K, Phommasone K, Chewapreecha C, Ashley EA and Batty EM

    Wellcome open research 2025;10;281

    PUBMED: 40861388; PMC: 12374155; DOI: 10.12688/wellcomeopenres.24138.2

  • The genome sequence of the Black Hairstreak, Satyrium pruni (Linnaeus, 1758) (Lepidoptera: Lycaenidae).

    Pohjoismaki J, Mutanen M, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;377

    PUBMED: 40931742; PMC: 12417987; DOI: 10.12688/wellcomeopenres.24619.1

  • The genome sequence of the bronze bream, Abramis brama (Linnaeus, 1758) (Cypriniformes: Leuciscidae).

    Nunn AD, Hänfling B, Pitman R, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;371

    PUBMED: 40969197; PMC: 12441676; DOI: 10.12688/wellcomeopenres.24606.1

  • The genome sequence of the Cranberry Fritillary, Boloria aquilonaris (Stichel, 1908) (Lepidoptera: Nymphalidae).

    Wymann HP, Suchackova Bartonova A, Lucek K, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;378

    PUBMED: 40786598; PMC: 12334919; DOI: 10.12688/wellcomeopenres.24620.1

  • The genome sequence of the Marsh Pennywort, Hydrocotyle vulgaris L. (Apiales: Araliaceae).

    Ruhsam M, Hollingsworth PM, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;370

    PUBMED: 40937467; PMC: 12421231; DOI: 10.12688/wellcomeopenres.24582.1

  • The genome sequence of the Mountain Clouded Yellow, Colias phicomone (Esper, 1780) (Lepidoptera: Pieridae).

    Linke D, Klečková I, Matos-Maraví P, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;379

    PUBMED: 40989963; PMC: 12451261; DOI: 10.12688/wellcomeopenres.24625.1

  • The genome sequence of the White-barred Clearwing, Synanthedon spheciformis (Denis & Schiffermüller), 1775 (Lepidoptera: Sesiidae).

    Pohjoismaki J, Mutanen M, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Project Psyche Community

    Wellcome open research 2025;10;373

    PUBMED: 40978457; PMC: 12449690; DOI: 10.12688/wellcomeopenres.24613.1

  • A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space.

    Harland LTG, Lohoff T, Koulena N, Pierson N, Pape C, Ameen F, Griffiths J, Theeuwes B, Wilson NK, Kreshuk A et al.

    Cell reports 2025;44;8;116047

    PUBMED: 40728928; DOI: 10.1016/j.celrep.2025.116047

  • Genomics of Neotropical biodiversity indicators: Two butterfly radiations with rampant chromosomal rearrangements and hybridization.

    van der Heijden ESM, Näsvall K, Seixas FA, Beserra Nobre CE, Maia ACD, Salazar-Carrión P, Walker JM, Szczerbowski D, Schulz S, Warren IA et al.

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;31;e2410939122

    PUBMED: 40720651; PMC: 12337270; DOI: 10.1073/pnas.2410939122

  • The genome sequence of the Alpine Milkvetch, Astragalus alpinus L. (Fabales: Fabaceae).

    Ruhsam M, Hollingsworth PM, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;366

    PUBMED: 40894105; PMC: 12398678; DOI: 10.12688/wellcomeopenres.24576.1

  • The genome sequence of the Mountain Bumble Bee, Bombus monticola Smith, 1849 (Hymenoptera: Apidae).

    Hislop L, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;367

    PUBMED: 40917439; PMC: 12409256; DOI: 10.12688/wellcomeopenres.24577.1

  • The genome sequence of the Pearly Heath, Coenonympha arcania Linnaeus, 1761 (Lepidoptera: Nymphalidae).

    Vila R, Vila S, Doniol-Valcroze P, Wright CJ, Meier JI, Blaxter ML, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;364

    PUBMED: 41019577; PMC: 12461188; DOI: 10.12688/wellcomeopenres.24624.1

  • Radiation with reproductive isolation in the near-absence of phylogenetic signal.

    Helmkampf M, Coulmance F, Heckwolf MJ, Acero P A, Balard A, Bista I, Dominguez OD, Frandsen PB, Torres-Oliva M, Santaquiteria A et al.

    Science advances 2025;11;30;eadt0973

    PUBMED: 40712024; PMC: 12292942; DOI: 10.1126/sciadv.adt0973

  • Within-host bacterial evolution and the emergence of pathogenicity.

    Tonkin-Hill G, Ruis C, Bentley SD, Lythgoe KA and Bryant JM

    Nature microbiology 2025;10;8;1829-1840

    PUBMED: 40715782; DOI: 10.1038/s41564-025-02036-1

  • An expanded method for malaria parasite genetic surveillance using targeted nanopore sequencing.

    Harrott AJR, Morang'a CM, Pearson RD, Sakyi ML, Osumanu A, Amoako EK, Bara FD, Hosmillo M, Rowe K, Aniweh Y et al.

    Gates open research 2025;9;49

    PUBMED: 40718588; PMC: 12290220; DOI: 10.12688/gatesopenres.16355.1

  • Deciphering the proteome of Escherichia coli K-12: Integrating transcriptomics and machine learning to annotate hypothetical proteins.

    Chakraborty S, Ardern Z, Aliyu H and Kaster AK

    Computational and structural biotechnology journal 2025;27;3565-3578

    PUBMED: 40821719; PMC: 12356324; DOI: 10.1016/j.csbj.2025.07.036

  • Genetics, energetics, and allostery in proteins with randomized cores and surfaces.

    Escobedo A, Voigt G, Faure AJ and Lehner B

    Science (New York, N.Y.) 2025;389;6758;eadq3948

    PUBMED: 40705891; DOI: 10.1126/science.adq3948

  • The chromosomal genome sequence of the photosymbiotic ascidian, Trididemnum clinides Kott, 1977 and its associated microbial metagenome sequences.

    Hirose E, Lopez JV, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V et al.

    Wellcome open research 2025;10;357

    PUBMED: 40949821; PMC: 12432502; DOI: 10.12688/wellcomeopenres.24563.1

  • The peculiar properties of mitochondrial carriers of the SLC25 family.

    Kunji ERS, Mavridou V, King MS, Cimadamore-Werthein C, Jaiquel Baron S, Jones SA, King AC, Springett R, Chand D, Palmer SM et al.

    The Biochemical journal 2025;482;15;1047-78

    PUBMED: 40706023; PMC: 12410006; DOI: 10.1042/BCJ20253171

  • Anti-Human Endogenous Retrovirus and Anti-Myelin Oligodendrocyte Glycoprotein Humoral Response in Cerebrospinal Fluid of Multiple Sclerosis Patients: A Case Control Study.

    Garcia KC, Santos SN, Flose BR, Juliano MA, Domingues RB, Neves LM, José Costa Silva G, Arruda LB, Penalva-de-Oliveira AC, de Andrade Matas SL et al.

    Microbiology and immunology 2025

    PUBMED: 40696868; DOI: 10.1111/1348-0421.70003

  • COVID-19 Surveillance in Madagascar and Urban Burkina Faso: Addressing Underreporting of Disease Burden Through Integrative Analysis of Diverse Data Streams.

    Rakotozandrindrainy N, Kang SSY, Wandji Nana LR, Sugimoto JD, Wang YT, Rakotozandrindrainy N, Razafindrabe TJL, Raminosoa TM, Hong SL, Razafindrakalia M et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2025;80;Supplement_1;S16-S28

    PUBMED: 40694513; DOI: 10.1093/cid/ciaf041

  • Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.

    Ashton PM, Mageiros L, Meiring JE, Chunga-Chirambo A, Khanam F, Dongol S, Banda H, Karkey A, Preciado-Llanes L, Thomaides-Brears H et al.

    Microbiome 2025;13;1;168

    PUBMED: 40696437; DOI: 10.1186/s40168-025-02125-7

  • Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro.

    Lawrence JEG, Woods S, Roberts K, Sumanaweera D, Balogh P, Li T, Predeus AV, He P, Polanski K, Prigmore E et al.

    Developmental cell 2025

    PUBMED: 40712580; DOI: 10.1016/j.devcel.2025.06.031

  • Evolutionary hotspots in bacterial genomes.

    Cazares A, Cazares D and Figueroa W

    Nature reviews. Microbiology 2025

    PUBMED: 40691347; DOI: 10.1038/s41579-025-01217-3

  • Application of image guided analyses to monitor fecal microbial composition and diversity in a human cohort.

    Zafeiropoulou K, Voermans B, Ngo H, Moreno J, Lee D, Derikx JPM, Luyer M, Zwinderman AH, Nieuwdorp M, de Goffau M et al.

    Scientific reports 2025;15;1;26237

    PUBMED: 40683926; PMC: 12276231; DOI: 10.1038/s41598-025-10629-3

  • ecDNA replication is disorganized and vulnerable to replication stress.

    Jaworski JJ, Pfuderer PL, Czyz P, Petris G, Boemo MA and Sale JE

    Nucleic acids research 2025;53;14

    PUBMED: 40744497; DOI: 10.1093/nar/gkaf711

  • A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections.

    Lilue J, Corvelo A, Gómez-Garrido J, Akagi K, Yang F, Green G, Ng BL, Fu B, Chorostecki UP, Warner SC et al.

    BMC biology 2025;23;1;217

    PUBMED: 40682131; PMC: 12275374; DOI: 10.1186/s12915-025-02316-6

  • Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks.

    Todd CD, Ijaz J, Torabi F, Dovgusha O, Bevan S, Cracknell O, Lohoff T, Clark S, Argelaguet R, Pierce J et al.

    Genome biology 2025;26;1;214

    PUBMED: 40682180; PMC: 12272991; DOI: 10.1186/s13059-025-03658-8

  • High diversity of Escherichia coli causing invasive disease in neonates in Malawi poses challenges for O-antigen based vaccine approach.

    Pearse O, Zuza A, Tewesa E, Siyabu P, Fraser AJ, Cornick J, Kawaza K, Musicha P, Thomson NR, Feasey NA and Heinz E

    Communications medicine 2025;5;1;298

    PUBMED: 40681780; PMC: 12274568; DOI: 10.1038/s43856-025-01007-1

  • Optimization and Characterization of the Antimalarial Activity of N-Aryl Acetamides that are Susceptible to Mutations in ROM8 and CSC1.

    Nguyen W, Boulet C, Dans MG, Loi K, Jarman KE, Barnes CBG, Yeo T, Sheth T, Mukherjee P, Chakraborty A et al.

    Journal of medicinal chemistry 2025

    PUBMED: 40680058; DOI: 10.1021/acs.jmedchem.5c01471

  • Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria.

    Serna C, Matamoros BR, Pulido-Vadillo M, Delgado-Blas JF, Jansen RR, Willems RJL, Almeida A, Harrison EM, Dupuy B, Coll F and Gonzalez-Zorn B

    Nature communications 2025;16;1;6360

    PUBMED: 40675954; DOI: 10.1038/s41467-025-61152-y

  • Functional Gonadotroph Adenomas in Male Patients: Clinical Characteristics, Surgical Outcomes, and Hormonal Follow-up.

    Peeran Z, Osorio RC, Perez M, Kabir AS, Mehari M, Dada A, Badani A, Khela HS, Young JS, El-Sayed IH et al.

    Operative neurosurgery (Hagerstown, Md.) 2025

    PUBMED: 40667987; DOI: 10.1227/ons.0000000000001693

  • High Propensity for Multidrug-Resistant Pneumococcal Shedding Among Adults Living With HIV on Stable Antiretroviral Therapy in Malawi.

    Sibale LL, Kalata N, Mitole N, Nyazika TK, Phiri JA, Kusakala A, Khwiya M, Sagawa G, Lo SW, Chaguza C et al.

    Open forum infectious diseases 2025;12;8;ofaf422

    PUBMED: 40799787; PMC: 12343114; DOI: 10.1093/ofid/ofaf422

  • The Lancet One Health Commission: harnessing our interconnectedness for equitable, sustainable, and healthy socioecological systems.

    Winkler AS, Brux CM, Carabin H, das Neves CG, Häsler B, Zinsstag J, Fèvre EM, Okello A, Laing G, Harrison WE et al.

    Lancet (London, England) 2025

    PUBMED: 40683291; DOI: 10.1016/S0140-6736(25)00627-0

  • Atlas of amnion development during the first trimester of human pregnancy.

    Hu W, Sancho-Serra C, Gantner CW, Szafranska HM, Solanky N, Metcalfe K, Vento-Tormo R and Zernicka-Goetz M

    Nature cell biology 2025;27;7;1175-1185

    PUBMED: 40659869; DOI: 10.1038/s41556-025-01696-9

  • Communicating clearly about data sharing in genomics.

    Thaldar D, Uberoi D, Thorogood A, Milne R, Newson AJ, Hall A, Glazer D, Esselaar P and Joly Y

    Human genomics 2025;19;1;80

    PUBMED: 40660395; PMC: 12257658; DOI: 10.1186/s40246-025-00784-z

  • Genomic characterization of multidrug-resistant extended-spectrum β-lactamase-producing Vibrio cholerae O1 strains from 2022 cholera outbreak in Kenya.

    Imoli D, Maingi JM, Mbae C, Kavai SM, Wairimu C, Mundalo S, Odityo G, Wairimu M, Mekuria Z, Gebreyes W and Kariuki S

    The Journal of antimicrobial chemotherapy 2025

    PUBMED: 40658488; DOI: 10.1093/jac/dkaf224

  • Individual-Level Analysis of the Efficacy of Albendazole and Albendazole-Ivermectin Fixed-Dose Coformulation (FDC) Against Trichuris trichiura and Hookworms.

    Fleitas PE, Gandasegui J, Gelaye W, Messa JA, Kepha S, van Lieshout L, Algorta J, de Jesus Á, Novela V, Mandomando I et al.

    Acta tropica 2025;107742

    PUBMED: 40669531; DOI: 10.1016/j.actatropica.2025.107742

  • Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets.

    Papaiakovou M, Waeschenbach A, Ajibola O, Ajjampur SS, Anderson RM, Bailey R, Benjamin-Chung J, Cambra-Pellejà M, Caro NR, Chaima D et al.

    Nature communications 2025;16;1;6374

    PUBMED: 40640199; DOI: 10.1038/s41467-025-61687-0

  • Somatic mutations in TBX3 promote hepatic clonal expansion by accelerating VLDL secretion.

    Mannino G, Quinn G, Zhu M, Wang Z, Wang X, Li B, Hsieh MH, Mathews T, Zacharias L, Gu W et al.

    The Journal of clinical investigation 2025

    PUBMED: 40638249; DOI: 10.1172/JCI191855

  • The scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet & Donadey, 1987, and its associated microbial metagenome sequences.

    de Goeij JM, Mueller B, Achlatis M, Campana S, Hudspith M, Kornder NA, Hentschel U, Oatley G, Sinclair E, Aunin E et al.

    Wellcome open research 2025;10;344

    PUBMED: 40894108; PMC: 12391866; DOI: 10.12688/wellcomeopenres.24281.1

  • Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture.

    Papaiakovou M, Waeschenbach A, Anderson RM, Cools P, Mekonnen Z, Littlewood DTJ, Cantacessi C and Doyle SR

    Molecular ecology resources 2025;e70005

    PUBMED: 40631469; DOI: 10.1111/1755-0998.70005

  • Whole-genome sequences provide insights into the formation and adaptation of human populations in the Himalayas.

    Arciero E, Almarri MA, Mezzavilla M, Xue Y, Hallast P, Hammoud C, Chen Y, Skov L, Kraaijenbrink T, Ayub Q et al.

    Current biology : CB 2025

    PUBMED: 40645174; DOI: 10.1016/j.cub.2025.06.048

  • The chromosomal genome sequence of the giant barrel sponge, Xestospongia muta Schmidt 1870 and its associated microbial metagenome sequences.

    Lopez JV, Pomponi SA, Hentschel U, Erpenbeck D, Pruzinsky N, Fiore C, Mulheron R, Oatley G, Sinclair E, Aunin E et al.

    Wellcome open research 2025;10;336

    PUBMED: 40894109; PMC: 12398682; DOI: 10.12688/wellcomeopenres.24173.1

  • The genome sequence of the eyed flat-backed millipede, Nanogona polydesmoides (Leach, 1814).

    Owen C, Sivell O, Sivell D, Twitchett RJ, Edgecombe GD, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;332

    PUBMED: 40786599; PMC: 12334921; DOI: 10.12688/wellcomeopenres.24341.1

  • Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing.

    Troman C, Horsfield ST, Abraham D, Mohan VR, Giri S, Nair S, Shaw AG, Dyson Z, Holt KE and Grassly NC

    PLoS neglected tropical diseases 2025;19;7;e0013211

    PUBMED: 40627640; PMC: 12237024; DOI: 10.1371/journal.pntd.0013211

  • Environmental carcinogens often exacerbate endogenous mutagenic processes to enhance tumor promotion.

    Xu M, Li J, Hsiao YC, Kovi RC, Li JL, Klimczak LJ, Riva L, Adams D, Bushel PR, Merrick BA et al.

    Cell reports 2025;44;7;115978

    PUBMED: 40638383; DOI: 10.1016/j.celrep.2025.115978

  • Genomic evidence of spatially structured gene flow and divergent insecticide resistance backgrounds of the malaria vector Anopheles funestus in Tanzania.

    Odero JO, Nambunga IH, Bwanary H, Mkandawile G, Paliga JM, Mapua SA, Mwinyi SH, Ngowo HS, Govella NJ, Kaindoa EW et al.

    Genetics 2025

    PUBMED: 40620209; DOI: 10.1093/genetics/iyaf117

  • Immunogenicity of autologous and allogeneic human primary cholangiocyte organoid cellular therapies.

    Petrus-Reurer S, Lei W, Tysoe O, Mairesse M, Baez-Ortega A, Jones J, Tan T, Rehakova S, Mahbubani KT, Brodie C et al.

    Cell reports. Medicine 2025;102205

    PUBMED: 40628261; DOI: 10.1016/j.xcrm.2025.102205

  • The genome sequence of the Little Snipefly, Chrysopilus asiliformis (Preyssler, 1791).

    Crowley LM, Taylor SC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;329

    PUBMED: 40861389; PMC: 12371324; DOI: 10.12688/wellcomeopenres.24326.1

  • The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types.

    Chan PY, Alexander D, Mehta I, Matsuyama LSAS, Harle V, Olvera-León R, Park JS, Arriaga-González FG, van der Weyden L, Cheema S et al.

    Nature genetics 2025

    PUBMED: 40615675; DOI: 10.1038/s41588-025-02222-1

  • Somatic loss-of-function mutations in CIDEB reduce hepatic steatosis by increasing lipolysis and fatty acid oxidation.

    Zeng Q, Patel S, Wang X, Hsieh MH, Li Z, Ren X, Wang J, Kim D, Li S, Gu X et al.

    Journal of hepatology 2025

    PUBMED: 40618957; DOI: 10.1016/j.jhep.2025.06.021

  • Genomic infrastructure for cetacean research and conservation: reference genomes for eight families spanning the cetacean tree of life

    Phillip A. Morin, Bernhard Bein, Chiara Bortoluzzi, Yury V. Bukhman, Taylor Hains, Dorothea Heimeier, Marcela Uliano-Silva, Dominic E. Absolon, Linelle Abueg, Jessica Antosiewicz-Bourget et al.

    Frontiers in Marine Science 2025

    DOI: 10.3389/fmars.2025.1562045; URL: https://doi.org/10.3389/fmars.2025.1562045

  • High quality transcriptome profiling confirms the transcriptional landscape of Treponema pallidum subsp. pallidum.

    Grillová L, Carrami EM, Roberts-Sengier W and Thomson NR

    Scientific reports 2025;15;1;23272

    PUBMED: 40604007; PMC: 12223175; DOI: 10.1038/s41598-025-06583-9

  • A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins.

    Sharapov S, Timoshchuk A, Zaytseva O, Maslov DE, Soplenkova A, Elgaeva EE, Tiys ES, Mangino M, Wittenbecher C, Karssen L et al.

    Nature communications 2025;16;1;5525

    PUBMED: 40593539; PMC: 12218978; DOI: 10.1038/s41467-025-60431-y

  • The long-term effects of chemotherapy on normal blood cells.

    Mitchell E, Pham MH, Clay A, Sanghvi R, Williams N, Pietsch S, Hsu JI, Jung H, Vedi A, Moody S et al.

    Nature genetics 2025

    PUBMED: 40596443; DOI: 10.1038/s41588-025-02234-x

  • Clonal evolution of hematopoietic stem cells after autologous stem cell transplantation.

    Uryu H, Saeki K, Haeno H, Kapadia CD, Furudate K, Nangalia J, Spencer Chapman M, Zhao L, Hsu JI, Zhao C et al.

    Nature genetics 2025

    PUBMED: 40596442; DOI: 10.1038/s41588-025-02235-w

  • Defining and benchmarking open problems in single-cell analysis.

    Luecken MD, Gigante S, Burkhardt DB, Cannoodt R, Strobl DC, Markov NS, Zappia L, Palla G, Lewis W, Dimitrov D et al.

    Nature biotechnology 2025

    PUBMED: 40595413; DOI: 10.1038/s41587-025-02694-w

  • Evidence that cultural groups differ in their abilities to detect fake accents: a follow up.

    Goodman JR and Foley RA

    Evolutionary human sciences 2025;7;e19

    PUBMED: 40809159; PMC: 12344596; DOI: 10.1017/ehs.2025.10007

  • Genomic surveillance reveals geographical heterogeneity and differences in known and novel insecticide resistance mechanisms in Anopheles arabiensis across Kenya.

    Polo B, Bennett KL, Barasa S, Brenas J, Agumba S, Mwangangi J, Wachira L, Kitur S, Matoke-Muhia D, Mburu DM et al.

    BMC genomics 2025;26;1;599

    PUBMED: 40597647; PMC: 12210584; DOI: 10.1186/s12864-025-11788-3

  • Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming.

    Lord E, Feinauer IS, Soares AER, Lagerholm VK, Näsvall K, Ersmark E, Olsen RA, Prost S, Kuzmina EA, Smirnov NG et al.

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;28;e2424333122

    PUBMED: 40587810; DOI: 10.1073/pnas.2424333122

  • Comprehensive profiling of the mutational landscape of hidradenoma papilliferum validates key role of alterations in the PI3K/AKT pathway.

    Cheema S, van der Weyden L, Wong K, Del Castillo Velasco-Herrera M, Billington J, Vermes I, Anderson E, Allen L, de Saint Aubain N, van der Horst MPJ et al.

    The British journal of dermatology 2025

    PUBMED: 40580495; DOI: 10.1093/bjd/ljaf257

  • PARPAL: PARalog Protein Redistribution using Abundance and Localization in Yeast Database.

    Greco BM, Zapata G, Dandage R, Papkov M, Pereira V, Lefebvre F, Bourque G, Parts L and Kuzmin E

    G3 (Bethesda, Md.) 2025

    PUBMED: 40580499; DOI: 10.1093/g3journal/jkaf148

  • Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii.

    Short FL, Maharjan R, Li L, Afrin N, Delgado N, Boinett CJ, Parkhill J, Cain AK and Paulsen IT

    mBio 2025;e0096625

    PUBMED: 40576344; DOI: 10.1128/mbio.00966-25

  • The postglacial history of Euphrasia micrantha in Scotland: evidence from genome skimming

    Ding, Y., Metherell, C., Ennos, R. A., Darwin Tree of Life Consortium, Hollingsworth, P. M. and Twyford, A. D.

    Plant Ecology & Diversity 2025;1-12

    DOI: 10.1080/17550874.2025.2519256; URL: https://doi.org/10.1080/17550874.2025.2519256

  • Nosema or Vairimorpha: Genomic/proteomic support to a complex socio-economic issue rooted in taxonomic change.

    Bojko J, Becnel J, Bessette E, Edwards S, Gao J, Huang WF, Katanić N, Khalaf A, Li T, Snow JW et al.

    Journal of invertebrate pathology 2025;108376

    PUBMED: 40571120; DOI: 10.1016/j.jip.2025.108376

  • Clinical Utility and Cost-Effectiveness of Pretreatment NUDT15 Pharmacogenetic Testing to Prevent Thiopurine-Induced Myelosuppression: A Genotype-First Reverse Phenotyping Cohort Study Within the UK NIHR Inflammatory Bowel Disease Bioresource.

    Roberts C, Peters J, Sazonvos A, Goodman N, Sharip M, Smith R, Bishara M, Bewshea C, Lin S, Chanchlani N et al.

    Alimentary pharmacology & therapeutics 2025

    PUBMED: 40548539; DOI: 10.1111/apt.70232

  • Eomes directs the formation of spatially and functionally diverse extraembryonic hematovascular tissues.

    Theeuwes B, Harland LTG, Bisia AM, Costello I, Ton MN, Lohoff T, Clark SJ, Argelaguet R, Wilson NK, Reik W et al.

    Developmental cell 2025

    PUBMED: 40562043; DOI: 10.1016/j.devcel.2025.06.001

  • Genome structure and molecular phylogeny of the only Eurasian Boechera species, Boechera falcata (Brassicaceae).

    Zilov D, Mandáková T, Popova M, Lysak MA, Windham MD and Brukhin V

    G3 (Bethesda, Md.) 2025

    PUBMED: 40539638; DOI: 10.1093/g3journal/jkaf117

  • NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation.

    Miller A, Biga V, Rowntree A, Chhatriwala M, Woods F, Noble B, Marinopoulou E, Kamath A, Vallier L and Papalopulu N

    Developmental cell 2025

    PUBMED: 40570854; DOI: 10.1016/j.devcel.2025.06.004

  • Single-cell transcriptional landscapes of Aedes aegypti midgut and fat body after a bloodmeal.

    Vial T, Lopez-Maestre H, Couderc E, Pinaud S, Howick V, Akorli J, Lawniczak M, Marti G and Merkling SH

    Cell genomics 2025;100924

    PUBMED: 40570845; DOI: 10.1016/j.xgen.2025.100924

  • Hybrid reference genome assemblies for Leishmania (Viannia) braziliensis, a primary agent of mucocutaneous leishmaniasis.

    Cotton JA, Van den Broeck F, Myler PJ, Akopyants NS, Berriman M and Beverley SM

    Microbiology resource announcements 2025;e0131724

    PUBMED: 40525854; DOI: 10.1128/mra.01317-24

  • Protist genomics: key to understanding eukaryotic evolution.

    Schoenle A, Francis O, Archibald JM, Burki F, de Vries J, Dumack K, Eme L, Florent I, Hehenberger E, Hoffmeyer TT et al.

    Trends in genetics : TIG 2025

    PUBMED: 40517085; DOI: 10.1016/j.tig.2025.05.004

  • Temporal multi-omics analysis of COVID-19 in end-stage kidney disease.

    Stephenson E, Macdonald-Dunlop E, Dratva LM, Lindeboom RGH, Tuong ZK, Tun WM, Kretschmer L, Buang NB, Ballereau S, Cabantaus M et al.

    Cell genomics 2025;100918

    PUBMED: 40532694; DOI: 10.1016/j.xgen.2025.100918

  • Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid radiation.

    Blumer LM, Burskaia V, Artiushin I, Saha J, Garcia JC, Jiménez FC, Hooft van der Huysdynen A, Elkin J, Fischer B, Van Houtte N et al.

    Science (New York, N.Y.) 2025;388;6752;eadr9961

    PUBMED: 40504893; DOI: 10.1126/science.adr9961

  • Massively parallel genetic perturbation suggests the energetic structure of an amyloid-β transition state.

    Arutyunyan A, Seuma M, Faure AJ, Bolognesi B and Lehner B

    Science advances 2025;11;24;eadv1422

    PUBMED: 40498820; DOI: 10.1126/sciadv.adv1422

  • Primary cutaneous dedifferentiated and undifferentiated melanoma.

    Ferreira I and Brenn T

    Seminars in diagnostic pathology 2025;42;5;150937

    PUBMED: 40532288; DOI: 10.1016/j.semdp.2025.150937

  • A comparison of approaches to studying relationships between lumbar spinal degeneration findings demonstrates advantages to interspace-level analyses over person-level analyses.

    Suri P, Elgaeva E, Jarvik J, Rundell S, Tsepilov Y, Williams F and Heagerty P

    European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society 2025

    PUBMED: 40493208; DOI: 10.1007/s00586-025-08976-w

  • How machine learning can help us understand what we have grown in the dish.

    Vento-Tormo R

    Nature reviews. Molecular cell biology 2025

    PUBMED: 40495046; DOI: 10.1038/s41580-025-00868-7

  • Widespread genetic signals of visual system adaptation in deepwater cichlid fishes.

    Camacho García JI, Malinsky M, Joyce DA, Santos ME, Vernaz G, Ngochera MJ and Svardal H

    Molecular biology and evolution 2025

    PUBMED: 40488307; DOI: 10.1093/molbev/msaf147

  • A machine-learning-based approach to predict early hallmarks of progressive hearing loss.

    Ceriani F, Giles J, Ingham NJ, Jeng JY, Lewis MA, Steel KP, Arvaneh M and Marcotti W

    Hearing research 2025;464;109328

    PUBMED: 40532491; DOI: 10.1016/j.heares.2025.109328

  • Validating data from multiplex assays of variant effect: A CanVIG-UK national survey of NHS clinical scientists.

    Allen S, Garrett A, Rowlands CF, Durkie M, Burghel GJ, Robinson R, Callaway A, Field J, Frugtniet B, Palmer-Smith S et al.

    American journal of human genetics 2025;112;6;1479-1488

    PUBMED: 40480200; DOI: 10.1016/j.ajhg.2025.04.006

  • The genome sequence of a long-legged fly, Argyra leucocephala (Meigen, 1824).

    Falk S, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;309

    PUBMED: 40823658; PMC: 12355172; DOI: 10.12688/wellcomeopenres.24307.1

  • The genome sequence of a phantom cranefly, Ptychoptera contaminata (Linnaeus, 1758).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;308

    PUBMED: 40823656; PMC: 12355170; DOI: 10.12688/wellcomeopenres.24276.1

  • The genome sequence of the Brown Moss-moth, Bryotropha terrella (Denis & Schiffermüller), 1775.

    Hutchinson F, Crowley LM, Broad GR, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;310

    PUBMED: 40904416; PMC: 12402767; DOI: 10.12688/wellcomeopenres.24324.1

  • Wilms tumor characteristics in children with heterozygous germline DIS3L2 variants.

    van Peer SE, Treger TD, Wegert J, Hol JA, Le Gall J, Jakkula EE, Kamihara J, Mullen EA, Graf N, Behjati S et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2025;101478

    PUBMED: 40481679; DOI: 10.1016/j.gim.2025.101478

  • The chromosomal genome sequence of the marine leech, Branchellion lobata Moore, 1952 and its associated microbial metagenome sequences.

    Goffredi SK, Appy R, Martín-Durán JM, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H et al.

    Wellcome open research 2025;10;304

    PUBMED: 40771652; PMC: 12326168; DOI: 10.12688/wellcomeopenres.24186.1

  • The genome sequence of a flea beetle, Altica lythri Aubé, 1843.

    Paul J, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;297

    PUBMED: 40931741; PMC: 12417985; DOI: 10.12688/wellcomeopenres.24269.1

  • The genome sequence of the banded centipede, Lithobius variegatus Leach, 1814.

    Edgecombe GD, Crowley LM, Telfer MG, Hughes L, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;285

    PUBMED: 40852602; PMC: 12368494; DOI: 10.12688/wellcomeopenres.24329.1

  • The genome sequence of the Dark Umber moth, Philereme transversata (Hufnagel, 1767).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;300

    PUBMED: 40697421; PMC: 12280868; DOI: 10.12688/wellcomeopenres.24265.1

  • The genome sequence of the Eurasian Curlew, Numenius arquata (Linnaeus, 1758).

    Walsh G, Donoghue BO, Höglund J, McMahon BJ, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, WellcomeSanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;298

    PUBMED: 40880729; PMC: 12381557; DOI: 10.12688/wellcomeopenres.24272.1

  • The genome sequence of the Poplar Cosmet moth, Batrachedra praeangusta (Haworth, 1828).

    Broad GR, Boyes C, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;288

    PUBMED: 40894107; PMC: 12395131; DOI: 10.12688/wellcomeopenres.24308.1

  • The genome sequence of the Small Dotted Buff moth, Photedes minima Haworth, 1809.

    Boyes D, Crowley LM, Adewumi T, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;299

    PUBMED: 40703330; PMC: 12284473; DOI: 10.12688/wellcomeopenres.24264.1

  • The genome sequence of the Small Sallow Mining Bee, Andrena praecox (Scopoli, 1763).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;290

    PUBMED: 40808700; PMC: 12344408; DOI: 10.12688/wellcomeopenres.24301.1

  • Long-term effects of azithromycin mass administration to reduce childhood mortality on Streptococcus pneumoniae antimicrobial resistance: a population-based, cross-sectional, follow-up carriage survey.

    Kalizang'oma A, Chan JM, Kalua K, Bonomali F, Brown C, Msefula J, Chaima D, Samikwa L, Meleke H, Hart JD et al.

    The Lancet. Infectious diseases 2025

    PUBMED: 40473452; DOI: 10.1016/S1473-3099(25)00212-9

  • Ocular Phenotyping of Knockout Mice Identifies Genes Associated With Late Adult Retinal Phenotypes.

    Hang A, Shao A, Shea M, Roux MJ, Imai-Leonard DM, Adams DJ, Amano T, Amarie OV, Berberovic Z, Bour R et al.

    Investigative ophthalmology & visual science 2025;66;6;64

    PUBMED: 40548636; PMC: 12186831; DOI: 10.1167/iovs.66.6.64

  • Performance of deep-learning-based approaches to improve polygenic scores.

    Kelemen M, Xu Y, Jiang T, Zhao JH, Anderson CA, Wallace C, Butterworth A and Inouye M

    Nature communications 2025;16;1;5122

    PUBMED: 40456720; PMC: 12130321; DOI: 10.1038/s41467-025-60056-1

  • Genomic analysis of invasive and non-invasive disease-causing Streptococcus pneumoniae isolated from children between 2014 and 2023 in Suzhou, China.

    Huang L, King AC, Liu Y, Hung HCH, Bentley SD, Jiang Y, Lv P, Xu X, Lo SW and Chen M

    Microbial genomics 2025;11;6

    PUBMED: 40455658; PMC: 12130468; DOI: 10.1099/mgen.0.001398

  • Enterococcus lactis is ecologically and genetically distinct from the major opportunistic pathogen Enterococcus faecium.

    Ross TA, Janice J, Arredondo-Alonso S, Löhr IH, Holsbø E, Corander J, Pöntinen AK, Kampffmeyer M and Hegstad K

    Microbial genomics 2025;11;6

    PUBMED: 40478766; PMC: 12144320; DOI: 10.1099/mgen.0.001420

  • The limitations of mobile phone data for measuring movement patterns of populations at risk of malaria.

    Tam G, Sinha I, Pongsoipetch K, Chindavongsa K, Mayxay M, Phalivong S, Cowling BJ, Miotto O, Mahaphontrakoon S, Xayvanghang S and Maude RJ

    Malaria journal 2025;24;1;174

    PUBMED: 40450347; PMC: 12126860; DOI: 10.1186/s12936-025-05416-4

  • Age-related disparities in treatment and outcomes for newly diagnosed multiple myeloma: a population-based study.

    Shan X, Kuiper R, Ding C, Munshi PN, Stadtmauer EA and Susanibar-Adaniya SP

    Haematologica 2025

    PUBMED: 40438975; DOI: 10.3324/haematol.2025.287506

  • High resolution clonal architecture of hypomutated Wilms tumours.

    Lee-Six H, Treger TD, Dave M, Coorens TH, Anderson ND, Tiersma Y, Derakhshan S, de Haan S, van den Heuvel-Eibrink MM, Wang Y et al.

    Nature communications 2025;16;1;4647

    PUBMED: 40442086; DOI: 10.1038/s41467-025-59854-4

  • SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.

    Elrick H, Sauer CM, Espejo Valle-Inclan J, Trevers K, Tanguy M, Zumalave S, De Noon S, Muyas F, Cascão R, Afonso A et al.

    Nature methods 2025

    PUBMED: 40437218; DOI: 10.1038/s41592-025-02708-0

  • The genome sequence of the solitary wasp, Cerceris ruficornis (Fabricius, 1793).

    Sivell O, Boyes C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;276

    PUBMED: 40917437; PMC: 12411840; DOI: 10.12688/wellcomeopenres.24270.1

  • Single-cell imaging of protein dynamics of paralogs reveals sources of gene retention

    Rohan Dandage, Mikhail Papkov, Brittany M. Greco, Vanessa Pereira, Dmytro Fishman, Helena Friesen, Kyle Wang, Erin B. Styles, Oren Kraus, Benjamin Grys et al.

    iScience 2025;28;7;112771

    DOI: 10.1016/j.isci.2025.112771; URL: https://doi.org/10.1016/j.isci.2025.112771

  • The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences.

    Maldonado M, Pita L, Hentschel U, Erpenbeck D, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M et al.

    Wellcome open research 2025;10;275

    PUBMED: 40520149; PMC: 12166358; DOI: 10.12688/wellcomeopenres.24154.1

  • The genome sequence of the great crested newt, Triturus cristatus (Laurenti, 1768).

    Streicher JW, Holt S, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;270

    PUBMED: 40470061; PMC: 12134737; DOI: 10.12688/wellcomeopenres.24257.1

  • The genome sequence of the Heath Bumblebee, Bombus jonellus (Kirby, 1802).

    Broad GR, Januszczak I, Fletcher C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;269

    PUBMED: 40520151; PMC: 12166357; DOI: 10.12688/wellcomeopenres.24256.1

  • The genome sequence of the Slender-footed Robberfly, Leptarthrus brevirostris (Meigen, 1804).

    Wolton R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;273

    PUBMED: 40656864; PMC: 12254722; DOI: 10.12688/wellcomeopenres.24277.1

  • Metagenomics distilled: new k-mer-based methods.

    Rozday TJ

    Nature reviews. Microbiology 2025

    PUBMED: 40410357; DOI: 10.1038/s41579-025-01192-9

  • Resistance to BRAF inhibitors drives melanoma sensitivity to Chk1 inhibition.

    Carvalho DG, Kenski JCN, Moreira DA, Rajão MA, Krijgsman O, Furtado C, Boroni M, Viola JPB, Peeper DS and Possik PA

    Pharmacological research 2025;107797

    PUBMED: 40414585; DOI: 10.1016/j.phrs.2025.107797

  • Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.

    Yang Y, Duan Y, Lang S, Fondevila MF, Schöler D, Harberts A, Cabré N, Chen S, Shao Y, Vervier K et al.

    Cell host & microbe 2025

    PUBMED: 40441146; DOI: 10.1016/j.chom.2025.05.003

  • Bi-allelic variants in POPDC2 cause an autosomal recessive syndrome presenting with cardiac conduction defects and hypertrophic cardiomyopathy.

    Nicastro M, Vermeer AMC, Postema PG, Tadros R, Bowling FZ, Aegisdottir HM, Tragante V, Mach L, Postma AV, Lodder EM et al.

    American journal of human genetics 2025

    PUBMED: 40409267; DOI: 10.1016/j.ajhg.2025.04.016

  • Genetic surveillance of Plasmodium falciparum populations following treatment policy revisions in the Greater Mekong Subregion.

    Wasakul V, Verschuuren TD, Thuy-Nhien N, Booth E, Quang HH, Thang ND, Chindavongsa K, Sovannaroth S, Banouvong V, Sengsavath V et al.

    Nature communications 2025;16;1;4689

    PUBMED: 40394107; PMC: 12092748; DOI: 10.1038/s41467-025-59946-1

  • The genome sequence of a lauxanid fly, Meiosimyza decipiens (Loew, 1847).

    McCulloch J, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;245

    PUBMED: 40666601; PMC: 12260490; DOI: 10.12688/wellcomeopenres.23785.1

  • The genome sequence of Bocage's wall lizard, Podarcis bocagei (Lopez-Seoane, 1885).

    Feiner N, Uller T, Carretero MA, Meier J, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2025;10;246

    PUBMED: 40666602; PMC: 12260489; DOI: 10.12688/wellcomeopenres.24032.1

  • Cell-intrinsic metabolic phenotypes identified in patients with glioblastoma, using mass spectrometry imaging of 13C-labelled glucose metabolism.

    Tsyben A, Dannhorn A, Hamm G, Pitoulias M, Couturier DL, Sawle A, Briggs M, Wright AJ, Brodie C, Mendil L et al.

    Nature metabolism 2025

    PUBMED: 40389678; DOI: 10.1038/s42255-025-01293-y

  • Wnt/β-catenin activation by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary basal cell adenoma.

    Wong K, Bishop JA, Weinreb I, Motta M, Del Castillo Velasco-Herrera M, Bellacchio E, Ferreira I, van der Weyden L, Boccacino JM, Lauri A et al.

    Nature communications 2025;16;1;4657

    PUBMED: 40389436; PMC: 12089348; DOI: 10.1038/s41467-025-59871-3

  • Knockout of SIN3B modulates transcriptional programs and cell survival in cutaneous melanoma.

    Sekimoto Matsuyama LSA, Harle V, Offord V, Droop A, Rabbie R, Garg M, Vázquez-Cruz ME, Robles-Espinoza CD, Turner G, Fraser D et al.

    Pharmacological research 2025;107785

    PUBMED: 40393534; DOI: 10.1016/j.phrs.2025.107785

  • The impact of ancestral, genetic, and environmental influences on germline de novo mutation rates and spectra.

    Garcia-Salinas OI, Hwang S, Huang QQ, Sanghvi R, Malawsky DS, Kaplanis J, Neville MDC, Day FR, Rahbari R, Scally A and Martin HC

    Nature communications 2025;16;1;4527

    PUBMED: 40374658; PMC: 12081642; DOI: 10.1038/s41467-025-59750-x

  • Psychological and behavioural considerations for integrating polygenic risk scores for disease into clinical practice.

    Sanderson SC and Inouye M

    Nature human behaviour 2025;9;6;1098-1106

    PUBMED: 40355674; DOI: 10.1038/s41562-025-02200-x

  • The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health.

    Dyson ZA, Cerdeira L, Sharma V, Carey ME, Holt KE and Global Typhoid Genomics Consortium

    Genome medicine 2025;17;1;51

    PUBMED: 40346656; PMC: 12063449; DOI: 10.1186/s13073-025-01470-4

  • Tools and challenges in the use of routine clinical data for antimicrobial resistance surveillance.

    Holt KE, Carey ME, Chandler C, Cross JH, Dyson ZA, Furnham N, Glover RE, Virgo M and Knight GM

    npj antimicrobials and resistance 2025;3;1;37

    PUBMED: 40346194; PMC: 12064641; DOI: 10.1038/s44259-025-00105-3

  • The Tree of Sex consortium: A global initiative for studying the evolution of reproduction in eukaryotes.

    Jeffries D, Benvenuto C, Böhne A, Fraisse C, Garcia S, Jay P, Kratochvíl L, McDonough-Goldstein CE, Ruiz-Herrera A, Sotero-Caio CG et al.

    Journal of evolutionary biology 2025

    PUBMED: 40336333; DOI: 10.1093/jeb/voaf053

  • Distinct pathways for genetic and epigenetic predisposition in familial and bilateral Wilms tumor.

    Wegert J, Appenzeller S, Treger TD, Streitenberger H, Ziegler B, Bausenwein S, Vokuhl C, Parks C, Jüttner E, Gramlich S et al.

    Genome medicine 2025;17;1;49

    PUBMED: 40340749; PMC: 12060375; DOI: 10.1186/s13073-025-01482-0

  • The genome sequence of the Ibiza wall lizard, Podarcis pityusensis (Boscá, 1883).

    Feiner N, Uller T, de la Cruz F, Garcia-Roa R, Meier J, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2025;10;235

    PUBMED: 40520148; PMC: 12163369; DOI: 10.12688/wellcomeopenres.24143.1

  • The genome sequences of the diplonemid protist Rhynchopus euleeides YPF1915 and its bacterial endosymbiont Candidatus Syngnamydia salmonis (Chlamydiota).

    Tashyreva D, Faktorová D, Horák A, Lukeš J, Archibald JM, Oatley G, Sinclair E, Santos C, Paulini M, Aunin E et al.

    Wellcome open research 2025;10;233

    PUBMED: 40528998; PMC: 12171722; DOI: 10.12688/wellcomeopenres.24014.1

  • Chromatin loops are an ancestral hallmark of the animal regulatory genome.

    Kim IV, Navarrete C, Grau-Bové X, Iglesias M, Elek A, Zolotarov G, Bykov NS, Montgomery SA, Ksiezopolska E, Cañas-Armenteros D et al.

    Nature 2025

    PUBMED: 40335694; DOI: 10.1038/s41586-025-08960-w

  • Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction.

    Xiang R, Ben-Eghan C, Liu Y, Roberts D, Ritchie S, Lambert SA, Xu Y, Takeuchi F and Inouye M

    Nature communications 2025;16;1;4260

    PUBMED: 40335489; PMC: 12059119; DOI: 10.1038/s41467-025-59525-4

  • Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

    FitzPatrick MEB, Antanaviciute A, Dunstan M, Künnapuu K, Trzupek D, Provine NM, Dooley K, Zhang JY, Irwin SL, Garner LC et al.

    Nature immunology 2025;26;6;947-962

    PUBMED: 40328997; PMC: 12133578; DOI: 10.1038/s41590-025-02146-2

  • Shelter dogs as reservoirs of international clones of Escherichia coli carrying mcr-1.1 and blaCTX-M resistance genes in Lima, Peru.

    Ayzanoa B, Salvatierra G, Cuicapuza D, Furlan JPR, Sellera FP, Chavez L, Esposito F, Tsukayama P and Lincopan N

    Veterinary microbiology 2025;305;110543

    PUBMED: 40339258; DOI: 10.1016/j.vetmic.2025.110543

  • The mutation burden of narrowband ultraviolet B phototherapy (NB-UVB) in human skin; relevance to NB-UVB lifetime exposures and skin cancer surveillance.

    Fowler JC, Sood RK, Coltart G, Lai C, Nadarajah N, Holloway JW, Rose-Zerilli MJJ, Diffey B, Jones PH and Healy E

    The British journal of dermatology 2025

    PUBMED: 40317189; DOI: 10.1093/bjd/ljaf173

  • Misspecification-robust likelihood-free inference in high dimensions

    Thomas, Owen, Sá-Leão, Raquel, de Lencastre, Hermínia, Kaski, Samuel, Corander, Jukka and Pesonen et al.

    Computational Statistics 2025

    DOI: 10.1007/s00180-025-01607-4

  • A tissue-specific atlas of protein-protein associations enables prioritization of candidate disease genes.

    Laman Trip DS, van Oostrum M, Memon D, Frommelt F, Baptista D, Panneerselvam K, Bradley G, Licata L, Hermjakob H, Orchard S et al.

    Nature biotechnology 2025

    PUBMED: 40316700; DOI: 10.1038/s41587-025-02659-z

  • Distinct type I and II interferon responses direct cortical and medullary thymic epithelial cell development.

    Mohammed A, Wang W, Arreola M, Solomon BD, Slepicka PF, Hubka KM, Nguyen HD, Zheng Z, Chavez MG, Yeh CY et al.

    Science immunology 2025;10;107;eado4720

    PUBMED: 40315299; DOI: 10.1126/sciimmunol.ado4720

  • MANIFEST: Multiomic Platform for Cancer Immunotherapy.

    Lim KHJ, Tippu Z, Corrie PG, Hubank M, Larkin J, Lawley TD, Stares M, Stewart GD, Strange A, Symeonides SN et al.

    Cancer discovery 2025;15;5;878-883

    PUBMED: 40313120; DOI: 10.1158/2159-8290.CD-25-0099

  • Aberrant basal cell clonal dynamics shape early lung carcinogenesis.

    Gómez-López S, Alhendi ASN, Przybilla MJ, Bordeu I, Whiteman ZE, Butler T, Rouhani MJ, Kalinke L, Uddin I, Otter KEJ et al.

    Science (New York, N.Y.) 2025;eads9145

    PUBMED: 40310937; DOI: 10.1126/science.ads9145

  • Systematic Ocular Phenotyping of Knockout Mouse Lines Identifies Genes Associated With Age-Related Corneal Dystrophies.

    Briere A, Vo P, Yang B, Adams D, Amano T, Amarie O, Berberovic Z, Bower L, Brown SDM, Burrill S et al.

    Investigative ophthalmology & visual science 2025;66;5;7

    PUBMED: 40323269; PMC: 12060066; DOI: 10.1167/iovs.66.5.7

  • A chromosome-level reference genome for the critically endangered Southern Corroboree frog ( Pseudophryne corroboree).

    Kosch TA, Berger L, Crawford AJ, Gilbert D, Goodall D, Hunter D, McFadden M, Abueg L, Formenti G, Collins J et al.

    Wellcome open research 2025;10;228

    PUBMED: 40756765; PMC: 12314482; DOI: 10.12688/wellcomeopenres.23820.1

  • The genome sequence of the Dark-triangle Button moth, Acleris laterana (Fabricius, 1794).

    Hutchinson F, Crowley LM, Lees DC, University of Oxford Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;231

    PUBMED: 40978456; PMC: 12449689; DOI: 10.12688/wellcomeopenres.24003.1

  • Draft genomic sequences of a rare environmental pathogen, Comamonas kerstersii, from immunocompromised patients with acute gastroenteritis.

    Ballal M, Bangera SR, Shetty V, Umakanth S, Sørensen LH and Hendriksen RS

    Microbiology resource announcements 2025;e0099824

    PUBMED: 40304601; DOI: 10.1128/mra.00998-24

  • Natural language processing in drug discovery: bridging the gap between text and therapeutics with artificial intelligence.

    Withers CA, Rufai AM, Venkatesan A, Tirunagari S, Lobentanzer S, Harrison M and Zdrazil B

    Expert opinion on drug discovery 2025;1-19

    PUBMED: 40298230; DOI: 10.1080/17460441.2025.2490835

  • Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.

    Garcia-Mauriño C, Shao Y, Miltz A, Lawley TD, Rodger A and Field N

    The Lancet. Microbe 2025;101072

    PUBMED: 40482668; DOI: 10.1016/j.lanmic.2024.101072

  • Urethral sarcomatoid urothelial carcinoma with heterologous elements in a dog.

    van der Weyden L, Bertram CA, Dinhopl N, Triebl M, Donovan TA and Compérat EM

    Journal of comparative pathology 2025;219;31-35

    PUBMED: 40300500; DOI: 10.1016/j.jcpa.2025.04.005

  • Variable rates of SARS-CoV-2 evolution in chronic infections.

    Smith EW, Hamilton WL, Warne B, Walker ER, Jahun AS, Hosmillo M, ISARIC Consortium, Gupta RK, Goodfellow I, Gkrania-Klotsas E et al.

    PLoS pathogens 2025;21;4;e1013109

    PUBMED: 40294077; DOI: 10.1371/journal.ppat.1013109

  • Widespread recessive effects on common diseases in a cohort of 44,000 British Pakistanis and Bangladeshis with high autozygosity.

    Heng TH, Walter K, Huang QQ, Karjalainen J, Daly MJ, Heyne HO, FinnGen, Malawsky DS, Kalantzis G, Genes & Health Research Team et al.

    American journal of human genetics 2025

    PUBMED: 40306283; DOI: 10.1016/j.ajhg.2025.03.020

  • The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences.

    Leys SP, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Erpenbeck D, Niu H et al.

    Wellcome open research 2025;10;222

    PUBMED: 40487152; PMC: 12141999; DOI: 10.12688/wellcomeopenres.23988.1

  • The genome sequence of a rove beetle, Philonthus spinipes Sharp, 1874.

    Mann DJ, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;217

    PUBMED: 40470059; PMC: 12134740; DOI: 10.12688/wellcomeopenres.23996.1

  • The genome sequence of petty spurge, Euphorbia peplus L. (Euphorbiaceae).

    Christenhusz MJM, Fay MF, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;219

    PUBMED: 40454263; PMC: 12125573; DOI: 10.12688/wellcomeopenres.24030.1

  • The genome sequence of the Vestal Cuckoo Bee, Bombus vestalis (Geoffroy, 1785).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;218

    PUBMED: 40416837; PMC: 12102655; DOI: 10.12688/wellcomeopenres.24004.1

  • Emergence and spread of ST5 methicillin-resistant Staphylococcus aureus with accessory gene regulator dysfunction: genomic insights and antibiotic resistance.

    Jiang S, Matuszewska M, Chen M, Hong Y, Chen Y, Wang Z, Zhuang H, Sun L, Zhu F, Wang H et al.

    Microbiological research 2025;297;128196

    PUBMED: 40311457; DOI: 10.1016/j.micres.2025.128196

  • The identification of functional regions of MEK1 using CRISPR tiling screens.

    Zhang Z, Abreu B, Brothwood JL, Alexander J, Sims MJ, Lyons JF, Munck JM and Hindley CJ

    Communications biology 2025;8;1;656

    PUBMED: 40274952; DOI: 10.1038/s42003-025-07966-4

  • Production of platelets in vitro in functionalised 3-dimensional scaffolds mimicking the bone marrow niche.

    Foster HR, Colzani M, Bouet G, Howard D, Di Buduo CA, Müller-Sienerth N, Waller AK, Sun Y, Davidenko N, Shepherd JH et al.

    Haematologica 2025

    PUBMED: 40270202; DOI: 10.3324/haematol.2024.286758

  • The genome sequence of the Bordered Sallow moth, Pyrrhia umbra (Hufnagel, 1766).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;208

    PUBMED: 40917440; PMC: 12411841; DOI: 10.12688/wellcomeopenres.24001.1

  • The genome sequence of the Common Grey moth, Scoparia ambigualis Treitschke, 1829.

    Hutchinson F, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;205

    PUBMED: 40718592; PMC: 12290446; DOI: 10.12688/wellcomeopenres.23998.1

  • The genome sequence of the common hop, Humulus lupulus L.

    Christenhusz MJM, Percival-Alwyn L, Hajdu K, Connell J, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2025;10;210

    PUBMED: 40528995; PMC: 12171724; DOI: 10.12688/wellcomeopenres.24025.1

  • The genome sequence of the common water plantain, Alisma plantago-aquatica L. (Alismataceae).

    Christenhusz MJM, Mian S, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;209

    PUBMED: 40454262; PMC: 12125570; DOI: 10.12688/wellcomeopenres.24005.1

  • Geographic and age variations in mutational processes in colorectal cancer.

    Díaz-Gay M, Dos Santos W, Moody S, Kazachkova M, Abbasi A, Steele CD, Vangara R, Senkin S, Wang J, Fitzgerald S et al.

    Nature 2025

    PUBMED: 40267983; DOI: 10.1038/s41586-025-09025-8

  • Integrative analysis of blood biomarkers and clinical variables improves early detection of aggressive prostate cancer.

    Lazareva O, Riediger A, Stegle O, Sültmann H, Hohenfellner M and Görtz M

    Scientific reports 2025;15;1;14071

    PUBMED: 40269068; DOI: 10.1038/s41598-025-98980-3

  • Treatment of acute myeloid leukemia models by targeting a cell surface RNA-binding protein.

    George BM, Eleftheriou M, Yankova E, Perr J, Chai P, Nestola G, Almahayni K, Evans S, Damaskou A, Hemberger H et al.

    Nature biotechnology 2025

    PUBMED: 40269321; DOI: 10.1038/s41587-025-02648-2

  • The genome sequence of the V-Pug moth, Chloroclystis v-ata (Haworth, 1809).

    Boyes D, Gardiner A, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;197

    PUBMED: 40786600; PMC: 12332475; DOI: 10.12688/wellcomeopenres.23965.1

  • Horizontal transfer of nuclear DNA in transmissible cancer.

    Gori K, Baez-Ortega A, Strakova A, Stammnitz MR, Wang J, Chan J, Hughes K, Belkhir S, Hammel M, Moralli D et al.

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;18;e2424634122

    PUBMED: 40261943; DOI: 10.1073/pnas.2424634122

  • The genome sequence of a small dung beetle,  Volinus sticticus (Panzer, 1798), formerly known as Aphodius sticticus.

    Sládeček F, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;195

    PUBMED: 40495928; PMC: 12149814; DOI: 10.12688/wellcomeopenres.23692.1

  • Phenotypic heterogeneity in DYNC2H1-related short-rib thoracic dysplasia: antenatal indicators and postnatal outcomes.

    Pattani N, Elkhateeb N, Joshi A, Del Rey Jimenez JC, Barber JL, Palmrich P, Firth H, Mehta SG, Kesh LAR, Campbell J et al.

    Journal of medical genetics 2025

    PUBMED: 40250984; DOI: 10.1136/jmg-2024-110369

  • Disparate co-evolution and prevalence of sulfadoxine and pyrimethamine resistance alleles and haplotypes at dhfr and dhps genes across Africa.

    White NFD, Whitton G, Wasakul V, Amenga-Etego L, Dara A, Andrianaranjaka V, Randrianarivelojosia M, Miotto O, D'Alessandro U, Djimdé A et al.

    Scientific reports 2025;15;1;13222

    PUBMED: 40247054; PMC: 12006366; DOI: 10.1038/s41598-025-98035-7

  • Desmosome mutations in keratinocytes fuel melanoma development.

    Possik PA, Marie KL and Adams DJ

    Nature genetics 2025

    PUBMED: 40240878; DOI: 10.1038/s41588-025-02133-1

  • Genomic Analysis Reveals a New Cryptic Taxon Within the Anopheles gambiae Complex With a Distinct Insecticide Resistance Profile in the Coast of East Africa.

    Mwinyi SH, Bennett KL, Nagi SC, Kabula B, Matowo J, Weetman D, Baldini F, Babayan SA, Donnelly MJ, Clarkson CS et al.

    Molecular ecology 2025;e17762

    PUBMED: 40241387; DOI: 10.1111/mec.17762

  • Mitochondrial metabolism sustains DNMT3A-R882-mutant clonal haematopoiesis.

    Gozdecka M, Dudek M, Wen S, Gu M, Stopforth RJ, Rak J, Damaskou A, Grice GL, McLoughlin MA, Bond L et al.

    Nature 2025

    PUBMED: 40239706; DOI: 10.1038/s41586-025-08980-6

  • Network-Based Approaches for Drug Target Identification.

    Koutsandreas T, Tsafou K, Horn H, Barrett I and Petsalaki E

    Annual review of biomedical data science 2025;8;1;423-446

    PUBMED: 40239307; DOI: 10.1146/annurev-biodatasci-101424-120950

  • Towards multimodal foundation models in molecular cell biology.

    Cui H, Tejada-Lapuerta A, Brbić M, Saez-Rodriguez J, Cristea S, Goodarzi H, Lotfollahi M, Theis FJ and Wang B

    Nature 2025;640;8059;623-633

    PUBMED: 40240854; DOI: 10.1038/s41586-025-08710-y

  • Cardiac Troponins and Cardiovascular Disease Risk Prediction: An Individual-Participant-Data Meta-Analysis.

    Shah ASV, Keene SJ, Pennells L, Kaptoge S, Kimenai DM, Walker M, Halley JD, Rocha S, Hoogeveen RC, Gudnason V et al.

    Journal of the American College of Cardiology 2025;85;14;1471-1484

    PUBMED: 40204376; DOI: 10.1016/j.jacc.2025.02.016

  • Guidelines for releasing a variant effect predictor.

    Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L et al.

    Genome biology 2025;26;1;97

    PUBMED: 40234898; DOI: 10.1186/s13059-025-03572-z

  • Staphylococcal toxin PVL ruptures model membranes under acidic conditions through interactions with cardiolipin and phosphatidic acid.

    Chow SH, Jeon Y, Deo P, Yeung ATY, Hale C, Sridhar S, Abraham G, Nickson J, Olivier FAB, Jiang JH et al.

    PLoS biology 2025;23;4;e3003080

    PUBMED: 40233125; DOI: 10.1371/journal.pbio.3003080

  • The genome sequence of the Bog Asphodel, Narthecium ossifragum (L.) Huds.

    Ruhsam M, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;194

    PUBMED: 40823657; PMC: 12351241; DOI: 10.12688/wellcomeopenres.24049.1

  • Genome-wide analyses identify 25 infertility loci and relationships with reproductive traits across the allele frequency spectrum.

    Venkatesh SS, Wittemans LBL, Palmer DS, Baya NA, Ferreira T, Hill B, Lassen FH, Parker MJ, Reibe S, Elhakeem A et al.

    Nature genetics 2025

    PUBMED: 40229599; DOI: 10.1038/s41588-025-02156-8

  • Optimization and Characterization of N-Acetamide Indoles as Antimalarials That Target PfATP4.

    Awalt JK, Ooi ZK, Ashton TD, Mansouri M, Calic PPS, Zhou Q, Vasanthan S, Lee S, Loi K, Jarman KE et al.

    Journal of medicinal chemistry 2025

    PUBMED: 40228810; DOI: 10.1021/acs.jmedchem.5c00614

  • Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease.

    Martin-Geary AC, Blakes AJM, Dawes R, Findlay SD, Lord J, Dong S, Walker S, Talbot-Martin J, Wieder N, D'Souza EN et al.

    Genome medicine 2025;17;1;40

    PUBMED: 40229884; PMC: 11998461; DOI: 10.1186/s13073-025-01464-2

  • Lingual hamartoma-like lipoblastoma: the diagnostic value of routine whole-genome sequencing.

    Kan SY, Ferro A, Watkins JA, Behjati S, Murray MJ, Coleman N, Roberts T, Cross J, Trotman J, Tarpey P et al.

    Histopathology 2025

    PUBMED: 40223173; DOI: 10.1111/his.15457

  • The genome sequence of a cluster fly, Pollenia pediculata Macquart, 1834.

    Falk S, Crowley LM, Sivell O, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;190

    PUBMED: 40454264; PMC: 12125572; DOI: 10.12688/wellcomeopenres.23961.1

  • The genome sequence of the Grouse Louse Fly, Ornithomya chloropus (Bergroth, 1901).

    Wawman DC, Insley H, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;191

    PUBMED: 40703329; PMC: 12284471; DOI: 10.12688/wellcomeopenres.23962.1

  • The genome sequence of the Tortix moth, Archips podanus (Scopoli, 1763).

    Boyes D, Fletcher C, Phillips D, Sivess L, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2025;10;189

    PUBMED: 40838167; PMC: 12361883; DOI: 10.12688/wellcomeopenres.23921.1

  • Early-life gut microbiome associates with positive vaccine take and shedding in neonatal schedule of the human neonatal rotavirus vaccine RV3-BB.

    Wagner J, Handley A, Donato CM, Lyons EA, Pavlic D, Ong DS, Bonnici R, Bogdanovic-Sakran N, Parker EPK, Bronowski C et al.

    Nature communications 2025;16;1;3432

    PUBMED: 40210877; DOI: 10.1038/s41467-025-58632-6

  • A single-cell and tissue-scale analysis suite resolves Mixl1's role in heart development.

    Strauss ME, Ton MN, Mason S, Bagri J, Harland LTG, Imaz-Rosshandler I, Wilson NK, Nichols J, Tyser RCV, Göttgens B et al.

    iScience 2025;28;5;112397

    PUBMED: 40330894; PMC: 12051648; DOI: 10.1016/j.isci.2025.112397

  • Two chromosomal reference genome sequences for the malaria mosquito, Anopheles ( Nyssorhynchus) darlingi, Root, 1926 from French Guiana and Peru.

    Gendrin M, Heu K, Moreno M, Gamboa D, Vinetz JM, Tong C, Conn JE, Johnson HF, Heaton H, Wagah MG et al.

    Wellcome open research 2025;10;187

    PUBMED: 41040652; PMC: 12485361; DOI: 10.12688/wellcomeopenres.23989.1

  • DNA-guided transcription factor interactions extend human gene regulatory code.

    Xie Z, Sokolov I, Osmala M, Yue X, Bower G, Pett JP, Chen Y, Wang K, Cavga AD, Popov A et al.

    Nature 2025

    PUBMED: 40205063; DOI: 10.1038/s41586-025-08844-z

  • Hepatitis B virus resistance to nucleos(t)ide analogue therapy: WHO consultation on questions, challenges, and a roadmap for the field.

    Lumley SF, Mokaya J, Maponga TG, Kramvis A, Dusheiko G, Irving W, Delphin M, Said Mohammed K, Downs LO, Waddilove E et al.

    The Lancet. Microbe 2025;101076

    PUBMED: 40220768; DOI: 10.1016/j.lanmic.2025.101076

  • In vivo evaluation of phage therapy against Klebsiella pneumoniae using the Galleria mellonella model and molecular characterization of a novel Drulisvirus phage species.

    Quispe-Villegas G, Alcántara-Lozano GI, Cuicapuza D, Laureano R, Ayzanoa B, Tsukayama P and Tamariz J

    Microbiology spectrum 2025;e0114524

    PUBMED: 40202337; DOI: 10.1128/spectrum.01145-24

  • Timing and trajectory of BCR::ABL1-driven chronic myeloid leukaemia.

    Kamizela AE, Leongamornlert D, Williams N, Wang X, Nyamondo K, Dawson K, Spencer Chapman M, Guo J, Lee J, Mane K et al.

    Nature 2025

    PUBMED: 40205062; DOI: 10.1038/s41586-025-08817-2

  • Translational genomics of osteoarthritis in 1,962,069 individuals.

    Hatzikotoulas K, Southam L, Stefansdottir L, Boer CG, McDonald ML, Pett JP, Park YC, Tuerlings M, Mulders R, Barysenka A et al.

    Nature 2025

    PUBMED: 40205036; DOI: 10.1038/s41586-025-08771-z

  • The genome sequence of a cave spider, Troglohyphantes excavatus Fage, 1919.

    Pavlek M, Rožman T, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2025;10;177

    PUBMED: 41040644; PMC: 12485337; DOI: 10.12688/wellcomeopenres.23920.1

  • The genome sequence of a snail-killing fly, Dichetophora obliterata (Fabricius, 1805).

    Crowley LM, Sivell O, Mitchell R, Sivell D, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;176

    PUBMED: 40433623; PMC: 12107236; DOI: 10.12688/wellcomeopenres.23993.1

  • The genome sequence of long-finned pilot whale, Globicephala melas (Traill, 1809).

    Davison NJ, Morin PA, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;180

    PUBMED: 40256617; PMC: 12009481; DOI: 10.12688/wellcomeopenres.23919.1

  • The genome sequence of the Brindled White-spot moth, Parectropis similaria (Hufnagel, 1767).

    Boyes D, Broad GR, Lees DC, Boyes C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;179

    PUBMED: 41040654; PMC: 12485357; DOI: 10.12688/wellcomeopenres.23984.1

  • The genome sequence of the European ground squirrel, Spermophilus citellus (Linnaeus, 1766).

    Rammou DL, Youlatos D, Triantafyllidis A, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2025;10;184

    PUBMED: 40433625; PMC: 12107237; DOI: 10.12688/wellcomeopenres.23974.1

  • The genome sequence of the harbour porpoise, Phocoena phocoena (Linnaeus, 1758).

    Davison NJ, Morin PA, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;181

    PUBMED: 40256618; PMC: 12006785; DOI: 10.12688/wellcomeopenres.24011.1

  • The genome sequence of the short-beaked common dolphin, Delphinus delphis Linnaeus, 1758.

    Davison NJ, Morin PA, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;178

    PUBMED: 40290354; PMC: 12022549; DOI: 10.12688/wellcomeopenres.23918.1

  • The genome sequence of the Sycamore-seed Pygmy moth, Ectoedemia decentella (Herrich-Schäffer, 1855) van Nieukerken, 1986.

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;182

    PUBMED: 41040647; PMC: 12485360; DOI: 10.12688/wellcomeopenres.23973.1

  • Improved genetic discovery and fine-mapping resolution through multivariate latent factor analysis of high-dimensional traits.

    Zhou F, Astle WJ, Butterworth AS and Asimit JL

    Cell genomics 2025;100847

    PUBMED: 40220762; DOI: 10.1016/j.xgen.2025.100847

  • KpnK48 clone driving hypervirulent carbapenem-resistant Escherichia coli epidemics: Insights into its evolutionary trajectory similar to Klebsiella pneumoniae.

    Wang M, Jin L, Wang R, Wang Q, Wang S, Wu X, Yao C, Corander J and Wang H

    Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy 2025;81;101243

    PUBMED: 40239363; DOI: 10.1016/j.drup.2025.101243

  • The genome sequence of Glossophaga mutica (Chiroptera, Phyllostomidae, Glossophaginae; Merriam, 1898).

    Simmons NB, Ingala MR, O'Toole BP, Abueg L, McCaffrey K, Koo B, Formenti G, Jarvis ED, Pieri M, Mai M et al.

    Wellcome open research 2025;10;174

    PUBMED: 40386544; PMC: 12082079; DOI: 10.12688/wellcomeopenres.23611.1

  • Protocol for the functional evaluation of genetic variants using saturation genome editing.

    Obolenski S, Olvera-León R, Sun D, Adams DJ and Waters AJ

    STAR protocols 2025;6;2;103710

    PUBMED: 40198219; DOI: 10.1016/j.xpro.2025.103710

  • Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study.

    Xie O, Chisholm RH, Featherstone L, Nguyen ANT, Hayes AJ, Jespersen MG, Zachreson C, Tellioglu N, Tonkin-Hill G, Dotel R et al.

    The Lancet. Microbe 2025;101053

    PUBMED: 40194534; DOI: 10.1016/j.lanmic.2024.101053

  • A new set of mutations in the second transmembrane helix of the Cox2p-W56R substantially improves its allotopic expression in Saccharomyces cerevisiae.

    Gombeau K, Hoffmann SA and Cai Y

    Genetics 2025

    PUBMED: 40178993; DOI: 10.1093/genetics/iyaf037

  • Microbial solutions for climate change require global partnership.

    Lennon JT, Rappuoli R, Bloom DE, Brooke C, Burckhardt RM, Dangour AD, Egamberdieva D, Gronvall GK, Lawley TD, Morhard R et al.

    mBio 2025;e0077825

    PUBMED: 40176258; DOI: 10.1128/mbio.00778-25

  • Plasmid-driven strategies for clone success in Escherichia coli.

    Arredondo-Alonso S, Pöntinen AK, Gama JA, Gladstone RA, Harms K, Tonkin-Hill G, Thorpe HA, Simonsen GS, Samuelsen Ø, Johnsen PJ et al.

    Nature communications 2025;16;1;2921

    PUBMED: 40180894; DOI: 10.1038/s41467-025-57940-1

  • A new strain of thought in gut metagenomics.

    Gichuki BM, Van Camp AG and Shao Y

    Nature reviews. Microbiology 2025

    PUBMED: 40175522; DOI: 10.1038/s41579-025-01176-9

  • The genome sequence of Artibeus lituratus (Chiroptera, Phyllostomidae, Stenodermatinae; Olfers, 1818).

    Simmons NB, Ingala MR, O'Toole BP, Formenti G, Philge P, Zhang N, Jarvis ED, Gray JL, McCaffrey K, Brajuka N et al.

    Wellcome open research 2025;10;170

    PUBMED: 40808701; PMC: 12344409; DOI: 10.12688/wellcomeopenres.23088.1

  • A Million Years of Mammoth Mitogenome Evolution.

    Chacón-Duque JC, Thomas Thorpe JA, Li W, Dehasque M, Pečnerová P, Barlow A, Díez-Del-Molino D, Henneberger K, Jin C, Moreland KN et al.

    Molecular biology and evolution 2025;42;4

    PUBMED: 40202893; PMC: 11980863; DOI: 10.1093/molbev/msaf065

  • Comparative pangenomics of Streptococcus pneumoniae from Malawi: uncovering genetic variability and pathogenicity.

    Iranzadeh A, Alisoltani A, Kiran AM, Breiman RF, Chaguza C, Peno C, Cornick JE, Everett DB and Mulder N

    Microbial genomics 2025;11;4

    PUBMED: 40232949; DOI: 10.1099/mgen.0.001370

  • Genomic characterization of group B Streptococcus from Argentina: insights into prophage diversity, virulence factors and antibiotic resistance genes.

    Kovacec V, Di Gregorio S, Pajon M, Khan UB, Poklepovich T, Campos J, Crestani C, Bentley SD, Jamrozy D, Mollerach M and Bonofiglio L

    Microbial genomics 2025;11;4

    PUBMED: 40266661; DOI: 10.1099/mgen.0.001399

  • The complexity of tobacco smoke-induced mutagenesis in head and neck cancer.

    Torrens L, Moody S, de Carvalho AC, Kazachkova M, Abedi-Ardekani B, Cheema S, Senkin S, Cattiaux T, Cortez Cardoso Penha R, Atkins JR et al.

    Nature genetics 2025

    PUBMED: 40164736; DOI: 10.1038/s41588-025-02134-0

  • Causal machine learning for single-cell genomics.

    Tejada-Lapuerta A, Bertin P, Bauer S, Aliee H, Bengio Y and Theis FJ

    Nature genetics 2025

    PUBMED: 40164735; DOI: 10.1038/s41588-025-02124-2

  • Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence.

    Cruz-Castillo C, Fumis L, Mehta C, Martinez-Osorio RE, Roldan-Romero JM, Cornu H, Uniyal P, Solano-Roman A, Carmona M, Ochoa D et al.

    Bioinformatics (Oxford, England) 2025;41;4

    PUBMED: 39936578; PMC: 11968318; DOI: 10.1093/bioinformatics/btaf070

  • Lit-OTAR framework for extracting biological evidences from literature.

    Tirunagari S, Saha S, Venkatesan A, Suveges D, Carmona M, Buniello A, Ochoa D, McEntyre J, McDonagh E and Harrison M

    Bioinformatics (Oxford, England) 2025;41;4

    PUBMED: 40097274; PMC: 11978389; DOI: 10.1093/bioinformatics/btaf113

  • Key priorities for the implementation of the 2023 ESC Guidelines for the management of cardiovascular disease in patients with diabetes in low-resource settings.

    Marx N, Schütt K, Müller-Wieland D, Di Angelantonio E, Herrington WG, Ajjan RA, Kautzky-Willer A, Rocca B, Sattar N, Fauchier L et al.

    European heart journal. Quality of care & clinical outcomes 2025

    PUBMED: 40152911; DOI: 10.1093/ehjqcco/qcae105

  • Optimal risk assessment intervals for primary prevention of cardiovascular disease: a population-based two-stage landmarking study.

    Gu Z, Gasperoni F, Paige E, Sweeting M, Usher-Smith J, Poppe K, Stevens D, Arnold M, Di Angelantonio E, Wood AM and Barrett JK

    BMJ public health 2025;3;1;e001241

    PUBMED: 40166609; PMC: 11956352; DOI: 10.1136/bmjph-2024-001241

  • A flexible framework for minimal biomarker signature discovery from clinical omics studies without library size normalisation.

    Rawlinson D, Zhou C, Kaforou M, Cao KL, Coin LJM and RAPIDS Study Group

    PLOS digital health 2025;4;3;e0000780

    PUBMED: 40138621; DOI: 10.1371/journal.pdig.0000780

  • The human endometrium: atlases, models, and prospects.

    Wong FC, Kim CE, Garcia-Alonso L and Vento-Tormo R

    Current opinion in genetics & development 2025;92;102341

    PUBMED: 40154154; DOI: 10.1016/j.gde.2025.102341

  • Dynamic roles of ILC3 in endometrial repair and regeneration.

    Cuff AO, Von Woon E, Bainton T, Browne B, Kirkwood PM, Collins F, Gibson DA, Saunders PTK, Horne AW, Johnson MR et al.

    Discovery immunology 2025;4;1;kyaf004

    PUBMED: 40303843; PMC: 12038238; DOI: 10.1093/discim/kyaf004

  • Interferon-Inducible ADAR1 p150 Is Essential for the Survival of Oral Squamous Cell Carcinoma.

    Yee PS, Chai AWY, Yee SM, Ooi S, Tan YH, Garnett MJ, Ng SK and Cheong SC

    Molecular carcinogenesis 2025

    PUBMED: 40135601; DOI: 10.1002/mc.23910

  • Socio-economic status is a social construct with heritable components and genetic consequences.

    Abdellaoui A, Martin HC, Kolk M, Rutherford A, Muthukrishna M, Tropf FC, Mills MC, Zietsch BP, Verweij KJH and Visscher PM

    Nature human behaviour 2025

    PUBMED: 40140606; DOI: 10.1038/s41562-025-02150-4

  • CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.

    Troulé K, Petryszak R, Cakir B, Cranley J, Harasty A, Prete M, Tuong ZK, Teichmann SA, Garcia-Alonso L and Vento-Tormo R

    Nature protocols 2025

    PUBMED: 40133495; DOI: 10.1038/s41596-024-01137-1

  • Microbes can capture carbon and degrade plastic - why aren't we using them?

    Rappuoli, R, Nguyen, NK, Bloom, DE, Brooke, C, Burckhardt, RM et al.

    Nature 2025;639;8056

    DOI: 10.1038/d41586-025-00875-w; URL: http://dx.doi.org/10.1038/d41586-025-00875-w

  • Streptococcus pneumoniae serotype 33H: a novel serotype with frameshift mutations in the acetyltransferase gene wciG.

    Manna S, Ortika BD, Werren JP, Pell CL, Gjuroski I, Lo SW, Hinds J, Tundev O, Dunne EM, Gessner BD et al.

    Pneumonia (Nathan Qld.) 2025;17;1;7

    PUBMED: 40128891; PMC: 11934437; DOI: 10.1186/s41479-025-00162-2

  • Large-scale combination screens reveal small-molecule sensitization of antibiotic-resistant gram-negative ESKAPE pathogens.

    Tse MW, Zhu M, Peters B, Hamami E, Chen J, Davis KP, Nitz S, Weller J, Warrier T, Hunt DK et al.

    Proceedings of the National Academy of Sciences of the United States of America 2025;122;13;e2402017122

    PUBMED: 40127266; DOI: 10.1073/pnas.2402017122

  • Differential neuronal vulnerability to C9orf72 repeat expansion driven by Xbp1-induced endoplasmic reticulum-associated degradation.

    Shen D, Vincent A, Udine E, Buhidma Y, Anoar S, Tsintzas E, Maeland M, Xu D, Carcolé M, Osumi-Sutherland D et al.

    Cell reports 2025;115459

    PUBMED: 40203833; DOI: 10.1016/j.celrep.2025.115459

  • Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.

    Bridges Y, Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ et al.

    BMC bioinformatics 2025;26;1;87

    PUBMED: 40121479; PMC: 11929307; DOI: 10.1186/s12859-025-06105-4

  • 2024 Revision of the level of evidence grading system for ESC clinical practice guideline recommendations II: diagnostic tests and prediction models.

    Di Angelantonio E, Pennells L, Abdelhamid M, Aboyans V, Asteggiano R, Čelutkienė J, Grobbee DE, Iung B, Jüni P, McEvoy JW et al.

    European heart journal 2025

    PUBMED: 40116738; DOI: 10.1093/eurheartj/ehaf016

  • Microvascular aberrations found in human polycystic kidneys are an early feature in a Pkd1 mutant mouse model.

    Jafree DJ, Perera C, Ball M, Tolomeo D, Pomeranz G, Wilson L, Davis B, Mason WJ, Funk EM, Kolatsi-Joannou M et al.

    Disease models & mechanisms 2025

    PUBMED: 40114603; DOI: 10.1242/dmm.052024

  • The genome sequence of a cave beetle, Leptodirus hochenwartii F.J.Schmidt, 1832.

    Delić T, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Tree of Life Core Informatics collective and Wellcome Sanger Institute Tree of Life Core Informatics team

    Wellcome open research 2025;10;159

    PUBMED: 40225906; PMC: 11992515; DOI: 10.12688/wellcomeopenres.23959.1

  • Myxozoan parasite genomes assembled from contaminated host data reveal extensive gene order conservation and rapid sequence evolution.

    Weber CC, Paulini M and Blaxter ML

    G3 (Bethesda, Md.) 2025

    PUBMED: 40112161; DOI: 10.1093/g3journal/jkaf061

  • The genome sequence of a beetle, Pycnomerus fuliginosus Erichson, 1842.

    Sivell O, Taylor SC, Barclay MVL, Skipp S, Geiser MF, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;144

    PUBMED: 40256616; PMC: 12006784; DOI: 10.12688/wellcomeopenres.23770.1

  • The genome sequence of a carabid beetle, Abax parallelepipedus (Piller & Mitterpacher, 1783).

    Sivell O, Sivell D, Mitchell R, Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;147

    PUBMED: 40386542; PMC: 12082080; DOI: 10.12688/wellcomeopenres.23888.1

  • The genome sequence of a cranefly, Tipula lateralis Meigen, 1804.

    Sivell D, Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;149

    PUBMED: 41040648; PMC: 12485334; DOI: 10.12688/wellcomeopenres.23899.1

  • The genome sequence of a snipefly, Rhagio lineola Fabricius, 1794.

    Sivell O, Sivell D, Mitchell R, Webb JA, Falk S, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2025;10;154

    PUBMED: 41063758; PMC: 12501595; DOI: 10.12688/wellcomeopenres.23901.1

  • The genome sequence of the Banded Ivy Tortrix moth, Clepsis dumicolana (Zeller, 1847).

    Lees DC, Sterling MJ, Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;153

    PUBMED: 41040655; PMC: 12485335; DOI: 10.12688/wellcomeopenres.23905.1

  • The genome sequence of the Common Pochard, Aythya ferina (Linnaeus, 1758).

    O'Brien MF, Lopez Colom R, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;152

    PUBMED: 40256619; PMC: 12009480; DOI: 10.12688/wellcomeopenres.23904.1

  • The genome sequence of the Four-spotted Footman moth, Lithosia quadra (Linnaeus, 1758).

    Hutchinson F, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;146

    PUBMED: 40302899; PMC: 12038344; DOI: 10.12688/wellcomeopenres.23788.1

  • The genome sequence of the Sandhill Knot-horn moth, Anerastia lotella Hübner, 1813.

    Boyes C, Martin JP, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;148

    PUBMED: 41040646; PMC: 12485358; DOI: 10.12688/wellcomeopenres.23898.1

  • The genome sequence of the Straw-barred Pearl moth, Pyrausta despicata Scopoli, 1763.

    Broad GR, Lees DC, Boyes D, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;151

    PUBMED: 40443799; PMC: 12120437; DOI: 10.12688/wellcomeopenres.23902.1

  • The somatic mutation landscape of normal gastric epithelium.

    Coorens THH, Collord G, Jung H, Wang Y, Moore L, Hooks Y, Mahbubani K, Law SYK, Yan HHN, Yuen ST et al.

    Nature 2025

    PUBMED: 40108450; DOI: 10.1038/s41586-025-08708-6

  • Enable, empower, succeed: a bioinformatics workshop Harnessing open web-based tools for surveillance of bacterial antimicrobial resistance.

    Founou LL, Lawal OU, Djiyou A, Odih EE, Amoako DG, Fadanka S, Aworh MK, Lukhele S, Nikolic D, Matimba A and Founou RC

    BMC microbiology 2025;25;1;156

    PUBMED: 40102762; PMC: 11921729; DOI: 10.1186/s12866-025-03865-0

  • The genome sequence of a bark-dwelling beetle, Silvanus unidentatus (Olivier, 1790).

    Barclay MVL, Turner T, Telfer MG, Geiser MF, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;136

    PUBMED: 40206407; PMC: 11979581; DOI: 10.12688/wellcomeopenres.23771.1

  • The genome sequence of an ichneumonid wasp, Polytribax perspicillator (Gravenhorst, 1807).

    Broad GR, Crowley LM, Januszczak I, Fletcher C, Barnes I, McCulloch J, De Ketelaere A, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management et al.

    Wellcome open research 2025;10;140

    PUBMED: 40271159; PMC: 12015431; DOI: 10.12688/wellcomeopenres.23769.1

  • The genome sequence of the Maple Pug moth, Eupithecia inturbata (Hübner, 1817).

    Hutchinson F, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;141

    PUBMED: 40225904; PMC: 11992513; DOI: 10.12688/wellcomeopenres.23796.1

  • The genome sequence of the True Lover's Knot moth, Lycophotia porphyrea (Denis & Schiffermüller), 1775.

    Davis J, Griffiths A, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;9;469

    PUBMED: 40115046; PMC: 11923537; DOI: 10.12688/wellcomeopenres.22897.2

  • Epidemiology of Group B Streptococcus: Maternal Colonization and Infant Disease in Kampala, Uganda.

    Kyohere M, Davies HG, Karampatsas K, Cantrell L, Musoke P, Nakimuli A, Tusubira V, Nsimire JS, Jamrozy D, Khan UB et al.

    Open forum infectious diseases 2025;12;4;ofaf167

    PUBMED: 40201722; PMC: 11977330; DOI: 10.1093/ofid/ofaf167

  • Quantitative characterization of cell niches in spatially resolved omics data.

    Birk S, Bonafonte-Pardàs I, Feriz AM, Boxall A, Agirre E, Memi F, Maguza A, Yadav A, Armingol E, Fan R et al.

    Nature genetics 2025

    PUBMED: 40102688; DOI: 10.1038/s41588-025-02120-6

  • Reassessing the association between age at menarche and cardiovascular disease: observational and Mendelian randomization analyses.

    Tschiderer L, Peters SAE, van der Schouw YT, Burgess S, Luijken J, Bijmolt C, Soliman H, Butterworth AS, Wood AM, Tong TYN et al.

    European journal of preventive cardiology 2025

    PUBMED: 40099743; DOI: 10.1093/eurjpc/zwaf051

  • The genome sequence of a chironomid fly, Chironomus tentans Fabricius, 1805.

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;133

    PUBMED: 40302898; PMC: 12038343; DOI: 10.12688/wellcomeopenres.23907.1

  • The genome sequence of the Bog Ant Fly, Microdon myrmicae Schönrogge et al., 2002.

    Wolton RJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;134

    PUBMED: 41040650; PMC: 12485359; DOI: 10.12688/wellcomeopenres.23903.1

  • Decoding pathogen evolution to curb antimicrobial resistance.

    Shetty V and Mutreja A

    Nature reviews. Microbiology 2025

    PUBMED: 40097639; DOI: 10.1038/s41579-025-01168-9

  • The genome sequence of the Triangle-marked Roller, Ancylis achatana (Denis & Schiffermüller), 1775.

    Boyes D, Lees DC, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;128

    PUBMED: 41040651; PMC: 12485347; DOI: 10.12688/wellcomeopenres.23897.1

  • The genome sequence of the Yellow-legged Gull, Larus michahellis Naumann, 1840.

    Ramos E, Schweizer M, Wu MY, Sahli C, Latt C, Lunak M, Crochet PA, Salzburger W, Meier J, Marques DA et al.

    Wellcome open research 2025;10;129

    PUBMED: 40386543; PMC: 12082078; DOI: 10.12688/wellcomeopenres.23849.1

  • Biomedical data and AI.

    Xu H, Zhou S, Zhu Z, Vitelli V, Chen L, Dai Z, Yang N, Lai L, Yang S, Ovchinnikov S et al.

    Science China. Life sciences 2025

    PUBMED: 40100542; DOI: 10.1007/s11427-024-2859-1

  • Cell envelope polysaccharide modifications alter the surface properties and interactions of Mycobacterium abscessus with innate immune cells in a morphotype-dependent manner.

    Lian E, Belardinelli JM, De K, Pandurangan AP, Angala SK, Palčeková Z, Grzegorzewicz AE, Bryant JM, Blundell TL, Parkhill J et al.

    mBio 2025;e0032225

    PUBMED: 40084888; DOI: 10.1128/mbio.00322-25

  • Chromosome-level haplotype-resolved genome assembly of bread wheat's wild relative Aegilops mutica.

    Grewal S, Yang CY, Krasheninnikova K, Collins J, Wood JMD, Ashling S, Scholefield D, Kaithakottil GG, Swarbreck D, Yao E et al.

    Scientific data 2025;12;1;438

    PUBMED: 40082453; PMC: 11906796; DOI: 10.1038/s41597-025-04737-y

  • Feature selection methods affect the performance of scRNA-seq data integration and querying.

    Zappia L, Richter S, Ramírez-Suástegui C, Kfuri-Rubens R, Vornholz L, Wang W, Dietrich O, Frishberg A, Luecken MD and Theis FJ

    Nature methods 2025

    PUBMED: 40082610; DOI: 10.1038/s41592-025-02624-3

  • Long term latency of highly mutated cells in normal mouse skin is reversed by exposure to tumor promoters and chronic tissue damage.

    Li YR, Kandyba E, Halliwill K, Delrosario R, Tran Q, Bayani N, Wu D, Mirzoeva OK, Reeves MQ, Islam SMA et al.

    Cancer discovery 2025

    PUBMED: 40073432; DOI: 10.1158/2159-8290.CD-24-1379

  • Focus on Tumours in Pet Animals

    van der Weyden, L

    VETERINARY SCIENCES 2025;12;3;266

    DOI: 10.3390/vetsci12030266; URL: http://dx.doi.org/10.3390/vetsci12030266

  • Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19.

    Lee JTH, Barnett SN, Roberts K, Ashwin H, Milross L, Cho JW, Huseynov A, Woodhams B, Aivazidis A, Li T et al.

    Nature communications 2025;16;1;1979

    PUBMED: 40064844; PMC: 11893906; DOI: 10.1038/s41467-025-56473-x

  • Selection for somatic escape variants in SERPINA1 in the liver of patients with alpha-1 antitrypsin deficiency.

    Brzozowska N, Wu LYD, Khodzhaeva V, Griffiths WJ, Duckworth A, Jung H, Coorens THH, Hooks Y, Chambers JE, Campbell PJ et al.

    Nature genetics 2025

    PUBMED: 40065168; DOI: 10.1038/s41588-025-02125-1

  • The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.

    Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ et al.

    Genetics 2025

    PUBMED: 40048704; DOI: 10.1093/genetics/iyaf027

  • ARHGAP12 and ARHGAP29 exert distinct regulatory effects on switching between two cell morphological states through GSK-3 activity.

    Cheng VWT, Vaughn-Beaucaire P, Shaw GC, Kriegs M, Droop A, Psakis G, Mittelbronn M, Humphries M, Esteves F, Hayes J et al.

    Cell reports 2025;44;3;115361

    PUBMED: 40053455; DOI: 10.1016/j.celrep.2025.115361

  • Aspirin prevents metastasis by limiting platelet TXA2 suppression of T cell immunity.

    Yang J, Yamashita-Kanemaru Y, Morris BI, Contursi A, Trajkovski D, Xu J, Patrascan I, Benson J, Evans AC, Conti AG et al.

    Nature 2025

    PUBMED: 40044852; DOI: 10.1038/s41586-025-08626-7

  • Clonal dynamics and somatic evolution of haematopoiesis in mouse.

    Kapadia CD, Williams N, Dawson KJ, Watson C, Yousefzadeh MJ, Le D, Nyamondo K, Kodavali S, Cagan A, Waldvogel S et al.

    Nature 2025

    PUBMED: 40044850; DOI: 10.1038/s41586-025-08625-8

  • The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes.

    Tokolyi A, Persyn E, Nath AP, Burnham KL, Marten J, Vanderstichele T, Tardaguila M, Stacey D, Farr B, Iyer V et al.

    Nature genetics 2025

    PUBMED: 40038547; DOI: 10.1038/s41588-025-02096-3

  • The genome sequence of the common crane, Grus grus (Linnaeus, 1758).

    O'Brien MF, Lopez Colom R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;119

    PUBMED: 40162188; PMC: 11953615; DOI: 10.12688/wellcomeopenres.23797.1

  • Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes.

    Henry A, Mo X, Finan C, Chaffin MD, Speed D, Issa H, Denaxas S, Ware JS, Zheng SL, Malarstig A et al.

    Nature genetics 2025

    PUBMED: 40038546; DOI: 10.1038/s41588-024-02064-3

  • Cell2fate infers RNA velocity modules to improve cell fate prediction.

    Aivazidis A, Memi F, Kleshchevnikov V, Er S, Clarke B, Stegle O and Bayraktar OA

    Nature methods 2025

    PUBMED: 40032996; DOI: 10.1038/s41592-025-02608-3

  • Identification of plasma proteomic markers underlying polygenic risk of type 2 diabetes and related comorbidities.

    Loesch DP, Garg M, Matelska D, Vitsios D, Jiang X, Ritchie SC, Sun BB, Runz H, Whelan CD, Holman RR et al.

    Nature communications 2025;16;1;2124

    PUBMED: 40032831; PMC: 11876343; DOI: 10.1038/s41467-025-56695-z

  • Agents for Change: Artificial Intelligent Workflows for Quantitative Clinical Pharmacology and Translational Sciences.

    Shahin MH, Goswami S, Lobentanzer S and Corrigan BW

    Clinical and translational science 2025;18;3;e70188

    PUBMED: 40055986; PMC: 11889410; DOI: 10.1111/cts.70188

  • Genomic characterization of Streptococcus pneumoniae isolates obtained from carriage and disease among paediatric patients in Addis Ababa, Ethiopia.

    Negash AA, Ferreira A, Asrat D, Aseffa A, Cools P, Van Simaey L, Vaneechoutte M, Bentley SD and Lo SW

    Microbial genomics 2025;11;3

    PUBMED: 40100271; DOI: 10.1099/mgen.0.001376

  • Glasswing butterfly (Mechanitis messenoides).

    Meier JI

    Nature ecology & evolution 2025;9;3;526

    PUBMED: 40069443; DOI: 10.1038/s41559-025-02655-1

  • Investigating two decades of Streptococcus pneumoniae bacteraemia in the Gelderland area, the Netherlands, using whole-genome sequencing.

    Sanches Ferreira AD, King AC, Wolters F, Wertheim HFL, Mulder B, Swanink CMA, van der Gaast-de Jongh CE, Arends DW, van Sorge NM, Schaars C et al.

    Microbial genomics 2025;11;3

    PUBMED: 40100258; PMC: 11936379; DOI: 10.1099/mgen.0.001377

  • Pregnant women as a sentinel population for genomic surveillance of malaria in the Democratic Republic of the Congo: a population-based study.

    Onyamboko M, Wasakul V, Bakomba SB, Kayembe DK, Nzambiwishe BK, Ekombolo PE, Badjanga BB, Maindombe JM, Ngavuka JN, Lwadi BN et al.

    The Lancet. Global health 2025;13;3;e479-e487

    PUBMED: 40021306; PMC: 11868776; DOI: 10.1016/S2214-109X(24)00497-2

  • The genome sequence of a long-legged fly, Scellus notatus (Fabricius, 1781).

    Falk S, Crowley LM, McCulloch J, Akinmusola RY, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;117

    PUBMED: 40104438; PMC: 11914874; DOI: 10.12688/wellcomeopenres.23764.1

  • The genome sequence of a mirid bug, Stenodema calcarata (Fallen, 1807).

    McCulloch J, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;115

    PUBMED: 40162190; PMC: 11950723; DOI: 10.12688/wellcomeopenres.23763.1

  • The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767).

    Broad GR, Holt S, Sivess L, Boyes D, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2025;10;111

    PUBMED: 40125538; PMC: 11926530; DOI: 10.12688/wellcomeopenres.23761.1

  • Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function.

    Beresford-Jones BS, Suyama S, Clare S, Soderholm A, Xia W, Sardar P, Lee J, Harcourt K, Lawley TD and Pedicord VA

    Microbiome 2025;13;1;61

    PUBMED: 40022210; PMC: 11869688; DOI: 10.1186/s40168-025-02050-9

  • Breaking barriers: we need a multidisciplinary approach to tackle cancer drug resistance.

    Ingham J, Ruan JL and Coelho MA

    BJC reports 2025;3;1;11

    PUBMED: 40016372; DOI: 10.1038/s44276-025-00129-2

  • A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758.

    Hesson JC, Haba Y, McBride CS, Sheerin E, Mathers TC, Paulini M, Pointon DB, Torrance JW, Sadasivan Baby C, Wood JMD et al.

    Wellcome open research 2025;10;107

    PUBMED: 40115327; PMC: 11923538; DOI: 10.12688/wellcomeopenres.23767.1

  • The genome sequence of the virgin bagworm, Luffia ferchaultella (Stephens, 1850).

    Whiteford S, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;108

    PUBMED: 40894110; PMC: 12391867; DOI: 10.12688/wellcomeopenres.23768.1

  • LLIN Evaluation in Uganda Project (LLINEUP2) - Effect of long-lasting insecticidal nets (LLINs) treated with pyrethroid plus pyriproxyfen vs LLINs treated with pyrethroid plus piperonyl butoxide in Uganda: A cluster-randomised trial.

    Gonahasa S, Namuganga JF, Nassali MJ, Maiteki-Sebuguzi C, Nabende I, Epstein A, Snyman K, Nankabirwa JI, Opigo J, Donnelly MJ et al.

    PLOS global public health 2025;5;2;e0003558

    PUBMED: 40009611; PMC: 11864545; DOI: 10.1371/journal.pgph.0003558

  • Cancer-independent somatic mutation of the wild-type NF1 allele in normal tissues in neurofibromatosis type 1.

    Oliver TRW, Lawson ARJ, Lee-Six H, Tollit A, Jung H, Hooks Y, Sanghvi R, Young MD, Butler TM, Nicola PA et al.

    Nature genetics 2025

    PUBMED: 40000831; DOI: 10.1038/s41588-025-02097-2

  • SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.

    Martino C, Kellman BP, Sandoval DR, Clausen TM, Cooper R, Benjdia A, Soualmia F, Clark AE, Garretson AF, Marotz CA et al.

    mBio 2025;e0401524

    PUBMED: 39998226; DOI: 10.1128/mbio.04015-24

  • The cellular and molecular cardiac tissue responses in human inflammatory cardiomyopathies after SARS-CoV-2 infection and COVID-19 vaccination.

    Maatz H, Lindberg EL, Adami E, López-Anguita N, Perdomo-Sabogal A, Cocera Ortega L, Patone G, Reichart D, Myronova A, Schmidt S et al.

    Nature cardiovascular research 2025

    PUBMED: 39994453; DOI: 10.1038/s44161-025-00612-6

  • The genome sequence of an orbweaving spider, Gibbaranea gibbosa (Walckenaer, 1802).

    Crowley LM, Wilding CS, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;97

    PUBMED: 40162187; PMC: 11953616; DOI: 10.12688/wellcomeopenres.23751.1

  • The genome sequence of the amphioxus, Branchiostoma lanceolatum (Pallas, 1774).

    Adkins P, Bishop J, Harley J, Holland PWH, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;95

    PUBMED: 40093594; PMC: 11907188; DOI: 10.12688/wellcomeopenres.23671.1

  • The genome sequence of the click beetle, Ampedus sanguinolentus sanguinolentus (Schrank, 1776).

    Sivell D, Telnov D, Geiser MF, Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;96

    PUBMED: 40134828; PMC: 11933788; DOI: 10.12688/wellcomeopenres.23712.1

  • The genome sequence of the Common Sheetweb Spider Linyphia triangularis (Clerck, 1757).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;92

    PUBMED: 40084296; PMC: 11904403; DOI: 10.12688/wellcomeopenres.23754.1

  • The genome sequence of the European mole, Talpa europaea Linnaeus, 1758.

    Pearce N, O'Brien MF, Lopez Colom R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;98

    PUBMED: 40093592; PMC: 11909498; DOI: 10.12688/wellcomeopenres.23759.1

  • The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767).

    Boyes D, Hutchinson F, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;101

    PUBMED: 40171521; PMC: 11959263; DOI: 10.12688/wellcomeopenres.23749.1

  • The genome sequence of the Tropical Bluetail Damselfly, Ischnura senegalensis (Rambur, 1842).

    Willink B, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2025;10;104

    PUBMED: 40290353; PMC: 12033981; DOI: 10.12688/wellcomeopenres.23747.1

  • Genomic and proteomic analyses of Nus-dependent non-lambdoid phages reveal a novel coliphage group prevalent in gut: mEpimmI.

    Negrete-Méndez H, Valencia-Toxqui G, Sepúlveda-Robles OA, Ríos-Castro E, Hurtado-Cortés JC, Flores V, Cázares A, Kameyama L, Martínez-Peñafiel E and Fernández-Ramírez F

    Frontiers in microbiology 2025;16;1480411

    PUBMED: 40066275; PMC: 11893012; DOI: 10.3389/fmicb.2025.1480411

  • Polygenic scores for autism are associated with reduced neurite density in adults and children from the general population.

    Gu Y, Maria-Stauffer E, Bedford SA, APEX consortium, iPSYCH-autism consortium, Romero-Garcia R, Grove J, Børglum AD, Martin H, Baron-Cohen S et al.

    Molecular psychiatry 2025

    PUBMED: 39994426; DOI: 10.1038/s41380-025-02927-z

  • The genome sequence of the black-headed gull, Chroicocephalus ridibundus (Linnaeus, 1766).

    Lopez Colom R, O'Brien M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;9;399

    PUBMED: 40134894; PMC: 11933786; DOI: 10.12688/wellcomeopenres.22741.2

  • The genome sequence of the pine hoverfly, Blera fallax (Linnaeus, 1758).

    Taylor HR, Ritchie-Parker H, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;8;89

    PUBMED: 40444016; PMC: 12120433; DOI: 10.12688/wellcomeopenres.19034.2

  • RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry.

    Perr J, Langen A, Almahayni K, Nestola G, Chai P, Lebedenko CG, Volk RF, Detrés D, Caldwell RM, Spiekermann M et al.

    Cell 2025

    PUBMED: 40020667; DOI: 10.1016/j.cell.2025.01.040

  • Understanding the potential contribution of polygenic risk scores to the prediction of gestational and type 2 diabetes in women from British Pakistani and Bangladeshi groups: a cohort study in Genes and Health.

    Zöllner J, Orazumbekova B, Hodgson S, van Heel DA, Genes and Health Research Team, Iliodromiti S, Siddiqui M, Mathur R, Finer S and Jardine J

    AJOG global reports 2025;5;2;100457

    PUBMED: 40201617; PMC: 11976246; DOI: 10.1016/j.xagr.2025.100457

  • A putative hepatitis B virus sequence motif associated with hepatocellular carcinoma in South African adults.

    Maponga TG, McNaughton AL, Campbell C, de Cesare M, Mokaya J, Lumley SF, Bonsall D, Ip CL, Chai H, Van Rensburg C et al.

    Annals of hepatology 2025;101763

    PUBMED: 39986372; DOI: 10.1016/j.aohep.2024.101763

  • Arboviral infections in southeast Europe: ongoing challenges for diagnosis, outbreak investigation, and preparedness.

    Burt FJ and Hewson R

    The Lancet. Infectious diseases 2025

    PUBMED: 39987928; DOI: 10.1016/S1473-3099(25)00076-3

  • Governing synthetic data in medical research: the time is now.

    Boraschi D, van der Schaar M, Costa A and Milne R

    The Lancet. Digital health 2025

    PUBMED: 39984419; DOI: 10.1016/j.landig.2025.01.012

  • The genome sequence of Hornet Plumehorn hoverfly, Volucella zonaria (Poda, 1761).

    Wolton RJ, Sivell O, Woodcock KJ, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;86

    PUBMED: 40470060; PMC: 12134739; DOI: 10.12688/wellcomeopenres.23738.1

  • The genome sequence of the false flower beetle, Anaspis frontalis (Linnaeus, 1758).

    Barclay MVL, Nikolaeva S, Telnov D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;82

    PUBMED: 40093595; PMC: 11909497; DOI: 10.12688/wellcomeopenres.23726.1

  • The genome sequence of the false flower beetle, Anaspis regimbarti Schilsky, 1895.

    Barclay MVL, Telnov D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;85

    PUBMED: 40162189; PMC: 11950724; DOI: 10.12688/wellcomeopenres.23737.1

  • The genome sequence of the Rock-rose Pot Beetle, Cryptocephalus primarius Harold, 1872.

    Mitchell R, Geiser MF, Turner T, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;77

    PUBMED: 40225903; PMC: 11986415; DOI: 10.12688/wellcomeopenres.23703.1

  • The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789).

    Sivell O, Sivell D, Mitchell R, Webb J, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;79

    PUBMED: 40099017; PMC: 11911719; DOI: 10.12688/wellcomeopenres.23708.1

  • What is the main bottleneck in deriving biological understanding from spatial transcriptomic profiling?

    Moffitt JR, Li M, Nie Q, Kanemaru K, Teichmann SA, Dar D, Kagohara LT, Itzkovitz S, Vento-Tormo R, Yanai I et al.

    Cell systems 2025;16;2;101200

    PUBMED: 39978311; DOI: 10.1016/j.cels.2025.101200

  • Exploration of the mutational landscape of cutaneous leiomyoma confirms FH as a driver gene and identifies targeting purine metabolism as a potential therapeutic strategy.

    van der Weyden L, Del Castillo Velasco-Herrera M, Cheema S, Wong K, Boccacino JM, Vermes I, Offord V, Droop A, Jones DRA, Anderson E et al.

    The British journal of dermatology 2025;192;3;551-553

    PUBMED: 39506538; PMC: 11833311; DOI: 10.1093/bjd/ljae432

  • UK Longitudinal Linkage Collaboration (UK LLC): The National Trusted Research Environment for Longitudinal Research.

    Boyd A, Evans KM, Turner EL, Flaig R, Oakley J, Campbell KC, Thomas R, McLachlan S, Crane M, Whitehorn R et al.

    International journal of population data science 2025;10;1;2468

    PUBMED: 40129687; PMC: 11931487; DOI: 10.23889/ijpds.v10i1.2468

  • Contribution of autosomal rare and de novo variants to sex differences in autism.

    Koko M, Satterstrom FK, Autism Sequencing Consortium, APEX consortium, Warrier V and Martin H

    American journal of human genetics 2025;112;3;599-614

    PUBMED: 39954678; PMC: 11947420; DOI: 10.1016/j.ajhg.2025.01.016

  • Developmental origins and evolution of pallial cell types and structures in birds.

    Zaremba B, Fallahshahroudi A, Schneider C, Schmidt J, Sarropoulos I, Leushkin E, Berki B, Van Poucke E, Jensen P, Senovilla-Ganzo R et al.

    Science (New York, N.Y.) 2025;387;6735;eadp5182

    PUBMED: 39946461; DOI: 10.1126/science.adp5182

  • The genome sequence of the Large Red Tailed Bumble Bee, Bombus lapidarius (Linnaeus, 1758).

    Sivell O, Sivell D, Smith MN, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;67

    PUBMED: 40191528; PMC: 11971630; DOI: 10.12688/wellcomeopenres.23624.1

  • Genomic data sharing: you don't know what you've got (till it's gone).

    Holt KE and Inouye M

    Nature reviews. Genetics 2025

    PUBMED: 39939811; DOI: 10.1038/s41576-025-00820-7

  • The genome sequence of the acute-angled fungus beetle, Cryptophagus acutangulus Gyllenhal, 1827.

    Barclay MVL, Telnov D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;58

    PUBMED: 40880728; PMC: 12381558; DOI: 10.12688/wellcomeopenres.23688.1

  • The genome sequence of a longhorn beetle, Rhagium mordax (Degeer, 1775).

    Barclay MVL, Telnov D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;51

    PUBMED: 40093593; PMC: 11909496; DOI: 10.12688/wellcomeopenres.23668.1

  • The genome sequence of the black scavenger fly, Nemopoda nitidula (Fallén, 1820).

    Falk S, Crowley LM, Akinmusola RY, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;49

    PUBMED: 40520150; PMC: 12163368; DOI: 10.12688/wellcomeopenres.23664.1

  • The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798.

    Boyes D, Januszczak I, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective et al.

    Wellcome open research 2025;10;50

    PUBMED: 40248649; PMC: 12004066; DOI: 10.12688/wellcomeopenres.23665.1

  • Age-stratified analysis of health-related quality of life in patients with early-stage breast cancer receiving adjuvant radiation therapy and endocrine therapy.

    Li K, Chadha M, Moshier E, Rosenstein BS and REQUITE consortium

    Journal of geriatric oncology 2025;16;2;102195

    PUBMED: 39919652; DOI: 10.1016/j.jgo.2025.102195

  • Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta.

    McIntyre J, Morrison A, Maitland K, Berger D, Price DRG, Dougan S, Grigoriadis D, Tracey A, Holroyd N, Bull K et al.

    PLoS pathogens 2025;21;2;e1012820

    PUBMED: 39913358; DOI: 10.1371/journal.ppat.1012820

  • Discovery of drug targets for heart failure with preserved and reduced ejection fraction.

    Ritchie SC

    Nature cardiovascular research 2025

    PUBMED: 39915328; DOI: 10.1038/s44161-024-00605-x

  • Agar-Dilution Is Comparable to Broth Dilution for MIC Determination in Streptococcus agalactiae.

    Portal EAR, Farley C, Iannetelli T, Coelho J, Efstratiou A, Bentley SD, Chalker VJ and Spiller OB

    Antibiotics (Basel, Switzerland) 2025;14;2

    PUBMED: 40001400; PMC: 11852353; DOI: 10.3390/antibiotics14020156

  • Clinical utility and implementation of polygenic risk scores for predicting cardiovascular disease.

    Schunkert H, Di Angelantonio E, Inouye M, Patel RS, Ripatti S, Widen E, Sanderson SC, Kaski JP, McEvoy JW, Vardas P et al.

    European heart journal 2025

    PUBMED: 39906985; DOI: 10.1093/eurheartj/ehae649

  • Lineage tracing of stem cells decades after blood and bone-marrow transplantation.

    No authors listed

    Nature 2025

    PUBMED: 39910360; DOI: 10.1038/d41586-025-00345-3

  • Supernumerary ring chromosome 1 syndrome leads to fusion-driven B-cell Acute Lymphoblastic Leukemia in monozygotic twins.

    Gutiérrez-Abril J, Gundem G, Fiala E, Liosis K, Farnoud N, Leongamornlert D, Amallraja A, Arango Ossa JEE, Domenico D, Levine MF et al.

    Blood advances 2025

    PUBMED: 39908462; DOI: 10.1182/bloodadvances.2024014869

  • Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia.

    Al-Ajli FO, Formenti G, Fedrigo O, Tracey A, Sims Y, Howe K, Al-Karkhi IM, Althani AA, Jarvis ED, Rahman S and Ayub Q

    Scientific reports 2025;15;1;4154

    PUBMED: 39900672; PMC: 11790892; DOI: 10.1038/s41598-025-88216-9

  • Suppressing recurrence in Sonic Hedgehog subgroup medulloblastoma using the OLIG2 inhibitor CT-179.

    Li Y, Lim C, Dismuke T, Malawsky DS, Oasa S, Bruce ZC, Offenhäuser C, Baumgartner U, D'Souza RCJ, Edwards SL et al.

    Nature communications 2025;16;1;1091

    PUBMED: 39904981; PMC: 11794477; DOI: 10.1038/s41467-024-54861-3

  • The genome sequence of a cluster fly, Pollenia griseotomentosa (Jacentkovský, 1944).

    Sivell O, Mitchell R, Falk S, Natural History Museum Genome Acquisition Lab, University of Oxford Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2025;10;42

    PUBMED: 40697422; PMC: 12280869; DOI: 10.12688/wellcomeopenres.23625.1

  • The genome sequence of a seed weevil, Aspidapion aeneum (Fabricius, 1775).

    Barclay MVL, Turner T, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;41

    PUBMED: 40104437; PMC: 11914875; DOI: 10.12688/wellcomeopenres.23613.1

  • The genome sequence of the Grey Arches moth, Polia nebulosa Hufnagel, 1766.

    Griffiths A, Prescott T, Forrester R, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;39

    PUBMED: 40191529; PMC: 11971629; DOI: 10.12688/wellcomeopenres.23608.1

  • Drug resistance-associated mutations in Plasmodium UBP-1 disrupt its essential deubiquitinating activity.

    Smith CJ, Eavis H, Briggs C, Henrici R, Karpiyevich M, Ansbro MR, Hoshizaki J, van der Heden van Noort GJ, Ascher DB, Sutherland CJ et al.

    The Journal of biological chemistry 2025;108266

    PUBMED: 39909372; DOI: 10.1016/j.jbc.2025.108266

  • Quinoxaline-based anti-schistosomal compounds have potent anti-plasmodial activity.

    Rawat M, Padalino G, Adika E, Okombo J, Yeo T, Brancale A, Fidock DA, Hoffmann KF and Lee MCS

    PLoS pathogens 2025;21;2;e1012216

    PUBMED: 39899599; DOI: 10.1371/journal.ppat.1012216

  • k-mer approaches for biodiversity genomics.

    Jenike KM, Campos-Domínguez L, Boddé M, Cerca J, Hodson CN, Schatz MC and Jaron KS

    Genome research 2025

    PUBMED: 39890468; DOI: 10.1101/gr.279452.124

  • Multiplex generation and single-cell analysis of structural variants in mammalian genomes.

    Pinglay S, Lalanne JB, Daza RM, Kottapalli S, Quaisar F, Koeppel J, Garge RK, Li X, Lee DS and Shendure J

    Science (New York, N.Y.) 2025;387;6733;eado5978

    PUBMED: 39883753; DOI: 10.1126/science.ado5978

  • Randomizing the human genome by engineering recombination between repeat elements.

    Koeppel J, Ferreira R, Vanderstichele T, Riedmayr LM, Peets EM, Girling G, Weller J, Murat P, Liberante FG, Ellis T et al.

    Science (New York, N.Y.) 2025;387;6733;eado3979

    PUBMED: 39883775; DOI: 10.1126/science.ado3979

  • Temporal profiling of human lymphoid tissues reveals coordinated defense against viral challenge.

    Coates ML, Richoz N, Tuong ZK, Bowyer GS, Lee CYC, Ferdinand JR, Gillman E, McClure M, Dratva L, Teichmann SA et al.

    Nature immunology 2025;26;2;215-229

    PUBMED: 39890933; PMC: 11785532; DOI: 10.1038/s41590-024-02064-9

  • tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.

    Brown MR, Gonzalez de La Rosa P and Blaxter M

    Bioinformatics (Oxford, England) 2025

    PUBMED: 39891350; DOI: 10.1093/bioinformatics/btaf049

  • The genome sequence of Greek sea-spurrey, Spergularia bocconei (Scheele) Graebn. (Caryophyllaceae).

    Power D, Christenhusz MJM, French C, Bennallick I, Mian S, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management et al.

    Wellcome open research 2025;10;34

    PUBMED: 40084295; PMC: 11904401; DOI: 10.12688/wellcomeopenres.23609.1

  • Mining microbiomes for microproteins.

    Neville BA and Lawley TD

    Nature reviews. Microbiology 2025

    PUBMED: 39885330; DOI: 10.1038/s41579-025-01154-1

  • Update on the evolving landscape of pneumococcal capsule types: new discoveries and way forward.

    Ganaie FA, Beall BW, Yu J, van der Linden M, McGee L, Satzke C, Manna S, Lo SW, Bentley SD, Ravenscroft N and Nahm MH

    Clinical microbiology reviews 2025;e0017524

    PUBMED: 39878373; DOI: 10.1128/cmr.00175-24

  • Overcoming research challenges in resource-limited settings: perspectives from Thailand.

    Chewapreecha C and Chewprecha T

    Nature reviews. Microbiology 2025

    PUBMED: 39875528; DOI: 10.1038/s41579-025-01148-z

  • Think zebras: challenges and opportunities for treating rare cancers.

    Behjati S, Boehm JS, Dun MD, Fröhling S, Huang PH, Jabado N, Li N and Robles-Espinoza CD

    Trends in cancer 2025

    PUBMED: 39875305; DOI: 10.1016/j.trecan.2025.01.004

  • A single-cell atlas of the Culex tarsalis midgut during West Nile virus infection.

    Fitzmeyer EA, Dutt TS, Pinaud S, Graham B, Gallichotte EN, Hill JL, Campbell CL, Ogg H, Howick V, Lawniczak MKN et al.

    PLoS pathogens 2025;21;1;e1012855

    PUBMED: 39869679; DOI: 10.1371/journal.ppat.1012855

  • Hatching of whipworm eggs induced by bacterial contact is serine-protease dependent.

    Goulding D, Tolley C, Mkandawire TT, Doyle SR, Hart E, Airs PM, Grencis RK, Berriman M and Duque-Correa MA

    PLoS pathogens 2025;21;1;e1012502

    PUBMED: 39869639; DOI: 10.1371/journal.ppat.1012502

  • Stratified distance space improves the efficiency of sequential samplers for approximate Bayesian computation

    Pesonen, Henri and Corander, Jukka

    Computational Statistics & Data Analysis 2025;207

    DOI: 10.1016/j.csda.2025.108141; URL: https://doi.org/10.1016/j.csda.2025.108141

  • Young, female and scientist: exploring barriers, challenges and opportunities.

    Derosiers N, Bernaerts E, Braun JL, Pozo Garcia V, Gencheva R, Paredes Garcia A and Tsagakis I

    FEBS open bio 2025

    PUBMED: 39854261; DOI: 10.1002/2211-5463.13972

  • Competitive behaviors in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment.

    Williams DJ, Hawkins A, Hernandez RE, Mariano G, Mathers K, Buchanan G, Stonier BJ, Inkster T, Leanord A, Chalmers JD et al.

    Cell host & microbe 2025

    PUBMED: 39884275; DOI: 10.1016/j.chom.2025.01.001

  • YAT2150 is irresistible in Plasmodium falciparum and active against Plasmodium vivax and Leishmania clinical isolates.

    Bouzón-Arnáiz I, Rawat M, Coyle R, Feufack-Donfack LB, Ea M, Orban A, Popovici J, Román-Álamo L, Fallica AN, Domínguez-Asenjo B et al.

    Scientific reports 2025;15;1;2941

    PUBMED: 39848983; DOI: 10.1038/s41598-025-85346-y

  • A platform for the biomedical application of large language models.

    Lobentanzer S, Feng S, Bruderer N, Maier A, BioChatter Consortium, Wang C, Baumbach J, Abreu-Vicente J, Krehl N, Ma Q et al.

    Nature biotechnology 2025

    PUBMED: 39843580; DOI: 10.1038/s41587-024-02534-3

  • Circulating proteomic profiles are associated with type 2 diabetes in Asian populations - a longitudinal study.

    Liang Y, Lim CGY, Ritchie SC, Bertin N, Chai JF, Yao J, Li Y, Tai ES, van Dam RM and Sim X

    The Journal of clinical endocrinology and metabolism 2025

    PUBMED: 39842943; DOI: 10.1210/clinem/dgaf045

  • Cohort profile: the BangladEsh Longitudinal Investigation of Emerging Vascular and nonvascular Events (BELIEVE) cohort study.

    Chowdhury R, Khan N, Pennells L, Iurilli MLC, Uddin Miah MT, Monower MM, Rahman KMT, Samin S, Saqeeb KN, Tasmin I et al.

    BMJ open 2025;15;1;e088338

    PUBMED: 39843382; DOI: 10.1136/bmjopen-2024-088338

  • Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.

    Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK et al.

    Genome biology 2025;26;1;14

    PUBMED: 39844208; DOI: 10.1186/s13059-025-03475-z

  • Time to invest in cholera

    Stout, Rebecca C., Feasey, Nicholas, Péchayre, Marion, Thomson, Nicholas and Chilima, Benson Z.

    eClinicalMedicine 2025;80;103044

    DOI: 10.1016/j.eclinm.2024.103044; URL: https://doi.org/10.1016/j.eclinm.2024.103044

  • Proteins Involved in Endothelial Function and Inflammation Are Implicated in Cerebral Small Vessel Disease.

    Sun Z, Harshfield EL, de Leeuw FE, Burgess S, Butterworth AS, Riksen NP, Mallat Z and Markus HS

    Stroke 2025

    PUBMED: 39818967; PMC: 7617319; DOI: 10.1161/STROKEAHA.124.049079

  • Rapid and relaying deleterious effects of a gastrointestinal pathogen, Citrobacter rodentium, on bone, an extra-intestinal organ.

    Sharan K, Brandt C, Yusuf MA, Singh P, Halder N, Edwards ME, Mangu SR, Das A, Mishra A, Kumar SS et al.

    iScience 2025;28;2;111802

    PUBMED: 39967874; PMC: 11834125; DOI: 10.1016/j.isci.2025.111802

  • TopoQual polishes circular consensus sequencing data and accurately predicts quality scores.

    Weerakoon M, Lee S, Mitchell E and Heaton H

    BMC bioinformatics 2025;26;1;17

    PUBMED: 39815230; PMC: 11737182; DOI: 10.1186/s12859-024-06020-0

  • The genome sequence of the Asparagus Beetle, Crioceris asparagi (Linnaeus, 1758).

    Geiser MF, Read F, Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;18

    PUBMED: 40528997; PMC: 12171721; DOI: 10.12688/wellcomeopenres.23460.1

  • A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease.

    Lim K, Rutherford EN, Delpiano L, He P, Lin W, Sun D, Van den Boomen DJH, Edgar JR, Bang JH, Predeus A et al.

    The EMBO journal 2025

    PUBMED: 39815007; DOI: 10.1038/s44318-024-00328-6

  • Prolonged persistence of mutagenic DNA lesions in somatic cells.

    Spencer Chapman M, Mitchell E, Yoshida K, Williams N, Fabre MA, Ranzoni AM, Robinson PS, Kregar LD, Wilk M, Boettcher S et al.

    Nature 2025

    PUBMED: 39814886; DOI: 10.1038/s41586-024-08423-8

  • The genome sequence of 18-spot Ladybird, Myrrha octodecimguttata (Linnaeus, 1758).

    Barclay MVL, Namintraporn T, Geiser MF, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2025;10;7

    PUBMED: 41019576; PMC: 12461194; DOI: 10.12688/wellcomeopenres.23455.1

  • The mutational landscape of Staphylococcus aureus during colonisation.

    Coll F, Blane B, Bellis KL, Matuszewska M, Wonfor T, Jamrozy D, Toleman MS, Geoghegan JA, Parkhill J, Massey RC et al.

    Nature communications 2025;16;1;302

    PUBMED: 39805814; PMC: 11730646; DOI: 10.1038/s41467-024-55186-x

  • Approximate Bayesian inference from noisy likelihoods with Gaussian process emulated MCMC

    Marko Järvenpää and Jukka Corander

    Journal of Machine Learning Research (JMLR) 2025;25;366;1-55

    URL: https://www.jmlr.org/papers/v25/21-0421.html

  • Implementing Mutational Epidemiology on a Global Scale: Lessons from Mutographs.

    Stratton MR, Humphreys L, Alexandrov LB, Balmain A, Brennan P, Campbell PJ and Phillips DH

    Cancer discovery 2025;15;1;22-27

    PUBMED: 39801236; DOI: 10.1158/2159-8290.CD-24-1687

  • Investigating misclassification of type 1 diabetes in a population-based cohort of British Pakistanis and Bangladeshis using polygenic risk scores.

    Liu T, Sankareswaran A, Paterson G, Genes & Health Research Team, Fraser DP, Hodgson S, Huang QQ, Heng TH, Ladwa M, Thomas N et al.

    Scientific reports 2025;15;1;1168

    PUBMED: 39805939; PMC: 11729895; DOI: 10.1038/s41598-024-80348-8

  • Emerging carbapenem-resistant Klebsiella pneumoniae in a tertiary care hospital in Lima, Peru.

    Krapp F, Cuicapuza D, Salvatierra G, Buteau JP, Amaro C, Astocondor L, Hinostroza N, Jacobs J, García C and Tsukayama P

    Microbiology spectrum 2025;e0182524

    PUBMED: 39792003; DOI: 10.1128/spectrum.01825-24

  • Nuclear and mitochondrial genome assemblies for the endangered wood-decaying fungus Somion occarium.

    Hill R, McGowan J, Brabcová V, McTaggart S, Irish N, Barker T, Knitlhoffer V, Lucchini S, Baker K, Catchpole L et al.

    Genome biology and evolution 2025

    PUBMED: 39791427; DOI: 10.1093/gbe/evaf003

  • Typing of feces-derived Candida albicans strains using a novel seven-locus microsatellite panel reveals associations with yeast phenotype in individuals with inflammatory bowel disease.

    van Thiel IAM, Kreulen IAM, Bénard MV, de Goffau MC, Theelen B, Heinsbroek SEM, Zylka PK, Ponsioen CY, Boekhout T, de Jonge WJ et al.

    Pathogens and disease 2025

    PUBMED: 39794285; DOI: 10.1093/femspd/ftaf001

  • A scalable variational inference approach for increased mixed-model association power.

    Loya H, Kalantzis G, Cooper F and Palamara PF

    Nature genetics 2025

    PUBMED: 39789286; DOI: 10.1038/s41588-024-02044-7

  • Predicting cell morphological responses to perturbations using generative modeling.

    Palma A, Theis FJ and Lotfollahi M

    Nature communications 2025;16;1;505

    PUBMED: 39779675; PMC: 11711326; DOI: 10.1038/s41467-024-55707-8

  • Site-saturation mutagenesis of 500 human protein domains.

    Beltran A, Jiang X, Shen Y and Lehner B

    Nature 2025

    PUBMED: 39779847; DOI: 10.1038/s41586-024-08370-4

  • Challenges associated with the development of "trial ready cohorts" for dementia prevention trials.

    Milne R, Richard E and Brayne C

    BMJ (Clinical research ed.) 2025;388;e080275

    PUBMED: 39773881; DOI: 10.1136/bmj-2024-080275

  • Investigating the origins of the mutational signatures in cancer.

    Boysen G, Alexandrov LB, Rahbari R, Nookaew I, Ussery D, Chao MR, Hu CW and Cooke MS

    Nucleic acids research 2025;53;1

    PUBMED: 39778866; PMC: 11707540; DOI: 10.1093/nar/gkae1303

  • Pervasive horizontal transmission of Wolbachia in natural populations of closely related and widespread tropical skipper butterflies.

    Ribeiro P, Butenko A, Linke D, Ghanavi HR, Meier JI, Wahlberg N and Matos-Maraví P

    BMC microbiology 2025;25;1;5

    PUBMED: 39773184; PMC: 11706079; DOI: 10.1186/s12866-024-03719-1

  • The B Chromosome of Pseudococcus viburni: A Selfish Chromosome that Exploits Whole-Genome Meiotic Drive.

    Vea IM, de la Filia AG, Jaron KS, Barlow SEJ, Herbette M, Mongue AJ, Nelson R, Ruiz-Ruano FJ and Ross L

    Genome biology and evolution 2025;17;1

    PUBMED: 39878751; PMC: 11776215; DOI: 10.1093/gbe/evae257

  • Analysis-ready VCF at Biobank scale using Zarr.

    Czech E, Tyler W, White T, Jeffery B, Millar TR, Elsworth B, Guez J, Hancox J, Karczewski KJ, Miles A et al.

    GigaScience 2025;14

    PUBMED: 40451243; PMC: 12127038; DOI: 10.1093/gigascience/giaf049

  • Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.

    Lawniczak MKN, Kocot KM, Astrin JJ, Blaxter M, Sotero-Caio CG, Barker KB, Childers AK, Coddington J, Davis P, Howe K et al.

    GigaScience 2025;14

    PUBMED: 40440092; DOI: 10.1093/gigascience/giaf041

  • Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes.

    Zhou Y, Jin J, Li X, Gedman G, Pelan S, Rhie A, Jiang C, Fedrigo O, Howe K, Phillippy AM et al.

    GigaScience 2025;14

    PUBMED: 39778707; DOI: 10.1093/gigascience/giae112

  • Evaluation of controls, quality control assays, and protocol optimisations for PacBio HiFi sequencing on diverse and challenging samples.

    Bronner IF, Dawson E, Park N, Piepenburg O and Quail MA

    Frontiers in genetics 2025;15;1505839

    PUBMED: 39845189; PMC: 11752452; DOI: 10.3389/fgene.2024.1505839

  • Interfacial water confers transcription factors with dinucleotide specificity.

    Morgunova E, Nagy G, Yin Y, Zhu F, Nayak SP, Xiao T, Sokolov I, Popov A, Laughton C, Grubmuller H and Taipale J

    Nature structural & molecular biology 2025

    PUBMED: 39753777; DOI: 10.1038/s41594-024-01449-6

  • Signalling and rich trustworthiness in data-driven healthcare: an interdisciplinary approach

    Jonathan R. Goodman and Richard Milne

    Data & Policy 2025;6;e26

    DOI: 10.1017/dap.2024.74; URL: https://doi.org/10.1017/dap.2024.74

  • Gliomagenesis mimics an injury response orchestrated by neural crest-like cells.

    Hamed AA, Hua K, Trinh QM, Simons BD, Marioni JC, Stein LD and Dirks PB

    Nature 2025

    PUBMED: 39743595; DOI: 10.1038/s41586-024-08356-2

2024

  • A complete assembly and annotation of the American shad genome yields insights into the origins of diadromy.

    Velotta JP, Iqbal AR, Glenn ES, Franckowiak RP, Formenti G, Mountcastle J, Balacco J, Tracey A, Sims Y, Howe K et al.

    Genome biology and evolution 2024

    PUBMED: 39786563; DOI: 10.1093/gbe/evae276

  • DNA replication initiation drives focal mutagenesis and rearrangements in human cancers.

    Murat P, Guilbaud G and Sale JE

    Nature communications 2024;15;1;10850

    PUBMED: 39738026; PMC: 11685606; DOI: 10.1038/s41467-024-55148-3

  • Wilms tumor primary cultures capture phenotypic heterogeneity and facilitate preclinical screening.

    Götz L, Wegert J, Paikari A, Appenzeller S, Bausenwein S, Vokuhl C, Treger TD, Drost J, Linderkamp C, Schneider DT et al.

    Translational oncology 2024;52;102263

    PUBMED: 39740515; DOI: 10.1016/j.tranon.2024.102263

  • Cardiovascular safety of assisted reproductive technology: a meta-analysis.

    Pivato CA, Inversetti A, Condorelli G, Chieffo A, Levi-Setti PE, Latini AC, Busnelli A, Messa M, Cristodoro M, Bragato RM et al.

    European heart journal 2024

    PUBMED: 39710934; DOI: 10.1093/eurheartj/ehae886

  • Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis.

    Schoenpflug LA, Chatzipli A, Sirinukunwattana K, Richman S, Blake A, Robineau J, Mertz KD, Verrill C, Leedham SJ, Hardy C et al.

    The Journal of pathology 2024

    PUBMED: 39710952; DOI: 10.1002/path.6376

  • Mutations in mexT bypass the stringent response dependency of virulence in Pseudomonas aeruginosa.

    Figueroa W, Cazares A, Ashworth EA, Weimann A, Kadioglu A, Floto RA and Welch M

    Cell reports 2024;44;1;115079

    PUBMED: 39708318; DOI: 10.1016/j.celrep.2024.115079

  • Conventional and regionally distinctive risk factors for first-onset myocardial infarction: the Bangladesh Risk of Acute Vascular Events (BRAVE) case-control study.

    Chowdhury R, Naheed A, Monower MM, Shahzad S, Raqib R, Tasmin I, Spackman S, Kaptoge S, Pennells L, Butterworth AS et al.

    The Lancet regional health. Southeast Asia 2024;32;100519

    PUBMED: 39811539; PMC: 11730263; DOI: 10.1016/j.lansea.2024.100519

  • Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

    Wright J, Baker K, Barker T, Catchpole L, Durrant A, Fraser F, Gharbi K, Harrison C, Henderson S, Irish N et al.

    Scientific data 2024;11;1;1368

    PUBMED: 39695199; DOI: 10.1038/s41597-024-04222-y

  • HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling.

    Otoničar J, Lazareva O, Mallm JP, Simovic-Lorenz M, Philippos G, Sant P, Parekh U, Hammann L, Li A, Yildiz U et al.

    Genome biology 2024;25;1;316

    PUBMED: 39696535; PMC: 11657747; DOI: 10.1186/s13059-024-03450-0

  • Spatiotemporal single-cell roadmap of human skin wound healing.

    Liu Z, Bian X, Luo L, Björklund ÅK, Li L, Zhang L, Chen Y, Guo L, Gao J, Cao C et al.

    Cell stem cell 2024

    PUBMED: 39729995; DOI: 10.1016/j.stem.2024.11.013

  • Leucocyte telomere length and conduction system ageing.

    van Duijvenboden S, Nelson CP, Raisi-Estabragh Z, Ramirez J, Orini M, Wang Q, Aung N, Codd V, Stoma S, Allara E et al.

    Heart (British Cardiac Society) 2024

    PUBMED: 39689933; DOI: 10.1136/heartjnl-2024-324875

  • The retinoic acid family-like nuclear receptor SmRAR identified by single-cell transcriptomics of ovarian cells controls oocyte differentiation in Schistosoma mansoni.

    Moescheid MF, Lu Z, Soria CD, Quack T, Puckelwaldt O, Holroyd N, Holzaepfel P, Haeberlein S, Rinaldi G, Berriman M and Grevelding CG

    Nucleic acids research 2024

    PUBMED: 39676663; DOI: 10.1093/nar/gkae1228

  • Bi-allelic variants in DAP3 result in reduced assembly of the mitoribosomal small subunit with altered apoptosis and a Perrault-syndrome-spectrum phenotype.

    Smith TB, Kopajtich R, Demain LAM, Rea A, Thomas HB, Schiff M, Beetz C, Joss S, Conway GS, Shukla A et al.

    American journal of human genetics 2024

    PUBMED: 39701103; DOI: 10.1016/j.ajhg.2024.11.007

  • Assessing the kinetics of oxygen-unloading from red cells using FlowScore, a flow-cytometric proxy of the functional quality of blood.

    Rabcuka J, Smethurst PA, Dammert K, Saker J, Aran G, Walsh GM, Tan JCG, Codinach M, McTaggart K, Marks DC et al.

    EBioMedicine 2024;111;105498

    PUBMED: 39674089; DOI: 10.1016/j.ebiom.2024.105498

  • Considerations for building and using integrated single-cell atlases.

    Hrovatin K, Sikkema L, Shitov VA, Heimberg G, Shulman M, Oliver AJ, Mueller MF, Ibarra IL, Wang H, Ramírez-Suástegui C et al.

    Nature methods 2024

    PUBMED: 39672979; DOI: 10.1038/s41592-024-02532-y

  • Predisposition footprints in the somatic genome of Wilms tumours.

    Treger TD, Wegert J, Wenger A, Coorens THH, Al-Saadi R, Kemps PG, Kennedy J, Parks C, Anderson ND, Hodder A et al.

    Cancer discovery 2024

    PUBMED: 39665570; DOI: 10.1158/2159-8290.CD-24-0878

  • The genomic and clinical consequences of replacing procarbazine with dacarbazine in escalated BEACOPP for Hodgkin lymphoma: a retrospective, observational study.

    Santarsieri A, Mitchell E, Pham MH, Sanghvi R, Jablonski J, Lee-Six H, Sturgess K, Brice P, Menne TF, Osborne W et al.

    The Lancet. Oncology 2024

    PUBMED: 39674188; DOI: 10.1016/S1470-2045(24)00598-9

  • New developments for the Quest for Orthologs benchmark service.

    Altenhoff A, Nevers Y, Tran V, Jyothi D, Martin M, Cosentino S, Majidian S, Marcet-Houben M, Fuentes-Palacios D, Persson E et al.

    NAR genomics and bioinformatics 2024;6;4;lqae167

    PUBMED: 39664814; PMC: 11632614; DOI: 10.1093/nargab/lqae167

  • Heterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma.

    Papargyriou A, Najajreh M, Cook DP, Maurer CH, Bärthel S, Messal HA, Ravichandran SK, Richter T, Knolle M, Metzler T et al.

    Nature biomedical engineering 2024

    PUBMED: 39658630; DOI: 10.1038/s41551-024-01273-9

  • Novel loci and biomedical consequences of iron homoeostasis variation.

    Allara E, Bell S, Smith R, Keene SJ, Gill D, Gaziano L, Morselli Gysi D, Wang F, Tragante V, Mason A et al.

    Communications biology 2024;7;1;1631

    PUBMED: 39643614; PMC: 11624196; DOI: 10.1038/s42003-024-07115-3

  • Entering the spatial age of parasite genomics.

    Buddenborg SK and Doyle SR

    Trends in parasitology 2024

    PUBMED: 39638657; DOI: 10.1016/j.pt.2024.11.010

  • Exome sequencing of UK birth cohorts.

    Koko M, Fabian L, Popov I, Eberhardt RY, Zakharov G, Huang QQ, Wade EE, Azad R, Danecek P, Ho K et al.

    Wellcome open research 2024;9;390

    PUBMED: 39839975; PMC: 11747307; DOI: 10.12688/wellcomeopenres.22697.2

  • The genome sequence of the straw spear-moss, Straminergon stramineum (Dicks. ex Brid.) Hedenas, 1993.

    Bell D, Kungu L, Long D, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;712

    PUBMED: 40225273; PMC: 11992514; DOI: 10.12688/wellcomeopenres.23432.1

  • Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system.

    Adameyko I, Bakken T, Bhaduri A, Chhatbar C, Filbin MG, Gate D, Hochgerner H, Kim CN, Krull J, La Manno G et al.

    Nature neuroscience 2024;27;12;2278-2291

    PUBMED: 39627588; DOI: 10.1038/s41593-024-01827-9

  • Implementation and validation of single-cell genomics experiments in neuroscience.

    Colonna M, Konopka G, Liddelow SA, Nowakowski T, Awatramani R, Bateup HS, Cadwell CR, Caglayan E, Chen JL, Gillis J et al.

    Nature neuroscience 2024;27;12;2310-2325

    PUBMED: 39627589; DOI: 10.1038/s41593-024-01814-0

  • Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.

    Bonev B, Gonçalo CB, Chen F, Codeluppi S, Corces MR, Fan J, Heiman M, Harris K, Inoue F, Kellis M et al.

    Nature neuroscience 2024;27;12;2292-2309

    PUBMED: 39627587; DOI: 10.1038/s41593-024-01806-0

  • Using multiplexed functional data to reduce variant classification inequities in underrepresented populations.

    Dawood M, Fayer S, Pendyala S, Post M, Kalra D, Patterson K, Venner E, Muffley LA, Fowler DM, Rubin AF et al.

    Genome medicine 2024;16;1;143

    PUBMED: 39627863; PMC: 11616159; DOI: 10.1186/s13073-024-01392-7

  • The Role of Hybridization in Species Formation and Persistence.

    Peñalba JV, Runemark A, Meier JI, Singh P, Wogan GOU, Sánchez-Guillén R, Mallet J, Rometsch SJ, Menon M, Seehausen O et al.

    Cold Spring Harbor perspectives in biology 2024;16;12

    PUBMED: 38438186; PMC: 11610762; DOI: 10.1101/cshperspect.a041445

  • MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data.

    Faure AJ and Lehner B

    Genome biology 2024;25;1;303

    PUBMED: 39617885; PMC: 11610129; DOI: 10.1186/s13059-024-03444-y

  • Quantifying conformational changes in the TCR:pMHC-I binding interface.

    McMaster B, Thorpe CJ, Rossjohn J, Deane CM and Koohy H

    Frontiers in immunology 2024;15;1491656

    PUBMED: 39687625; PMC: 11646856; DOI: 10.3389/fimmu.2024.1491656

  • B cells infiltrate cutaneous T cell lymphomas.

    No authors listed

    Nature immunology 2024;25;12;2180-2181

    PUBMED: 39562743; DOI: 10.1038/s41590-024-02022-5

  • Phenotypic and Genotypic Correlates of the NaHCO3-Responsive Phenotype Among Methicillin-Resistant Staphylococcus aureus (MRSA) Isolates from Skin and Soft Tissue Infections (SSTIs).

    Ersoy SC, Madrigal SL, Chen L, Mediavilla J, Kreiswirth B, Flores EA, Miller LG, Xiong YQ, Harrison EM, Blane B et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2024

    PUBMED: 39626860; DOI: 10.1016/j.cmi.2024.11.034

  • MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models.

    Clarke AW, Høye E, Hembrom AA, Paynter VM, Vinther J, Wyrożemski Ł, Biryukova I, Formaggioni A, Ovchinnikov V, Herlyn H et al.

    Nucleic acids research 2024

    PUBMED: 39673268; DOI: 10.1093/nar/gkae1094

  • SARS-CoV-2 human challenge reveals biomarkers that discriminate early and late phases of respiratory viral infections.

    Rosenheim J, Gupta RK, Thakker C, Mann T, Bell LCK, Broderick CM, Madon K, Papargyris L, Dayananda P, Kwok AJ et al.

    Nature communications 2024;15;1;10434

    PUBMED: 39616162; PMC: 11608262; DOI: 10.1038/s41467-024-54764-3

  • Conference report of the 2024 Antimicrobial Resistance Meeting.

    Chong CE, Pham TM, Carey ME, Wee BA, Taouk ML, Favieres JF, Moore CE, Dyson ZA, Lim C, Brown CL et al.

    npj antimicrobials and resistance 2024;2;1;43

    PUBMED: 39843763; DOI: 10.1038/s44259-024-00058-z

  • New pneumococcal serotype 20C is a WciG O-acetyltransferase deficient variant of canonical serotype 20B.

    Yu J, Ravenscroft N, Davey P, Liyanage R, Lorenz O, Kuttel MM, Lo SW, Ganaie FA and Nahm MH

    Microbiology spectrum 2024;e0244324

    PUBMED: 39612217; DOI: 10.1128/spectrum.02443-24

  • Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning.

    Cai Z, Apolinário S, Baião AR, Pacini C, Sousa MD, Vinga S, Reddel RR, Robinson PJ, Garnett MJ, Zhong Q and Gonçalves E

    Nature communications 2024;15;1;10390

    PUBMED: 39614072; PMC: 11607321; DOI: 10.1038/s41467-024-54771-4

  • Systematic in vitro evolution in Plasmodium falciparum reveals key determinants of drug resistance.

    Luth MR, Godinez-Macias KP, Chen D, Okombo J, Thathy V, Cheng X, Daggupati S, Davies H, Dhingra SK, Economy JM et al.

    Science (New York, N.Y.) 2024;386;6725;eadk9893

    PUBMED: 39607932; DOI: 10.1126/science.adk9893

  • COVID-19 progression and convalescence in common variable immunodeficiency patients show dysregulated adaptive immune responses and persistent type I interferon and inflammasome activation.

    Rodríguez-Ubreva J, Calafell-Segura J, Calvillo CL, Keller B, Ciudad L, Handfield LF, de la Calle-Fabregat C, Godoy-Tena G, Andrés-León E, Hoo R et al.

    Nature communications 2024;15;1;10344

    PUBMED: 39609471; PMC: 11605083; DOI: 10.1038/s41467-024-54732-x

  • CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data.

    CZI Cell Science Program, Abdulla S, Aevermann B, Assis P, Badajoz S, Bell SM, Bezzi E, Cakir B, Chaffer J, Chambers S et al.

    Nucleic acids research 2024

    PUBMED: 39607691; DOI: 10.1093/nar/gkae1142

  • EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

    Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE et al.

    Nucleic acids research 2024

    PUBMED: 39607697; DOI: 10.1093/nar/gkae1089

  • Evolutionary genomics of Leishmania braziliensis across the neotropical realm.

    Heeren S, Sanders M, Shaw JJ, Pinto Brandão-Filho S, Côrtes Boité M, Motta Cantanhêde L, Chourabi K, Maes I, Llanos-Cuentas A, Arevalo J et al.

    Communications biology 2024;7;1;1587

    PUBMED: 39609617; DOI: 10.1038/s42003-024-07278-z

  • Genetic variation at 11q23.1 confers colorectal cancer risk by dysregulation of colonic tuft cell transcriptional activator POU2AF2.

    Rajasekaran V, Harris BT, Osborn RT, Smillie C, Donnelly K, Bacou M, Esiri-Bloom E, Ooi LY, Allan M, Walker M et al.

    Gut 2024

    PUBMED: 39609081; DOI: 10.1136/gutjnl-2024-332121

  • The interplay of DNA repair context with target sequence predictably biases Cas9-generated mutations.

    Pallaseni A, Peets EM, Girling G, Crepaldi L, Kuzmin I, Moor M, Muñoz-Subirana N, Schimmel J, Serçin Ö, Mardin BR et al.

    Nature communications 2024;15;1;10271

    PUBMED: 39592573; PMC: 11599590; DOI: 10.1038/s41467-024-54566-7

  • Evolutionary plasticity in nematode Hox gene complements and genomic loci arrangement.

    Kirangwa J, Laetsch DR, King E, Stevens L, Blaxter M, Holovachov O and Schiffer P

    Scientific reports 2024;14;1;29513

    PUBMED: 39604390; PMC: 11603191; DOI: 10.1038/s41598-024-79962-3

  • Shigella sonnei: epidemiology, evolution, pathogenesis, resistance and host interactions.

    Scott TA, Baker KS, Trotter C, Jenkins C, Mostowy S, Hawkey J, Schmidt H, Holt KE, Thomson NR and Baker S

    Nature reviews. Microbiology 2024

    PUBMED: 39604656; DOI: 10.1038/s41579-024-01126-x

  • Systemic coordination of whole-body tissue remodeling during local regeneration in sea anemones.

    Cheung S, Bredikhin D, Gerber T, Steenbergen PJ, Basu S, Bailleul R, Hansen P, Paix A, Benton MA, Korswagen HC et al.

    Developmental cell 2024

    PUBMED: 39615481; DOI: 10.1016/j.devcel.2024.11.001

  • A Mendelian randomization study finds no evidence for causal effects of C-reactive protein (CRP) on chronic pain conditions.

    Suri P, Tsepilov YA, Elgaeva EE, Williams FMK, Freidin MB and Stanaway IB

    Pain medicine (Malden, Mass.) 2024

    PUBMED: 39589921; DOI: 10.1093/pm/pnae122

  • Genotes - a 'just-in-time' genomics education resource co-designed with clinicians.

    Frost A, Kelly A, Bishop M, Bogue D, Copson E, Gompertz L, Hay E, Hayward J, Hendriks E, McVeigh T et al.

    BMC medical education 2024;24;1;1378

    PUBMED: 39593035; DOI: 10.1186/s12909-024-06059-w

  • Risk factors for vasovagal reactions in blood donors: A systematic review and meta-analysis.

    Wu Y, Qi H, Di Angelantonio E, Kaptoge S, Wood AM and Kim LG

    Transfusion 2024

    PUBMED: 39587929; DOI: 10.1111/trf.18078

  • Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells.

    Michaels YS, Major MC, Bonham-Carter B, Zhang J, Heydari T, Edgar JM, Siu MM, Greenstreet L, Vilarrasa-Blasi R, Kim S et al.

    Cell systems 2024

    PUBMED: 39615483; DOI: 10.1016/j.cels.2024.11.001

  • Haplotype-phased genome assemblies and annotation of the northern white-cheeked gibbon (Nomascus leucogenys).

    Luo Z, Jiang L, Xu J, Wang J, Nie W, Ning Z and Yang F

    Scientific data 2024;11;1;1279

    PUBMED: 39587154; DOI: 10.1038/s41597-024-04073-7

  • Macrophages and nociceptor neurons form a sentinel unit around fenestrated capillaries to defend the synovium from circulating immune challenge.

    Hasegawa T, Lee CYC, Hotchen AJ, Fleming A, Singh R, Suzuki K, Yuzaki M, Watanabe M, Birch MA, McCaskie AW et al.

    Nature immunology 2024;25;12;2270-2283

    PUBMED: 39587345; DOI: 10.1038/s41590-024-02011-8

  • Plasmodium falciparum molecular surveillance to inform the Mozambican National Malaria Control Programme strategy: protocol.

    da Silva C, Matambisso G, Boene S, Rovira-Vallbona E, Pujol A, Comiche K, Sánchez A, Greenhouse B, Chidimatembue A, Aranda-Díaz A et al.

    BMJ open 2024;14;11;e092590

    PUBMED: 39581722; DOI: 10.1136/bmjopen-2024-092590

  • Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instability.

    Smirnov P, Przybilla MJ, Simovic-Lorenz M, Parra RG, Susak H, Ratnaparkhe M, Wong JK, Körber V, Mallm JP, Philippos G et al.

    Nature communications 2024;15;1;10183

    PUBMED: 39580568; PMC: 11585558; DOI: 10.1038/s41467-024-54547-w

  • Cancer incidence and competing mortality risk following 15 presenting symptoms in primary care: a population-based cohort study using electronic healthcare records.

    Barclay ME, Renzi C, Harrison H, Torralbo A, White B, Ip SHY, Usher-Smith J, Lange J, Pashayan N, Denaxas S et al.

    BMJ oncology 2024;3;1;e000500

    PUBMED: 39886176; PMC: 11660325; DOI: 10.1136/bmjonc-2024-000500

  • The commitment of the human cell atlas to humanity.

    Amit I, Ardlie K, Arzuaga F, Awandare G, Bader G, Bernier A, Carninci P, Donnelly S, Eils R, Forrest ARR et al.

    Nature communications 2024;15;1;10019

    PUBMED: 39567491; PMC: 11579494; DOI: 10.1038/s41467-024-54306-x

  • The genome sequence of the whiskered bat, Myotis mystacinus (Kuhl, 1817).

    Ryan H, Vernes SC, Teeling EC, Mai M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;684

    PUBMED: 39635244; PMC: 11615438; DOI: 10.12688/wellcomeopenres.23345.1

  • The genome sequence of the white-beaked dolphin, Lagenorhynchus albirostris (Gray, 1846).

    Davison NJ, Morin P, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;687

    PUBMED: 39635243; PMC: 11615437; DOI: 10.12688/wellcomeopenres.23369.1

  • A multi-omic atlas of human embryonic skeletal development.

    To K, Fei L, Pett JP, Roberts K, Blain R, Polański K, Li T, Yayon N, He P, Xu C et al.

    Nature 2024;635;8039;657-667

    PUBMED: 39567793; DOI: 10.1038/s41586-024-08189-z

  • An organotypic atlas of human vascular cells.

    Barnett SN, Cujba AM, Yang L, Maceiras AR, Li S, Kedlian V, Pett JP, Polanski K, Miranda AMA, Xu C et al.

    Nature medicine 2024

    PUBMED: 39566559; DOI: 10.1038/s41591-024-03376-x

  • A spatial human thymus cell atlas mapped to a continuous tissue axis.

    Yayon N, Kedlian VR, Boehme L, Suo C, Wachter BT, Beuschel RT, Amsalem O, Polanski K, Koplev S, Tuck E et al.

    Nature 2024;635;8039;708-718

    PUBMED: 39567784; DOI: 10.1038/s41586-024-07944-6

  • HOX gene expression in the developing human spine.

    Lawrence JEG, Roberts K, Tuck E, Li T, Mamanova L, Balogh P, Usher I, Piapi A, Mazin P, Anderson ND et al.

    Nature communications 2024;15;1;10023

    PUBMED: 39567486; PMC: 11579336; DOI: 10.1038/s41467-024-54187-0

  • multiDGD: A versatile deep generative model for multi-omics data.

    Schuster V, Dann E, Krogh A and Teichmann SA

    Nature communications 2024;15;1;10031

    PUBMED: 39567490; PMC: 11579284; DOI: 10.1038/s41467-024-53340-z

  • Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of P. falciparum genes.

    Lee C, Ünlü ES, White NFD, Almagro-Garcia J, Ariani C and Pearson RD

    Bioinformatics (Oxford, England) 2024

    PUBMED: 39565917; DOI: 10.1093/bioinformatics/btae673

  • Single-cell integration reveals metaplasia in inflammatory gut diseases.

    Oliver AJ, Huang N, Bartolome-Casado R, Li R, Koplev S, Nilsen HR, Moy M, Cakir B, Polanski K, Gudiño V et al.

    Nature 2024;635;8039;699-707

    PUBMED: 39567783; PMC: 11578898; DOI: 10.1038/s41586-024-07571-1

  • Dominant negative variants in ITPR3 impair T cell Ca2+ dynamics causing combined immunodeficiency.

    Blanco E, Camps C, Bahal S, Kerai MD, Ferla MP, Rochussen AM, Handel AE, Golwala ZM, Spiridou Goncalves H, Kricke S et al.

    The Journal of experimental medicine 2024;222;1

    PUBMED: 39560673; DOI: 10.1084/jem.20220979

  • Risks of major arterial and venous thrombotic diseases after hospitalisation for influenza, pneumonia, and COVID-19: A population-wide cohort in 2.6 million people in Wales.

    Keene S, Abbasizanjani H, Torabi F, Knight R, Walker V, Raffetti E, Cezard G, Ip S, Sampri A, Bolton T et al.

    Thrombosis research 2024;245;109213

    PUBMED: 39608301; DOI: 10.1016/j.thromres.2024.109213

  • Cutaneous T cell lymphoma atlas reveals malignant TH2 cells supported by a B cell-rich tumor microenvironment.

    Li R, Strobl J, Poyner EFM, Balbaa A, Torabi F, Mazin PV, Chipampe NJ, Stephenson E, Ramírez-Suástegi C, Shanmugiah VBM et al.

    Nature immunology 2024;25;12;2320-2330

    PUBMED: 39558094; PMC: 11588665; DOI: 10.1038/s41590-024-02018-1

  • Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution.

    Silva M, Mazzoni Zerbinato Andrade Silva D, Castro JP, Makunin AI, Barby FF, de Oliveira EHC, Liehr T, Cioffi MB, Porto-Foresti F, Foresti F and Artoni RF

    PloS one 2024;19;11;e0313896

    PUBMED: 39556552; PMC: 11573200; DOI: 10.1371/journal.pone.0313896

  • Shared immunohistochemical and genomic features of the low- and high-grade components of a cutaneous secretory carcinoma with epidermotrophism and lymph node involvement.

    Marusic Z, van der Weyden L, Suárez Vilela D, Suárez Sánchez F, Méndez Álvarez JR, Velasco-Herrera MDC, Ferreira I, Adams DJ and Calonje E

    Histopathology 2024

    PUBMED: 39557498; DOI: 10.1111/his.15351

  • Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli.

    Mäklin T, Taira A, Arredondo-Alonso S, Shao Y, Stratton MR, Lawley TD, Aaltonen LA and Corander J

    The Lancet. Microbe 2024;101015

    PUBMED: 39644909; DOI: 10.1016/j.lanmic.2024.101015

  • Exploring the driver events of eccrine poromas and porocarcinomas: A retrospective, cross-institutional study of 54 cases.

    Arends MJ, Del Castillo Velasco-Herrera M, Cheema S, Wong K, Boccacino JM, Vermes I, Roberts K, Anderson E, van der Horst MPJ, de Saint Aubain N et al.

    The British journal of dermatology 2024

    PUBMED: 39546556; DOI: 10.1093/bjd/ljae447

  • Mutational landscape induced by chronic exposure to environmental PM10 and PM2.5 in A549 lung epithelial cell.

    Quezada-Maldonado EM, Cerrato-Izaguirre D, Morales-Bárcenas R, Bautista-Ocampo Y, Santibáñez-Andrade M, Quintana-Belmares R, Chirino YI, Basurto-Lozada P, Robles-Espinoza CD, Sánchez-Pérez Y and García-Cuellar CM

    Chemosphere 2024;143766

    PUBMED: 39551196; DOI: 10.1016/j.chemosphere.2024.143766

  • Primary cartilage transcriptional signatures reflect cell-type-specific molecular pathways underpinning osteoarthritis.

    Katsoula G, Lawrence JEG, Arruda AL, Tutino M, Balogh P, Southam L, Swift D, Behjati S, Teichmann SA, Wilkinson JM and Zeggini E

    American journal of human genetics 2024

    PUBMED: 39579762; DOI: 10.1016/j.ajhg.2024.10.019

  • A consensus statement on dual purpose pathogen surveillance systems: The always on approach.

    van der Westhuizen HM, Soundararajan S, Berry T, Agus D, Carmona S, Ma P, Davis J, Walker S, Mokaya J, Bentley SD et al.

    PLOS global public health 2024;4;11;e0003762

    PUBMED: 39541405; DOI: 10.1371/journal.pgph.0003762

  • The genome sequence of an ichneumonid wasp, Gelis areator (Panzer, 1804).

    McCulloch J, Crowley LM, Broad GR, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;679

    PUBMED: 40771345; PMC: 12326167; DOI: 10.12688/wellcomeopenres.23342.1

  • A river of resistant genes uncovered by metagenomics.

    Neo O, Singh N and Cazares A

    Nature reviews. Microbiology 2024

    PUBMED: 39543347; DOI: 10.1038/s41579-024-01127-w

  • The genome sequence of the glistening inkcap, Coprinellus micaceus Coprinellus; Coprinellus micaceus ((Bull.) Vilgalys, Hopple & Jacq. Johnson, 2001).

    Wright R, Woof K, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;677

    PUBMED: 39640371; PMC: 11617826; DOI: 10.12688/wellcomeopenres.23349.1

  • The genome sequence of the sycamore periphyllus aphid, Periphyllus acericola (Walker, 1848).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;676

    PUBMED: 39629217; PMC: 11612552; DOI: 10.12688/wellcomeopenres.23341.1

  • Deep-amplicon sequencing of the complete beta-tubulin gene in Trichuris trichiura before and after albendazole treatment.

    Gandasegui J, Grau-Pujol B, Novela V, Muchisse O, Cambra-Pellejà M, Cossa A, Jamine JC, Sacoor C, Brienen EAT, Catala-Moll F et al.

    International journal for parasitology. Drugs and drug resistance 2024;26;100570

    PUBMED: 39546832; DOI: 10.1016/j.ijpddr.2024.100570

  • Integrative ensemble modelling of cetuximab sensitivity in colorectal cancer patient-derived xenografts.

    Perron U, Grassi E, Chatzipli A, Viviani M, Karakoc E, Trastulla L, Brochier LM, Isella C, Zanella ER, Klett H et al.

    Nature communications 2024;15;1;9139

    PUBMED: 39528460; PMC: 11555063; DOI: 10.1038/s41467-024-53163-y

  • Microsporidia and invertebrate hosts: genome-informed taxonomy surrounding a new lineage of crayfish-infecting Nosema spp. (Nosematida)

    Stratton, Cheyenne E., Bolds, Sara A., Reisinger, Lindsey S., Behringer, Donald C., Khalaf, Amjad et al.

    Fungal Diversity 2024

    DOI: 10.1007/s13225-024-00543-w; URL: https://doi.org/10.1007/s13225-024-00543-w

  • Un/Diagnosed: Family Experience of Genomic Diagnoses and the Re-Making of (Rare) Disease in the UK.

    Costa A

    Medical anthropology 2024;43;7;655-668

    PUBMED: 39526903; DOI: 10.1080/01459740.2024.2420117

  • Performance of stool-based molecular tests and processing methods for paediatric tuberculosis diagnosis: a systematic review and meta-analysis.

    Carratalà-Castro L, Munguambe S, Saavedra-Cervera B, de Haas P, Kay A, Marcy O, Nabeta P, Ssengooba W, Ghimenton-Walters E, Acácio S et al.

    The Lancet. Microbe 2024;100963

    PUBMED: 39547244; DOI: 10.1016/j.lanmic.2024.100963

  • Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding.

    Li K, Smith ML, Blazier JC, Kochan KJ, Wood JMD, Howe K, Kwitek AE, Dwinell MR, Chen H, Ciosek JL et al.

    Genome research 2024

    PUBMED: 39516046; DOI: 10.1101/gr.279292.124

  • Modeling the increase of electronic waste due to generative AI.

    Lannelongue L

    Nature computational science 2024

    PUBMED: 39516374; DOI: 10.1038/s43588-024-00726-0

  • Profiling immune cell tissue niches in the spatial "omics" era.

    Lee CY, McCaffrey J, McGovern D and Clatworthy MR

    The Journal of allergy and clinical immunology 2024

    PUBMED: 39522655; DOI: 10.1016/j.jaci.2024.11.001

  • Variation Exists in Service Delivery: Similarities and Differences in the Provision of a Whole Genome Sequencing Service for Paediatric Rare Disease Patients in the National Health Service in England.

    Laskowski NM, Clarke A, Patch C, Pichini A, Hill M, Whyte S and Lewis C

    Public health genomics 2024;28;1;1-18

    PUBMED: 39522508; DOI: 10.1159/000542027

  • The genome sequence of the confused eyebright, Euphrasia confusa Pugsley.

    Twyford AD, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;662

    PUBMED: 39649626; PMC: 11624436; DOI: 10.12688/wellcomeopenres.23301.1

  • The genome sequence of the Scalloped Hook-tip moth, Falcaria lacertinaria (Linnaeus, 1758).

    Griffiths A, Prescott T, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;659

    PUBMED: 39649622; PMC: 11624438; DOI: 10.12688/wellcomeopenres.23258.1

  • Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis.

    Miotto O, Amambua-Ngwa A, Amenga-Etego LN, Abdel Hamid MM, Adam I, Aninagyei E, Apinjoh T, Awandare GA, Bejon P, Bertin GI et al.

    The Lancet. Microbe 2024;100941

    PUBMED: 39522520; DOI: 10.1016/j.lanmic.2024.07.004

  • Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.

    Tagirdzhanova G, Saary P, Cameron ES, Allen CCG, Garber AI, Escandón DD, Cook AT, Goyette S, Nogerius VT, Passo A et al.

    PLoS biology 2024;22;11;e3002862

    PUBMED: 39509454; PMC: 11542873; DOI: 10.1371/journal.pbio.3002862

  • The genome sequence of the Common Wainscot moth, Mythimna pallens Linnaeus, 1758.

    Holt S, Sivess L, Januszczak I, Broad GR, Fletcher C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;654

    PUBMED: 39649620; PMC: 11624437; DOI: 10.12688/wellcomeopenres.23320.1

  • Curating genomic disease-gene relationships with Gene2Phenotype (G2P).

    Yates TM, Ansari M, Thompson L, Hunt SE, Uhalte EC, Hobson RJ, Marsh JA, Wright CF and Firth HV

    Genome medicine 2024;16;1;127

    PUBMED: 39506859; DOI: 10.1186/s13073-024-01398-1

  • Fine-mapping and molecular characterisation of primary sclerosing cholangitis genetic risk loci.

    Goode EC, Fachal L, Panousis N, Moutsianas L, McIntyre RE, Bai BYH, Kawasaki N, Wittmann A, Raine T, Rushbrook SM and Anderson CA

    Nature communications 2024;15;1;9594

    PUBMED: 39505854; PMC: 11541731; DOI: 10.1038/s41467-024-53602-w

  • The genome sequence of a soliderfly, Stratiomys singularior (Harris, 1776).

    Sivell O, Sivell D, Mitchell R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;646

    PUBMED: 39606619; PMC: 11599808; DOI: 10.12688/wellcomeopenres.23294.1

  • The genome sequence of an ichneumonid wasp, Pimpla contemplator (Muller, 1776).

    Crowley LM, Broad GR, McCulloch J, De Ketelaere A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;647

    PUBMED: 39659995; PMC: 11628944; DOI: 10.12688/wellcomeopenres.23303.1

  • The genome sequence of the Figwort Sawfly Tenthredo scrophulariae Linnaeus, 1758.

    Falk S, Crowley LM, Green A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;650

    PUBMED: 39575232; PMC: 11579585; DOI: 10.12688/wellcomeopenres.23304.1

  • Crucial role of biosensors in the detection of helminth biomarkers in public health programmes.

    Cambra-Pellejà M, van Lieshout L, Baptista-Pires L, Vilaplana M, Muñoz J, Gandasegui J and Parolo C

    The Lancet. Microbe 2024;100964

    PUBMED: 39515358; DOI: 10.1016/j.lanmic.2024.100964

  • Gut Microbiome in Human Melioidosis: Composition and Resistome Dynamics from Diagnosis to Discovery.

    Chowdhury S, Kullberg RFJ, Haak BW, Duran C, Earny VA, Eshwara VK, Lawley TD, Wiersinga WJ and Mukhopadhyay C

    Open forum infectious diseases 2024;11;11;ofae654

    PUBMED: 39553288; PMC: 11568386; DOI: 10.1093/ofid/ofae654

  • The genome sequence of knotweed leaf beetle, Gastrophysa polygoni (Linnaeus, 1758).

    McCulloch J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;642

    PUBMED: 39640370; PMC: 11617825; DOI: 10.12688/wellcomeopenres.23293.1

  • The genome sequence of spotted medick, Medicago arabica (L.) Huds. (Fabaceae).

    Christenhusz MJM, Fay MF, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;116

    PUBMED: 39563952; PMC: 11574327; DOI: 10.12688/wellcomeopenres.20996.2

  • The genome sequence of the Case-bearing Clothes moth, Tinea pellionella (Linnaeus, 1758).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;119

    PUBMED: 39494195; PMC: 11530743; DOI: 10.12688/wellcomeopenres.21015.1

  • Contemporary epidemiology of hospitalised heart failure with reduced versus preserved ejection fraction in England: a retrospective, cohort study of whole-population electronic health records.

    Fletcher RA, Rockenschaub P, Neuen BL, Walter IJ, Conrad N, Mizani MA, Bolton T, Lawson CA, Tomlinson C, Logothetis SB et al.

    The Lancet. Public health 2024;9;11;e871-e885

    PUBMED: 39486903; DOI: 10.1016/S2468-2667(24)00215-9

  • MicroRNA Quantification as an Accurate and Cost-Effective Method to Diagnose Acral Melanoma.

    Gutiérrez-García C and Robles-Espinoza CD

    The Journal of investigative dermatology 2024

    PUBMED: 39488783; DOI: 10.1016/j.jid.2024.09.002

  • Bacteria divide to conquer antibiotics.

    Harrison E

    Science (New York, N.Y.) 2024;386;6721;494-495

    PUBMED: 39480952; DOI: 10.1126/science.adt0042

  • Decoding the human prenatal immune system with single-cell multi-omics.

    Haniffa M, Maartens A, Winheim E and Jardine L

    Nature reviews. Immunology 2024;25;4;285-297

    PUBMED: 39482372; DOI: 10.1038/s41577-024-01099-1

  • Large-Scale Pharmacogenomics Analysis of Patients With Cancer Within the 100,000 Genomes Project Combining Whole-Genome Sequencing and Medical Records to Inform Clinical Practice.

    Leong IUS, Cabrera CP, Cipriani V, Ross PJ, Turner RM, Stuckey A, Sanghvi S, Pasko D, Moutsianas L, Odhams CA et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2024;JCO2302761

    PUBMED: 39481076; DOI: 10.1200/JCO.23.02761

  • Not All Carcinogens Are Directly Mutagenic: A Holistic View of the Environmental Exposure–Cancer Connection

    Derick Okwan-Duodu, Arun R. Pandiri and David J. Adams

    Annual Review of Cancer Biology 2024;9;21-41

    DOI: 10.1146/annurev-cancerbio-060424-052905; URL: https://doi.org/10.1146/annurev-cancerbio-060424-052905

  • The genome sequence of a woodlouse fly, Melanophora roralis (Linnaeus, 1758).

    Mitchell R, Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;637

    PUBMED: 39659996; PMC: 11628945; DOI: 10.12688/wellcomeopenres.23295.1

  • Clonal dynamics after allogeneic haematopoietic cell transplantation.

    Spencer Chapman M, Wilk CM, Boettcher S, Mitchell E, Dawson K, Williams N, Müller J, Kovtonyuk L, Jung H, Caiado F et al.

    Nature 2024

    PUBMED: 39478227; DOI: 10.1038/s41586-024-08128-y

  • Phylogenomics supports a single origin of terrestriality in isopods.

    Thomas Thorpe JA

    Proceedings. Biological sciences 2024;291;2033;20241042

    PUBMED: 39471855; PMC: 11521608; DOI: 10.1098/rspb.2024.1042

  • Polyclonality overcomes fitness barriers in Apc-driven tumorigenesis.

    Sadien ID, Adler S, Mehmed S, Bailey S, Sawle A, Couturier DL, Eldridge M, Adams DJ, Kemp R, Lourenço FC and Winton DJ

    Nature 2024;634;8036;1196-1203

    PUBMED: 39478206; PMC: 11525183; DOI: 10.1038/s41586-024-08053-0

  • The genome sequence of Hoary Whitlowgrass, Draba incana L.

    Ruhsam M, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;630

    PUBMED: 39629218; PMC: 11612554; DOI: 10.12688/wellcomeopenres.23202.1

  • The genome sequence of the alder spittlebug, Aphrophora alni (Fallén, 1805).

    Griffiths A, Moran S, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;632

    PUBMED: 39575233; PMC: 11579584; DOI: 10.12688/wellcomeopenres.23248.1

  • Computer-Aided formulation design for pharmaceutical drug product development, part 01: Materials exploration through a visualization tool.

    Piccione PM, Lang MN, Amado Becker F, Hofstetter A, Marchal S, Ly K, Legras V, Ewert A, Kohler D, Maurer R et al.

    International journal of pharmaceutics 2024;124891

    PUBMED: 39481812; DOI: 10.1016/j.ijpharm.2024.124891

  • β-Carboline-3-carboxamide Antimalarials: Structure-Activity Relationship, ADME-Tox Studies, and Resistance Profiling.

    Mathew J, Zhou B, Haney RS, Kunz KA, Do Amaral LS, Roy Chowdhury R, Butler JH, Li H, Chakraborty AJ, Tabassum A et al.

    ACS infectious diseases 2024

    PUBMED: 39466084; DOI: 10.1021/acsinfecdis.4c00653

  • Common misconceptions of speciation.

    Walker JM, van der Heijden ESM, Maulana A, Rueda-M N, Näsvall K, Salazar PA, Meyer M and Meier JI

    Evolutionary journal of the Linnean Society 2024;3;1;kzae029

    PUBMED: 39600713; PMC: 11590199; DOI: 10.1093/evolinnean/kzae029

  • Novel risk loci in LGI1-antibody encephalitis: genome-wide association study discovery and validation cohorts.

    Binks SNM, Elliott KS, Muñiz-Castrillo S, Gilbert E, Kawasaki de Araujo T, Harper AR, Brown AC, Chong AY, Band G, Peris Sempere V et al.

    Brain : a journal of neurology 2024

    PUBMED: 39454566; DOI: 10.1093/brain/awae349

  • Multidrug-resistant Salmonella Typhi among symptomatic and asymptomatic children in informal settlements in Nairobi, Kenya.

    Kavai SM, Oyugi J, Mbae C, Kering K, Muturi P, Kebenei C, Omulo S and Kariuki S

    BMC infectious diseases 2024;24;1;1205

    PUBMED: 39455953; PMC: 11515195; DOI: 10.1186/s12879-024-10104-w

  • The importance of family-based sampling for biobanks.

    Davies NM, Hemani G, Neiderhiser JM, Martin HC, Mills MC, Visscher PM, Yengo L, Young AS and Keller MC

    Nature 2024;634;8035;795-803

    PUBMED: 39443775; PMC: 11623399; DOI: 10.1038/s41586-024-07721-5

  • Examining the healthy human microbiome concept.

    Joos R, Boucher K, Lavelle A, Arumugam M, Blaser MJ, Claesson MJ, Clarke G, Cotter PD, De Sordi L, Dominguez-Bello MG et al.

    Nature reviews. Microbiology 2024

    PUBMED: 39443812; DOI: 10.1038/s41579-024-01107-0

  • Genetic variation, structural analysis, and virulence implications of BimA and BimC in clinical isolates of Burkholderia pseudomallei in Thailand.

    Cagape CMS, Seng R, Saiprom N, Tandhavanant S, Chewapreecha C, Boonyuen U, West TE and Chantratita N

    Scientific reports 2024;14;1;24966

    PUBMED: 39443499; PMC: 11499645; DOI: 10.1038/s41598-024-74922-3

  • The genome sequence of a hoverfly, Cheilosia grossa (Fallén, 1817).

    Mitchell R, Falk S, Woodcock KJ, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;616

    PUBMED: 39563953; PMC: 11574337; DOI: 10.12688/wellcomeopenres.23189.1

  • The Hopes and Fears Lab: enabling dialogue on discovery science

    Milne, Richard, Galloway, Catherine, Rashid, Mariam, Boraschi, Daniela, Burch, Claudette et al.

    Journal of Science Communication 2024;23;7;N05

    DOI: 10.22323/2.23070805; URL: https://doi.org/10.22323/2.23070805

  • Building pangenome graphs.

    Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C et al.

    Nature methods 2024

    PUBMED: 39433878; DOI: 10.1038/s41592-024-02430-3

  • Causal inference can lead us to modifiable mechanisms and informative archetypes in sepsis.

    Baillie JK, Angus D, Burnham K, Calandra T, Calfee C, Gutteridge A, Hacohen N, Khatri P, Langley R, Ma'ayan A et al.

    Intensive care medicine 2024

    PUBMED: 39432104; DOI: 10.1007/s00134-024-07665-4

  • Fecal Microbiota Transplantation Outcome and Gut Microbiota Composition in Ulcerative Colitis: a Systematic Review and Meta-analysis.

    Bénard MV, de Goffau MC, Blonk J, Hugenholtz F, van Buuren J, Paramsothy S, Kaakoush NO, D'Haens GRAM, Borody TJ, Kamm MA and Ponsioen CY

    Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association 2024

    PUBMED: 39442743; DOI: 10.1016/j.cgh.2024.10.001

  • Pathological mechanisms and candidate therapeutic approaches in the hearing loss of mice carrying human MIR96 mutations.

    Lewis MA, Lachgar-Ruiz M, Di Domenico F, Duddy G, Chen J, Fernandez S, Morin M, Williams G, Moreno Pelayo MA and Steel KP

    Genome medicine 2024;16;1;121

    PUBMED: 39434156; PMC: 11492784; DOI: 10.1186/s13073-024-01394-5

  • The genome sequence of a fungus weevil, Pseudeuparius sepicola (Fabricius, 1792).

    Booth R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;615

    PUBMED: 39568558; PMC: 11576567; DOI: 10.12688/wellcomeopenres.23209.1

  • The genome sequence of a picture-winged fly, Melieria crassipennis (Fabricius, 1794).

    Mitchell R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;614

    PUBMED: 39554247; PMC: 11569385; DOI: 10.12688/wellcomeopenres.23224.1

  • Base editing screens define the genetic landscape of cancer drug resistance mechanisms.

    Coelho MA, Strauss ME, Watterson A, Cooper S, Bhosle S, Illuzzi G, Karakoc E, Dinçer C, Vieira SF, Sharma M et al.

    Nature genetics 2024

    PUBMED: 39424923; DOI: 10.1038/s41588-024-01948-8

  • Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of Streptococcus pneumoniae.

    Ramos-Sevillano E, Ercoli G, Betts M, Guerra-Assunção JA, Iverson A, Frank M, Partridge F, Lo SW, Fernandes VE, Nasher F et al.

    mBio 2024;e0175824

    PUBMED: 39422467; DOI: 10.1128/mbio.01758-24

  • Scalable identification of lineage-specific gene regulatory networks from metacells with NetID.

    Wang W, Wang Y, Lyu R and Grün D

    Genome biology 2024;25;1;275

    PUBMED: 39425176; DOI: 10.1186/s13059-024-03418-0

  • The genome sequence of black elder, Sambucus nigra Linnaeus, 1753 (Adoxaceae).

    Christenhusz MJM, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;609

    PUBMED: 39534534; PMC: 11555357; DOI: 10.12688/wellcomeopenres.23147.1

  • The genome sequence of Inga leiocalycina Benth.

    Schley RJ, Pennington RT, Twyford AD, Dexter KG, Kidner C, Michael TP, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;606

    PUBMED: 39494196; PMC: 11531642; DOI: 10.12688/wellcomeopenres.23131.1

  • The genome sequence of Inga oerstediana Benth.

    Schley RJ, Pennington RT, Twyford AD, Dexter KG, Kidner C, Michael TP, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;607

    PUBMED: 39606618; PMC: 11599804; DOI: 10.12688/wellcomeopenres.23146.1

  • The genome sequence of the acorn piercer, Pammene fasciana (Linnaeus, 1761).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Lewin T and Darwin Tree of Life Consortium

    Wellcome open research 2024;7;258

    PUBMED: 39464235; PMC: 11512137; DOI: 10.12688/wellcomeopenres.18114.2

  • The genome sequence of the common awl robberfly, Neoitamus cyanurus (Loew, 1849).

    Crowley LM, Akinmusola RY, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;289

    PUBMED: 39439929; PMC: 11494275; DOI: 10.12688/wellcomeopenres.22253.2

  • The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773).

    Boyes D, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;6;300

    PUBMED: 39600916; PMC: 11589414; DOI: 10.12688/wellcomeopenres.17349.2

  • The genome sequence of the planthopper, Conomelus anceps (Germar, 1821).

    Moran S, Griffiths A, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;605

    PUBMED: 39534535; PMC: 11555367; DOI: 10.12688/wellcomeopenres.23104.1

  • The genome sequence of the willow leaf beetle, Lochmaea capreae Linnaeus, 1758.

    Barclay MVL, Vassiliades D, Bayfield-Farrell W, Cristóvão J, Matsumoto K, Geiser M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;304

    PUBMED: 39464373; PMC: 11503005; DOI: 10.12688/wellcomeopenres.22424.2

  • An unbiased lncRNA dropout CRISPR-Cas9 screen reveals RP11-350G8.5 as a novel therapeutic target for multiple myeloma.

    Grillone K, Ascrizzi S, Cremaschi P, Amato J, Polerà N, Croci O, Rocca R, Riillo C, Conforti F, Graziano R et al.

    Blood 2024;144;16;1705-1721

    PUBMED: 39158066; DOI: 10.1182/blood.2023021991

  • Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

    Toro S, Anagnostopoulos AV, Bello SM, Blumberg K, Cameron R, Carmody L, Diehl AD, Dooley DM, Duncan WD, Fey P et al.

    Journal of biomedical semantics 2024;15;1;19

    PUBMED: 39415214; PMC: 11484368; DOI: 10.1186/s13326-024-00320-3

  • A prenatal skin atlas reveals immune regulation of human skin morphogenesis.

    Gopee NH, Winheim E, Olabi B, Admane C, Foster AR, Huang N, Botting RA, Torabi F, Sumanaweera D, Le AP et al.

    Nature 2024;635;8039;679-689

    PUBMED: 39415002; PMC: 11578897; DOI: 10.1038/s41586-024-08002-x

  • Genetic architecture of routinely acquired blood tests in a British South Asian cohort.

    Jacobs BM, Stow D, Hodgson S, Zöllner J, Samuel M, Kanoni S, Bidi S, Genes & Health Research Team, Walter K, Langenberg C et al.

    Nature communications 2024;15;1;8929

    PUBMED: 39414775; PMC: 11484750; DOI: 10.1038/s41467-024-53091-x

  • Investigation of parasite genetic variation and systemic immune responses in patients presenting with different clinical presentations of cutaneous leishmaniasis caused by Leishmania aethiopica.

    Yizengaw E, Takele Y, Franssen S, Gashaw B, Yimer M, Adem E, Nibret E, Yismaw G, Cruz Cervera E, Ejigu K et al.

    Infectious diseases of poverty 2024;13;1;76

    PUBMED: 39415297; PMC: 11484111; DOI: 10.1186/s40249-024-01244-x

  • The genome sequence of a lauxaniid fly, Tricholauxania praeusta (Fallén, 1820).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;586

    PUBMED: 39563950; PMC: 11574340; DOI: 10.12688/wellcomeopenres.23099.1

  • The genome sequence of a leaf beetle, Galeruca laticollis Sahlberg, C.R., 1838.

    Booth R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;594

    PUBMED: 39575234; PMC: 11579587; DOI: 10.12688/wellcomeopenres.23195.1

  • The genome sequence of Langmaid's Yellow Underwing moth, Noctua janthina (Denis & Schiffermüller) 1775.

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;592

    PUBMED: 39554246; PMC: 11569387; DOI: 10.12688/wellcomeopenres.23192.1

  • The genome sequence of lesser burdock, Arctium minus (Hill) Bernh. (Asteraceae).

    Christenhusz MJM, Martin CA, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;589

    PUBMED: 39563949; PMC: 11574341; DOI: 10.12688/wellcomeopenres.23160.1

  • The genome sequence of the Golden-tabbed robberfly, Eutolmus rufibarbis (Meigen, 1820).

    Nash WJ, Halstead A, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;593

    PUBMED: 39611124; PMC: 11602699; DOI: 10.12688/wellcomeopenres.23162.1

  • The genome sequence of the Long-tailed duck, Clangula hyemalis (Linnaeus, 1758).

    O'Brien MF, Lopez Colom R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;475

    PUBMED: 39606616; PMC: 11599803; DOI: 10.12688/wellcomeopenres.22779.2

  • The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).

    Weir JC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium and Boyes D

    Wellcome open research 2024;8;314

    PUBMED: 39464503; PMC: 11502997; DOI: 10.12688/wellcomeopenres.19480.2

  • Integrating Genomic Data with the Development of CRISPR-Based Point-of-Care-Testing for Bacterial Infections

    Wanitchanon, Thanyapat, CHEWAPREECHA, CLAIRE and Uttamapinant, Chayasith

    Current Clinical Microbiology Reports 2024;11;241–258

    PMC: 11541280; DOI: 10.1007/s40588-024-00236-7; URL: https://doi.org/10.1007/s40588-024-00236-7

  • Taxonomy Identifiers (TaxId) for Biodiversity Genomics: a guide to getting TaxId for submission of data to public databases.

    Blaxter M, Pauperio J, Schoch C and Howe K

    Wellcome open research 2024;9;591

    PUBMED: 39526195; PMC: 11544195; DOI: 10.12688/wellcomeopenres.22949.1

  • Large-scale evaluation of outcomes after a genetic diagnosis in children with severe developmental disorders.

    Copeland H, Low KJ, Wynn SL, Ahmed A, Arthur V, Balasubramanian M, Bennett K, Berg J, Bertoli M, Bryson L et al.

    Genetics in medicine open 2024;2;101864

    PUBMED: 39822267; PMC: 11736166; DOI: 10.1016/j.gimo.2024.101864

  • The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;8;300

    PUBMED: 39449983; PMC: 11499843; DOI: 10.12688/wellcomeopenres.19647.2

  • The genome sequence of the Orange-tipped sea squirt, Corella eumyota Traustedt, 1882.

    Bishop J, Wood C, Mrowicki RJ, Harley J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;146

    PUBMED: 39439930; PMC: 11494272; DOI: 10.12688/wellcomeopenres.21141.2

  • The genome sequence of the Satin Lutestring moth, Tetheella fluctuosa (Hübner, 1803).

    Prescott T, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;576

    PUBMED: 39534536; PMC: 11555359; DOI: 10.12688/wellcomeopenres.23076.1

  • The genome sequence of the Sprawler moth, Asteroscopus sphinx Hufnagel, 1766.

    Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;505

    PUBMED: 39600925; PMC: 11589413; DOI: 10.12688/wellcomeopenres.22920.2

  • The genome sequence of the Black Medic, Medicago lupulina L.

    Ruhsam M, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;574

    PUBMED: 39464371; PMC: 11503012; DOI: 10.12688/wellcomeopenres.23134.1

  • The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758).

    Pálsson S, Skarphéðinsson KH, Heintz J, Quarfordt P, Strand AS, Bunikis I, Pettersson OV, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;575

    PUBMED: 39534533; PMC: 11555360; DOI: 10.12688/wellcomeopenres.23089.1

  • Harmonize rules for digital sequence information benefit-sharing across UN frameworks.

    Sett S, Kress WJ, Halewood M, Nicholson D, Nuñez-Vega G, Faggionato D, Rouard M, Jaspars M, da Silva M, Prat C et al.

    Nature communications 2024;15;1;8745

    PUBMED: 39384744; PMC: 11464523; DOI: 10.1038/s41467-024-52994-z

  • A diagnosis of Noonan syndrome through routine whole genome sequencing in a child with an intracranial nongerminomatous germ cell tumor.

    Mahmood S, Leiter SM, Phyu P, Craven C, Horan G, Gains J, Briggs M, Blanco E, Behjati S, Watkins J et al.

    Pediatric blood & cancer 2024;e31368

    PUBMED: 39380176; DOI: 10.1002/pbc.31368

  • Phenotypic variation in the lipopolysaccharide O-antigen of Salmonella Paratyphi A and implications for vaccine development.

    Mylona E, Pereira-Dias J, Keane JA, Karkey A, Dongol S, Khokhar F, Tran TA, Cormie C, Higginson E and Baker S

    Vaccine 2024;42;26;126404

    PUBMED: 39383552; DOI: 10.1016/j.vaccine.2024.126404

  • The genome sequence of Inga laurina (Sw.) Willd.

    Schley RJ, Pennington RT, Twyford AD, Dexter KG, Kidner C, Michael TP, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2024;9;567

    PUBMED: 39540104; PMC: 11558168; DOI: 10.12688/wellcomeopenres.23057.1

  • The genome sequence of the common alder, Alnus glutinosa (L.) Gaertn. (Betulaceae).

    Christenhusz MJM, Goodwin Z, Bell DG, Martin CA, Royal Botanic Gardens Kew Genome Acquisition Lab, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;570

    PUBMED: 39512383; PMC: 11541074; DOI: 10.12688/wellcomeopenres.23137.1

  • The genome sequence of the giant tachinid fly, Tachina grossa (Linnaeus, 1758).

    Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;571

    PUBMED: 39611123; PMC: 11602700; DOI: 10.12688/wellcomeopenres.23102.1

  • Discovery of Knock-Down Resistance in the Major African Malaria Vector Anopheles funestus.

    Odero JO, Dennis TPW, Polo B, Nwezeobi J, Boddé M, Nagi SC, Hernandez-Koutoucheva A, Nambunga IH, Bwanary H, Mkandawile G et al.

    Molecular ecology 2024;e17542

    PUBMED: 39374937; DOI: 10.1111/mec.17542

  • Genome-wide association testing beyond SNPs.

    Harris L, McDonagh EM, Zhang X, Fawcett K, Foreman A, Daneck P, Sergouniotis PI, Parkinson H, Mazzarotto F, Inouye M et al.

    Nature reviews. Genetics 2024

    PUBMED: 39375560; DOI: 10.1038/s41576-024-00778-y

  • Maintenance of hematopoietic stem cells by tyrosine-unphosphorylated STAT5 and JAK inhibition.

    Williams MJ, Wang X, Bastos HP, Grondys-Kotarba G, Wu Q, Jin S, Johnson CS, Mende N, Calderbank EF, Wantoch M et al.

    Blood advances 2024

    PUBMED: 39374575; DOI: 10.1182/bloodadvances.2024014046

  • Association of circulating fatty acids with cardiovascular disease risk: Analysis of individual-level data in three large prospective cohorts and updated meta-analysis.

    Shi F, Chowdhury R, Sofianopoulou E, Koulman A, Sun L, Steur M, Aleksandrova K, Dahm CC, Schulze MB, van der Schouw YT et al.

    European journal of preventive cardiology 2024

    PUBMED: 39365172; DOI: 10.1093/eurjpc/zwae315

  • Whole genomes from the extinct Xerces Blue butterfly can help identify declining insect species.

    de Dios Martinez T, Fontsere C, Renom P, Stiller J, Llovera L, Uliano-Silva M, Sánchez-Gracia A, Wright C, Lizano E, Caballero B et al.

    eLife 2024;12

    PUBMED: 39365295; DOI: 10.7554/eLife.87928

  • High TNF and NF-ĸB pathway dependency are associated with AZD5582 sensitivity in OSCC via CASP8-dependent apoptosis.

    Chai AWY, Tan YH, Ooi S, Yee PS, Yee SM, Lightfoot H, Barthorpe S, Garnett MJ and Cheong SC

    Cancer research communications 2024

    PUBMED: 39360810; DOI: 10.1158/2767-9764.CRC-24-0136

  • The genome sequence of the Heart and Dart moth, Agrotis exclamationis (Linnaeus, 1758).

    Forrester R, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;563

    PUBMED: 39444547; PMC: 11496940; DOI: 10.12688/wellcomeopenres.23042.1

  • Towards integrated malaria molecular surveillance in Africa.

    Dada N, Simpson VJ, Amenga-Etego LN, Oriero E, Miotto O, Torok ME, Juma EO, Williams NA, Rajatileka S, Ariani CV et al.

    Trends in parasitology 2024

    PUBMED: 39477780; DOI: 10.1016/j.pt.2024.09.005

  • The genome sequence of the yellow-girdled Dasysyrphus, Dasysyrphus tricinctus (Fallén, 1817).

    Crowley LM, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;561

    PUBMED: 39450190; PMC: 11499735; DOI: 10.12688/wellcomeopenres.22892.1

  • Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae.

    Tsang KK, Lam MMC, Wick RR, Wyres KL, Bachman M, Baker S, Barry K, Brisse S, Campino S, Chiaverini A et al.

    Microbial genomics 2024;10;10

    PUBMED: 39432416; PMC: 11493186; DOI: 10.1099/mgen.0.001294

  • Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.

    Meier R, Lawniczak MKN and Srivathsan A

    Annual review of entomology 2024

    PUBMED: 39353093; DOI: 10.1146/annurev-ento-040124-014001

  • Inflammatory Gene Expression in Livers Undergoing Ex Situ Normothermic Perfusion Is Attenuated by Leukocyte Removal From the Perfusate.

    Bahadori K, Lee CYC, Ferdinand JR, Cabantous M, Butler AJ, Rouhani FJ, Watson CJE and Clatworthy MR

    Transplantation 2024

    PUBMED: 39350310; DOI: 10.1097/TP.0000000000005214

  • ReNU syndrome - a newly discovered prevalent neurodevelopmental disorder.

    Burns VF and Radford EJ

    Trends in genetics : TIG 2024

    PUBMED: 39358183; DOI: 10.1016/j.tig.2024.09.005

  • Revisiting typing systems for group B Streptococcus prophages: an application in prophage detection and classification in group B Streptococcus isolates from Argentina.

    Kovacec V, Di Gregorio S, Pajon M, Crestani C, Poklepovich T, Campos J, Basit Khan U, Bentley SD, Jamrozy D, Mollerach M and Bonofiglio L

    Microbial genomics 2024;10;10

    PUBMED: 39418095; PMC: 11485964; DOI: 10.1099/mgen.0.001297

  • Spatial Transcriptomics of the Respiratory System.

    Megas S, Wilbrey-Clark A, Maartens A, Teichmann SA and Meyer KB

    Annual review of physiology 2024

    PUBMED: 39353142; DOI: 10.1146/annurev-physiol-022724-105144

  • Surveillance of travel-associated isolates elucidates the diversity of non-pandemic Vibrio cholerae.

    Bote L, Taylor-Brown A, Maes M, Ingle DJ, Valcanis M, Howden BP and Thomson NR

    Microbial genomics 2024;10;10

    PUBMED: 39412871; DOI: 10.1099/mgen.0.001307

  • Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines.

    Elrick H, Peterson KA, Willis BJ, Lanza DG, Acar EF, Ryder EJ, Teboul L, Kasparek P, Birling MC, Adams DJ et al.

    Scientific reports 2024;14;1;22626

    PUBMED: 39349521; PMC: 11443006; DOI: 10.1038/s41598-024-72418-8

  • Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children.

    Lekhuleni C, Ndlangisa K, Gladstone RA, Chochua S, Metcalf BJ, Li Y, Kleynhans J, de Gouveia L, Hazelhurst S, Ferreira ADS et al.

    Nature communications 2024;15;1;8401

    PUBMED: 39333488; PMC: 11436952; DOI: 10.1038/s41467-024-52459-3

  • Long-term 3D primary epithelioid cultures reveal genes that regulate esophageal cell fitness.

    No authors listed

    Nature genetics 2024

    PUBMED: 39333767; DOI: 10.1038/s41588-024-01887-4

  • A chromosomal reference genome sequence for the malaria mosquito, Anopheles marshallii, Theobald, 1903.

    Makanga BK, Ayala D, Rahola N, Bouafou LBA, Johnson HF, Heaton H, Wagah MG, Collins JC, Krasheninnikova K, Pelan SE et al.

    Wellcome open research 2024;9;554

    PUBMED: 39507815; PMC: 11538599; DOI: 10.12688/wellcomeopenres.22989.1

  • The genome sequence of the cephid sawfly, Cephus spinipes (Panzer, 1800).

    Broad GR, Sivess L, Holt S, Fletcher C, Januszczak I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;557

    PUBMED: 39439928; PMC: 11494279; DOI: 10.12688/wellcomeopenres.23068.1

  • The genome sequence of the cuckoo wrasse, Labrus mixtus Linnaeus 1758.

    Heaton B, Brittain R, Adkins P, Scott-Somme K, Harley J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;549

    PUBMED: 39544313; PMC: 11561382; DOI: 10.12688/wellcomeopenres.23063.1

  • Chromosomal reference genome sequences for the malaria mosquito, Anopheles coustani, Laveran, 1900.

    Bouafou LBA, Ayala D, Makanga BK, Rahola N, Johnson HF, Heaton H, Wagah MG, Collins JC, Krasheninnikova K, Pelan SE et al.

    Wellcome open research 2024;9;551

    PUBMED: 39429628; PMC: 11490835; DOI: 10.12688/wellcomeopenres.22983.1

  • Enhancing the Polygenic Score Catalog with tools for score calculation and ancestry normalization.

    Lambert SA, Wingfield B, Gibson JT, Gil L, Ramachandran S, Yvon F, Saverimuttu S, Tinsley E, Lewis E, Ritchie SC et al.

    Nature genetics 2024

    PUBMED: 39327485; DOI: 10.1038/s41588-024-01937-x

  • Mortality, morbidity and educational outcomes in children of consanguineous parents in the Born in Bradford cohort.

    Small N, Kelly B, Malawsky DS, Lodh R, Oddie S and Wright J

    Wellcome open research 2024;9;319

    PUBMED: 39372840; PMC: 11452767; DOI: 10.12688/wellcomeopenres.22547.2

  • The genetic architecture of protein stability.

    Faure AJ, Martí-Aranda A, Hidalgo-Carcedo C, Beltran A, Schmiedel JM and Lehner B

    Nature 2024;634;8035;995-1003

    PUBMED: 39322666; PMC: 11499273; DOI: 10.1038/s41586-024-07966-0

  • Integration of variant annotations using deep set networks boosts rare variant association testing.

    Clarke B, Holtkamp E, Öztürk H, Mück M, Wahlberg M, Meyer K, Munzlinger F, Brechtmann F, Hölzlwimmer FR, Lindner J et al.

    Nature genetics 2024

    PUBMED: 39322779; DOI: 10.1038/s41588-024-01919-z

  • Single-cell multi-omics map of human fetal blood in Down syndrome.

    Marderstein AR, De Zuani M, Moeller R, Bezney J, Padhi EM, Wong S, Coorens THH, Xie Y, Xue H, Montgomery SB and Cvejic A

    Nature 2024

    PUBMED: 39322663; DOI: 10.1038/s41586-024-07946-4

  • The power of arts-based film interventions to encourage Black blood donors.

    Mills R, Okubanjo A, Acheampong N, Croucher M, Eaton N, Kazi A, di Angelantonio E, Wood A, Masser B and Ferguson E

    Transfusion 2024

    PUBMED: 39311593; DOI: 10.1111/trf.17963

  • Federated analysis of autosomal recessive coding variants in 29,745 developmental disorder patients from diverse populations.

    Chundru VK, Zhang Z, Walter K, Lindsay SJ, Danecek P, Eberhardt RY, Gardner EJ, Malawsky DS, Wigdor EM, Torene R et al.

    Nature genetics 2024;56;10;2046-2053

    PUBMED: 39313616; PMC: 11525179; DOI: 10.1038/s41588-024-01910-8

  • Microbiome signature suggestive of lactose-intolerance in rhesus macaques (Macaca mulatta) with intermittent chronic diarrhea.

    Maaskant A, Voermans B, Levin E, de Goffau MC, Plomp N, Schuren F, Remarque EJ, Smits A, Langermans JAM, Bakker J and Montijn R

    Animal microbiome 2024;6;1;53

    PUBMED: 39313845; PMC: 11421201; DOI: 10.1186/s42523-024-00338-z

  • Self-sustaining long-term 3D epithelioid cultures reveal drivers of clonal expansion in esophageal epithelium.

    Herms A, Fernandez-Antoran D, Alcolea MP, Kalogeropoulou A, Banerjee U, Piedrafita G, Abby E, Valverde-Lopez JA, Ferreira IS, Caseda I et al.

    Nature genetics 2024;56;10;2158-2173

    PUBMED: 39313617; PMC: 11525200; DOI: 10.1038/s41588-024-01875-8

  • Diverse epistatic effects in barley-powdery mildew interactions localize to host chromosome hotspots.

    Velásquez-Zapata V, Smith S, Surana P, Chapman AVE, Jaiswal N, Helm M and Wise RP

    iScience 2024;27;10;111013

    PUBMED: 39445108; PMC: 11497433; DOI: 10.1016/j.isci.2024.111013

  • Evaluation of the Master's in Genomic Medicine framework: A national, multiprofessional program to educate health care professionals in NHS England.

    Nightingale KP, Bishop M, Avitabile N, Simpson S, Freidoony L, Buckley S and Tatton-Brown K

    Genetics in medicine : official journal of the American College of Medical Genetics 2024;27;1;101277

    PUBMED: 39315528; DOI: 10.1016/j.gim.2024.101277

  • The genome sequence of the Brindled Ochre moth, Dasypolia templi (Thunberg, 1792).

    Griffiths A, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;542

    PUBMED: 39484641; PMC: 11525101; DOI: 10.12688/wellcomeopenres.23054.1

  • The genome sequence of the Broom moth, Ceramica pisi Linnaeus, 1758.

    Griffiths A, Wawman DC, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;539

    PUBMED: 39554249; PMC: 11568375; DOI: 10.12688/wellcomeopenres.23050.1

  • The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906).

    Boyes D, Crowley LM, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;540

    PUBMED: 39526196; PMC: 11549545; DOI: 10.12688/wellcomeopenres.23060.1

  • The genome sequence of the Small Argent and Sable moth, Epirrhoe tristata (Linnaeus, 1758).

    Botham M, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;541

    PUBMED: 41041147; PMC: 12485329; DOI: 10.12688/wellcomeopenres.23055.1

  • Marmoset and human trophoblast stem cells differ in signaling requirements and recapitulate divergent modes of trophoblast invasion.

    Siriwardena D, Munger C, Penfold C, Kohler TN, Weberling A, Linneberg-Agerholm M, Slatery E, Ellermann AL, Bergmann S, Clark SJ et al.

    Cell stem cell 2024

    PUBMED: 39321797; DOI: 10.1016/j.stem.2024.09.004

  • Gene-level alignment of single-cell trajectories.

    Sumanaweera D, Suo C, Cujba AM, Muraro D, Dann E, Polanski K, Steemers AS, Lee W, Oliver AJ, Park JE et al.

    Nature methods 2024

    PUBMED: 39300283; DOI: 10.1038/s41592-024-02378-4

  • Improved species assignments across the entire Anopheles genus using targeted sequencing.

    Boddé M, Makunin A, Teltscher F, Akorli J, Andoh NE, Bei A, Chaumeau V, Desamours I, Ekpo UF, Govella NJ et al.

    Frontiers in genetics 2024;15;1456644

    PUBMED: 39364005; PMC: 11446804; DOI: 10.3389/fgene.2024.1456644

  • The genome sequence of an Entiminae weevil, Polydrusus pterygomalis Boheman, 1840.

    Telfer MG, Bickerstaff J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;528

    PUBMED: 39439931; PMC: 11494282; DOI: 10.12688/wellcomeopenres.23048.1

  • The genome sequence of barren brome, Bromus sterilis L. (Poaceae).

    Christenhusz MJM, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;534

    PUBMED: 39386963; PMC: 11462126; DOI: 10.12688/wellcomeopenres.22994.1

  • The genome sequence of the European conger eel, Conger conger (Linnaeus, 1758).

    Adkins P, Brittain R, Harley J, Modepali V, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;532

    PUBMED: 39415785; PMC: 11480707; DOI: 10.12688/wellcomeopenres.23052.1

  • The genome sequence of the Pale Oak Beauty, Hypomecis punctinalis (Scopoli, 1763).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;531

    PUBMED: 41064473; PMC: 12501592; DOI: 10.12688/wellcomeopenres.23061.1

  • The genome sequence of the ruby bryozoan, Bugula neritina (Linnaeus, 1758).

    Uhl R, Bishop J, Jenkins H, Wood C, Adkins P, Azzopardi F, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;533

    PUBMED: 39415781; PMC: 11480708; DOI: 10.12688/wellcomeopenres.23056.1

  • Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo.

    Dennis TPW, Pescod P, Barasa S, Cerdeira LT, Lucas ER, Clarkson CS, Miles A, Asidi A, Manzambi EZ, Metelo E et al.

    Scientific reports 2024;14;1;21782

    PUBMED: 39294180; DOI: 10.1038/s41598-024-70885-7

  • High-resolution functional mapping of RAD51C by saturation genome editing.

    Olvera-León R, Zhang F, Offord V, Zhao Y, Tan HK, Gupta P, Pal T, Robles-Espinoza CD, Arriaga-González FG, Matsuyama LSAS et al.

    Cell 2024;187;20;5719-5734.e19

    PUBMED: 39299233; DOI: 10.1016/j.cell.2024.08.039

  • Mechanisms of transcriptional regulation in Anopheles gambiae revealed by allele-specific expression.

    Dyer NA, Lucas ER, Nagi SC, McDermott DP, Brenas JH, Miles A, Clarkson CS, Mawejje HD, Wilding CS, Halfon MS et al.

    Proceedings. Biological sciences 2024;291;2031;20241142

    PUBMED: 39288798; DOI: 10.1098/rspb.2024.1142

  • Treatment of mosaic ALPK1 driven Blaschkoid cylindroma with Mohs micrographic surgery.

    Carson L, Roberts C, Carson N, Bray A, Adams DJ and Rajan N

    Clinical and experimental dermatology 2024

    PUBMED: 39292106; DOI: 10.1093/ced/llae383

  • The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

    Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitão HG, Diedericks G, Kirangwa J, Morselli M, Salces-Ortiz J et al.

    npj biodiversity 2024;3;1;28

    PUBMED: 39289538; DOI: 10.1038/s44185-024-00054-6

  • Whole-genome sequencing of major malaria vectors reveals the evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso.

    Kientega M, Clarkson CS, Traoré N, Hui TJ, O'Loughlin S, Millogo AA, Epopa PS, Yao FA, Belem AMG, Brenas J et al.

    Malaria journal 2024;23;1;280

    PUBMED: 39285410; DOI: 10.1186/s12936-024-05106-7

  • Genotypic Diversity among Salmonella Typhi Isolated from Children Living in Informal Settlements in Nairobi, Kenya.

    Kavai SM, Oyugi J, Mbae C, Wairimu C, Kering K, Kebenei C, Muturi P, Omulo S and Kariuki S

    International journal of clinical microbiology 2024;1;3;18-27

    PUBMED: 39483419; PMC: 11526766; DOI: 10.14302/issn.2690-4721.ijcm-24-5195

  • Overexpression of Igf2-derived Mir483 inhibits Igf1 expression and leads to developmental growth restriction and metabolic dysfunction in mice.

    Sandovici I, Fernandez-Twinn DS, Campbell N, Cooper WN, Sekita Y, Zvetkova I, Ferland-McCollough D, Prosser HM, Oyama LM, Pantaleão LC et al.

    Cell reports 2024;43;9;114750

    PUBMED: 39283743; DOI: 10.1016/j.celrep.2024.114750

  • Multifocal, multiphenotypic tumours arising from an MTOR mutation acquired in early embryogenesis.

    Pacyna CN, Anandapadamanaban M, Loudon KW, Hay IM, Perisic O, Li R, Byrne M, Allen L, Roberts K, Hooks Y et al.

    Oncogene 2024

    PUBMED: 39271965; DOI: 10.1038/s41388-024-03137-7

  • The European Health Data Space can be a boost for research beyond borders.

    Ganna A, Carracedo A, Christiansen CF, Di Angelantonio E, Dykstra PA, Dzhambov AM, Eils R, Green S, Schneider KL, Varga TV et al.

    Nature medicine 2024

    PUBMED: 39266746; DOI: 10.1038/s41591-024-03246-6

  • The genome sequence of Molossus alvarezi González-Ruiz, Ramírez-Pulido and Arroyo-Cabrales, 2011 (Chiroptera, Molossidae).

    Simmons NB, Ingala MR, Pieri M, O'Toole BP, Gray JL, Philge P, L Volkert T, Zhang N, Abueg L, Brajuka N et al.

    Wellcome open research 2024;9;522

    PUBMED: 39411461; PMC: 11474149; DOI: 10.12688/wellcomeopenres.22726.1

  • A lipidomic dataset for epidemiological studies of acute myocardial infarction.

    Castro C, Harshfield EL, Butterworth AS, Wood AM, Koulman A and Griffin JL

    Data in brief 2024;57;110925

    PUBMED: 39411341; PMC: 11474276; DOI: 10.1016/j.dib.2024.110925

  • Exploiting human immune repertoire transgenic mice for protective monoclonal antibodies against antimicrobial resistant Acinetobacter baumannii.

    Baker S, Krishna A, Higham S, Naydenova P, O'Leary S, Scott JB, Harcourt K, Forrest S, Goulding D, Thi Nguyen TN et al.

    Nature communications 2024;15;1;7979

    PUBMED: 39266557; PMC: 11392949; DOI: 10.1038/s41467-024-52357-8

  • Archetypes of Open Science Partnerships: connecting aims and means in open biomedical research collaborations

    Norn, Maria Theresa, Priego, Laia Pujol, Ramos-Vielba, Irene, Ryan, Thomas Kjeldager, Conradsen, Marie Louise et al.

    Humanities and Social Sciences Communications 2024;11;1184

    DOI: 10.1057/s41599-024-03682-2

  • Genetic links between ovarian ageing, cancer risk and de novo mutation rates.

    Stankovic S, Shekari S, Huang QQ, Gardner EJ, Ivarsdottir EV, Owens NDL, Mavaddat N, Azad A, Hawkes G, Kentistou KA et al.

    Nature 2024;633;8030;608-614

    PUBMED: 39261734; PMC: 11410666; DOI: 10.1038/s41586-024-07931-x

  • Widespread geographic distribution of Aedes aegypti (Diptera: Culicidae) kdr variants in Panama.

    García J, Chong M, Rojas AL, McMillan WO, Bennett KL, Lenhart AE, Chaves LF and Loaiza JR

    Journal of medical entomology 2024

    PUBMED: 39259661; DOI: 10.1093/jme/tjae115

  • Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.

    Klein JA, Predeus AV, Greissl AR, Clark-Herrera MM, Cruz E, Cundiff JA, Haeberle AL, Howell M, Lele A, Robinson DJ et al.

    Infection and immunity 2024;e0031424

    PUBMED: 39254346; DOI: 10.1128/iai.00314-24

  • Population genomic evidence of a putative 'far-west' African cryptic taxon in the Anopheles gambiae complex.

    Caputo B, De Marco CM, Pichler V, Bottà G, Bennett KL, Amambua-Ngwa A, Assogba SB, Opondo KO, Clarkson CS, Tennessen JA et al.

    Communications biology 2024;7;1;1115

    PUBMED: 39256556; DOI: 10.1038/s42003-024-06809-y

  • Bin2cell reconstructs cells from high resolution visium HD data.

    Polański K, Bartolomé-Casado R, Sarropoulos I, Xu C, England N, Jahnsen FL, Teichmann SA and Yayon N

    Bioinformatics (Oxford, England) 2024

    PUBMED: 39250728; DOI: 10.1093/bioinformatics/btae546

  • Defining and pursuing diversity in human genetic studies.

    Raven-Adams MC, Hernandez-Boussard T, Joly Y, Knoppers BM, Chandrasekharan S, Thorogood A, Kumuthini J, Ho CWL, Gonzlez A, Nelson SC et al.

    Nature genetics 2024

    PUBMED: 39251787; DOI: 10.1038/s41588-024-01903-7

  • Rediscovering plasmid-dependent phages.

    Cazares D, Figueroa W and Cazares A

    Nature reviews. Microbiology 2024

    PUBMED: 39251838; DOI: 10.1038/s41579-024-01102-5

  • ThP3.3 - Prophylactic Endoluminal Vacuum Therapy – towards an era of reducing leak related morbidity after elective oesophago-gastric resection

    Saqib, Imad-ud-din, Al-Ani, Zena, Ribbits, Alexander, Gourgiotis, Stavros, Bennett, John et al.

    British Journal of Surgery 2024;111;Supplement_8;11-21

    DOI: 10.1093/bjs/znae197.249; URL: https://doi.org/10.1093/bjs/znae197.249

  • A New Method for Conditional Gene-Based Analysis Effectively Accounts for the Regional Polygenic Background.

    Svishcheva GR, Belonogova NM, Kirichenko AV, Tsepilov YA and Axenovich TI

    Genes 2024;15;9

    PUBMED: 39336765; PMC: 11431718; DOI: 10.3390/genes15091174

  • Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data.

    Pascoe B, Futcher G, Pensar J, Bayliss SC, Mourkas E, Calland JK, Hitchings MD, Joseph LA, Lane CG, Greenlee T et al.

    The Journal of infection 2024;89;5;106265

    PUBMED: 39245152; PMC: 7617841; DOI: 10.1016/j.jinf.2024.106265

  • Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases.

    Kalizang'oma A, Richard D, Kwambana-Adams B, Coelho J, Broughton K, Pichon B, Hopkins KL, Chalker V, Beleza S, Bentley SD et al.

    Nature communications 2024;15;1;7812

    PUBMED: 39242612; PMC: 11379897; DOI: 10.1038/s41467-024-52120-z

  • Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly.

    Shao Y, Garcia-Mauriño C, Clare S, Dawson NJR, Mu A, Adoum A, Harcourt K, Liu J, Browne HP, Stares MD et al.

    Nature microbiology 2024;9;10;2570-2582

    PUBMED: 39242817; PMC: 11445081; DOI: 10.1038/s41564-024-01804-9

  • The genome sequence of the marsh cinquefoil, Comarum palustre L., also known as Potentilla palustris (L.) Scop. (Rosaceae).

    Christenhusz MJM, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;518

    PUBMED: 39526193; PMC: 11549540; DOI: 10.12688/wellcomeopenres.23016.1

  • Assessing mechanisms of potential local adaptation through a seascape genomic approach in a marine gastropod, Littoraria flava.

    Cortez T, Sonoda GG, Santos CA and Andrade SCS

    Genome biology and evolution 2024

    PUBMED: 39235041; DOI: 10.1093/gbe/evae194

  • Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis across different settings.

    Mariner-Llicer C, Goig GA, Torres-Puente M, Vashakidze S, Villamayor LM, Saavedra-Cervera B, Mambuque E, Khurtsilava I, Avaliani Z, Rosenthal A et al.

    Nature communications 2024;15;1;7114

    PUBMED: 39237504; PMC: 11377819; DOI: 10.1038/s41467-024-51266-0

  • Genomic changes and stabilization following homoploid hybrid speciation of the Oxford ragwort Senecio squalidus.

    Nevado B, Chapman MA, Brennan AC, Clark JW, Wong ELY, Batstone T, McCarthy SA, Tracey A, Torrance J, Sims Y et al.

    Current biology : CB 2024

    PUBMED: 39260362; DOI: 10.1016/j.cub.2024.08.009

  • The genome sequence of fat-hen, Chenopodium album L.

    Mian S, Christenhusz MJM, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;508

    PUBMED: 39372839; PMC: 11452771; DOI: 10.12688/wellcomeopenres.23015.1

  • Recurrent evolution and selection shape structural diversity at the amylase locus.

    Bolognini D, Halgren A, Lou RN, Raveane A, Rocha JL, Guarracino A, Soranzo N, Chin CS, Garrison E and Sudmant PH

    Nature 2024

    PUBMED: 39232174; DOI: 10.1038/s41586-024-07911-1

  • The genome sequence of an ichneumonid wasp, Hyposoter dolosus (Gravenhorst, 1829).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;499

    PUBMED: 39355654; PMC: 11443231; DOI: 10.12688/wellcomeopenres.22895.1

  • The genome sequence of the Dogs-Mercury Flea Beetle, Hermaeophaga mercurialis (Fabricius, 1792).

    Crowley LM, Telfer M, Barclay MVL, Phillips D, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;503

    PUBMED: 39429629; PMC: 11489834; DOI: 10.12688/wellcomeopenres.22896.1

  • The genome sequence of the Eurasian minnow, Phoxinus phoxinus (Linnaeus, 1758).

    Nunn AD, Moccetti P, Hänfling B, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;504

    PUBMED: 39606613; PMC: 11599798; DOI: 10.12688/wellcomeopenres.22867.1

  • The genome sequence of the Scarce Cardinal Beetle, Schizotus pectinicornis (Linnaeus, 1758).

    Lyszkowski R, Telnov D, Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;501

    PUBMED: 39640369; PMC: 11617827; DOI: 10.12688/wellcomeopenres.22888.1

  • The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839).

    Boyes D, Hutchinson F, Crowley LM, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;500

    PUBMED: 39568559; PMC: 11576566; DOI: 10.12688/wellcomeopenres.22890.1

  • The genome sequence of the Streak, Chesias legatella (Denis & Schiffermüller, 1775).

    Lees D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;8;205

    PUBMED: 39247705; PMC: 11377919; DOI: 10.12688/wellcomeopenres.19298.2

  • The genome sequence of the thistle gall fly, Urophora cardui (Linnaeus 1758).

    Franzen L, Crowley LM, Medd N, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;502

    PUBMED: 39345341; PMC: 11427867; DOI: 10.12688/wellcomeopenres.22919.1

  • Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides.

    Amaya Romero JE, Chenal C, Ben Chehida Y, Miles A, Clarkson CS, Pedergnana V, Wertheim B and Fontaine MC

    Genome biology and evolution 2024;16;9

    PUBMED: 39226386; PMC: 11370803; DOI: 10.1093/gbe/evae172

  • Noncoding variants are a rare cause of recessive developmental disorders in trans with coding variants.

    Lord J, Oquendo CJ, Wai HA, Holloway JG, Martin-Geary A, Blakes AJM, Arciero E, Domcke S, Childs AM, Low K et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2024;26;12;101249

    PUBMED: 39243181; DOI: 10.1016/j.gim.2024.101249

  • Cancer drug-tolerant persister cells: from biological questions to clinical opportunities.

    Russo M, Chen M, Mariella E, Peng H, Rehman SK, Sancho E, Sogari A, Toh TS, Balaban NQ, Batlle E et al.

    Nature reviews. Cancer 2024

    PUBMED: 39223250; DOI: 10.1038/s41568-024-00737-z

  • Rare Genetic Variants in LDLR, APOB, and PCSK9 are Associated with Aortic Stenosis.

    Rämö J, Jurgens SJ, Kany S, Choi SH, Wang X, Smirnov AN, Friedman SF, Maddah M, Khurshid S, Ellinor PT and Pirruccello JP

    Circulation 2024

    PUBMED: 39222019; DOI: 10.1161/CIRCULATIONAHA.124.070982

  • Topical Anti-Inflammatory Treatments for Eczema: A Cochrane Systematic Review and Network Meta-Analysis.

    Lax SJ, Van Vogt E, Candy B, Steele L, Reynolds C, Stuart B, Parker R, Axon E, Roberts A, Doyle M et al.

    Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2024

    PUBMED: 39219446; DOI: 10.1111/cea.14556

  • Leave no transcripts behind.

    Moy M, Kyany'a C and Maes M

    Nature reviews. Microbiology 2024;22;9;527

    PUBMED: 39048838; DOI: 10.1038/s41579-024-01074-6

  • Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution.

    Nadalin F, Marzi MJ, Pirra Piscazzi M, Fuentes-Bravo P, Procaccia S, Climent M, Bonetti P, Rubolino C, Giuliani B, Papatheodorou I et al.

    Nature communications 2024;15;1;7609

    PUBMED: 39218912; PMC: 11366763; DOI: 10.1038/s41467-024-51424-4

  • Variation in bacterial pathotype is consistent with the sit-and-wait hypothesis.

    Rayner E, Lavenir A, Murray GGR, Matusewska M, Tucker AW, Welch JJ and Weinert LA

    Microbiology (Reading, England) 2024;170;9

    PUBMED: 39287974; DOI: 10.1099/mic.0.001500

  • scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood.

    Bonder MJ, Clark SJ, Krueger F, Luo S, Agostinho de Sousa J, Hashtroud AM, Stubbs TM, Stark AK, Rulands S, Stegle O et al.

    Nature communications 2024;15;1;7567

    PUBMED: 39217176; PMC: 11366017; DOI: 10.1038/s41467-024-51833-5

  • A long noncoding RNA at the cortex locus controls adaptive coloration in butterflies.

    Livraghi L, Hanly JJ, Evans E, Wright CJ, Loh LS, Mazo-Vargas A, Kamrava K, Carter A, van der Heijden ESM, Reed RD et al.

    Proceedings of the National Academy of Sciences of the United States of America 2024;121;36;e2403326121

    PUBMED: 39213180; DOI: 10.1073/pnas.2403326121

  • Conference report: The first Bacterial Genome Sequencing Pan-European Network Conference.

    Germuskova Z, Sosa E, Lagos AC, Aamot HV, Beale MA, Bertelli C, Björkmann J, Couto N, Feige L, Greub G et al.

    Microbes and infection 2024;105410

    PUBMED: 39218348; DOI: 10.1016/j.micinf.2024.105410

  • The genetic landscape of neuro-related proteins in human plasma.

    Repetto L, Chen J, Yang Z, Zhai R, Timmers PRHJ, Feng X, Li T, Yao Y, Maslov D, Timoshchuk A et al.

    Nature human behaviour 2024

    PUBMED: 39210026; DOI: 10.1038/s41562-024-01963-z

  • Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.

    Ishigohoka J, Bascón-Cardozo K, Bours A, Fuß J, Rhie A, Mountcastle J, Haase B, Chow W, Collins J, Howe K et al.

    Evolution; international journal of organic evolution 2024

    PUBMED: 39208288; DOI: 10.1093/evolut/qpae117

  • An integrated single-cell reference atlas of the human endometrium.

    Marečková M, Garcia-Alonso L, Moullet M, Lorenzi V, Petryszak R, Sancho-Serra C, Oszlanczi A, Icoresi Mazzeo C, Wong FCK, Kelava I et al.

    Nature genetics 2024

    PUBMED: 39198675; DOI: 10.1038/s41588-024-01873-w

  • A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture.

    Attenborough T, Rawlinson KA, Diaz Soria CL, Ambridge K, Sankaranarayanan G, Graham J, Cotton JA, Doyle SR, Rinaldi G and Berriman M

    eLife 2024;13

    PUBMED: 39190022; PMC: 11349301; DOI: 10.7554/eLife.95628

  • Molecular connectomics: Placing cells into morphological tissue context.

    Megas S, Yayon N, Meyer KB and Teichmann SA

    PLoS biology 2024;22;8;e3002803

    PUBMED: 39186794; DOI: 10.1371/journal.pbio.3002803

  • COVID-19 diagnosis, vaccination during pregnancy, and adverse pregnancy outcomes of 865,654 women in England and Wales: a population-based cohort study.

    Raffetti E, Bolton T, Nolan J, Zuccolo L, Denholm R, Smith G, Akbari A, Harron K, Curry G, Allara E et al.

    The Lancet regional health. Europe 2024;45;101037

    PUBMED: 39262452; PMC: 11388188; DOI: 10.1016/j.lanepe.2024.101037

  • Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules.

    Toledano I, Supek F and Lehner B

    Nature genetics 2024;56;9;1914-1924

    PUBMED: 39174735; PMC: 11387191; DOI: 10.1038/s41588-024-01878-5

  • COVID-19 and Mental Illnesses in Vaccinated and Unvaccinated People.

    Walker VM, Patalay P, Cuitun Coronado JI, Denholm R, Forbes H, Stafford J, Moltrecht B, Palmer T, Walker A, Thompson EJ et al.

    JAMA psychiatry 2024

    PUBMED: 39167370; DOI: 10.1001/jamapsychiatry.2024.2339

  • Organismal metabolism regulates the expansion of oncogenic PIK3CA mutant clones in normal esophagus.

    Herms A, Colom B, Piedrafita G, Kalogeropoulou A, Banerjee U, King C, Abby E, Murai K, Caseda I, Fernandez-Antoran D et al.

    Nature genetics 2024;56;10;2144-2157

    PUBMED: 39169259; PMC: 11525199; DOI: 10.1038/s41588-024-01891-8

  • The Fanconi anemia pathway induces chromothripsis and ecDNA-driven cancer drug resistance.

    Engel JL, Zhang X, Wu M, Wang Y, Espejo Valle-Inclán J, Hu Q, Woldehawariat KS, Sanders MA, Smogorzewska A, Chen J et al.

    Cell 2024

    PUBMED: 39181133; DOI: 10.1016/j.cell.2024.08.001

  • A pan-cancer screen identifies drug combination benefit in cancer cell lines at the individual and population level.

    Vis DJ, Jaaks P, Aben N, Coker EA, Barthorpe S, Beck A, Hall C, Hall J, Lightfoot H, Lleshi E et al.

    Cell reports. Medicine 2024;5;8;101687

    PUBMED: 39168097; DOI: 10.1016/j.xcrm.2024.101687

  • Pneumococcal carriage and changes in serotype distribution post- PCV13 introduction in children in Matiari, Pakistan.

    Iqbal I, Shahid S, Kanwar S, Kabir F, Umrani F, Ahmed S, Khan W, Qazi MF, Aziz F, Muneer S et al.

    Vaccine 2024;42;23;126238

    PUBMED: 39168078; DOI: 10.1016/j.vaccine.2024.126238

  • Investigating genomic diversity of Staphylococcus aureus associated with pediatric atopic dermatitis in South Africa.

    Ndhlovu GON, Javkar KG, Matuvhunye T, Ngondoh F, Jamrozy D, Bentley S, Shittu AO and Dube FS

    Frontiers in microbiology 2024;15;1422902

    PUBMED: 39224215; PMC: 11366657; DOI: 10.3389/fmicb.2024.1422902

  • WebAtlas pipeline for integrated single-cell and spatial transcriptomic data.

    Li T, Horsfall D, Basurto-Lozada D, Roberts K, Prete M, Lawrence JEG, He P, Tuck E, Moore J, Yoldas AK et al.

    Nature methods 2024

    PUBMED: 39160302; DOI: 10.1038/s41592-024-02371-x

  • Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study.

    Thorpe HA, Pesonen M, Corbella M, Pesonen H, Gaiarsa S, Boinett CJ, Tonkin-Hill G, Mäklin T, Pöntinen AK, MacAlasdair N et al.

    The Lancet. Microbe 2024;100890

    PUBMED: 39178869; DOI: 10.1016/S2666-5247(24)00113-7

  • The mRNA content of plasma extracellular vesicles provides a window into molecular processes in the brain during cerebral malaria.

    Kioko M, Mwangi S, Pance A, Ochola-Oyier LI, Kariuki S, Newton C, Bejon P, Rayner JC and Abdi AI

    Science advances 2024;10;33;eadl2256

    PUBMED: 39151016; PMC: 11328904; DOI: 10.1126/sciadv.adl2256

  • Disentangling Cobionts and Contamination in Long-Read Genomic Data using Sequence Composition.

    Weber CC

    G3 (Bethesda, Md.) 2024

    PUBMED: 39148415; DOI: 10.1093/g3journal/jkae187

  • Measuring and reducing the carbon footprint of fMRI preprocessing in fMRIPrep.

    Souter NE, Bhagwat N, Racey C, Wilkinson R, Duncan NW, Samuel G, Lannelongue L, Selvan R and Rae CL

    Human brain mapping 2024;45;12;e70003

    PUBMED: 39185668; PMC: 11345634; DOI: 10.1002/hbm.70003

  • The genome sequence of a green lacewing, Nineta flava (Scopoli, 1763).

    Broad GR, Hall DW, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;477

    PUBMED: 39502860; PMC: 11535497; DOI: 10.12688/wellcomeopenres.22777.1

  • The genome sequence of a tephritid fruit fly, Merzomyia westermanni Meigen 1826.

    Falk S, Crowley LM, Medd NC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;480

    PUBMED: 39386962; PMC: 11462123; DOI: 10.12688/wellcomeopenres.22873.1

  • The genome sequence of an ichneumonid wasp, Cylloceria caligata (Gravenhorst, 1829).

    Boparai J, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;478

    PUBMED: 39429634; PMC: 11489849; DOI: 10.12688/wellcomeopenres.22776.1

  • The genome sequence of an ichneumonid wasp, Rhimphoctona ( Xylophylax) megacephalus (Gravenhorst, 1829).

    Boparai J, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;472

    PUBMED: 39411462; PMC: 11474148; DOI: 10.12688/wellcomeopenres.22865.1

  • The genome sequence of the Purple Clay moth, Diarsia brunnea (Denis & Schiffermüller) 1775.

    Davis J, Menzies D, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;471

    PUBMED: 39309223; PMC: 11413557; DOI: 10.12688/wellcomeopenres.22868.1

  • The genomic basis of childhood T-lineage acute lymphoblastic leukaemia.

    Pölönen P, Di Giacomo D, Seffernick AE, Elsayed A, Kimura S, Benini F, Montefiori LE, Wood BL, Xu J, Chen C et al.

    Nature 2024

    PUBMED: 39143224; DOI: 10.1038/s41586-024-07807-0

  • Loss of histone deubiquitinase Bap1 triggers anti-tumor immunity.

    Chang H, Li M, Zhang L, Li M, Ong SH, Zhang Z, Zheng J, Xu X, Zhang Y, Wang J et al.

    Cellular oncology (Dordrecht, Netherlands) 2024

    PUBMED: 39141316; DOI: 10.1007/s13402-024-00978-y

  • The genome sequence of a braconid wasp, Aleiodes leptofemur van Achterberg & Shaw, 2016.

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;460

    PUBMED: 39309226; PMC: 11416704; DOI: 10.12688/wellcomeopenres.22769.1

  • The genome sequence of a braconid wasp, Dinocampus coccinellae (Schrank, 1802).

    Barclay MVL, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;461

    PUBMED: 39391068; PMC: 11464979; DOI: 10.12688/wellcomeopenres.22862.1

  • The genome sequence of a ground beetle, Clivina fossor (Linnaeus, 1758).

    Crowley LM, Telfer M, Barclay MVL, Badham XR, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;438

    PUBMED: 39415780; PMC: 11480717; DOI: 10.12688/wellcomeopenres.22898.1

  • The genome sequence of a lichen-forming fungus, Platismatia glauca Linnaeus, 1753.

    Yahr R, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;457

    PUBMED: 39415779; PMC: 11480706; DOI: 10.12688/wellcomeopenres.22842.1

  • The genome sequence of a robberfly Leptogaster cylindrica (De Geer, 1776).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;443

    PUBMED: 39415782; PMC: 11480716; DOI: 10.12688/wellcomeopenres.22761.1

  • The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820.

    Sivell O, Sivell D, Webb JA, Mitchell R, Ashworth M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;440

    PUBMED: 39403309; PMC: 11472010; DOI: 10.12688/wellcomeopenres.22884.1

  • The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808).

    Lohse K, Vila R, Hayward A, Laetsch DR, Harnqvist S, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;452

    PUBMED: 39415784; PMC: 11480711; DOI: 10.12688/wellcomeopenres.22847.1

  • The genome sequence of the Hawthorn Fruit Fly, Anomoia purmunda (Harris, 1780).

    Crowley LM, McCulloch J, Medd N, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;466

    PUBMED: 39364081; PMC: 11447438; DOI: 10.12688/wellcomeopenres.22849.1

  • The genome sequence of the Small Scabious Mining Bee, Andrena marginata Fabricius, 1776.

    Mitchell R, Monks J, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;447

    PUBMED: 39450192; PMC: 11499740; DOI: 10.12688/wellcomeopenres.22772.1

  • The genome sequence of the yellow mealworm beetle, Tenebrio molitor Linnaeus, 1758.

    Mann D, Crowley LM, Merino Recalde N, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;459

    PUBMED: 39540103; PMC: 11558167; DOI: 10.12688/wellcomeopenres.22863.1

  • Age and sex specific thresholds for risk stratification of cardiovascular disease and clinical decision making: prospective open cohort study.

    Xu Z, Usher-Smith J, Pennells L, Chung R, Arnold M, Kim L, Kaptoge S, Sperrin M, Di Angelantonio E and Wood AM

    BMJ medicine 2024;3;1;e000633

    PUBMED: 39175920; PMC: 11340247; DOI: 10.1136/bmjmed-2023-000633

  • Diversity and specificity of molecular functions in cyanobacterial symbionts.

    Cameron ES, Sanchez S, Goldman N, Blaxter ML and Finn RD

    Scientific reports 2024;14;1;18658

    PUBMED: 39134591; PMC: 11319675; DOI: 10.1038/s41598-024-69215-8

  • Genomic and functional determinants of host spectrum in Group B Streptococcus.

    Crestani C, Forde TL, Bell J, Lycett SJ, Oliveira LMA, Pinto TCA, Cobo-Ángel CG, Ceballos-Márquez A, Phuoc NN, Sirimanapong W et al.

    PLoS pathogens 2024;20;8;e1012400

    PUBMED: 39133742; DOI: 10.1371/journal.ppat.1012400

  • Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.

    Kuronen J, Horsfield ST, Pöntinen AK, Mallawaarachchi S, Arredondo-Alonso S, Thorpe H, Gladstone RA, Willems RJL, Bentley SD, Croucher NJ et al.

    Genome research 2024

    PUBMED: 39134411; DOI: 10.1101/gr.278485.123

  • Proteome- and Transcriptome-Wide Genetic Analysis Identifies Biological Pathways and Candidate Drug Targets for Preeclampsia.

    Ardissino M, Truong B, Slob EAW, Schuermans A, Yoshiji S, Morley AP, Burgess S, Ng FS, de Marvao A, Natarajan P et al.

    Circulation. Genomic and precision medicine 2024;e004755

    PUBMED: 39119725; DOI: 10.1161/CIRCGEN.124.004755

  • The genome sequence of the blonde ray, Raja brachyura Lafont, 1871.

    Adkins P, Brittain R, Scott-Somme K, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;436

    PUBMED: 39211808; PMC: 11358690; DOI: 10.12688/wellcomeopenres.22825.1

  • Bright New Resources for Syphilis Research: Genetically Encoded Fluorescent Tags for Treponema pallidum and Sf1Ep Cells.

    Grillová L, Romeis E, Lieberman NAP, Tantalo LC, Xu LH, Molini B, Trejos AT, Lacey G, Goulding D, Thomson NR et al.

    Molecular microbiology 2024

    PUBMED: 39115038; DOI: 10.1111/mmi.15304

  • Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites.

    Siegel SV, Trimarsanto H, Amato R, Murie K, Taylor AR, Sutanto E, Kleinecke M, Whitton G, Watson JA, Imwong M et al.

    Nature communications 2024;15;1;6757

    PUBMED: 39117628; PMC: 11310204; DOI: 10.1038/s41467-024-51015-3

  • The genome sequence of a leaf beetle, Chrysolina haemoptera (Linnaeus, 1758).

    Levey B, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;427

    PUBMED: 39669693; PMC: 11635191; DOI: 10.12688/wellcomeopenres.22887.1

  • The genome sequence of a segmented worm, Terebella lapidaria Linnaeus, 1767.

    Darbyshire T, Adkins P, Holmes A, Bishop J, Mieszkowska N, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;432

    PUBMED: 39221441; PMC: 11364976; DOI: 10.12688/wellcomeopenres.22823.1

  • The genome sequence of the Broad-barred Knot-horn, Acrobasis consociella (Hübner, 1813).

    Boyes D, Crowley LC, Hutchinson F, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;429

    PUBMED: 39649625; PMC: 11624432; DOI: 10.12688/wellcomeopenres.21553.1

  • The genome sequence of the Cotton Bollworm moth, Helicoverpa armigera (Hübner, 1808).

    Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;428

    PUBMED: 39386961; PMC: 11462122; DOI: 10.12688/wellcomeopenres.22882.1

  • The genome sequence of the sand star, Astropecten irregularis (Pennant, 1777).

    Adkins P, Harley J, Bishop J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;431

    PUBMED: 39415778; PMC: 11480709; DOI: 10.12688/wellcomeopenres.22821.1

  • The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis & Schiffermüller), 1775.

    Boyes D, Young MR, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;433

    PUBMED: 39618809; PMC: 11605175; DOI: 10.12688/wellcomeopenres.22844.1

  • Topical anti-inflammatory treatments for eczema: network meta-analysis.

    Lax SJ, Van Vogt E, Candy B, Steele L, Reynolds C, Stuart B, Parker R, Axon E, Roberts A, Doyle M et al.

    The Cochrane database of systematic reviews 2024;8;8;CD015064

    PUBMED: 39105474; PMC: 11301992; DOI: 10.1002/14651858.CD015064.pub2

  • The genome sequence of the endemic Mexican common mustached Bat, Pteronotus mexicanus. Miller, 1902 [Mormoopidae; Pteronotus].

    Sánchez-de la Vega G, Gasca-Pineda J, Martínez-Cárdenas A, Vernes SC, Teeling EC, Mai M, Aguirre-Planter E, Eguiarte LE, Phillips CD and Ortega J

    Gene 2024;929;148821

    PUBMED: 39111456; DOI: 10.1016/j.gene.2024.148821

  • Incidence of diabetes after SARS-CoV-2 infection in England and the implications of COVID-19 vaccination: a retrospective cohort study of 16 million people.

    Taylor K, Eastwood S, Walker V, Cezard G, Knight R, Al Arab M, Wei Y, Horne EMF, Teece L, Forbes H et al.

    The lancet. Diabetes & endocrinology 2024;12;8;558-568

    PUBMED: 39054034; DOI: 10.1016/S2213-8587(24)00159-1

  • Risk estimation for the primary prevention of cardiovascular disease: considerations for appropriate risk prediction model selection.

    van Daalen KR, Zhang D, Kaptoge S, Paige E, Di Angelantonio E and Pennells L

    The Lancet. Global health 2024;12;8;e1343-e1358

    PUBMED: 39030064; DOI: 10.1016/S2214-109X(24)00210-9

  • Toward learning a foundational representation of cells and genes.

    Lotfollahi M

    Nature methods 2024;21;8;1416-1417

    PUBMED: 39122939; DOI: 10.1038/s41592-024-02367-7

  • Cohort study of cardiovascular safety of different COVID-19 vaccination doses among 46 million adults in England.

    Ip S, North TL, Torabi F, Li Y, Abbasizanjani H, Akbari A, Horne E, Denholm R, Keene S, Denaxas S et al.

    Nature communications 2024;15;1;6085

    PUBMED: 39085208; PMC: 11291640; DOI: 10.1038/s41467-024-49634-x

  • The genome sequence of the springtail, Dicyrtomina minuta (O.Fabricius, 1783).

    Jaron KS, Schneider C, Hodson CN, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;417

    PUBMED: 39301438; PMC: 11411247; DOI: 10.12688/wellcomeopenres.22765.1

  • Genetic factors associated with reasons for clinical trial stoppage.

    Razuvayevskaya O, Lopez I, Dunham I and Ochoa D

    Nature genetics 2024;56;9;1862-1867

    PUBMED: 39075208; PMC: 11387188; DOI: 10.1038/s41588-024-01854-z

  • Mining alternative splicing patterns in scRNA-seq data using scASfind.

    Song Y, Parada G, Lee JTH and Hemberg M

    Genome biology 2024;25;1;197

    PUBMED: 39075577; PMC: 11285346; DOI: 10.1186/s13059-024-03323-6

  • The genome sequence of a braconid wasp, Aleiodes testaceus (Telenga, 1941).

    Broad GR, Cunningham-Eurich I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;408

    PUBMED: 39360220; PMC: 11445644; DOI: 10.12688/wellcomeopenres.22738.1

  • The genome sequence of a jewel beetle, Agrilus biguttatus (Fabricius, 1776).

    Garland S, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;413

    PUBMED: 39411460; PMC: 11474228; DOI: 10.12688/wellcomeopenres.22762.1

  • The genome sequence of the Dark Crimson Underwing moth, Catocala sponsa Linnaeus, 1767.

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;412

    PUBMED: 39315356; PMC: 11417456; DOI: 10.12688/wellcomeopenres.22759.1

  • The genome sequence of the harvestman spider, Odiellus spinosus (Bosc, 1792).

    Henriques S, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;407

    PUBMED: 39464375; PMC: 11503004; DOI: 10.12688/wellcomeopenres.22760.1

  • The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis Méhely, 1893.

    Halpern B, Vörös J, Mc Cartney AM, Formenti G, Mouton A, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2024;9;404

    PUBMED: 39345343; PMC: 11427866; DOI: 10.12688/wellcomeopenres.22694.1

  • The genome sequence of the Northern Bottlenose Whale, Hyperoodon ampullatus (Forster, 1770).

    Feyrer LJ, de Greef E, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;410

    PUBMED: 39649623; PMC: 11621617; DOI: 10.12688/wellcomeopenres.22743.1

  • The genome sequence of the particolored bat, Vespertilio murinus Linnaeus, 1758.

    Vandendriessche B, Martel A, Mai M, Teeling EC, Vernes SC, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;403

    PUBMED: 39239168; PMC: 11375412; DOI: 10.12688/wellcomeopenres.22606.1

  • Genomic insights into the 2022-2023Vibrio cholerae outbreak in Malawi.

    Chaguza C, Chibwe I, Chaima D, Musicha P, Ndeketa L, Kasambara W, Mhango C, Mseka UL, Bitilinyu-Bangoh J, Mvula B et al.

    Nature communications 2024;15;1;6291

    PUBMED: 39060226; PMC: 11282309; DOI: 10.1038/s41467-024-50484-w

  • Social, clinical and biological barriers to hepatitis B virus suppression with nucleos/tide analogue therapy: who is at risk and what should we do about it?

    Im YR, Mohammed KS, Martyn E, Lumley S, Ko J, Mokaya J, Flanagan S and Matthews PC

    Sexually transmitted infections 2024;100;5;259-263

    PUBMED: 39059818; DOI: 10.1136/sextrans-2023-056089

  • Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction.

    Kalizang'oma A, Swarthout TD, Mwalukomo TS, Kamng'ona A, Brown C, Msefula J, Demetriou H, Chan JM, Roalfe L, Obolski U et al.

    The Journal of infectious diseases 2024;230;1;e189-e198

    PUBMED: 39052729; DOI: 10.1093/infdis/jiae040

  • Optix and cortex/ivory/mir-193 again: the repeated use of two mimicry hotspot loci.

    Orteu A, Hornett EA, Reynolds LA, Warren IA, Hurst GDD, Martin SH and Jiggins CD

    Proceedings. Biological sciences 2024;291;2027;20240627

    PUBMED: 39045691; PMC: 11267468; DOI: 10.1098/rspb.2024.0627

  • The genome sequence of a hydroid, Candelabrum cocksii (Cocks, 1854).

    Adkins P, Mrowicki R, Modepalli V, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;393

    PUBMED: 39355656; PMC: 11443189; DOI: 10.12688/wellcomeopenres.22705.1

  • The genome sequence of the chalcid wasp, Chalcis sispes Linnaeus, 1761.

    Sivell O, Mitchell R, Webb J, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;391

    PUBMED: 39355655; PMC: 11443186; DOI: 10.12688/wellcomeopenres.22693.1

  • The genome sequence of the European harvest mouse, Micromys minutus (Pallas, 1771).

    O'Brien MF, Lopez Colom R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;394

    PUBMED: 39411465; PMC: 11474158; DOI: 10.12688/wellcomeopenres.22747.1

  • The genome sequence of the jumping weevil, Orchestes rusci (Herbst, 1795).

    Moran S, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;398

    PUBMED: 39290368; PMC: 11406132; DOI: 10.12688/wellcomeopenres.22745.1

  • The genome sequence of the moss carder bee, Bombus muscorum (Linnaeus, 1758).

    Broad GR, Barnes I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;397

    PUBMED: 39421651; PMC: 11484540; DOI: 10.12688/wellcomeopenres.22739.1

  • Use or abuse of trophy hunting for conservation genomics?

    Klinga, Peter, Pečnerová, Patrícia, Blaxter, Mark and Höglund, Jacob

    Journal of wildlife management 2024

    DOI: 10.1002/jwmg.22631; URL: https://doi.org/10.1002/jwmg.22631

  • The genome sequence of a sawfly Macrophya annulata (Geoffroy, 1785).

    Crowley LM, Green A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;388

    PUBMED: 39290365; PMC: 11406137; DOI: 10.12688/wellcomeopenres.22612.1

  • The genome sequence of the Cow Parsley Leaf Beetle, Chrysolina oricalcia (O.F. Müller, 1776).

    Sivell O, Sivell D, Geiser M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;8;400

    PUBMED: 39193091; PMC: 11347920; DOI: 10.12688/wellcomeopenres.19985.2

  • Genomic evidence reveals three W-autosome fusions in Heliconius butterflies.

    Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD et al.

    PLoS genetics 2024;20;7;e1011318

    PUBMED: 39024186; PMC: 11257349; DOI: 10.1371/journal.pgen.1011318

  • Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE.

    Missarova A, Dann E, Rosen L, Satija R and Marioni J

    Genome biology 2024;25;1;189

    PUBMED: 39026254; DOI: 10.1186/s13059-024-03334-3

  • The genome sequence of the Sandhill Rustic moth Luperina nickerlii (Freyer, 1845) subspecies leechi Goater, 1976.

    Spalding A, Traut W, Ffrench-Constant RH, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;382

    PUBMED: 39450193; PMC: 11499737; DOI: 10.12688/wellcomeopenres.22623.1

  • Misexpression of inactive genes in whole blood is associated with nearby rare structural variants.

    Vanderstichele T, Burnham KL, de Klein N, Tardaguila M, Howell B, Walter K, Kundu K, Koeppel J, Lee W, Tokolyi A et al.

    American journal of human genetics 2024

    PUBMED: 39053458; DOI: 10.1016/j.ajhg.2024.06.017

  • Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5.

    Wang LT, Cooper AJR, Farrell B, Miura K, Diouf A, Müller-Sienerth N, Crosnier C, Purser L, Kirtley PJ, Maciuszek M et al.

    Cell 2024

    PUBMED: 39059381; DOI: 10.1016/j.cell.2024.06.037

  • Study protocol for a randomised, phase II, double-blind, experimental medicine study of obinutuzumab versus rituximab in ANCA-associated vasculitis: ObiVas.

    McGovern DP, McClure ME, Coates M, Bond S, Martinez Del Pero M, Mynard K, Lee J, Smith RM, Jayne DR, Clatworthy MR et al.

    BMJ open 2024;14;7;e083277

    PUBMED: 39019638; PMC: 11256062; DOI: 10.1136/bmjopen-2023-083277

  • The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876).

    Morales HE, Groombridge JJ, Tollington S, Henshaw S, Tatayah V, Ruhomaun K, van Oosterhout C, Gilbert MTP, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;378

    PUBMED: 39301440; PMC: 11411241; DOI: 10.12688/wellcomeopenres.22583.1

  • The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.

    Li R, Li J, Lopez JV, Oatley G, Clayton-Lucey IA, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M et al.

    Wellcome open research 2024;9;375

    PUBMED: 39429632; PMC: 11490831; DOI: 10.12688/wellcomeopenres.22618.1

  • The genome sequence of wood avens, Geum urbanum L., 1753.

    Christenhusz MJM, Lu M, Royal Botanic Gardens Kew Genome Acquisition Lab, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;8;371

    PUBMED: 39157738; PMC: 11327653; DOI: 10.12688/wellcomeopenres.19664.2

  • Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes.

    Urzúa-Traslaviña CG, van Lieshout T, Boulogne F, Domanegg K, Zidan M, Bakker OB, Claringbould A, de Ridder J, Zwart W, Westra HJ et al.

    BMC medical genomics 2024;17;1;186

    PUBMED: 39010058; DOI: 10.1186/s12920-024-01941-4

  • Embryonic microenvironment suppresses YY1 and YY1-related genes in prostate cancer stem cells.

    Taskiran A, Oktem G, Demir A, Oltulu F, Ozcinar E, Duzagac F, Guven U, Karakoc E, Cakir A, Ayla S et al.

    Pathology, research and practice 2024;260;155467

    PUBMED: 39047662; DOI: 10.1016/j.prp.2024.155467

  • Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFβ as key predictors.

    Domingo E, Rathee S, Blake A, Samuel L, Murray G, Sebag-Montefiore D, Gollins S, West N, Begum R, Richman S et al.

    EBioMedicine 2024;106;105228

    PUBMED: 39013324; DOI: 10.1016/j.ebiom.2024.105228

  • Whole genome amplification and sequencing of individual Dirofilaria immitis microfilariae.

    Power RI, Doyle SR and Šlapeta J

    Experimental parasitology 2024;108806

    PUBMED: 39009178; DOI: 10.1016/j.exppara.2024.108806

  • De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome.

    Chen Y, Dawes R, Kim HC, Ljungdahl A, Stenton SL, Walker S, Lord J, Lemire G, Martin-Geary AC, Ganesh VS et al.

    Nature 2024;632;8026;832-840

    PUBMED: 38991538; PMC: 11338827; DOI: 10.1038/s41586-024-07773-7

  • Non-pharmaceutical interventions for COVID-19 transiently reduced pneumococcal and Haemophilus influenzae carriage in a cross-sectional pediatric cohort in Southampton, UK.

    Cleary DW, Campling J, Lahuerta M, Hayford K, Southern J, Gessner BD, Lo SW, Bentley SD, Faust SN and Clarke SC

    Microbiology spectrum 2024;e0022424

    PUBMED: 38990033; DOI: 10.1128/spectrum.00224-24

  • Pulmonary Adenocarcinoma with Cutaneous Metastasis in a Dog.

    Greyling A, van der Weyden L, Lensink AV and O'Dell N

    Veterinary sciences 2024;11;7

    PUBMED: 39057996; PMC: 11281710; DOI: 10.3390/vetsci11070312

  • The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.

    Obbard DJ, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;365

    PUBMED: 39229001; PMC: 11369588; DOI: 10.12688/wellcomeopenres.22584.1

  • The genome sequence of an ichneumonid wasp, Netelia fuscicornis (Holmgren, 1860).

    Price BW, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;363

    PUBMED: 39421652; PMC: 11484535; DOI: 10.12688/wellcomeopenres.22578.1

  • The genome sequence of Blair's Shoulder-knot, Lithophane leautieri (Boisduval, 1829).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;369

    PUBMED: 39381070; PMC: 11459115; DOI: 10.12688/wellcomeopenres.22610.1

  • The genome sequence of Rhynchonycteris naso, Peters, 1867 (Chiroptera, Emballonuridae, Rhynchonycteris).

    Alvarez van Tussenbroek I, Knörnschild M, Nagy M, O'Toole BP, Formenti G, Philge P, Zhang N, Abueg L, Brajuka N, Jarvis E et al.

    Wellcome open research 2024;9;361

    PUBMED: 39239167; PMC: 11375410; DOI: 10.12688/wellcomeopenres.19959.1

  • The genome sequence of Reeves' muntjac, Muntiacus reevesi (Ogilby, 1839).

    Ewart N, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;368

    PUBMED: 39345346; PMC: 11427868; DOI: 10.12688/wellcomeopenres.22608.1

  • The genome sequence of the European chub, Squalius cephalus (Linnaeus, 1758).

    Pitman R, Hänfling B, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;364

    PUBMED: 39364080; PMC: 11447678; DOI: 10.12688/wellcomeopenres.22579.1

  • The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869).

    Li R, Li J, Lemer S, Lopez JV, Oatley G, Sinclair E, Clayton-Lucey IA, Aunin E, Gettle N, Santos C et al.

    Wellcome open research 2024;9;366

    PUBMED: 39398938; PMC: 11467648; DOI: 10.12688/wellcomeopenres.22585.1

  • The genome sequence of the Large Red Damselfly Pyrrhosoma nymphula (Sulzer, 1776).

    Crowley LM, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;367

    PUBMED: 39184129; PMC: 11342034; DOI: 10.12688/wellcomeopenres.22586.1

  • Parallel evolution in mosquito vectors - a duplicated esterase locus is associated with resistance to pirimiphos-methyl in An. gambiae.

    Nagi SC, Lucas ER, Egyir-Yawson A, Essandoh J, Dadzie S, Chabi J, Djogbénou LS, Medjigbodo AA, Edi CV, Ketoh GK et al.

    Molecular biology and evolution 2024

    PUBMED: 38985692; DOI: 10.1093/molbev/msae140

  • Protein Condensate Atlas from predictive models of heteromolecular condensate composition.

    Saar KL, Scrutton RM, Bloznelyte K, Morgunov AS, Good LL, Lee AA, Teichmann SA and Knowles TPJ

    Nature communications 2024;15;1;5418

    PUBMED: 38987300; PMC: 11237133; DOI: 10.1038/s41467-024-48496-7

  • The functional evolution of collembolan Ubx on the regulation of abdominal appendage formation.

    Liang Y and Luan YX

    Development genes and evolution 2024

    PUBMED: 38980376; DOI: 10.1007/s00427-024-00718-0

  • Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand.

    Seng R, Chomkatekaew C, Tandhavanant S, Saiprom N, Phunpang R, Thaipadungpanit J, Batty EM, Day NPJ, Chantratita W, West TE et al.

    Nature communications 2024;15;1;5699

    PUBMED: 38972886; PMC: 11228029; DOI: 10.1038/s41467-024-50067-9

  • Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.

    Dyson ZA, Ashton PM, Khanam F, Chunga Chirambo A, Shakya M, Meiring JE, Tonks S, Karkey A, Msefula C, Clemens JD et al.

    The Lancet. Microbe 2024

    PUBMED: 38996496; DOI: 10.1016/S2666-5247(24)00047-8

  • Phenotypic and Genomic Characterization of a Small Colony Variant of Klebsiella pneumoniae Isolated from Urine of a Prostate cancer case.

    Afreen S, Singh N, Kaur M, Chaudhary N, Kumar A, Pahil S, Mohan B and Taneja N

    Indian journal of medical microbiology 2024;100664

    PUBMED: 38977132; DOI: 10.1016/j.ijmmb.2024.100664

  • A data science roadmap for open science organizations engaged in early-stage drug discovery.

    Edfeldt K, Edwards AM, Engkvist O, Günther J, Hartley M, Hulcoop DG, Leach AR, Marsden BD, Menge A, Misquitta L et al.

    Nature communications 2024;15;1;5640

    PUBMED: 38965235; PMC: 11224410; DOI: 10.1038/s41467-024-49777-x

  • The genome sequence of the Barred Chestnut moth, Diarsia dahlii (Hübner, 1813).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;357

    PUBMED: 39290367; PMC: 11406134; DOI: 10.12688/wellcomeopenres.22587.1

  • Evolution and host-specific adaptation of Pseudomonas aeruginosa.

    Weimann A, Dinan AM, Ruis C, Bernut A, Pont S, Brown K, Ryan J, Santos L, Ellison L, Ukor E et al.

    Science (New York, N.Y.) 2024;385;6704;eadi0908

    PUBMED: 38963857; DOI: 10.1126/science.adi0908

  • Saturation genome editing of BAP1 functionally classifies somatic and germline variants.

    Waters AJ, Brendler-Spaeth T, Smith D, Offord V, Tan HK, Zhao Y, Obolenski S, Nielsen M, van Doorn R, Murphy JE et al.

    Nature genetics 2024;56;7;1434-1445

    PUBMED: 38969833; PMC: 11250367; DOI: 10.1038/s41588-024-01799-3

  • Geographical migration and fitness dynamics of Streptococcus pneumoniae.

    Belman S, Lefrancq N, Nzenze S, Downs S, du Plessis M, Lo SW, Global Pneumococcal Sequencing Consortium, McGee L, Madhi SA, von Gottberg A et al.

    Nature 2024;631;8020;386-392

    PUBMED: 38961295; PMC: 11236706; DOI: 10.1038/s41586-024-07626-3

  • Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data.

    Drost F, An Y, Bonafonte-Pardàs I, Dratva LM, Lindeboom RGH, Haniffa M, Teichmann SA, Theis F, Lotfollahi M and Schubert B

    Nature communications 2024;15;1;5577

    PUBMED: 38956082; PMC: 11220149; DOI: 10.1038/s41467-024-49806-9

  • Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects.

    Frandsen PB, Holzenthal RW, Espeland M, Breinholt J, Thomas Thorpe JA, Simon S, Kawahara AY, Plotkin D, Hotaling S, Li Y et al.

    Proceedings. Biological sciences 2024;291;2026;20240514

    PUBMED: 38955232; DOI: 10.1098/rspb.2024.0514

  • Benefits for children with suspected cancer from routine whole-genome sequencing.

    Hodder A, Leiter SM, Kennedy J, Addy D, Ahmed M, Ajithkumar T, Allinson K, Ancliff P, Bailey S, Barnard G et al.

    Nature medicine 2024;30;7;1905-1912

    PUBMED: 38956197; PMC: 11271414; DOI: 10.1038/s41591-024-03056-w

  • Evidence for widespread translation of 5' untranslated regions.

    Rodriguez JM, Abascal F, Cerdán-Vélez D, Gómez LM, Vázquez J and Tress ML

    Nucleic acids research 2024

    PUBMED: 38953162; DOI: 10.1093/nar/gkae571

  • High-dimensional single-cell analysis of human natural killer cell heterogeneity.

    Rebuffet L, Melsen JE, Escalière B, Basurto-Lozada D, Bhandoola A, Björkström NK, Bryceson YT, Castriconi R, Cichocki F, Colonna M et al.

    Nature immunology 2024;25;8;1474-1488

    PUBMED: 38956378; PMC: 11291291; DOI: 10.1038/s41590-024-01883-0

  • Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping.

    Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, Brownlie D, Michaëlsson J, Marquardt N, Clancy T et al.

    Nature immunology 2024;25;8;1445-1459

    PUBMED: 38956379; PMC: 11291284; DOI: 10.1038/s41590-024-01884-z

  • Multidimensional Analysis of the Adult Human Heart in Health and Disease Using Hierarchical Phase-Contrast Tomography.

    Brunet J, Cook AC, Walsh CL, Cranley J, Tafforeau P, Engel K, Arthurs O, Berruyer C, Burke O'Leary E, Bellier A et al.

    Radiology 2024;312;1;e232731

    PUBMED: 39012246; DOI: 10.1148/radiol.232731

  • Splicing variants of versican in CD133+/CD44+ prostate cancer stem cells.

    Ayla S, Karakoc E, Byrne YY, Parlayan C, Keskin I, Karahuseyinoglu S, Taskiran A and Oktem G

    Pathology, research and practice 2024;260;155440

    PUBMED: 38964119; DOI: 10.1016/j.prp.2024.155440

  • Tracking pathogen evolution through climate change.

    Bote L and Maes M

    Nature reviews. Microbiology 2024;22;7;390

    PUBMED: 38755479; DOI: 10.1038/s41579-024-01057-7

  • Understanding the genetic complexity of puberty timing across the allele frequency spectrum.

    Kentistou KA, Kaisinger LR, Stankovic S, Vaudel M, Mendes de Oliveira E, Messina A, Walters RG, Liu X, Busch AS, Helgason H et al.

    Nature genetics 2024;56;7;1397-1411

    PUBMED: 38951643; PMC: 11250262; DOI: 10.1038/s41588-024-01798-4

  • A haplotype-resolved genome reveals the genetic basis of spine formation in Atelerix albiventris.

    Jiang L, Xu J, Zhu M, Lv Z, Ning Z and Yang F

    Journal of genetics and genomics = Yi chuan xue bao 2024

    PUBMED: 38950858; DOI: 10.1016/j.jgg.2024.06.012

  • The genome sequence of the Banded Burying beetle, Nicrophorus investigator Zetterstedt, 1824.

    Crowley LM, Broad GR, Fletcher C, Januszczak I, Barnes I, Whiffin AL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;343

    PUBMED: 39267991; PMC: 11391189; DOI: 10.12688/wellcomeopenres.21496.1

  • The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.

    Boyes D, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;348

    PUBMED: 39309222; PMC: 11416703; DOI: 10.12688/wellcomeopenres.21493.1

  • The genome sequence of the oak bush-cricket, Meconema thalassinum (De Geer, 1773).

    Crowley LM, Hotaling S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;346

    PUBMED: 39398939; PMC: 11467643; DOI: 10.12688/wellcomeopenres.21500.1

  • The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi.

    Carey ME, Thi Nguyen TN, Tran DHN, Dyson ZA, Keane JA, Pham Thanh D, Mylona E, Nair S, Chattaway M and Baker S

    Communications biology 2024;7;1;775

    PUBMED: 38942806; PMC: 11213900; DOI: 10.1038/s42003-024-06451-8

  • A systematic review and meta-analysis of the risk of hepatitis B virus (HBV) resistance in people treated with entecavir or tenofovir.

    Lumley SF, Delphin M, Mokaya JF, Tan CCS, Martyn E, Anderson M, Li KC, Waddilove E, Sukali G, Downs LO et al.

    Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2024;174;105711

    PUBMED: 38991458; DOI: 10.1016/j.jcv.2024.105711

  • Loss of transient receptor potential channel 5 causes obesity and postpartum depression.

    Li Y, Cacciottolo TM, Yin N, He Y, Liu H, Liu H, Yang Y, Henning E, Keogh JM, Lawler K et al.

    Cell 2024

    PUBMED: 38959890; DOI: 10.1016/j.cell.2024.06.001

  • The association of lumbar intervertebral disc degeneration with low back pain is modified by underlying genetic propensity to pain.

    Suri P, Naeini MK, Heagerty PJ, Freidin MB, Smith IG, Elgaeva EE, Compte R, Tsepilov YA and Williams FMK

    The spine journal : official journal of the North American Spine Society 2024;25;1;8-17

    PUBMED: 38942297; PMC: 11637947; DOI: 10.1016/j.spinee.2024.05.018

  • Characterising plasmacytoid and myeloid AXL+ SIGLEC-6+ dendritic cell functions and their interactions with HIV.

    Warner van Dijk FA, Tong O, O'Neil TR, Bertram KM, Hu K, Baharlou H, Vine EE, Jenns K, Gosselink MP, Toh JW et al.

    PLoS pathogens 2024;20;6;e1012351

    PUBMED: 38924030; DOI: 10.1371/journal.ppat.1012351

  • 2,8-Disubstituted-1,5-naphthyridines as Dual Inhibitors of Plasmodium falciparum Phosphatidylinositol-4-kinase and Hemozoin Formation with In Vivo Efficacy.

    Dziwornu GA, Seanego D, Fienberg S, Clements M, Ferreira J, Sypu VS, Samanta S, Bhana AD, Korkor CM, Garnie LF et al.

    Journal of medicinal chemistry 2024

    PUBMED: 38918002; DOI: 10.1021/acs.jmedchem.4c01154

  • Gut microbiota and immune profiling of microbiota-humanised versus wildtype mouse models of hepatointestinal schistosomiasis.

    Stark KA, Rinaldi G, Costain A, Clare S, Tolley C, Almeida A, McCarthy C, Harcourt K, Brandt C, Lawley TD et al.

    Animal microbiome 2024;6;1;36

    PUBMED: 38918824; PMC: 11201864; DOI: 10.1186/s42523-024-00318-3

  • A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project.

    Twyford AD, Beasley J, Barnes I, Allen H, Azzopardi F, Bell D, Blaxter ML, Broad G, Campos-Dominguez L, Choonea D et al.

    Wellcome open research 2024;9;339

    PUBMED: 39386966; PMC: 11462125; DOI: 10.12688/wellcomeopenres.21143.1

  • The genome sequence of a bluebottle fly, Calliphora vicina (Linnaeus, 1758).

    Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;335

    PUBMED: 39473873; PMC: 11519611; DOI: 10.12688/wellcomeopenres.22469.1

  • The genome sequence of a cranefly, Tipula ( Savtshenkia) confusa van der Wulp, 1883.

    Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;337

    PUBMED: 39429631; PMC: 11489842; DOI: 10.12688/wellcomeopenres.22470.1

  • Widespread chromatin context-dependencies of DNA double-strand break repair proteins.

    Vergara X, Manjón AG, de Haas M, Morris B, Schep R, Leemans C, Friskes A, Beijersbergen RL, Sanders MA, Medema RH and van Steensel B

    Nature communications 2024;15;1;5334

    PUBMED: 38909016; PMC: 11193718; DOI: 10.1038/s41467-024-49232-x

  • The Bioinformatic Applications of Hi-C and Linked Reads.

    Jiang L, Quail MA, Fraser-Govi J, Wang H, Shi X, Oliver K, Mellado Gomez E, Yang F and Ning Z

    Genomics, proteomics & bioinformatics 2024

    PUBMED: 38905513; DOI: 10.1093/gpbjnl/qzae048

  • The genome sequence of an anthomyiid fly, Pegoplata infirma (Meigen, 1826) (Diptera, Anthomyiidae).

    Falk S, Brighton P, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;330

    PUBMED: 40144701; PMC: 11937944; DOI: 10.12688/wellcomeopenres.22463.1

  • The genome sequence of the Coccidian parasite, Eimeria praecox (Apicomplexa: Eucoccidiorida).

    Blake DP, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;331

    PUBMED: 39262407; PMC: 11387943; DOI: 10.12688/wellcomeopenres.22464.1

  • The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758.

    Boyes D, Hutchinson F, Crowley LM, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;329

    PUBMED: 39398940; PMC: 11470982; DOI: 10.12688/wellcomeopenres.22461.1

  • The genome sequence of the European pine marten, Martes martes (Linnaeus, 1758).

    O'Brien D, Januszczak I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;325

    PUBMED: 39233901; PMC: 11372345; DOI: 10.12688/wellcomeopenres.22458.1

  • The genome sequence of the yellow-legged black legionnaire, Beris chalybata (Forster, 1771).

    Crowley LM, Akinmusola RY, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;151

    PUBMED: 39267993; PMC: 11391196; DOI: 10.12688/wellcomeopenres.21159.2

  • Developmental and stem cell biology's bright future.

    Lewis J, Schuh M, Hanna JH, Zernicka-Goetz M, Srivastava M, Tan T, Behjati S, Liu Z, Petridou NI and Mendjan S

    Cell 2024;187;13;3224-3228

    PUBMED: 38906097; DOI: 10.1016/j.cell.2024.05.037

  • Evaluation of polygenic scoring methods in five biobanks shows larger variation between biobanks than methods and finds benefits of ensemble learning.

    Monti R, Eick L, Hudjashov G, Läll K, Kanoni S, Wolford BN, Wingfield B, Pain O, Wharrie S, Jermy B et al.

    American journal of human genetics 2024

    PUBMED: 38908374; DOI: 10.1016/j.ajhg.2024.06.003

  • The genome sequence of the Common Alderfly, Sialis lutaria (Linnaeus, 1758).

    Farr A, Hall DW, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;322

    PUBMED: 39386967; PMC: 11462116; DOI: 10.12688/wellcomeopenres.22466.1

  • Human SARS-CoV-2 challenge uncovers local and systemic response dynamics.

    Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L et al.

    Nature 2024;631;8019;189-198

    PUBMED: 38898278; PMC: 11222146; DOI: 10.1038/s41586-024-07575-x

  • Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.

    Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK and Porazinska DL

    BMC genomics 2024;25;1;615

    PUBMED: 38890582; DOI: 10.1186/s12864-024-10500-1

  • Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.

    Khawaja T, Mäklin T, Kallonen T, Gladstone RA, Pöntinen AK, Mero S, Thorpe HA, Samuelsen Ø, Parkhill J, Izhar M et al.

    Nature communications 2024;15;1;5196

    PUBMED: 38890378; PMC: 11189469; DOI: 10.1038/s41467-024-49591-5

  • Community methicillin-resistant Staphylococcus aureus outbreaks in areas of low prevalence.

    Bellis KL, Dissanayake OM, Harrison EM and Aggarwal D

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2024;31;2;182-189

    PUBMED: 38897351; DOI: 10.1016/j.cmi.2024.06.006

  • SMIM1 absence is associated with reduced energy expenditure and excess weight.

    Stefanucci L, Moslemi C, Tomé AR, Virtue S, Bidault G, Gleadall NS, Watson LPE, Kwa JE, Burden F, Farrow S et al.

    Med (New York, N.Y.) 2024

    PUBMED: 38906141; DOI: 10.1016/j.medj.2024.05.015

  • Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis.

    Easter QT, Fernandes Matuck B, Beldorati Stark G, Worth CL, Predeus AV, Fremin B, Huynh K, Ranganathan V, Ren Z, Pereira D et al.

    Nature communications 2024;15;1;5016

    PUBMED: 38876998; PMC: 11178863; DOI: 10.1038/s41467-024-49037-y

  • The genome sequence of a cased caddisfly, Molanna angustata Curtis, 1834.

    Coleman D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;315

    PUBMED: 39464372; PMC: 11502996; DOI: 10.12688/wellcomeopenres.22271.1

  • The genome sequence of a cased caddisfly, Mystacides longicornis (Linnaeus, 1758).

    Coleman D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;310

    PUBMED: 39246518; PMC: 11380072; DOI: 10.12688/wellcomeopenres.22272.1

  • The genome sequence of the flea beetle, Crepidodera aurea (Geoffrey, 1785).

    Telfer MG, Blomfield-Smith H, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;318

    PUBMED: 39323607; PMC: 11422754; DOI: 10.12688/wellcomeopenres.22454.1

  • The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).

    Morales HE, Norris K, Henshaw S, Tatayah V, Ruhomaun K, van Oosterhout C, Groombridge JJ, Gilbert MTP, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;312

    PUBMED: 39221442; PMC: 11362723; DOI: 10.12688/wellcomeopenres.22452.1

  • The genome sequence of the Plain Longtail butterfly, Spicauda simplicius (Stoll, 1807).

    Ribeiro P, Matos-Maraví P, Linke D, Meier J, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2024;9;314

    PUBMED: 39246520; PMC: 11377922; DOI: 10.12688/wellcomeopenres.22457.1

  • The genome sequence of the tree-moss, Climacium dendroides (Hedw.) F.Weber & D.Mohr (Climaciaceae).

    Bell D, Long DG, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;311

    PUBMED: 39464370; PMC: 11503002; DOI: 10.12688/wellcomeopenres.22450.1

  • Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium.

    Tran TA, Sridhar S, Reece ST, Lunguya O, Jacobs J, Van Puyvelde S, Marks F, Dougan G, Thomson NR, Nguyen BT et al.

    Nature communications 2024;15;1;5074

    PUBMED: 38871710; PMC: 11176356; DOI: 10.1038/s41467-024-49433-4

  • eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis.

    Burnham KL, Milind N, Lee W, Kwok AJ, Cano-Gamez K, Mi Y, Geoghegan CG, Zhang P, GAinS Investigators, McKechnie S et al.

    Cell genomics 2024;100587

    PUBMED: 38897207; DOI: 10.1016/j.xgen.2024.100587

  • High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis.

    Davison A, Chowdhury M, Johansen M, Wellcome Sanger Institute Tree of Life programme, Uliano-Silva M and Blaxter M

    BMC genomics 2024;25;1;596

    PUBMED: 38872121; DOI: 10.1186/s12864-024-10505-w

  • Unlocking a genetic model of NK-cell transformation.

    Dufva O

    Blood 2024;143;24;2443-2444

    PUBMED: 38869919; DOI: 10.1182/blood.2024024550

  • Variant ranking pipeline for complex familial disorders.

    Ralli S, Vira T, Robles-Espinoza CD, Adams DJ and Brooks-Wilson AR

    Scientific reports 2024;14;1;13599

    PUBMED: 38866901; PMC: 11169219; DOI: 10.1038/s41598-024-64169-3

  • An EMT-like signature as a potential driver of myeloid sarcoma.

    Zorn KE, Alvarez-Argote J, Meyer AE, Cunningham A, Hintzke M, Giever E, Stelloh C, Atallah E, Vassiliou GS and Rao S

    Blood neoplasia 2024;1;3

    PUBMED: 40060005; PMC: 11887653; DOI: 10.1016/j.bneo.2024.100024

  • Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork.

    Calland JK, Pesonen ME, Mehat J, Pascoe B, Haydon DJ, Lourenco J, Lukasiewicz B, Mourkas E, Hitchings MD, La Ragione RM et al.

    NPJ vaccines 2024;9;1;105

    PUBMED: 38866805; PMC: 11169640; DOI: 10.1038/s41541-024-00879-z

  • High Prevalence and Genetic Diversity of Multidrug Resistant and Extended Spectrum ß-Lactamase Producing Escherichia coli and Klebsiella pneumoniae in Mothers and Neonates in a Cameroonian Labour Ward.

    Njeuna A, Founou LL, Founou RC, Koudoum PL, Mbossi A, Blocker A, Bentley SD and Sone LE

    American journal of infection control 2024

    PUBMED: 38876168; DOI: 10.1016/j.ajic.2024.06.002

  • Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution.

    Zhang X, Blaxter M, Wood JMD, Tracey A, McCarthy S, Thorpe P, Rayner JG, Zhang S, Sikkink KL, Balenger SL and Bailey NW

    Nature communications 2024;15;1;5001

    PUBMED: 38866741; PMC: 11169259; DOI: 10.1038/s41467-024-49344-4

  • The genome sequence of a soldier beetle, Cantharis flavilabris Fallén, 1807.

    Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;303

    PUBMED: 39280726; PMC: 11399767; DOI: 10.12688/wellcomeopenres.22422.1

  • The genome sequence of the grey gurnard, Eutrigla gurnardus (Linnaeus, 1758).

    Brittain R, Adkins P, Harley J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;307

    PUBMED: 39246517; PMC: 11377927; DOI: 10.12688/wellcomeopenres.22453.1

  • The genome sequence of the oak pinhole borer, Platypus cylindrus Fabricius, 1792.

    Barclay MVL, Vassiliades D, Bayfield Farrell W, Cristóvão J, Matsumoto K, Geiser M, Telfer MG, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective et al.

    Wellcome open research 2024;9;305

    PUBMED: 39301439; PMC: 11411242; DOI: 10.12688/wellcomeopenres.22425.1

  • AI and immunology.

    Germain RN, Van Allen EM, Trynka G, Tsang JS, Grün D, Kiemen AL, Shi Y, Pugh Bernard A and Nolan GP

    Immunity 2024;57;6;1177-1181

    PUBMED: 38865960; DOI: 10.1016/j.immuni.2024.05.016

  • Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.

    Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y et al.

    Nature biotechnology 2024

    PUBMED: 38862616; DOI: 10.1038/s41587-024-02250-y

  • Human milk antibodies to global pathogens reveal geographic and interindividual variations in IgA and IgG.

    Campo JJ, Seppo AE, Randall AZ, Pablo J, Hung C, Teng A, Shandling AD, Truong J, Oberai A, Miller J et al.

    The Journal of clinical investigation 2024;134;15

    PUBMED: 39087469; DOI: 10.1172/JCI168789

  • IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway.

    Moran EA, Salas-Briceno K, Zhao W, Enya T, Aguilera AN, Acosta I, Alonzo F, Kiani D, Behnsen J, Alvarez C et al.

    mBio 2024;e0120924

    PUBMED: 38860764; DOI: 10.1128/mbio.01209-24

  • Microarray analysis demonstrates upregulation of the endothelin-1 gene with compensatory downregulation of the ETA receptor gene in human portal vein.

    Davenport AP, Owen NE, Williams TL, Maguire JJ, Kuc RE and Davenport EE

    Bioscience reports 2024

    PUBMED: 38860875; DOI: 10.1042/BSR20240528

  • The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the Tree of Life.

    McKenna V, Archibald JM, Beinart R, Dawson MN, Hentschel U, Keeling PJ, Lopez JV, Martín-Durán JM, Petersen JM, Sigwart JD et al.

    Wellcome open research 2024;6;254

    PUBMED: 40438199; PMC: 12117321; DOI: 10.12688/wellcomeopenres.17222.2

  • Methods applied to neonatal dried blood spot samples for secondary research purposes: a scoping review.

    Canning J, Strawbridge RJ, Miedzybrodzka Z, Marioni RE, Melbye M, Porteous DJ, Hurles ME, Sattar N, Sudlow CLM, Collins R et al.

    Critical reviews in clinical laboratory sciences 2024;1-24

    PUBMED: 38855982; DOI: 10.1080/10408363.2024.2360996

  • Human γδ T cells in diverse tissues exhibit site-specific maturation dynamics across the life span.

    Gray JI, Caron DP, Wells SB, Guyer R, Szabo P, Rainbow D, Ergen C, Rybkina K, Bradley MC, Matsumoto R et al.

    Science immunology 2024;9;96;eadn3954

    PUBMED: 38848342; DOI: 10.1126/sciimmunol.adn3954

  • Detecting co-selection through excess linkage disequilibrium in bacterial genomes.

    Mallawaarachchi S, Tonkin-Hill G, Pöntinen AK, Calland JK, Gladstone RA, Arredondo-Alonso S, MacAlasdair N, Thorpe HA, Top J, Sheppard SK et al.

    NAR genomics and bioinformatics 2024;6;2;lqae061

    PUBMED: 38846349; PMC: 11155488; DOI: 10.1093/nargab/lqae061

  • DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts.

    Rimoldi M, Wang N, Zhang J, Villar D, Odom DT, Taipale J, Flicek P and Roller M

    Genome biology 2024;25;1;146

    PUBMED: 38844976; DOI: 10.1186/s13059-024-03218-6

  • LLIN Evaluation in Uganda Project (LLINEUP): modelling the impact of COVID-19-related disruptions on delivery of long-lasting insecticidal nets on malaria indicators in Uganda.

    Okiring J, Gonahasa S, Maiteki-Sebuguzi C, Katureebe A, Bagala I, Mutungi P, Kigozi SP, Namuganga JF, Nankabirwa JI, Kamya MR et al.

    Malaria journal 2024;23;1;180

    PUBMED: 38844987; DOI: 10.1186/s12936-024-05008-8

  • Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics.

    Palmer JA, Rosenthal N, Teichmann SA and Litvinukova M

    Circulation research 2024;134;12;1681-1702

    PUBMED: 38843288; DOI: 10.1161/CIRCRESAHA.124.323672

  • A disease-associated gene desert directs macrophage inflammation through ETS2.

    Stankey CT, Bourges C, Haag LM, Turner-Stokes T, Piedade AP, Palmer-Jones C, Papa I, Silva Dos Santos M, Zhang Q, Cameron AJ et al.

    Nature 2024;630;8016;447-456

    PUBMED: 38839969; PMC: 11168933; DOI: 10.1038/s41586-024-07501-1

  • Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction.

    Schormair B, Zhao C, Bell S, Didriksen M, Nawaz MS, Schandra N, Stefani A, Högl B, Dauvilliers Y, Bachmann CG et al.

    Nature genetics 2024;56;6;1090-1099

    PUBMED: 38839884; PMC: 11176086; DOI: 10.1038/s41588-024-01763-1

  • High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response.

    Mi Y, Burnham KL, Charles PD, Heilig R, Vendrell I, Whalley J, Torrance HD, Antcliffe DB, May SM, Neville MJ et al.

    Science translational medicine 2024;16;750;eadh0185

    PUBMED: 38838133; DOI: 10.1126/scitranslmed.adh0185

  • Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data.

    Cheng HR, Belman S, Salje H, Dagan R and Bentley SD

    Microbial genomics 2024;10;6

    PUBMED: 38913413; DOI: 10.1099/mgen.0.001262

  • Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi.

    Cave R, Kalizang'oma A, Chaguza C, Mwalukomo TS, Kamng'ona A, Brown C, Msefula J, Bonomali F, Nyirenda R, Swarthout TD et al.

    Microbial genomics 2024;10;6

    PUBMED: 38896467; DOI: 10.1099/mgen.0.001264

  • Novel somatic mutations in blood driving age-related clonal hematopoiesis.

    No authors listed

    Nature genetics 2024;56;6;1049-1050

    PUBMED: 38806715; DOI: 10.1038/s41588-024-01756-0

  • Host preference patterns in domestic and wild settings: Insights into Anopheles feeding behavior.

    Bouafou L, Makanga BK, Rahola N, Boddé M, Ngangué MF, Daron J, Berger A, Mouillaud T, Makunin A, Korlević P et al.

    Evolutionary applications 2024;17;6;e13693

    PUBMED: 38828055; PMC: 11143308; DOI: 10.1111/eva.13693

  • An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity.

    Faure AJ, Lehner B, Miró Pina V, Serrano Colome C and Weghorn D

    PLoS computational biology 2024;20;5;e1012132

    PUBMED: 38805561; PMC: 11161127; DOI: 10.1371/journal.pcbi.1012132

  • Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system.

    Badja C, Momen S, Koh GCC, Boushaki S, Roumeliotis TI, Kozik Z, Jones I, Bousgouni V, Dias JML, Krokidis MG et al.

    Cell reports 2024;43;6;114243

    PUBMED: 38805398; DOI: 10.1016/j.celrep.2024.114243

  • Emergence of High-Level Gentamicin Resistance in Streptococcus agalactiae Hypervirulent Serotype IV ST1010 (CC452) Strains by Acquisition of a Novel Integrative and Conjugative Element.

    Creti R, Imperi M, Khan UB, Berardi A, Recchia S, Alfarone G and Gherardi G

    Antibiotics (Basel, Switzerland) 2024;13;6

    PUBMED: 38927158; PMC: 11201010; DOI: 10.3390/antibiotics13060491

  • ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance.

    da Silva AF, da Silva Neto AM, Aksenen CF, Jeronimo PMC, Dezordi FZ, Almeida SP, Costa HMP, Salvato RS, Campos TL, Wallau GDL and Of The Fiocruz Genomic Network OB

    NAR genomics and bioinformatics 2024;6;2;lqae056

    PUBMED: 38800829; PMC: 11127631; DOI: 10.1093/nargab/lqae056

  • The genome sequence of a hoverfly  Eristalinus aeneus (Scopoli, 1763).

    Sivell O, Raper C, Mitchell R, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;69

    PUBMED: 38813464; PMC: 11134147; DOI: 10.12688/wellcomeopenres.20636.2

  • The genome sequence of the nematode Caenorhabditis drosophilae (Rhabditida, Rhabditidae) (Kiontke, 1997).

    Kieninger M, Stevens L, Collins JC, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Tree of Life Core Informatics team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations and Blaxter M

    Wellcome open research 2024;9;292

    PUBMED: 39114493; PMC: 11303941; DOI: 10.12688/wellcomeopenres.22416.1

  • Fasting before Intra-Gastric Dosing with Antigen Improves Intestinal Humoral Responses in Syrian Hamsters.

    Wood L, Hughes J, Trussell M, Bishop AL and Griffin R

    Vaccines 2024;12;6

    PUBMED: 38932302; PMC: 11209237; DOI: 10.3390/vaccines12060572

  • Genome evolution in intracellular parasites: Microsporidia and Apicomplexa.

    Khalaf A, Francis O and Blaxter ML

    The Journal of eukaryotic microbiology 2024;e13033

    PUBMED: 38785208; DOI: 10.1111/jeu.13033

  • Intratumoral antigen signaling traps CD8+ T cells to confine exhaustion to the tumor site.

    Takahashi M, So TY, Chamberlain-Evans V, Hughes R, Yam-Puc JC, Kania K, Ruhle M, Mann T, Schuijs MJ, Coupland P et al.

    Science immunology 2024;9;95;eade2094

    PUBMED: 38787961; DOI: 10.1126/sciimmunol.ade2094

  • NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome.

    Chen R, Lukianova E, van der Loeff IS, Spegarova JS, Willet JDP, James KD, Ryder EJ, Griffin H, IJspeert H, Gajbhiye A et al.

    Science immunology 2024;9;95;eade5705

    PUBMED: 38787962; DOI: 10.1126/sciimmunol.ade5705

  • An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding.

    Perry WB, Seymour M, Orsini L, Jâms IB, Milner N, Edwards F, Harvey R, de Bruyn M, Bista I, Walsh K et al.

    Nature communications 2024;15;1;4372

    PUBMED: 38782932; PMC: 11116482; DOI: 10.1038/s41467-024-48640-3

  • MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions.

    Farr E, Dimitrov D, Schmidt C, Turei D, Lobentanzer S, Dugourd A and Saez-Rodriguez J

    Briefings in bioinformatics 2024;25;4

    PUBMED: 39038934; DOI: 10.1093/bib/bbae347

  • Single-cell and spatial transcriptomics analysis of non-small cell lung cancer.

    De Zuani M, Xue H, Park JS, Dentro SC, Seferbekova Z, Tessier J, Curras-Alonso S, Hadjipanayis A, Athanasiadis EI, Gerstung M et al.

    Nature communications 2024;15;1;4388

    PUBMED: 38782901; PMC: 11116453; DOI: 10.1038/s41467-024-48700-8

  • The genome sequence of the Grey Sedge caddis fly, Odontocerum albicorne (Scopoli, 1769).

    Skipp S, Wallace I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;8;445

    PUBMED: 38784714; PMC: 11112305; DOI: 10.12688/wellcomeopenres.20124.2

  • Acquisition of epithelial plasticity in human chronic liver disease.

    Gribben C, Galanakis V, Calderwood A, Williams EC, Chazarra-Gil R, Larraz M, Frau C, Puengel T, Guillot A, Rouhani FJ et al.

    Nature 2024;630;8015;166-173

    PUBMED: 38778114; PMC: 11153150; DOI: 10.1038/s41586-024-07465-2

  • The genome sequence of the cut surfclam, Spisula subtruncata (da Costa, 1778).

    Adkins P, Holmes A, Mackie A, Darbyshire T, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;286

    PUBMED: 39015612; PMC: 11249531; DOI: 10.12688/wellcomeopenres.22286.1

  • The genome sequence of the Marbled Minor moth, Oligia strigilis (Linnaeus, 1758).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;282

    PUBMED: 39345345; PMC: 11437290; DOI: 10.12688/wellcomeopenres.21679.1

  • The genome sequence of the Muslin Footman moth, Nudaria mundana (Linnaeus, 1761).

    Crowley LM, Hutchinson F, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;283

    PUBMED: 39411458; PMC: 11474146; DOI: 10.12688/wellcomeopenres.22252.1

  • The genome sequence of the Pacific oyster, Magallana gigas (Thunberg, 1793).

    Mrowicki R, Uhl R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;284

    PUBMED: 39050697; PMC: 11267148; DOI: 10.12688/wellcomeopenres.22255.1

  • Protective role for kidney TREM2high macrophages in obesity- and diabetes-induced kidney injury.

    Subramanian A, Vernon KA, Zhou Y, Marshall JL, Alimova M, Arevalo C, Zhang F, Slyper M, Waldman J, Montesinos MS et al.

    Cell reports 2024;43;6;114253

    PUBMED: 38781074; DOI: 10.1016/j.celrep.2024.114253

  • The genome sequence of the Brown Litter Worm, Bimastos eiseni (Levinsen, 1884).

    Brown KD, Sherlock E, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;279

    PUBMED: 39296368; PMC: 11408909; DOI: 10.12688/wellcomeopenres.21622.1

  • Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children.

    Zhang Z, Kean IRL, Dratva LM, Clark JA, Syrimi E, Khan N, Daubney E, White D, O'Neill L, Chisholm C et al.

    Nature communications 2024;15;1;4227

    PUBMED: 38762592; PMC: 11102542; DOI: 10.1038/s41467-024-48699-y

  • The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis & Schiffermüller) 1775.

    Boyes D, Lees DC, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;271

    PUBMED: 39309224; PMC: 11415762; DOI: 10.12688/wellcomeopenres.21665.1

  • The impact of inversions across 33,924 families with rare disease from a national genome sequencing project.

    Pagnamenta AT, Yu J, Walker S, Noble AJ, Lord J, Dutta P, Hashim M, Camps C, Green H, Devaiah S et al.

    American journal of human genetics 2024

    PUBMED: 38776926; DOI: 10.1016/j.ajhg.2024.04.018

  • A screen for Plasmodium falciparum sporozoite surface protein binding to human hepatocyte surface receptors identifies novel host-pathogen interactions.

    Segireddy RR, Belda H, Yang ASP, Dundas K, Knoeckel J, Galaway F, Wood L, Quinkert D, Knuepfer E, Treeck M et al.

    Malaria journal 2024;23;1;151

    PUBMED: 38755636; PMC: 11098746; DOI: 10.1186/s12936-024-04913-2

  • APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes.

    Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basílio Lobo G, Bao SN et al.

    Scientific reports 2024;14;1;11242

    PUBMED: 38755230; PMC: 11099048; DOI: 10.1038/s41598-024-61295-w

  • Improving the care of children with GENetic Rare disease: Observational Cohort study (GenROC)-a study protocol.

    Low KJ, Watford A, Blair P, Nabney I, Powell J, Wynn SL, Foreman J, Firth H and Ingram J

    BMJ open 2024;14;5;e085237

    PUBMED: 38760043; PMC: 11103197; DOI: 10.1136/bmjopen-2024-085237

  • Inflammatory Memory in Psoriasis: From Remission to Recurrence.

    Francis L, Capon F, Smith CH, Haniffa M and Mahil SK

    The Journal of allergy and clinical immunology 2024

    PUBMED: 38761994; DOI: 10.1016/j.jaci.2024.05.008

  • The genome sequence of purple glasswort, Salicornia ramosissima Woods (Amaranthaceae).

    Mian S, Christenhusz MJM, Leitch IJ, Leitch AR, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;257

    PUBMED: 39411459; PMC: 11474152; DOI: 10.12688/wellcomeopenres.21552.1

  • The genome sequence of the Fig-leaf Skeletoniser, Choreutis nemorana (Hübner, [1799]).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;268

    PUBMED: 39290366; PMC: 11406129; DOI: 10.12688/wellcomeopenres.21624.1

  • The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758).

    Boyes D, Crowley LM, Morley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;260

    PUBMED: 39398937; PMC: 11467647; DOI: 10.12688/wellcomeopenres.21568.1

  • The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).

    Lohse K, Vila R, Hayward A, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;266

    PUBMED: 39257624; PMC: 11384194; DOI: 10.12688/wellcomeopenres.21627.1

  • The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).

    Boyes D, Broad GR, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;258

    PUBMED: 39267994; PMC: 11391193; DOI: 10.12688/wellcomeopenres.21567.1

  • The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758).

    Martin SH, Lohse K, Ebdon S, Mackintosh A, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;267

    PUBMED: 39386964; PMC: 11462119; DOI: 10.12688/wellcomeopenres.21586.1

  • The genome sequence of the Rusty-dot Pearl moth, Udea ferrugalis (Hübner, 1796).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;259

    PUBMED: 39372843; PMC: 11452769; DOI: 10.12688/wellcomeopenres.21571.1

  • AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation.

    Nagi SC, Ashraf F, Miles A and Donnelly MJ

    Wellcome open research 2024;9;255

    PUBMED: 39184128; PMC: 11342028; DOI: 10.12688/wellcomeopenres.20998.1

  • Phage-plasmids: missed links between mobile genetic elements.

    Figueroa W, Cazares D and Cazares A

    Trends in microbiology 2024

    PUBMED: 38755022; DOI: 10.1016/j.tim.2024.04.014

  • Analysis of somatic mutations in whole blood from 200,618 individuals identifies pervasive positive selection and novel drivers of clonal hematopoiesis.

    Bernstein N, Spencer Chapman M, Nyamondo K, Chen Z, Williams N, Mitchell E, Campbell PJ, Cohen RL and Nangalia J

    Nature genetics 2024;56;6;1147-1155

    PUBMED: 38744975; PMC: 11176083; DOI: 10.1038/s41588-024-01755-1

  • EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays.

    Megas S, Lorenzi V and Marioni JC

    Genome biology 2024;25;1;121

    PUBMED: 38741206; DOI: 10.1186/s13059-024-03259-x

  • High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response.

    Mentzer AJ, Dilthey AT, Pollard M, Gurdasani D, Karakoc E, Carstensen T, Muhwezi A, Cutland C, Diarra A, da Silva Antunes R et al.

    Nature medicine 2024;30;5;1384-1394

    PUBMED: 38740997; PMC: 11108778; DOI: 10.1038/s41591-024-02944-5

  • Complexities of modelling the bone marrow microenvironment to facilitate haematopoietic research.

    Busch C, Nyamondo K and Wheadon H

    Experimental hematology 2024;104233

    PUBMED: 38740324; DOI: 10.1016/j.exphem.2024.104233

  • Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.

    Speak SA, Birley T, Bortoluzzi C, Clark MD, Percival-Alwyn L, Morales HE and van Oosterhout C

    Molecular ecology resources 2024;e13967

    PUBMED: 38727721; DOI: 10.1111/1755-0998.13967

  • The future of rapid and automated single-cell data analysis using reference mapping.

    Lotfollahi M, Yuhan Hao, Theis FJ and Satija R

    Cell 2024;187;10;2343-2358

    PUBMED: 38729109; DOI: 10.1016/j.cell.2024.03.009

  • The genome sequence of a tachinid fly, Linnaemya tessellans (Robineau-Desvoidy, 1830).

    Falk S, Smith MN, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;243

    PUBMED: 39132670; PMC: 11310650; DOI: 10.12688/wellcomeopenres.21499.1

  • The genome sequence of the Brown Ash Ermine moth, Zelleria hepariella Stainton, 1849.

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;242

    PUBMED: 39109332; PMC: 11301138; DOI: 10.12688/wellcomeopenres.21495.1

  • The genome sequence of the Brown Long-eared bat, Plecotus auritus (Linnaeus 1758).

    Millar A, Vernes SC, Teeling EC, Mai M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;246

    PUBMED: 39045151; PMC: 11263909; DOI: 10.12688/wellcomeopenres.21501.1

  • Analyzing the functional effects of DNA variants with gene editing.

    Cooper S, Obolenski S, Waters AJ, Bassett AR and Coelho MA

    Cell reports methods 2024;100776

    PUBMED: 38744287; DOI: 10.1016/j.crmeth.2024.100776

  • In the Murine and Bovine Maternal Mammary Gland Signal Transducer and Activator of Transcription 3 is Activated in Clusters of Epithelial Cells around the Day of Birth.

    Hardwick LJA, Davies BP, Pensa S, Burge-Rogers M, Davies C, Baptista AF, Knott R, S McCrone I, Po E, Strugnell BW et al.

    Journal of mammary gland biology and neoplasia 2024;29;1;10

    PUBMED: 38722417; PMC: 11081984; DOI: 10.1007/s10911-024-09561-5

  • The genome sequence of the Winter Shade, Tortricodes alternella [Denis & Schiffermüller], 1775.

    Crowley LM, Morley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;236

    PUBMED: 38903871; PMC: 11187527; DOI: 10.12688/wellcomeopenres.21494.1

  • Integrated Proteomics Analysis of Baseline Protein Expression in Pig Tissues.

    Wang S, Collins A, Prakash A, Fexova S, Papatheodorou I, Jones AR and Vizcaíno JA

    Journal of proteome research 2024

    PUBMED: 38717300; DOI: 10.1021/acs.jproteome.3c00741

  • Oxidative DNA damage promotes vascular aging associated with changes in extracellular matrix-regulating proteins.

    Foote K, Rienks M, Schmidt L, Theofilatos K, Yasmin, Ozols M, Eckersley A, Shah A, Figg N, Finigan A et al.

    Cardiovascular research 2024

    PUBMED: 38717632; DOI: 10.1093/cvr/cvae091

  • Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.

    Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K et al.

    Database : the journal of biological databases and curation 2024;2024

    PUBMED: 38713862; DOI: 10.1093/database/baae031

  • Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations.

    Heinz E, Pearse O, Zuza A, Bilima S, Msefula C, Musicha P, Siyabu P, Tewesa E, Graf FE, Lester R et al.

    Genome medicine 2024;16;1;67

    PUBMED: 38711148; PMC: 11073982; DOI: 10.1186/s13073-024-01342-3

  • Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

    Peona V, Martelossi J, Almojil D, Bocharkina J, Brännström I, Brown M, Cang A, Carrasco-Valenzuela T, DeVries J, Doellman M et al.

    Mobile DNA 2024;15;1;10

    PUBMED: 38711146; PMC: 11071193; DOI: 10.1186/s13100-024-00319-8

  • A single cell atlas of sexual development in Plasmodium falciparum.

    Dogga SK, Rop JC, Cudini J, Farr E, Dara A, Ouologuem D, Djimdé AA, Talman AM and Lawniczak MKN

    Science (New York, N.Y.) 2024;384;6695;eadj4088

    PUBMED: 38696552; DOI: 10.1126/science.adj4088

  • Patent Foramen Ovale Closure in Older Patients With Stroke: Patient Selection for Trial Feasibility.

    Wang AY, Rothwell PM, Nelson J, Saver JL, Kasner SE, Carroll J, Mas JL, Derumeaux G, Chatellier G, Furlan AJ et al.

    Neurology 2024;102;10;e209388

    PUBMED: 38701403; DOI: 10.1212/WNL.0000000000209388

  • Systematic identification of structure-specific protein-protein interactions.

    Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA et al.

    Molecular systems biology 2024;20;6;651-675

    PUBMED: 38702390; PMC: 11148107; DOI: 10.1038/s44320-024-00037-6

  • Cachd1 interacts with Wnt receptors and regulates neuronal asymmetry in the zebrafish brain.

    Powell GT, Faro A, Zhao Y, Stickney H, Novellasdemunt L, Henriques P, Gestri G, Redhouse White E, Ren J, Lu W et al.

    Science (New York, N.Y.) 2024;384;6695;573-579

    PUBMED: 38696577; DOI: 10.1126/science.ade6970

  • Clinical Use of Molecular Biomarkers in Canine and Feline Oncology: Current and Future.

    Aupperle-Lellbach H, Kehl A, de Brot S and van der Weyden L

    Veterinary sciences 2024;11;5

    PUBMED: 38787171; PMC: 11126050; DOI: 10.3390/vetsci11050199

  • Developmental Dysregulation of Childhood Cancer.

    Oliver TRW and Behjati S

    Cold Spring Harbor perspectives in medicine 2024

    PUBMED: 38692740; DOI: 10.1101/cshperspect.a041580

  • Generation of Mammalian Astrocyte Functional Heterogeneity.

    Bartels T, Rowitch DH and Bayraktar OA

    Cold Spring Harbor perspectives in biology 2024

    PUBMED: 38692833; DOI: 10.1101/cshperspect.a041351

  • Geographic variation of mutagenic exposures in kidney cancer genomes.

    Senkin S, Moody S, Díaz-Gay M, Abedi-Ardekani B, Cattiaux T, Ferreiro-Iglesias A, Wang J, Fitzgerald S, Kazachkova M, Vangara R et al.

    Nature 2024;629;8013;910-918

    PUBMED: 38693263; PMC: 11111402; DOI: 10.1038/s41586-024-07368-2

  • Monitoring pathogens in wastewater.

    Wongprommoon A, Chomkatekaew C and Chewapreecha C

    Nature reviews. Microbiology 2024;22;5;261

    PUBMED: 38413815; DOI: 10.1038/s41579-024-01033-1

  • Multimodal decoding of human liver regeneration.

    Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA, Fercoq F, May S, Zajdel E, Beltran M, Sutherland EF, Mackey JBG et al.

    Nature 2024;630;8015;158-165

    PUBMED: 38693268; PMC: 11153152; DOI: 10.1038/s41586-024-07376-2

  • Systematic analysis of muscle aging using joint single-cell and single-nucleus sequencing.

    No authors listed

    Nature aging 2024;4;5;621-622

    PUBMED: 38658781; DOI: 10.1038/s43587-024-00629-9

  • Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment.

    Handley BL, Sokana O, Addo KK, Wagner J, Fookes M, Harding-Esch E, Marks M, Thomson NR and Doyle RM

    Microbial genomics 2024;10;5

    PUBMED: 38739120; DOI: 10.1099/mgen.0.001234

  • Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits.

    Keaton JM, Kamali Z, Xie T, Vaez A, Williams A, Goleva SB, Ani A, Evangelou E, Hellwege JN, Yengo L et al.

    Nature genetics 2024;56;5;778-791

    PUBMED: 38689001; PMC: 11096100; DOI: 10.1038/s41588-024-01714-w

  • The genome sequences of the marine diatom Epithemia pelagica strain UHM3201 (Schvarcz, Stancheva & Steward, 2022) and its nitrogen-fixing, endosymbiotic cyanobacterium.

    Schvarcz CR, Stancheva R, Turk-Kubo KA, Wilson ST, Zehr JP, Edwards KF, Steward GF, Archibald JM, Oatley G, Sinclair E et al.

    Wellcome open research 2024;9;232

    PUBMED: 38867757; PMC: 11167328; DOI: 10.12688/wellcomeopenres.21534.1

  • Acute response to pathogens in the early human placenta at single-cell resolution.

    Hoo R, Ruiz-Morales ER, Kelava I, Rawat M, Mazzeo CI, Tuck E, Sancho-Serra C, Chelaghma S, Predeus AV, Murray S et al.

    Cell systems 2024

    PUBMED: 38703772; DOI: 10.1016/j.cels.2024.04.002

  • Assessment of biological organ age using molecular pathology in pre-transplant kidney biopsies.

    Zhang R, Trotter PB, McCaffrey J, Fitzroy R, Trivioli G, Stewart BJ, Ferdinand JR, Loudon KW, Riding A, West J et al.

    Kidney international 2024

    PUBMED: 38692408; DOI: 10.1016/j.kint.2024.03.028

  • Epistasis, core-genome disharmony, and adaptation in recombining bacteria.

    Taylor AJ, Yahara K, Pascoe B, Ko S, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA et al.

    mBio 2024;15;6;e0058124

    PUBMED: 38683013; PMC: 11237541; DOI: 10.1128/mbio.00581-24

  • Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing.

    Pol S, Kallonen T, Mäklin T, Sar P, Hopkins J, Soeng S, Miliya T, Ling CL, Bentley SD, Corander J and Turner P

    mBio 2024;e0078424

    PUBMED: 38682956; DOI: 10.1128/mbio.00784-24

  • shaPRS: Leveraging shared genetic effects across traits or ancestries improves accuracy of polygenic scores.

    Kelemen M, Vigorito E, Fachal L, Anderson CA and Wallace C

    American journal of human genetics 2024

    PUBMED: 38703768; DOI: 10.1016/j.ajhg.2024.04.009

  • The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa.

    Kamau L, Bennett KL, Ochomo E, Herren J, Agumba S, Otieno S, Omoke D, Matoke-Muhia D, Mburu D, Mwangangi J et al.

    Malaria journal 2024;23;1;122

    PUBMED: 38671462; PMC: 11046809; DOI: 10.1186/s12936-024-04950-x

  • Long-Term Co-Circulation of Host-Specialist and Host-Generalist Lineages of Group B Streptococcus in Brazilian Dairy Cattle with Heterogeneous Antimicrobial Resistance Profiles.

    Oliveira LMA, Simões LC, Crestani C, Costa NS, Pantoja JCF, Rabello RF, Teixeira LM, Khan UB, Bentley S, Jamrozy D et al.

    Antibiotics (Basel, Switzerland) 2024;13;5

    PUBMED: 38786118; PMC: 11117364; DOI: 10.3390/antibiotics13050389

  • The genome sequence of an anthomyiid fly, Eustalomyia histrio (Zetterstedt, 1838).

    Falk S, Brighton P, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;230

    PUBMED: 39502861; PMC: 11535493; DOI: 10.12688/wellcomeopenres.21264.1

  • The genome sequence of black poplar, Populus nigra subsp. betulifolia L., 1753 (Salicaceae).

    Christenhusz MJM, Bastiaanse H, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;228

    PUBMED: 39224767; PMC: 11367076; DOI: 10.12688/wellcomeopenres.21300.1

  • The genome sequence of lesser trefoil or Irish shamrock, Trifolium dubium Sibth. (Fabaceae).

    Ruhsam M, Hollingsworth PM, Mc Cartney AM, Herron KE, Hughes GM, Christenhusz MJM, Fay MF, Leitch IJ, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective et al.

    Wellcome open research 2024;9;229

    PUBMED: 39258550; PMC: 11384199; DOI: 10.12688/wellcomeopenres.21191.1

  • The genome sequence of the marbled rockcod, Notothenia rossii Richardson, 1844.

    Bista I, Collins M, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team and Tree of Life Core Informatics collective

    Wellcome open research 2024;9;227

    PUBMED: 39221438; PMC: 11362733; DOI: 10.12688/wellcomeopenres.21270.1

  • The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835.

    Boyes D, Lees DC, Sims I, Phillips D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;226

    PUBMED: 39381069; PMC: 11459120; DOI: 10.12688/wellcomeopenres.21284.1

  • Evolution and genetic architecture of sex-limited polymorphism in cuckoos.

    Merondun J, Marques CI, Andrade P, Meshcheryagina S, Galván I, Afonso S, Alves JM, Araújo PM, Bachurin G, Balacco J et al.

    Science advances 2024;10;17;eadl5255

    PUBMED: 38657058; DOI: 10.1126/sciadv.adl5255

  • Fecal Shedding, Antimicrobial Resistance and In Vitro Biofilm formation on Simulated Gallstones by Salmonella Typhi Isolated from Typhoid Cases and Asymptomatic Carriers in Nairobi, Kenya.

    Muturi P, Wachira P, Wagacha M, Mbae C, Kavai S, Muhammed M, Gunn JS and Kariuki S

    International journal of clinical microbiology 2024;1;2;23-36

    PUBMED: 39319013; PMC: 11421374; DOI: 10.14302/issn.2690-4721.ijcm-24-5030

  • Genome-wide CRISPR screens identify the YAP/TEAD axis as a driver of persister cells in EGFR mutant lung cancer.

    Pfeifer M, Brammeld JS, Price S, Pilling J, Bhavsar D, Farcas A, Bateson J, Sundarrajan A, Miragaia RJ, Guan N et al.

    Communications biology 2024;7;1;497

    PUBMED: 38658677; PMC: 11043391; DOI: 10.1038/s42003-024-06190-w

  • The genome sequence of a false flower beetle, Anaspis maculata (Geoffroy in Fourcroy, 1785).

    Telfer MG, Barclay MVL, Phillips D, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;212

    PUBMED: 39022324; PMC: 11252652; DOI: 10.12688/wellcomeopenres.21283.1

  • The genome sequence of the beech bark beetle, Taphrorychus bicolor (Herbst, 1793).

    Telfer MG, Badham XR, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;213

    PUBMED: 39355659; PMC: 11443188; DOI: 10.12688/wellcomeopenres.21265.1

  • The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839).

    Boyes D, Crowley LM, McCulloch J, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;211

    PUBMED: 39139614; PMC: 11320048; DOI: 10.12688/wellcomeopenres.21267.1

  • A genomic basis of vocal rhythm in birds.

    Sebastianelli M, Lukhele SM, Secomandi S, de Souza SG, Haase B, Moysi M, Nikiforou C, Hutfluss A, Mountcastle J, Balacco J et al.

    Nature communications 2024;15;1;3095

    PUBMED: 38653976; PMC: 11039653; DOI: 10.1038/s41467-024-47305-5

  • Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?

    McMaster B, Thorpe C, Ogg G, Deane CM and Koohy H

    Nature methods 2024;21;5;766-776

    PUBMED: 38654083; DOI: 10.1038/s41592-024-02240-7

  • Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii.

    Grewal S, Yang CY, Scholefield D, Ashling S, Ghosh S, Swarbreck D, Collins J, Yao E, Sen TZ, Wilson M et al.

    Scientific data 2024;11;1;420

    PUBMED: 38653999; PMC: 11039740; DOI: 10.1038/s41597-024-03260-w

  • Spatial genomics: mapping human steatotic liver disease.

    Matchett KP, Paris J, Teichmann SA and Henderson NC

    Nature reviews. Gastroenterology & hepatology 2024;21;9;646-660

    PUBMED: 38654090; DOI: 10.1038/s41575-024-00915-2

  • Secondary messenger signalling influences Pseudomonas aeruginosa adaptation to sinus and lung environments.

    Ruhluel D, Fisher L, Barton TE, Leighton H, Kumar S, Morillo PA, O'Brien S, Fothergill JL and Neill DR

    The ISME journal 2024

    PUBMED: 38647527; DOI: 10.1093/ismejo/wrae065

  • A panel of recombinant Leishmania donovani cell surface and secreted proteins identifies LdBPK_323600.1 as a serological marker of symptomatic infection.

    Roberts AJ, Ong HB, Clare S, Brandt C, Harcourt K, Takele Y, Ghosh P, Toepp A, Waugh M, Matano D et al.

    mBio 2024;e0085924

    PUBMED: 38639536; DOI: 10.1128/mbio.00859-24

  • Minimum information and guidelines for reporting a multiplexed assay of variant effect.

    Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Nguyen Ba AN, Riehle K, Roth FP et al.

    Genome biology 2024;25;1;100

    PUBMED: 38641812; PMC: 11027375; DOI: 10.1186/s13059-024-03223-9

  • The genome sequence of the chaffinch, Fringilla coelebs Linnaeus, 1758.

    van Grouw H, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;207

    PUBMED: 39114491; PMC: 11303953; DOI: 10.12688/wellcomeopenres.21279.1

  • The genome sequence of the lesser stag beetle, Dorcus parallelipipedus (Linnaeus, 1758).

    Crowley LM, Phillips D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;202

    PUBMED: 39184130; PMC: 11342025; DOI: 10.12688/wellcomeopenres.21262.1

  • The genome sequence of the Lesser Yellow Underwing, Noctua comes Hübner, 1813.

    Boyes D, Crowley LM, Hutchinson F, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;200

    PUBMED: 39193399; PMC: 11347922; DOI: 10.12688/wellcomeopenres.21223.1

  • The genome sequence of the Lunar Marbled Brown, Drymonia ruficornis (Hufnagel, 1766).

    Langdon WBV, Morley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;201

    PUBMED: 39411464; PMC: 11474161; DOI: 10.12688/wellcomeopenres.21225.1

  • Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine.

    Wyatt NJ, Watson H, Anderson CA, Kennedy NA, Raine T, Ahmad T, Allerton D, Bardgett M, Clark E, Clewes D et al.

    BMJ open 2024;14;4;e073639

    PUBMED: 38631839; DOI: 10.1136/bmjopen-2023-073639

  • Lipoarabinomannan modification as a source of phenotypic heterogeneity in host-adapted Mycobacterium abscessus isolates.

    De K, Belardinelli JM, Pandurangan AP, Ehianeta T, Lian E, Palčeková Z, Lam H, Gonzalez-Juarrero M, Bryant JM, Blundell TL et al.

    Proceedings of the National Academy of Sciences of the United States of America 2024;121;17;e2403206121

    PUBMED: 38630725; DOI: 10.1073/pnas.2403206121

  • The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838.

    Butlin R, Mérot C, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;197

    PUBMED: 39114490; PMC: 11303939; DOI: 10.12688/wellcomeopenres.21222.1

  • The genome sequence of the Bordered Straw, Heliothis peltigera (Denis & Schiffermüller) 1775.

    Wawman DC, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;195

    PUBMED: 39135756; PMC: 11318084; DOI: 10.12688/wellcomeopenres.21221.1

  • The genome sequence of the Western Capercaillie Tetrao urogallus Linnaeus, 1758.

    Ball A, Robertson C, Doubleday M, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;198

    PUBMED: 38706509; PMC: 11066522; DOI: 10.12688/wellcomeopenres.21261.1

  • Age-specific nasal epithelial responses to SARS-CoV-2 infection.

    Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, Yoshida M, Polanski K, Huang N, Lindeboom RGH, Mamanova L et al.

    Nature microbiology 2024;9;5;1293-1311

    PUBMED: 38622380; PMC: 11087271; DOI: 10.1038/s41564-024-01658-1

  • Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods.

    Neavin D, Senabouth A, Arora H, Lee JTH, Ripoll-Cladellas A, sc-eQTLGen Consortium, Franke L, Prabhakar S, Ye CJ, McCarthy DJ et al.

    Genome biology 2024;25;1;94

    PUBMED: 38622708; PMC: 11020463; DOI: 10.1186/s13059-024-03224-8

  • Human skeletal muscle aging atlas.

    Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, Tudor C, Shen Z, Fasouli ES, Prigmore E, Kleshchevnikov V et al.

    Nature aging 2024;4;5;727-744

    PUBMED: 38622407; PMC: 11108788; DOI: 10.1038/s43587-024-00613-3

  • Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders.

    Wigdor EM, Samocha KE, Eberhardt RY, Chundru VK, Firth HV, Wright CF, Hurles ME and Martin HC

    Scientific reports 2024;14;1;8708

    PUBMED: 38622173; PMC: 11018828; DOI: 10.1038/s41598-024-58894-y

  • The genome sequence of an ichneumonid wasp, Oxytorus armatus Thomson, 1883.

    Broad GR, Fletcher C, Januszczak I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;190

    PUBMED: 39246521; PMC: 11380729; DOI: 10.12688/wellcomeopenres.21215.1

  • The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).

    Jentoft S, Tørresen OK, Tooming-Klunderud A, Skage M, Kollias S, Jakobsen KS, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;189

    PUBMED: 39224768; PMC: 11367075; DOI: 10.12688/wellcomeopenres.21122.1

  • The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009).

    Rüber L, Britz R, Conway K, Bista I, McCarthy S, Wood J, Smith M, Oliver K, Howe K and Durbin R

    Wellcome open research 2024;9;194

    PUBMED: 39224769; PMC: 11367074; DOI: 10.12688/wellcomeopenres.21117.1

  • Human Genetics and Genomics for Drug Target Identification and Prioritization: Open Targets' Perspective.

    McDonagh EM, Trynka G, McCarthy M, Holzinger ER, Khader S, Nakic N, Hu X, Cornu H, Dunham I and Hulcoop D

    Annual review of biomedical data science 2024

    PUBMED: 38608311; DOI: 10.1146/annurev-biodatasci-102523-103838

  • Tissue-specific inflammation and insulin sensitivity in subjects with obesity.

    Oussaada SM, Kilicarslan M, de Weijer BA, Gilijamse PW, Şekercan A, Virtue S, Janssen IMC, van de Laar A, Demirkiran A, van Wagensveld BA et al.

    Diabetes research and clinical practice 2024;211;111663

    PUBMED: 38616042; DOI: 10.1016/j.diabres.2024.111663

  • Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation.

    Abnizova I, Stapel C, Boekhorst RT, Lee JTH and Hemberg M

    BMC biology 2024;22;1;78

    PUBMED: 38600550; PMC: 11005181; DOI: 10.1186/s12915-024-01869-2

  • Mapping Human Immunity and the Education of Waldeyer's Ring.

    Talks BJ, Mather MW, Chahal M, Coates M, Clatworthy MR and Haniffa M

    Annual review of genomics and human genetics 2024

    PUBMED: 38594932; DOI: 10.1146/annurev-genom-120522-012938

  • Novel WRN Helicase Inhibitors Selectively Target Microsatellite Unstable Cancer Cells.

    Picco G, Rao Y, Al Saedi A, Lee Y, Vieira SF, Bhosle S, May K, Herranz-Ors C, Walker SJ, Shenje R et al.

    Cancer discovery 2024

    PUBMED: 38587317; DOI: 10.1158/2159-8290.CD-24-0052

  • Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis.

    De Jode A, Faria R, Formenti G, Sims Y, Smith TP, Tracey A, Wood JMD, Zagrodzka ZB, Johannesson K, Butlin RK and Leder EH

    Genome biology and evolution 2024

    PUBMED: 38584387; DOI: 10.1093/gbe/evae076

  • The Virtual Child.

    Gilbertson RJ, Behjati S, Böttcher AL, Bronner ME, Burridge M, Clausing H, Clifford H, Danaher T, Donovan LK, Drost J et al.

    Cancer discovery 2024;14;4;663-668

    PUBMED: 38571421; DOI: 10.1158/2159-8290.CD-23-1500

  • Immune microniches shape intestinal Treg function.

    Gu Y, Bartolomé-Casado R, Xu C, Bertocchi A, Janney A, Heuberger C, Pearson CF, Teichmann SA, Thornton EE and Powrie F

    Nature 2024;628;8009;854-862

    PUBMED: 38570678; PMC: 11041794; DOI: 10.1038/s41586-024-07251-0

  • Making predictions under interventions: a case study from the PREDICT-CVD cohort in New Zealand primary care.

    Lin L, Poppe K, Wood A, Martin GP, Peek N and Sperrin M

    Frontiers in epidemiology 2024;4;1326306

    PUBMED: 38633209; PMC: 11021700; DOI: 10.3389/fepid.2024.1326306

  • The genome sequence of the Spruce-seed moth, Cydia strobilella (Linnaeus, 1758).

    Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;177

    PUBMED: 39323608; PMC: 11422755; DOI: 10.12688/wellcomeopenres.21214.1

  • Clonal hematopoiesis in people with advanced HIV and associated inflammatory syndromes.

    Rocco JM, Zhou Y, Liu NS, Laidlaw E, Galindo F, Anderson MV, Rupert A, Lage SL, Ortega-Villa AM, Yu S et al.

    JCI insight 2024;9;9

    PUBMED: 38564303; DOI: 10.1172/jci.insight.174783

  • A region of suppressed recombination misleads neoavian phylogenomics.

    Mirarab S, Rivas-González I, Feng S, Stiller J, Fang Q, Mai U, Hickey G, Chen G, Brajuka N, Fedrigo O et al.

    Proceedings of the National Academy of Sciences of the United States of America 2024;121;15;e2319506121

    PUBMED: 38557186; DOI: 10.1073/pnas.2319506121

  • Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions.

    Blane B, Raven KE, Brown NM, Harrison EM, Coll F, Thaxter R, Enoch DA, Gouliouris T, Leek D, Girgis ST et al.

    Microbial genomics 2024;10;4

    PUBMED: 38630616; DOI: 10.1099/mgen.0.001235

  • Identifying the best PCR enzyme for library amplification in NGS.

    Quail MA, Corton C, Uphill J, Keane J and Gu Y

    Microbial genomics 2024;10;4

    PUBMED: 38578268; PMC: 11092157; DOI: 10.1099/mgen.0.001228

  • Melioidosis in Patients with COVID-19 Exposed to Contaminated Tap Water, Thailand, 2021.

    Tantirat P, Chantarawichian Y, Taweewigyakarn P, Kripattanapong S, Jitpeera C, Doungngern P, Phiancharoen C, Tangwangvivat R, Hinjoy S, Sujariyakul A et al.

    Emerging infectious diseases 2024;30;4;791-794

    PUBMED: 38526300; PMC: 10977828; DOI: 10.3201/eid3004.231476

  • Colonisation of hospital surfaces from low- and middle-income countries by extended spectrum β-lactamase- and carbapenemase-producing bacteria.

    Nieto-Rosado M, Sands K, Portal EAR, Thomson KM, Carvalho MJ, Mathias J, Milton R, Dyer C, Akpulu C, Boostrom I et al.

    Nature communications 2024;15;1;2758

    PUBMED: 38553439; PMC: 10980694; DOI: 10.1038/s41467-024-46684-z

  • The genome sequence of  Tenthredo notha Klug, 1814, a sawfly.

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Broad GR and Darwin Tree of Life Consortium

    Wellcome open research 2024;7;120

    PUBMED: 38586560; PMC: 10997988; DOI: 10.12688/wellcomeopenres.17811.2

  • A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast.

    Reed AD, Pensa S, Steif A, Stenning J, Kunz DJ, Porter LJ, Hua K, He P, Twigger AJ, Siu AJQ et al.

    Nature genetics 2024;56;4;652-662

    PUBMED: 38548988; PMC: 11018528; DOI: 10.1038/s41588-024-01688-9

  • What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species.

    Basenko EY, Shanmugasundram A, Böhme U, Starns D, Wilkinson PA, Davison HR, Crouch K, Maslen G, Harb OS, Amos B et al.

    Genetics 2024

    PUBMED: 38529759; DOI: 10.1093/genetics/iyae035

  • The genome sequence of the common green furrow bee, Lasioglossum morio (Fabricius, 1793).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Monks J and Darwin Tree of Life Consortium

    Wellcome open research 2024;8;28

    PUBMED: 38699201; PMC: 11063680; DOI: 10.12688/wellcomeopenres.18715.2

  • Integration of polygenic and gut metagenomic risk prediction for common diseases.

    Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P et al.

    Nature aging 2024;4;4;584-594

    PUBMED: 38528230; PMC: 11031402; DOI: 10.1038/s43587-024-00590-7

  • CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues.

    Vathrakokoili Pournara A, Miao Z, Beker OY, Nolte N, Brazma A and Papatheodorou I

    Bioinformatics advances 2024;4;1;vbae048

    PUBMED: 38638280; PMC: 11023940; DOI: 10.1093/bioadv/vbae048

  • A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.

    de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W et al.

    Cell genomics 2024;100527

    PUBMED: 38537634; DOI: 10.1016/j.xgen.2024.100527

  • The genome sequence of the grey top shell, Steromphala cineraria (Linnaeus, 1758).

    Adkins P, Mrowicki R, Harley J, Mieszkowska N, Ferreira JGRN, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;7;44

    PUBMED: 38715953; PMC: 11074690; DOI: 10.12688/wellcomeopenres.17677.3

  • The genome sequence of rosebay willowherb Chamaenerion angustifolium (L.) Scop., 1771 (syn. Epilobium angustifolium L., 1753) (Onagraceae).

    Christenhusz MJM, Leitch AR, Leitch IJ, Fay MF, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;163

    PUBMED: 38903872; PMC: 11187524; DOI: 10.12688/wellcomeopenres.21163.1

  • The genome sequence of the Lesser Skullcap, Scutellaria minor Huds., 1762 (Lamiaceae).

    Mian S, Christenhusz MJM, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;165

    PUBMED: 39206280; PMC: 11350328; DOI: 10.12688/wellcomeopenres.21164.1

  • The genome sequence of the Orange-tailed Clearwing, Synanthedon andrenaeformis (Laspeyres, 1801).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;160

    PUBMED: 39092001; PMC: 11292182; DOI: 10.12688/wellcomeopenres.21110.1

  • Estimating Between Country Migration in Pneumococcal Populations.

    Belman S, Pesonen H, Croucher NJ, Bentley SD and Corander J

    G3 (Bethesda, Md.) 2024

    PUBMED: 38507601; DOI: 10.1093/g3journal/jkae058

  • Implementation and external validation of the Cambridge Multimorbidity Score in the UK Biobank cohort.

    Harrison H, Ip S, Renzi C, Li Y, Barclay M, Usher-Smith J, Lyratzopoulos G, Wood A and Antoniou AC

    BMC medical research methodology 2024;24;1;71

    PUBMED: 38509467; PMC: 10953059; DOI: 10.1186/s12874-024-02175-9

  • Integrating AIPSS-MF and molecular predictors: A comparative analysis of prognostic models for myelofibrosis.

    Mosquera-Orgueira A, Arellano-Rodrigo E, Garrote M, Martín I, Pérez-Encinas M, Gómez-Casares MT, Hernández-Sánchez A, Ferrer-Marín F, Mora E, Velez P et al.

    HemaSphere 2024;8;3;e60

    PUBMED: 38510992; PMC: 10951878; DOI: 10.1002/hem3.60

  • SpatialData: an open and universal data framework for spatial omics.

    Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB et al.

    Nature methods 2024;22;1;58-62

    PUBMED: 38509327; PMC: 11725494; DOI: 10.1038/s41592-024-02212-x

  • Venous-plexus-associated lymphoid hubs support meningeal humoral immunity.

    Fitzpatrick Z, Ghabdan Zanluqui N, Rosenblum JS, Tuong ZK, Lee CYC, Chandrashekhar V, Negro-Demontel ML, Stewart AP, Posner DA, Buckley M et al.

    Nature 2024;628;8008;612-619

    PUBMED: 38509366; PMC: 11482273; DOI: 10.1038/s41586-024-07202-9

  • The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758).

    Li R, Li J, Lopez JV, Oatley G, Clayton-Lucey IA, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M et al.

    Wellcome open research 2024;9;145

    PUBMED: 38800516; PMC: 11116938; DOI: 10.12688/wellcomeopenres.21136.1

  • The genome sequence of the John Dory, Zeus faber Linnaeus, 1758.

    Adkins P, Harley J, Brittain R, Scott-Somme K, Azzopardi F, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;150

    PUBMED: 38881949; PMC: 11179049; DOI: 10.12688/wellcomeopenres.21140.1

  • The genome sequence of the thickback sole, Microchirus variegatus (Donovan, 1808).

    Brittain R, Adkins P, Mrowicki RJ, Harley J, Modepali V, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;152

    PUBMED: 38938521; PMC: 11208857; DOI: 10.12688/wellcomeopenres.21139.1

  • Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases.

    Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH and Natarajan P

    Cell genomics 2024;4;4;100523

    PUBMED: 38508198; PMC: 11019356; DOI: 10.1016/j.xgen.2024.100523

  • The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).

    Boyes D, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Skojec C, Plotkin D, Kawahara AY and Darwin Tree of Life Consortium

    Wellcome open research 2024;7;197

    PUBMED: 39323974; PMC: 11422757; DOI: 10.12688/wellcomeopenres.17924.2

  • hERG, Plasmodium Life Cycle, and Cross Resistance Profiling of New Azabenzimidazole Analogues of Astemizole.

    Mambwe D, Coertzen D, Leshabane M, Mulubwa M, Njoroge M, Gibhard L, Girling G, Wicht KJ, Lee MCS, Wittlin S et al.

    ACS medicinal chemistry letters 2024;15;4;463-469

    PUBMED: 38628794; PMC: 11017395; DOI: 10.1021/acsmedchemlett.3c00496

  • Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.

    Lin GL, Drysdale SB, Snape MD, O'Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Ansari MA, Bonsall D et al.

    Nature communications 2024;15;1;2379

    PUBMED: 38493135; PMC: 10944482; DOI: 10.1038/s41467-024-46648-3

  • Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis.

    Xie O, Morris JM, Hayes AJ, Towers RJ, Jespersen MG, Lees JA, Ben Zakour NL, Berking O, Baines SL, Carter GP et al.

    Nature communications 2024;15;1;2286

    PUBMED: 38480728; PMC: 10937727; DOI: 10.1038/s41467-024-46530-2

  • Impact of CRISPR/HDR editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques.

    Lee BC, Gin A, Wu C, Singh K, Grice M, Mortlock R, Abraham D, Fan X, Zhou Y, AlJanahi A et al.

    Cell stem cell 2024

    PUBMED: 38508195; DOI: 10.1016/j.stem.2024.02.010

  • Patient stratification using plasma cytokines and their regulators in sepsis: relationship to outcomes, treatment effect and leucocyte transcriptomic subphenotypes.

    Antcliffe DB, Mi Y, Santhakumaran S, Burnham KL, Prevost AT, Ward JK, Marshall TJ, Bradley C, Al-Beidh F, Hutton P et al.

    Thorax 2024

    PUBMED: 38471792; DOI: 10.1136/thorax-2023-220538

  • Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators.

    Diaz Soria CL, Attenborough T, Lu Z, Fontenla S, Graham J, Hall C, Thompson S, Andrews TGR, Rawlinson KA, Berriman M and Rinaldi G

    Scientific reports 2024;14;1;5974

    PUBMED: 38472267; PMC: 10933418; DOI: 10.1038/s41598-024-55790-3

  • The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;143

    PUBMED: 39139615; PMC: 11319900; DOI: 10.12688/wellcomeopenres.21090.1

  • The genome sequence of the Judas Tree Seed Beetle, Bruchidius siliquastri Delobel, 2007.

    Barclay MVL, Geiser M, Matsumoto K, Pash E, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;142

    PUBMED: 39132672; PMC: 11316170; DOI: 10.12688/wellcomeopenres.21109.1

  • Dietary intake of plant- and animal-derived protein and incident cardiovascular diseases: the pan-European EPIC-CVD case-cohort study.

    Zheng JS, Steur M, Imamura F, Freisling H, Johnson L, van der Schouw YT, Tong TYN, Weiderpass E, Bajracharya R, Crous-Bou M et al.

    The American journal of clinical nutrition 2024

    PUBMED: 38479550; DOI: 10.1016/j.ajcnut.2024.03.006

  • Impact of vaccination on the association of COVID-19 with cardiovascular diseases: An OpenSAFELY cohort study.

    Cezard GI, Denholm RE, Knight R, Wei Y, Teece L, Toms R, Forbes HJ, Walker AJ, Fisher L, Massey J et al.

    Nature communications 2024;15;1;2173

    PUBMED: 38467603; PMC: 10928172; DOI: 10.1038/s41467-024-46497-0

  • The genome sequence of Gwynne's mining bee, Andrena bicolor Fabricius, 1775.

    Falk S, Monks J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;140

    PUBMED: 38846929; PMC: 11153990; DOI: 10.12688/wellcomeopenres.21104.1

  • The genome sequence of the Beautiful China-mark moth Nymphula nitidulata (Hufnagel, 1767).

    Boyes D, Mulhair PO, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;135

    PUBMED: 39109333; PMC: 11301135; DOI: 10.12688/wellcomeopenres.21102.1

  • The genome sequence of the Four-banded Bee-grabber, Conops quadrifasciatus De Geer, 1776.

    Falk S, Crowley LM, Clements DK, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;136

    PUBMED: 38784436; PMC: 11112309; DOI: 10.12688/wellcomeopenres.21106.1

  • The genome sequence of the Summer Chafer, Amphimallon solstitiale (Linnaeus, 1758).

    Boyes D, Crowley LM, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;138

    PUBMED: 38784435; PMC: 11112308; DOI: 10.12688/wellcomeopenres.21100.1

  • The genome sequence of the Water Veneer, Acentria ephemerella (Denis & Schiffermüller, 1775).

    Boyes D, Mulhair PO, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;134

    PUBMED: 38779149; PMC: 11109561; DOI: 10.12688/wellcomeopenres.21099.1

  • Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations.

    Bashi AC, Coker EA, Bulusu KC, Jaaks P, Crafter C, Lightfoot H, Milo M, McCarten K, Jenkins DF, van der Meer D et al.

    Cancer discovery 2024;OF1-OF20

    PUBMED: 38456804; DOI: 10.1158/2159-8290.CD-23-0388

  • The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).

    Li R, Li J, Lemer S, Lopez JV, Oatley G, Clayton-Lucey IA, Sinclair E, Aunin E, Gettle N, Santos C et al.

    Wellcome open research 2024;9;129

    PUBMED: 38989474; PMC: 11234083; DOI: 10.12688/wellcomeopenres.21134.1

  • Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1.

    Ang CE, Olmos VH, Vodehnal K, Zhou B, Lee QY, Sinha R, Narayanaswamy A, Mall M, Chesnov K, Dominicus CS et al.

    Proceedings of the National Academy of Sciences of the United States of America 2024;121;11;e2308401121

    PUBMED: 38446849; DOI: 10.1073/pnas.2308401121

  • Genome-wide characterization of circulating metabolic biomarkers.

    Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K et al.

    Nature 2024;628;8006;130-138

    PUBMED: 38448586; PMC: 10990933; DOI: 10.1038/s41586-024-07148-y

  • The genome sequence of the meadow plant bug, Leptopterna dolabrata (Linnaeus, 1758).

    Crowley LM, Livermore L, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;128

    PUBMED: 39415783; PMC: 11480713; DOI: 10.12688/wellcomeopenres.21005.1

  • The genome sequence of the Rivulet moth, Perizoma affinitatum (Stephens, 1831).

    Broad GR, Sivess L, Fletcher C, Januszczak I, Holt S, Phillips D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team et al.

    Wellcome open research 2024;9;127

    PUBMED: 39345342; PMC: 11427865; DOI: 10.12688/wellcomeopenres.21016.1

  • Benchmarking CRISPR-BP34 for point-of-care melioidosis detection in low-income and middle-income countries: a molecular diagnostics study.

    Pakdeerat S, Boonklang P, Angchagun K, Chomkatekaew C, Apichaidejudom N, Dokket Y, Faosap A, Wongsuwan G, Wuthiekanun V, Aramrueung P et al.

    The Lancet. Microbe 2024

    PUBMED: 38493790; DOI: 10.1016/S2666-5247(23)00378-6

  • Round Table Discussion on Optimal Clinical Trial Design in Precursor Multiple Myeloma.

    Ghobrial IM, Gormley N, Kumar SK, Mateos MV, Bergsagel PL, Chesi M, Dhodapkar MV, Dispenzieri A, Fonseca R, Getz G et al.

    Blood cancer discovery 2024;OF1-OF7

    PUBMED: 38441243; DOI: 10.1158/2643-3230.BCD-24-0022

  • Workshop report: the clinical application of data from multiplex assays of variant effect (MAVEs), 12 July 2023.

    Allen S, Garrett A, Muffley L, Fayer S, Foreman J, Adams DJ, Hurles M, Rubin AF, Roth FP, Starita LM et al.

    European journal of human genetics : EJHG 2024;32;5;593-600

    PUBMED: 38433264; PMC: 11061192; DOI: 10.1038/s41431-024-01566-2

  • High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding

    Michell, Craig, Collins, Joanna, Laine, Pia K., Fekete, Zsófia, Tapanainen, Riikka et al.

    Peer Community Journal 2024;4;e26

    DOI: 10.24072/pci.genomics.100299; URL: https://doi.org/10.24072/pci.genomics.100299

  • The genome sequence of a soldier beetle, Malthinus flaveolus (Herbst, 1786).

    Telfer MG, Geiser MF, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;121

    PUBMED: 39301443; PMC: 11411255; DOI: 10.12688/wellcomeopenres.21086.1

  • The genome sequence of common knotgrass, Polygonum aviculare L. (Polygonaceae).

    Christenhusz MJM, Hollingsworth PM, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;112

    PUBMED: 39101050; PMC: 11294812; DOI: 10.12688/wellcomeopenres.21001.1

  • The genome sequence of Daubenton's bat, Myotis daubentonii (Kuhl, 1817).

    Ruedi M, Vernes SC, Teeling EC, Mai M, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;107

    PUBMED: 39022322; PMC: 11252650; DOI: 10.12688/wellcomeopenres.21081.1

  • The genome sequence of field madder, Sherardia arvensis L., 1753 (Rubiaceae).

    Christenhusz MJM, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;126

    PUBMED: 39139616; PMC: 11320180; DOI: 10.12688/wellcomeopenres.21027.1

  • The genome sequence of great wood-rush, Luzula sylvatica (Huds) Gaudin.

    Goodwin ZA, Bell D, Hart ML, Hollingsworth PM, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;124

    PUBMED: 39246514; PMC: 11380069; DOI: 10.12688/wellcomeopenres.20997.1

  • The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae).

    Christenhusz MJM, Pannell JR, Twyford AD, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;102

    PUBMED: 38854694; PMC: 11157195; DOI: 10.12688/wellcomeopenres.21004.1

  • The genome sequence of the big-headed mining bee, Andrena bucephala (Stephens, 1846).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;111

    PUBMED: 39144162; PMC: 11322697; DOI: 10.12688/wellcomeopenres.21003.1

  • The genome sequence of the Black Lace-weaver spider, Amaurobius ferox (Walckenaer, 1830).

    Henriques S, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;105

    PUBMED: 39015616; PMC: 11249506; DOI: 10.12688/wellcomeopenres.21080.1

  • The genome sequence of the Blood-vein moth, Timandra comae Schmidt, 1931.

    Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;100

    PUBMED: 39267990; PMC: 11391194; DOI: 10.12688/wellcomeopenres.21088.1

  • The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;104

    PUBMED: 39239169; PMC: 11375399; DOI: 10.12688/wellcomeopenres.21012.1

  • The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;117

    PUBMED: 39233902; PMC: 11372352; DOI: 10.12688/wellcomeopenres.21014.1

  • The genome sequence of the ten-spot ladybird, Adalia decempunctata (Linnaeus, 1758).

    Crowley LM, Roy HE, Brown PMJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;106

    PUBMED: 38966305; PMC: 11222777; DOI: 10.12688/wellcomeopenres.21008.1

  • The genome sequence of the wood-carving leafcutter bee, Megachile ligniseca (Kirby, 1802).

    Crowley LM, Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;103

    PUBMED: 38903870; PMC: 11187525; DOI: 10.12688/wellcomeopenres.21002.1

  • A gut microbial signature for combination immune checkpoint blockade across cancer types.

    Gunjur A, Shao Y, Rozday T, Klein O, Mu A, Haak BW, Markman B, Kee D, Carlino MS, Underhill C et al.

    Nature medicine 2024;30;3;797-809

    PUBMED: 38429524; PMC: 10957475; DOI: 10.1038/s41591-024-02823-z

  • Bayesian modelling of antimicrobial resistance in enteric fever in understudied areas.

    Bote L and Maes M

    The Lancet. Global health 2024;12;3;e346-e347

    PUBMED: 38365399; DOI: 10.1016/S2214-109X(24)00030-5

  • Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy.

    Töpf A, Cox D, Zaharieva IT, Di Leo V, Sarparanta J, Jonson PH, Sealy IM, Smolnikov A, White RJ, Vihola A et al.

    Nature genetics 2024

    PUBMED: 38429495; DOI: 10.1038/s41588-023-01651-0

  • Genomic analysis of clinical Aeromonas isolates reveals genetic diversity but little evidence of genetic determinants for diarrhoeal disease.

    Klemm EJ, Nisar MI, Bawn M, Nasrin D, Qamar FN, Page A, Qadri F, Shakoor S, Zaidi AK, Levine MM et al.

    Microbial genomics 2024;10;3

    PUBMED: 38451244; DOI: 10.1099/mgen.0.001211

  • Genus-wide research provides insights into pathogen evolution.

    McGimpsey S and Beale MA

    Nature reviews. Microbiology 2024;22;3;121

    PUBMED: 38253794; DOI: 10.1038/s41579-024-01009-1

  • The genome sequence of a conopid fly, Myopa testacea (Linnaeus, 1767).

    Falk S, Poole O, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;99

    PUBMED: 38689759; PMC: 11058451; DOI: 10.12688/wellcomeopenres.20647.1

  • The genome sequence of Tadarida brasiliensis I. Geoffroy Saint-Hilaire, 1824 [Molossidae; Tadarida].

    Webster CF, Smotherman M, Pippel M, Brown T, Winkler S, Pieri M, Mai M, Myers EW, Teeling EC, Vernes SC and Bat1K Consortium

    Wellcome open research 2024;9;98

    PUBMED: 38800517; PMC: 11128047; DOI: 10.12688/wellcomeopenres.20603.1

  • The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).

    Boyes D, Januszczak I, Lees DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;96

    PUBMED: 39257623; PMC: 11384207; DOI: 10.12688/wellcomeopenres.20841.1

  • Genomic evolution shapes prostate cancer disease type.

    Woodcock DJ, Sahli A, Teslo R, Bhandari V, Gruber AJ, Ziubroniewicz A, Gundem G, Xu Y, Butler A, Anokian E et al.

    Cell genomics 2024;4;3;100511

    PUBMED: 38428419; PMC: 10943594; DOI: 10.1016/j.xgen.2024.100511

  • Review of Molecular Technologies for Investigating Canine Cancer.

    Kehl A, Aupperle-Lellbach H, de Brot S and van der Weyden L

    Animals : an open access journal from MDPI 2024;14;5

    PUBMED: 38473154; DOI: 10.3390/ani14050769

  • Mechanistic causes of sign epistasis and its applications.

    Zhang J, Chen F and Li X

    Frontiers in genetics 2024;15;1366917

    PUBMED: 38482385; PMC: 10932960; DOI: 10.3389/fgene.2024.1366917

  • NFIL3 contributes to cytotoxic T lymphocyte-mediated killing.

    Douanne T, Strege K, Del Castillo Velasco-Herrera M, Rochussen AM, Adams DJ and Griffiths GM

    Open biology 2024;14;2;230456

    PUBMED: 38412963; DOI: 10.1098/rsob.230456

  • Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni.

    Brann T, Beltramini A, Chaparro C, Berriman M, Doyle SR and Protasio AV

    BMC genomics 2024;25;1;217

    PUBMED: 38413905; PMC: 10900676; DOI: 10.1186/s12864-024-10032-8

  • Unravelling the complex interplay between antibiotic consumption and adaptive changes in methicillin-resistant Staphylococcus aureus.

    van Hal SJ, Jensen SO, Tong SYC, Bentley S and Holden MT

    The Journal of antimicrobial chemotherapy 2024

    PUBMED: 38412336; DOI: 10.1093/jac/dkae048

  • Case Report: Cutaneous melanocytic schwannoma with concomitant melanocytoma in a canine.

    Monakali OH, O'Dell N and van der Weyden L

    Wellcome open research 2024;8;364

    PUBMED: 38911282; PMC: 11190644; DOI: 10.12688/wellcomeopenres.19694.2

  • Dynein and dynactin move long-range but are delivered separately to the axon tip.

    Fellows AD, Bruntraeger M, Burgold T, Bassett AR and Carter AP

    The Journal of cell biology 2024;223;5

    PUBMED: 38407313; PMC: 10896695; DOI: 10.1083/jcb.202309084

  • Pervasive mimicry in flight behavior among aposematic butterflies.

    Page E, Queste LM, Rosser N, Salazar PA, Nadeau NJ, Mallet J, Srygley RB, McMillan WO and Dasmahapatra KK

    Proceedings of the National Academy of Sciences of the United States of America 2024;121;11;e2300886121

    PUBMED: 38408213; DOI: 10.1073/pnas.2300886121

  • Transposable element insertions are associated with Batesian mimicry in the pantropical butterfly Hypolimnas misippus.

    Orteu A, Kucka M, Gordon IJ, Ng'iru I, van der Heijden ESM, Talavera G, Warren IA, Collins S, Ffrench-Constant RH, Martins DJ et al.

    Molecular biology and evolution 2024

    PUBMED: 38401262; DOI: 10.1093/molbev/msae041

  • The genome sequence of the Mournful Wasp, Pemphredon lugubris (Fabricius, 1793).

    Falk S, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;93

    PUBMED: 39221445; PMC: 11364974; DOI: 10.12688/wellcomeopenres.20948.1

  • Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples.

    Coorens THH, Spencer Chapman M, Williams N, Martincorena I, Stratton MR, Nangalia J and Campbell PJ

    Nature protocols 2024;19;6;1866-1886

    PUBMED: 38396041; DOI: 10.1038/s41596-024-00962-8

  • CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.

    Critical Assessment of Genome Interpretation Consortium

    Genome biology 2024;25;1;53

    PUBMED: 38389099; PMC: 10882881; DOI: 10.1186/s13059-023-03113-6

  • Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera.

    Wright CJ, Stevens L, Mackintosh A, Lawniczak M and Blaxter M

    Nature ecology & evolution 2024;8;4;777-790

    PUBMED: 38383850; PMC: 11009112; DOI: 10.1038/s41559-024-02329-4

  • Prevalence of persistent SARS-CoV-2 in a large community surveillance study.

    Ghafari M, Hall M, Golubchik T, Ayoubkhani D, House T, MacIntyre-Cockett G, Fryer HR, Thomson L, Nurtay A, Kemp SA et al.

    Nature 2024;626;8001;1094-1101

    PUBMED: 38383783; PMC: 10901734; DOI: 10.1038/s41586-024-07029-4

  • Targeted action to increase inclusion at the Wellcome Sanger Institute.

    Ahmed S, Adams DJ, Haniffa M, Maartens A and Arruda MA

    eLife 2024;13

    PUBMED: 38381132; PMC: 10881119; DOI: 10.7554/eLife.94732

  • A high-quality blue whale genome, segmental duplications, and historical demography.

    Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J et al.

    Molecular biology and evolution 2024

    PUBMED: 38376487; DOI: 10.1093/molbev/msae036

  • Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning.

    Ren Y, Li C, Nanayakkara Sapugahawatte D, Zhu C, Spänig S, Jamrozy D, Rothen J, Daubenberger CA, Bentley SD, Ip M and Heider D

    Computers in biology and medicine 2024;171;108185

    PUBMED: 38401454; DOI: 10.1016/j.compbiomed.2024.108185

  • Prediction, screening and characterization of novel bioactive tetra-peptide matrikines for skin rejuvenation.

    Jariwala N, Ozols M, Eckersley A, Mambwe B, Watson REB, Zeef L, Gilmore A, Debelle L, Bell M, Bradley EJ et al.

    The British journal of dermatology 2024

    PUBMED: 38375775; DOI: 10.1093/bjd/ljae061

  • A catalogue of chromosome counts for Phylum Nematoda.

    Blaxter ML, Leech C and Lunt DH

    Wellcome open research 2024;9;55

    PUBMED: 39534537; PMC: 11555361; DOI: 10.12688/wellcomeopenres.20550.1

  • The genome sequence of a barkfly, Mesopsocus fuscifrons Meinander, 1966.

    Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;72

    PUBMED: 39114494; PMC: 11303940; DOI: 10.12688/wellcomeopenres.20641.1

  • The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).

    Obbard DJ, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;56

    PUBMED: 39015613; PMC: 11249525; DOI: 10.12688/wellcomeopenres.20631.1

  • The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).

    Falk S, Poole O, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;74

    PUBMED: 39027808; PMC: 11255551; DOI: 10.12688/wellcomeopenres.20624.1

  • The genome sequence of a hoverfly, Merodon equestris (Fabricius, 1794).

    Sivell O, Crowley LM, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;67

    PUBMED: 38911901; PMC: 11192019; DOI: 10.12688/wellcomeopenres.20654.1

  • The genome sequence of a hoverfly, Syrphus vitripennis (Meigen, 1822).

    Sivell O, Sivell D, Falk S, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;78

    PUBMED: 38894705; PMC: 11184275; DOI: 10.12688/wellcomeopenres.20837.1

  • The genome sequence of a metallic wood-boring beetle, Agrilus cyanescens (Ratzeburg, 1837).

    Telfer MG, Phillips D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;46

    PUBMED: 38779150; PMC: 11109541; DOI: 10.12688/wellcomeopenres.20877.1

  • The genome sequence of a muscid fly, Hydrotaea cyrtoneurina (Zetterstedt, 1845).

    Falk S, Grzywacz A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;60

    PUBMED: 38725453; PMC: 11079579; DOI: 10.12688/wellcomeopenres.20638.1

  • The genome sequence of a muscid fly, Polietes domitor (Harris, 1780).

    Falk S, Sivell D, Webb J, Grzywacz A, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequence Operations et al.

    Wellcome open research 2024;9;58

    PUBMED: 39301441; PMC: 11411267; DOI: 10.12688/wellcomeopenres.20648.1

  • The genome sequence of a pipunculid fly, Nephrocerus scutellatus (Macquart, 1834).

    Falk S, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;41

    PUBMED: 39022323; PMC: 11252644; DOI: 10.12688/wellcomeopenres.20677.1

  • The genome sequence of Ramsons hoverfly, Portevinia maculata (Fallén, 1817).

    Crowley LM, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;52

    PUBMED: 39267988; PMC: 11391197; DOI: 10.12688/wellcomeopenres.20649.1

  • The genome sequence of the black-footed limpet, Patella depressa (Pennant, 1777).

    Hawkins SJ, Mieszkowska N, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;47

    PUBMED: 38779153; PMC: 11109591; DOI: 10.12688/wellcomeopenres.20687.1

  • The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;42

    PUBMED: 39015611; PMC: 11249505; DOI: 10.12688/wellcomeopenres.20840.1

  • The genome sequence of the drosophilid fruit fly, Drosophila phalerata (Meigen, 1830).

    Obbard DJ, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;63

    PUBMED: 38800521; PMC: 11126896; DOI: 10.12688/wellcomeopenres.20634.1

  • The genome sequence of the Emperor moth, Saturnia pavonia (Linnaeus, 1758).

    Crowley LM, Baker E, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;48

    PUBMED: 38764484; PMC: 11101921; DOI: 10.12688/wellcomeopenres.20652.1

  • The genome sequence of the giant willow aphid, Tuberolachnus salignus (Gmelin, 1790).

    Crowley LM, McCulloch J, James R, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;59

    PUBMED: 39114489; PMC: 11303955; DOI: 10.12688/wellcomeopenres.20646.1

  • The genome sequence of the hawthorn leaf beetle, Lochmaea crataegi (Forster, 1771).

    Crowley LM, Telfer MG, Escalona HE, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;80

    PUBMED: 39246515; PMC: 11380073; DOI: 10.12688/wellcomeopenres.20911.1

  • The genome sequence of the Hebrew Character, Orthosia gothica (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;90

    PUBMED: 39429633; PMC: 11487229; DOI: 10.12688/wellcomeopenres.20904.1

  • The genome sequence of the Lobe-spurred Furrow Bee, Lasioglossum pauxillum (Schenck, 1853).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;86

    PUBMED: 39176035; PMC: 11339594; DOI: 10.12688/wellcomeopenres.20950.1

  • The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;65

    PUBMED: 39015615; PMC: 11249503; DOI: 10.12688/wellcomeopenres.20637.1

  • The genome sequence of the parsley Cheilosia, Cheilosia pagana (Meigen, 1822).

    Falk S, Poole O, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;54

    PUBMED: 38813465; PMC: 11134149; DOI: 10.12688/wellcomeopenres.20627.1

  • The genome sequence of the Peppered Grey, Eudonia truncicolella (Stainton, 1849).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;44

    PUBMED: 38800520; PMC: 11126902; DOI: 10.12688/wellcomeopenres.20680.1

  • The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;88

    PUBMED: 39290364; PMC: 11406127; DOI: 10.12688/wellcomeopenres.20834.1

  • The genome sequence of the spotted Meliscaeva, Meliscaeva auricollis (Meigen, 1822).

    Falk S, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;82

    PUBMED: 39132673; PMC: 11316168; DOI: 10.12688/wellcomeopenres.20843.1

  • The genome sequence of the White-point, Mythimna albipuncta (Denis & Schiffermüller, 1775).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;62

    PUBMED: 38911902; PMC: 11193084; DOI: 10.12688/wellcomeopenres.20682.1

  • Challenges and perspectives in computational deconvolution of genomics data.

    Garmire LX, Li Y, Huang Q, Xu C, Teichmann SA, Kaminski N, Pellegrini M, Nguyen Q and Teschendorff AE

    Nature methods 2024;21;3;391-400

    PUBMED: 38374264; DOI: 10.1038/s41592-023-02166-6

  • Genetic drivers of heterogeneity in type 2 diabetes pathophysiology.

    Suzuki K, Hatzikotoulas K, Southam L, Taylor HJ, Yin X, Lorenz KM, Mandla R, Huerta-Chagoya A, Melloni GEM, Kanoni S et al.

    Nature 2024;627;8003;347-357

    PUBMED: 38374256; PMC: 10937372; DOI: 10.1038/s41586-024-07019-6

  • Genetic influences on circulating retinol and its relationship to human health.

    Reay WR, Kiltschewskij DJ, Di Biase MA, Gerring ZF, Kundu K, Surendran P, Greco LA, Clarke ED, Collins CE, Mondul AM et al.

    Nature communications 2024;15;1;1490

    PUBMED: 38374065; PMC: 10876955; DOI: 10.1038/s41467-024-45779-x

  • Recent advances in polygenic scores: translation, equitability, methods and FAIR tools.

    Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M and Lambert SA

    Genome medicine 2024;16;1;33

    PUBMED: 38373998; PMC: 10875792; DOI: 10.1186/s13073-024-01304-9

  • Past, Present and Future of Software for Bayesian Inference

    Strumbelj, Erik, Bouchard-Cote, Alexandre, Corander, Jukka, Gelman, Andrew, Rue, Havard et al.

    Statistical Science 2024;39;1;46-61

    DOI: 10.1214/23-STS907

  • Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing.

    Yuan CU, Quah FX and Hemberg M

    Molecular aspects of medicine 2024;96;101255

    PUBMED: 38368637; DOI: 10.1016/j.mam.2024.101255

  • The genome sequence of the Oak Beauty, Biston strataria (Hufnagel, 1767).

    Boyes D, Lees DC, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2024;9;35

    PUBMED: 39101049; PMC: 11294811; DOI: 10.12688/wellcomeopenres.20835.1

  • The genome sequence of the spotted cranefly, Nephrotoma appendiculata (Pierre, 1919).

    Crowley LM, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;38

    PUBMED: 38779147; PMC: 11109560; DOI: 10.12688/wellcomeopenres.20886.1

  • The genome sequence of the Stripe-backed Dasysyrphus, Dasysyrphus albostriatus (Fallén, 1817).

    Crowley LM, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;34

    PUBMED: 39132671; PMC: 11310654; DOI: 10.12688/wellcomeopenres.20887.1

  • Establishment and characterization of an Epstein-Barr virus-positive cell line from a non-keratinizing differentiated primary nasopharyngeal carcinoma.

    Chai AWY, Yee SM, Lee HM, Abdul Aziz N, Yee PS, Marzuki M, Wong KW, Chiang AKS, Chow LK, Dai W et al.

    Cancer research communications 2024

    PUBMED: 38358347; DOI: 10.1158/2767-9764.CRC-23-0341

  • Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study.

    Ashton PM, Chunga Chirambo A, Meiring JE, Patel PD, Mbewe M, Silungwe N, Chizani K, Banda H, Heyderman RS, Dyson ZA et al.

    The Lancet. Microbe 2024

    PUBMED: 38387472; DOI: 10.1016/S2666-5247(23)00327-0

  • Genetic determinants of micronucleus formation in vivo.

    Adams DJ, Barlas B, McIntyre RE, Salguero I, van der Weyden L, Barros A, Vicente JR, Karimpour N, Haider A, Ranzani M et al.

    Nature 2024;627;8002;130-136

    PUBMED: 38355793; PMC: 10917660; DOI: 10.1038/s41586-023-07009-0

  • MarkerScan: Separation and assembly of cobionts sequenced alongside target species in biodiversity genomics projects.

    Vancaester E and Blaxter ML

    Wellcome open research 2024;9;33

    PUBMED: 38617467; PMC: 11016177; DOI: 10.12688/wellcomeopenres.20730.1

  • The genome sequence of a sawfly, Macrophya alboannulata (Costa, 1859).

    Falk S, Green A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;28

    PUBMED: 39211806; PMC: 11358680; DOI: 10.12688/wellcomeopenres.20897.1

  • The genome sequence of a stiletto fly, Thereva unica (Harris, 1780).

    Drake M, Spilling C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;27

    PUBMED: 38764483; PMC: 11099511; DOI: 10.12688/wellcomeopenres.20828.1

  • The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;31

    PUBMED: 39233899; PMC: 11372354; DOI: 10.12688/wellcomeopenres.20833.1

  • Genomic attributes of airway commensal bacteria and mucosa.

    Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA et al.

    Communications biology 2024;7;1;171

    PUBMED: 38347162; PMC: 10861553; DOI: 10.1038/s42003-024-05840-3

  • Proteomic and metabolomic signatures of rectal tumor discriminate patients with different responses to preoperative radiotherapy.

    Wojakowska A, Marczak L, Zeman M, Chekan M, Zembala-Nożyńska E, Polanski K, Strugała A, Widlak P and Pietrowska M

    Frontiers in oncology 2024;14;1323961

    PUBMED: 38410100; PMC: 10896604; DOI: 10.3389/fonc.2024.1323961

  • The dynamic genetic determinants of increased transcriptional divergence in spermatids.

    Panten J, Heinen T, Ernst C, Eling N, Wagner RE, Satorius M, Marioni JC, Stegle O and Odom DT

    Nature communications 2024;15;1;1272

    PUBMED: 38341412; PMC: 10858866; DOI: 10.1038/s41467-024-45133-1

  • Morphological and molecular evidence for a new species of the genus Milnesium Doyère, 1840 (Tardigrada: Apochela) from south America

    Brotto-Guidetti, Emiliana, Morek, Witold and Garraffoni, Andre R. S.

    Zoologischer Anzeiger 2024;309;55-65

    DOI: 10.1016/j.jcz.2024.01.004

  • vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis.

    Bhuva DD, Tan CW, Liu N, Whitfield HJ, Papachristos N, Lee SC, Kharbanda M, Mohamed A and Davis MJ

    BMC bioinformatics 2024;25;1;64

    PUBMED: 38331751; PMC: 10854147; DOI: 10.1186/s12859-024-05676-y

  • Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.

    Bukhman YV, Meyer S, Chu LF, Abueg L, Antosiewicz-Bourget J, Balacco J, Brecht M, Dinatale E, Fedrigo O, Formenti G et al.

    Scientific data 2024;11;1;176

    PUBMED: 38326333; PMC: 10850158; DOI: 10.1038/s41597-024-03011-x

  • IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy.

    Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K et al.

    Genome biology 2024;25;1;45

    PUBMED: 38326875; PMC: 10848526; DOI: 10.1186/s13059-024-03172-3

  • The Mutographs biorepository: A unique genomic resource to study cancer around the world.

    Perdomo S, Abedi-Ardekani B, de Carvalho AC, Ferreiro-Iglesias A, Gaborieau V, Cattiaux T, Renard H, Chopard P, Carreira C, Spanu A et al.

    Cell genomics 2024;4;3;100500

    PUBMED: 38325367; PMC: 10943582; DOI: 10.1016/j.xgen.2024.100500

  • Functional validation of novel levamisole resistance marker S168T in Haemonchus contortus.

    Antonopoulos A, Charvet CL, Maitland K, Doyle SR, Neveu C and Laing R

    International journal for parasitology. Drugs and drug resistance 2024;24;100524

    PUBMED: 38346379; DOI: 10.1016/j.ijpddr.2024.100524

  • Aneuploid embryonic stem cells drive teratoma metastasis.

    Xiao R, Xu D, Zhang M, Chen Z, Cheng L, Du S, Lu M, Zhou T, Li R, Bai F and Huang Y

    Nature communications 2024;15;1;1087

    PUBMED: 38316790; PMC: 10844504; DOI: 10.1038/s41467-024-45265-4

  • Cutaneous Plasmacytoma with Systemic Metastases in a Cape Serotine Bat (Laephotis capensis).

    van der Weyden L, Avenant A and O'Dell N

    Veterinary sciences 2024;11;2

    PUBMED: 38393090; PMC: 10892064; DOI: 10.3390/vetsci11020072

  • Identification of a core transcriptional program driving the human renal mesenchymal-to-epithelial transition.

    Ng-Blichfeldt JP, Stewart BJ, Clatworthy MR, Williams JM and Röper K

    Developmental cell 2024

    PUBMED: 38340720; DOI: 10.1016/j.devcel.2024.01.011

  • DNA metabarcoding reveals the impact of Cu2+ on soil cercozoan diversity.

    Lourenço L, Ellegaard Bager S, Ng DYK, Sheikh S, Lunding Kindtler N, Broman Nielsen I, Guldberg Frøslev T and Ekelund F

    Protist 2024;175;2;126016

    PUBMED: 38350284; DOI: 10.1016/j.protis.2024.126016

  • Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids.

    Alves-Lopes JP, Wong FCK and Surani MA

    Nature protocols 2024

    PUBMED: 38302732; DOI: 10.1038/s41596-023-00945-1

  • Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase.

    Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES et al.

    Nature communications 2024;15;1;937

    PUBMED: 38297033; PMC: 10831071; DOI: 10.1038/s41467-024-45224-z

  • An atlas of cells in the human tonsil.

    Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S et al.

    Immunity 2024

    PUBMED: 38301653; DOI: 10.1016/j.immuni.2024.01.006

  • Detection and characterization of copy-number variants from exome sequencing in the DDD study.

    Danecek P, Gardner EJ, Fitzgerald TW, Gallone G, Kaplanis J, Eberhardt RY, Wright CF, Firth HV and Hurles ME

    Genetics in medicine open 2024;2;101818

    PUBMED: 39669630; PMC: 11613862; DOI: 10.1016/j.gimo.2024.101818

  • Prioritize environmental sustainability in use of AI and data science methods

    Jay, Caroline, Yu, Yurong, Crawford, Ian, Archer-Nicholls, Scott, James, Philip et al.

    Nature Geoscience 2024

    DOI: 10.1038/s41561-023-01369-y

  • Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.

    Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K et al.

    Nature biotechnology 2024

    PUBMED: 38278971; DOI: 10.1038/s41587-023-02100-3

  • Genome-wide transcriptome analysis of Echinococcus multilocularis larvae and germinative cell cultures reveals genes involved in parasite stem cell function.

    Herz M, Zarowiecki M, Wessels L, Pätzel K, Herrmann R, Braun C, Holroyd N, Huckvale T, Bergmann M, Spiliotis M et al.

    Frontiers in cellular and infection microbiology 2024;14;1335946

    PUBMED: 38333034; PMC: 10850878; DOI: 10.3389/fcimb.2024.1335946

  • Help biocurators to maximize the reach of your data.

    Holmes A, Carvalho-Silva D, Sondka Z, Ahmed M, Argasinska J, Lyne R, Sangrador-Vegas A and Ward S

    PLoS biology 2024;22;1;e3002477

    PUBMED: 38271296; DOI: 10.1371/journal.pbio.3002477

  • Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity.

    Dean I, Lee CYC, Tuong ZK, Li Z, Tibbitt CA, Willis C, Gaspal F, Kennedy BC, Matei-Rascu V, Fiancette R et al.

    Nature communications 2024;15;1;683

    PUBMED: 38267402; PMC: 10808449; DOI: 10.1038/s41467-024-44789-z

  • Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity.

    Lee CYC, Kennedy BC, Richoz N, Dean I, Tuong ZK, Gaspal F, Li Z, Willis C, Hasegawa T, Whiteside SK et al.

    Nature communications 2024;15;1;682

    PUBMED: 38267413; PMC: 10808534; DOI: 10.1038/s41467-024-44787-1

  • Changing course at the dawn of a genomics revolution.

    Teichmann SA

    Nature cell biology 2024

    PUBMED: 38263275; DOI: 10.1038/s41556-023-01301-x

  • Deep learning in spatially resolved transcriptfomics: a comprehensive technical view.

    Zahedi R, Ghamsari R, Argha A, Macphillamy C, Beheshti A, Alizadehsani R, Lovell NH, Lotfollahi M and Alinejad-Rokny H

    Briefings in bioinformatics 2024;25;2

    PUBMED: 38483255; DOI: 10.1093/bib/bbae082

  • A chromosome-level genome assembly for the dugong (Dugong dugon).

    Baker DN, Abueg L, Escalona M, Farquharson KA, Lanyon JM, Le Duc D, Schöneberg T, Absolon D, Sims Y, Fedrigo O et al.

    The Journal of heredity 2024

    PUBMED: 38245832; DOI: 10.1093/jhered/esae003

  • Harnessing human microbiomes for disease prediction.

    Liu Y, Fachrul M, Inouye M and Méric G

    Trends in microbiology 2024

    PUBMED: 38246848; DOI: 10.1016/j.tim.2023.12.004

  • The histone chaperone SPT2 regulates chromatin structure and function in Metazoa.

    Saredi G, Carelli FN, Rolland SGM, Furlan G, Piquet S, Appert A, Sanchez-Pulido L, Price JL, Alcon P, Lampersberger L et al.

    Nature structural & molecular biology 2024

    PUBMED: 38238586; DOI: 10.1038/s41594-023-01204-3

  • Genetic history of Cambridgeshire before and after the Black Death.

    Hui R, Scheib CL, D'Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQA, Griffith SJ, Solnik A et al.

    Science advances 2024;10;3;eadi5903

    PUBMED: 38232165; DOI: 10.1126/sciadv.adi5903

  • Inherited polygenic effects on common hematological traits influence clonal selection on JAK2V617F and the development of myeloproliferative neoplasms.

    Guo J, Walter K, Quiros PM, Gu M, Baxter EJ, Danesh J, Di Angelantonio E, Roberts D, Guglielmelli P, Harrison CN et al.

    Nature genetics 2024

    PUBMED: 38233595; DOI: 10.1038/s41588-023-01638-x

  • Resistance against two lytic phage variants attenuates virulence and antibiotic resistance in Pseudomonas aeruginosa.

    García-Cruz JC, Rebollar-Juarez X, Limones-Martinez A, Santos-Lopez CS, Toya S, Maeda T, Ceapă CD, Blasco L, Tomás M, Díaz-Velásquez CE et al.

    Frontiers in cellular and infection microbiology 2024;13;1280265

    PUBMED: 38298921; PMC: 10828002; DOI: 10.3389/fcimb.2023.1280265

  • Tissue Organoid Cultures Metabolize Dietary Carcinogens Proficiently and Are Effective Models for DNA Adduct Formation.

    Caipa Garcia AL, Kucab JE, Al-Serori H, Beck RSS, Bellamri M, Turesky RJ, Groopman JD, Francies HE, Garnett MJ, Huch M et al.

    Chemical research in toxicology 2024

    PUBMED: 38232180; DOI: 10.1021/acs.chemrestox.3c00255

  • The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes.

    Stevens L, Kieninger M, Chan B, Wood JMD, Gonzalez de la Rosa P, Allen J and Blaxter M

    PLoS genetics 2024;20;1;e1011116

    PUBMED: 38227589; DOI: 10.1371/journal.pgen.1011116

  • scSNV-seq: high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics.

    Cooper SE, Coelho MA, Strauss ME, Gontarczyk AM, Wu Q, Garnett MJ, Marioni JC and Bassett AR

    Genome biology 2024;25;1;20

    PUBMED: 38225637; PMC: 10789043; DOI: 10.1186/s13059-024-03169-y

  • Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas.

    Ijaz J, Harry E, Raine K, Menzies A, Beal K, Quail MA, Zumalave S, Jung H, Coorens THH, Lawson ARJ et al.

    Cell genomics 2024;100484

    PUBMED: 38232733; DOI: 10.1016/j.xgen.2023.100484

  • Polyploidy is widespread in Microsporidia.

    Khalaf A, Lawniczak MKN, Blaxter ML and Jaron KS

    Microbiology spectrum 2024;e0366923

    PUBMED: 38214524; DOI: 10.1128/spectrum.03669-23

  • Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data.

    Coll F, Gouliouris T, Blane B, Yeats CA, Raven KE, Ludden C, Khokhar FA, Wilson HJ, Roberts LW, Harrison EM et al.

    The Lancet. Microbe 2024

    PUBMED: 38219758; DOI: 10.1016/S2666-5247(23)00297-5

  • Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma.

    Obacz J, Antonio Valer J, Nibhani R, Adams TS, Schupp JC, Veale N, Lewis-Wade A, Flint J, Hogan J, Aresu G et al.

    The European respiratory journal 2024

    PUBMED: 38212075; DOI: 10.1183/13993003.00143-2023

  • The selection landscape and genetic legacy of ancient Eurasians.

    Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F et al.

    Nature 2024;625;7994;312-320

    PUBMED: 38200293; DOI: 10.1038/s41586-023-06705-1

  • 100 ancient genomes show repeated population turnovers in Neolithic Denmark.

    Allentoft ME, Sikora M, Fischer A, Sjögren KG, Ingason A, Macleod R, Rosengren A, Schulz Paulsson B, Jørkov MLS, Novosolov M et al.

    Nature 2024;625;7994;329-337

    PUBMED: 38200294; DOI: 10.1038/s41586-023-06862-3

  • Human uterine natural killer cells regulate differentiation of extravillous trophoblast early in pregnancy.

    Li Q, Sharkey A, Sheridan M, Magistrati E, Arutyunyan A, Huhn O, Sancho-Serra C, Anderson H, McGovern N, Esposito L et al.

    Cell stem cell 2024

    PUBMED: 38237587; DOI: 10.1016/j.stem.2023.12.013

  • Pitfalls of machine learning models for protein-protein interaction networks.

    Lannelongue L and Inouye M

    Bioinformatics (Oxford, England) 2024

    PUBMED: 38200587; DOI: 10.1093/bioinformatics/btae012

  • Prospective study design and data analysis in UK Biobank.

    Allen NE, Lacey B, Lawlor DA, Pell JP, Gallacher J, Smeeth L, Elliott P, Matthews PM, Lyons RA, Whetton AD et al.

    Science translational medicine 2024;16;729;eadf4428

    PUBMED: 38198570; DOI: 10.1126/scitranslmed.adf4428

  • Molecular characterization of carbapenemase-producing Enterobacterales in a tertiary hospital in Lima, Peru.

    Cuicapuza D, Loyola S, Velásquez J, Fernández N, Llanos C, Ruiz J, Tsukayama P and Tamariz J

    Microbiology spectrum 2024;e0250323

    PUBMED: 38193666; DOI: 10.1128/spectrum.02503-23

  • Transcriptional signals of transformation in human cancer.

    Kildisiute G, Kalyva M, Elmentaite R, van Dongen S, Thevanesan C, Piapi A, Ambridge K, Prigmore E, Haniffa M, Teichmann SA et al.

    Genome medicine 2024;16;1;8

    PUBMED: 38195504; PMC: 10775554; DOI: 10.1186/s13073-023-01279-z

  • The genome sequence of an ichneumonid wasp, Exephanes ischioxanthus (Gravenhorst, 1829).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;8

    PUBMED: 39233900; PMC: 11372355; DOI: 10.12688/wellcomeopenres.20498.1

  • The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796).

    Boyes D, Gibbs M, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: Sequencing Operations collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;9

    PUBMED: 38560613; PMC: 10980857; DOI: 10.12688/wellcomeopenres.20413.1

  • The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794).

    Boyes D, Sims I, Lees DC, Eagles M, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2024;9;6

    PUBMED: 38405013; PMC: 10891431; DOI: 10.12688/wellcomeopenres.20572.1

  • The genome sequence of the Hoary Footman, Eilema caniola (Hübner, 1808).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;5

    PUBMED: 38779146; PMC: 11109690; DOI: 10.12688/wellcomeopenres.20574.1

  • The genome sequence of the Marbled White Spot, Protodeltote pygarga (Hufnagel, 1766).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;7

    PUBMED: 38867756; PMC: 11167331; DOI: 10.12688/wellcomeopenres.20571.1

  • Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci.

    Croucher NJ, Campo JJ, Le TQ, Pablo JV, Hung C, Teng AA, Turner C, Nosten F, Bentley SD, Liang X et al.

    Nature communications 2024;15;1;355

    PUBMED: 38191887; PMC: 10774285; DOI: 10.1038/s41467-023-44584-2

  • Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.

    Viner C, Ishak CA, Johnson J, Walker NJ, Shi H, Sjöberg-Herrera MK, Shen SY, Lardo SM, Adams DJ, Ferguson-Smith AC et al.

    Genome biology 2024;25;1;11

    PUBMED: 38191487; PMC: 10773111; DOI: 10.1186/s13059-023-03070-0

  • COSMIC: a curated database of somatic variants and clinical data for cancer.

    Sondka Z, Dhir NB, Carvalho-Silva D, Jupe S, Madhumita, McLaren K, Starkey M, Ward S, Wilding J, Ahmed M et al.

    Nucleic acids research 2024;52;D1;D1210-D1217

    PUBMED: 38183204; PMC: 10767972; DOI: 10.1093/nar/gkad986

  • Inherited blood cancer predisposition through altered transcription elongation.

    Zhao J, Cato LD, Arora UP, Bao EL, Bryant SC, Williams N, Jia Y, Goldman SR, Nangalia J, Erb MA et al.

    Cell 2024

    PUBMED: 38218188; DOI: 10.1016/j.cell.2023.12.016

  • Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study.

    Pöntinen AK, Gladstone RA, Pesonen H, Pesonen M, Cléon F, Parcell BJ, Kallonen T, Simonsen GS, Croucher NJ, McNally A et al.

    The Lancet. Microbe 2024

    PUBMED: 38219757; DOI: 10.1016/S2666-5247(23)00292-6

  • Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference.

    Meng X, Navoly G, Giannakopoulou O, Levey DF, Koller D, Pathak GA, Koen N, Lin K, Adams MJ, Rentería ME et al.

    Nature genetics 2024;56;2;222-233

    PUBMED: 38177345; PMC: 10864182; DOI: 10.1038/s41588-023-01596-4

  • "A very big challenge": a qualitative study to explore the early barriers and enablers to implementing a national genomic medicine service in England.

    Friedrich B, Vindrola-Padros C, Lucassen AM, Patch C, Clarke A, Lakhanpaul M and Lewis C

    Frontiers in genetics 2024;14;1282034

    PUBMED: 38239852; PMC: 10794539; DOI: 10.3389/fgene.2023.1282034

  • A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization.

    Pacini C, Duncan E, Gonçalves E, Gilbert J, Bhosle S, Horswell S, Karakoc E, Lightfoot H, Curry E, Muyas F et al.

    Cancer cell 2024

    PUBMED: 38215750; DOI: 10.1016/j.ccell.2023.12.016

  • The genome sequence of the English holly, Ilex aquifolium L. (Aquifoliaceae).

    Christenhusz MJM, Fay MF, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;1

    PUBMED: 38779152; PMC: 11109700; DOI: 10.12688/wellcomeopenres.20748.1

  • The genome sequence of the Tipped Oak Case-bearer, Coleophora flavipennella (Duponchel 1843).

    Boyes D, Blaxter ML, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2024;9;3

    PUBMED: 38686023; PMC: 11056683; DOI: 10.12688/wellcomeopenres.19917.1

  • Genetic Associations of Circulating Cardiovascular Proteins With Gestational Hypertension and Preeclampsia.

    Schuermans A, Truong B, Ardissino M, Bhukar R, Slob EAW, Nakao T, Dron JS, Small AM, Cho SMJ, Yu Z et al.

    JAMA cardiology 2024

    PUBMED: 38170504; DOI: 10.1001/jamacardio.2023.4994

  • Benchmark Software and Data for Evaluating CRISPR-Cas9 Experimental Pipelines Through the Assessment of a Calibration Screen.

    Iannuzzi RM, Manipur I, Pacini C, Behan FM, Guarracino MR, Garnett MJ, Savino A and Iorio F

    The CRISPR journal 2024

    PUBMED: 38165445; DOI: 10.1089/crispr.2023.0040

  • De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus.

    Souza-Borges CH, Utsunomia R, Varani AM, Uliano-Silva M, Lira LVG, Butzge AJ, Gomez Agudelo JF, Manso S, Freitas MV, Ariede RB et al.

    GigaScience 2024;13

    PUBMED: 39589439; DOI: 10.1093/gigascience/giae085

  • Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma.

    Ganier C, Mazin P, Herrera-Oropeza G, Du-Harpur X, Blakeley M, Gabriel J, Predeus AV, Cakir B, Prete M, Harun N et al.

    Proceedings of the National Academy of Sciences of the United States of America 2024;121;2;e2313326120

    PUBMED: 38165934; DOI: 10.1073/pnas.2313326120

  • Association of Sickle Cell Disease, Malaria and HIV in Multi Drug Resistant Invasive Non-typhoidal Salmonella Isolated from Outpatient and Hospitalised Children Below 16 Years in Informal Settlements in Nairobi County, Kenya.

    Kavai SM, Mbae C, Wairimu C, Ngetich R, Wakio Z, Onsaŕe R and Kariuki S

    East Africa science 2024;6;1;48-54

    PUBMED: 39544623; PMC: 11561362; DOI: 10.24248/easci.v6i1.92

  • Bicycle: Intervention-Based Causal Discovery with Cycles

    Rohbeck, Martin, Clarke, Brian, Mikulik, Katharina, Pettet, Alexandra, STEGLE, OLIVER and Ueltzhöffer et al.

    Proceedings of Machine Learning Research 2024;236;209-242

    URL: https://proceedings.mlr.press/v236/rohbeck24a/rohbeck24a.pdf

  • Boosting microbiome science worldwide could save millions of children's lives.

    Browne HP, Iqbal NT, Osman M, Tigoi C, Lawley TD, Gordon JI, Ahmed T and Kariuki S

    Nature 2024;625;7994;237-240

    PUBMED: 38191714; PMC: 10810019; DOI: 10.1038/d41586-024-00017-8

  • MAARS Software for Automatic and Quantitative Analysis of Mitotic Progression.

    Li T, Gachet Y and Tournier S

    Methods in molecular biology (Clifton, N.J.) 2024;2740;275-293

    PUBMED: 38393482; DOI: 10.1007/978-1-0716-3557-5_17

  • Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan.

    Javaid N, Lo SW, Nisar MI, Basharat A, Jaleel H, Rasool K, Sultana Q, Kabir F, Hotwani A, Breiman RF et al.

    Microbial genomics 2024;10;1

    PUBMED: 38270581; DOI: 10.1099/mgen.0.001163

2023

  • The genome sequence of a solitary sea squirt, Ascidia mentula (Müller, 1776).

    Bishop J, Wood C, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;583

    PUBMED: 38779044; PMC: 11109543; DOI: 10.12688/wellcomeopenres.20415.1

  • Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy.

    Wienke J, Visser LL, Kholosy WM, Keller KM, Barisa M, Poon E, Munnings-Tomes S, Himsworth C, Calton E, Rodriguez A et al.

    Cancer cell 2023

    PUBMED: 38181797; DOI: 10.1016/j.ccell.2023.12.008

  • Splicing defects and CRISPR-Cas9 correction in isogenic homozygous photoreceptor precursors harboring clustered deep-intronic ABCA4 variants.

    De Angeli P, Flores-Tufiño A, Stingl K, Kühlewein L, Roschi E, Wissinger B and Kohl S

    Molecular therapy. Nucleic acids 2023;35;1;102113

    PUBMED: 38274366; PMC: 10809099; DOI: 10.1016/j.omtn.2023.102113

  • Identifying candidate genes underlying isolated congenital anosmia.

    Kamarck ML, Trimmer C, Murphy NR, Gregory KM, Manoel D, Logan DW, Saraiva LR and Mainland JD

    Clinical genetics 2023

    PUBMED: 38148624; DOI: 10.1111/cge.14470

  • Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19.

    Milross L, Hunter B, McDonald D, Merces G, Thomson A, Hilkens CMU, Wills J, Rees P, Jiwa K, Cooper N et al.

    EBioMedicine 2023;99;104945

    PUBMED: 38142637; DOI: 10.1016/j.ebiom.2023.104945

  • Automatic cell-type harmonization and integration across Human Cell Atlas datasets.

    Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB and Teichmann SA

    Cell 2023;186;26;5876-5891.e20

    PUBMED: 38134877; DOI: 10.1016/j.cell.2023.11.026

  • Single-cell genomics sheds light on kidney tissue immunity.

    Stewart AP and Clatworthy MR

    Nature reviews. Nephrology 2023

    PUBMED: 38129546; DOI: 10.1038/s41581-023-00802-0

  • The genome sequence of Ashworth's Rustic, Xestia ashworthii (Doubleday, 1855).

    Mulley JF, Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;578

    PUBMED: 39157737; PMC: 11327654; DOI: 10.12688/wellcomeopenres.20499.1

  • Molecular markers for malaria genetic epidemiology: progress and pitfalls.

    Ruybal-Pesántez S, McCann K, Vibin J, Siegel S, Auburn S and Barry AE

    Trends in parasitology 2023

    PUBMED: 38129280; DOI: 10.1016/j.pt.2023.11.006

  • Vaccination to Reduce Antimicrobial Resistance Burden-Data Gaps and Future Research.

    Tadesse BT, Keddy KH, Rickett NY, Zhusupbekova A, Poudyal N, Lawley T, Osman M, Dougan G, Kim JH, Lee JS et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2023;77;Supplement_7;S597-S607

    PUBMED: 38118013; PMC: 10732565; DOI: 10.1093/cid/ciad562

  • Novel stem cell technologies are powerful tools to understand the impact of human factors on Plasmodium falciparum malaria.

    Pance A, Ng BL, Mwikali K, Koutsourakis M, Agu C, Rouhani FJ, Montandon R, Law F, Ponstingl H and Rayner JC

    Frontiers in cellular and infection microbiology 2023;13;1287355

    PUBMED: 38173794; PMC: 10762799; DOI: 10.3389/fcimb.2023.1287355

  • A distinct human cell type expressing MHCII and RORγt with dual characteristics of dendritic cells and type 3 innate lymphoid cells.

    Ulezko Antonova A, Lonardi S, Monti M, Missale F, Fan C, Coates ML, Bugatti M, Jaeger N, Fernandes Rodrigues P, Brioschi S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2023;120;52;e2318710120

    PUBMED: 38109523; PMC: 10756205; DOI: 10.1073/pnas.2318710120

  • The energetic and allosteric landscape for KRAS inhibition.

    Weng C, Faure AJ, Escobedo A and Lehner B

    Nature 2023;626;7999;643-652

    PUBMED: 38109937; PMC: 10866706; DOI: 10.1038/s41586-023-06954-0

  • Diversity and dissemination of viruses in pathogenic protozoa.

    Heeren S, Maes I, Sanders M, Lye LF, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM et al.

    Nature communications 2023;14;1;8343

    PUBMED: 38102141; PMC: 10724245; DOI: 10.1038/s41467-023-44085-2

  • Early human lung immune cell development and its role in epithelial cell fate.

    Barnes JL, Yoshida M, He P, Worlock KB, Lindeboom RGH, Suo C, Pett JP, Wilbrey-Clark A, Dann E, Mamanova L et al.

    Science immunology 2023;8;90;eadf9988

    PUBMED: 38100545; DOI: 10.1126/sciimmunol.adf9988

  • Phenotypes and rates of cancer-relevant symptoms and tests in the year before cancer diagnosis in UK Biobank and CPRD Gold.

    Barclay M, Renzi C, Antoniou A, Denaxas S, Harrison H, Ip S, Pashayan N, Torralbo A, Usher-Smith J, Wood A and Lyratzopoulos G

    PLOS digital health 2023;2;12;e0000383

    PUBMED: 38100737; PMC: 10723831; DOI: 10.1371/journal.pdig.0000383

  • The genome sequence of the white-footed hoverfly, Platycheirus albimanus (Fabricius, 1781).

    Crowley LM, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;572

    PUBMED: 38836070; PMC: 11148528; DOI: 10.12688/wellcomeopenres.20494.1

  • A recurrent de novo MAX p.Arg60Gln variant causes a syndromic overgrowth disorder through differential expression of c-Myc target genes.

    Harris EL, Roy V, Montagne M, Rose AMS, Livesey H, Reijnders MRF, Hobson E, Sansbury FH, Willemsen MH, Pfundt R et al.

    American journal of human genetics 2023

    PUBMED: 38141607; DOI: 10.1016/j.ajhg.2023.11.010

  • Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment.

    Díaz-Gay M, Vangara R, Barnes M, Wang X, Islam SMA, Vermes I, Duke S, Narasimman NB, Yang T, Jiang Z et al.

    Bioinformatics (Oxford, England) 2023

    PUBMED: 38096571; DOI: 10.1093/bioinformatics/btad756

  • Genetically divergent Francisella philomiragia associated with septic arthritis, Montevideo, Uruguay.

    Riera N, Salazar C, Rivera B, Galiana A, Durán R, Portela MM, Antelo V, Pi B, González Ó and Iraola G

    New microbes and new infections 2023;57;101210

    PUBMED: 38261949; PMC: 10797181; DOI: 10.1016/j.nmni.2023.101210

  • Wilms Tumor With Raised Serum Alpha-Fetoprotein: Highlighting the Need for Novel Circulating Biomarkers.

    Green R, Ahmed A, Fleming B, Long AM, Behjati S, Trotman J, Tarpey P, Nicholson JC, Coleman N, Elizabeth Hook C and Murray MJ

    Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society 2023;10935266231213467

    PUBMED: 38098239; DOI: 10.1177/10935266231213467

  • Real-time single-base specific detection of the Haemonchus contortus S168T variant associated with levamisole resistance using loop-primer endonuclease cleavage loop-mediated isothermal amplification.

    Antonopoulos A, Higgins O, Doyle SR, Bartley D, Morrison A, Shalaby MM, Reboud J, Devaney E, Smith TJ, Laing R and Busin V

    Molecular and cellular probes 2023;101946

    PUBMED: 38097144; DOI: 10.1016/j.mcp.2023.101946

  • Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean.

    Lee YH, Abueg L, Kim JK, Kim YW, Fedrigo O, Balacco J, Formenti G, Howe K, Tracey A, Wood J et al.

    Scientific data 2023;10;1;880

    PUBMED: 38066002; PMC: 10709322; DOI: 10.1038/s41597-023-02782-z

  • Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type.

    Manna S, Werren JP, Ortika BD, Bellich B, Pell CL, Nikolaou E, Gjuroski I, Lo S, Hinds J, Tundev O et al.

    Microbiology spectrum 2023;e0357923

    PUBMED: 38059623; DOI: 10.1128/spectrum.03579-23

  • The genome sequence of the Ochreous Pearl, Anania crocealis (Hübner, 1796).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;568

    PUBMED: 38911283; PMC: 11193085; DOI: 10.12688/wellcomeopenres.20573.1

  • The genome sequence of the Webb's Wainscot, Globia sparganii (Esper, 1790).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;565

    PUBMED: 39417200; PMC: 11480736; DOI: 10.12688/wellcomeopenres.20181.1

  • A human embryonic limb cell atlas resolved in space and time.

    Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L et al.

    Nature 2023

    PUBMED: 38057666; DOI: 10.1038/s41586-023-06806-x

  • Cancer Evolution: A Multifaceted Affair.

    Ciriello G, Magnani L, Aitken SJ, Akkari L, Behjati S, Hanahan D, Landau DA, Lopez-Bigas N, Lupiáñez DG, Marine JC et al.

    Cancer discovery 2023;OF1-OF13

    PUBMED: 38047596; DOI: 10.1158/2159-8290.CD-23-0530

  • Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation.

    Radford EJ, Tan HK, Andersson MHL, Stephenson JD, Gardner EJ, Ironfield H, Waters AJ, Gitterman D, Lindsay S, Abascal F et al.

    Nature communications 2023;14;1;7702

    PUBMED: 38057330; PMC: 10700591; DOI: 10.1038/s41467-023-43041-4

  • The genome sequence of a caddisfly, Limnephilus auricula (Curtis, 1834).

    McCulloch J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;560

    PUBMED: 38779042; PMC: 11109698; DOI: 10.12688/wellcomeopenres.20383.1

  • The genome sequence of a cranefly, Tipula unca (Wiedemann, 1817).

    Sivell O, Webb J, Mitchell R, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;559

    PUBMED: 39440226; PMC: 11494271; DOI: 10.12688/wellcomeopenres.20298.1

  • The genome sequence of a tachinid fly, Thelaira solivaga (Harris, 1780).

    Falk S, Smith MN, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;564

    PUBMED: 38764971; PMC: 11101925; DOI: 10.12688/wellcomeopenres.19639.1

  • The genome sequence of a weevil, Polydrusus cervinus (Linnaeus, 1758).

    Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: Sequencing Operations collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;563

    PUBMED: 38846515; PMC: 11153995; DOI: 10.12688/wellcomeopenres.20414.1

  • The genome sequence of the European flat oyster, Ostrea edulis (Linnaeus, 1758).

    Adkins P, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;556

    PUBMED: 38558925; PMC: 10979132; DOI: 10.12688/wellcomeopenres.19916.1

  • The genome sequence of the Figure of Eight, Diloba caeruleocephala (Linnaeus, 1758).

    Crowley LM, Hutchinson F, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;554

    PUBMED: 39071793; PMC: 11282394; DOI: 10.12688/wellcomeopenres.20497.1

  • The genome sequence of the nine-spined stickleback, Pungitius pungitius (Linnaeus, 1758).

    Hänfling B, Smith A, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;555

    PUBMED: 39114814; PMC: 11303943; DOI: 10.12688/wellcomeopenres.20354.1

  • The hypermorphic PLCγ2 S707Y variant dysregulates microglial cell function - Insight into PLCγ2 activation in brain health and disease, and opportunities for therapeutic modulation.

    Bull D, Matte JC, Navarron CM, McIntyre R, Whiting P, Katan M, Ducotterd F and Magno L

    Biochimica et biophysica acta. Molecular basis of disease 2023;166978

    PUBMED: 38061598; DOI: 10.1016/j.bbadis.2023.166978

  • Colonization factors of human and animal-specific enterotoxigenic Escherichia coli (ETEC).

    von Mentzer A and Svennerholm AM

    Trends in microbiology 2023

    PUBMED: 38052687; DOI: 10.1016/j.tim.2023.11.001

  • Selenoprotein deficiency disorder predisposes to aortic aneurysm formation.

    Schoenmakers E, Marelli F, Jørgensen HF, Visser WE, Moran C, Groeneweg S, Avalos C, Jurgens SJ, Figg N, Finigan A et al.

    Nature communications 2023;14;1;7994

    PUBMED: 38042913; PMC: 10693596; DOI: 10.1038/s41467-023-43851-6

  • The genome sequence of a digger wasp, Ectemnius lituratus (Panzer,1805).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Wellcome Sanger Institute Tree of Life Core Informatics Team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;552

    PUBMED: 39188773; PMC: 11345589; DOI: 10.12688/wellcomeopenres.20337.1

  • The management of myelofibrosis: A British Society for Haematology Guideline.

    McLornan DP, Psaila B, Ewing J, Innes A, Arami S, Brady J, Butt NM, Cargo C, Cross NCP, Francis S et al.

    British journal of haematology 2023

    PUBMED: 38037886; DOI: 10.1111/bjh.19186

  • Environmental Impacts of Machine Learning Applications in Protein Science.

    Lannelongue L and Inouye M

    Cold Spring Harbor perspectives in biology 2023;15;12

    PUBMED: 38040454; PMC: 10691472; DOI: 10.1101/cshperspect.a041473

  • Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.

    Ban M, Bredikhin D, Huang Y, Bonder MJ, Katarzyna K, Oliver AJ, Wilson NK, Coupland P, Hadfield J, Göttgens B et al.

    Brain : a journal of neurology 2023

    PUBMED: 38038362; DOI: 10.1093/brain/awad404

  • How developmental cell atlases inform stem cell embryo models.

    Haniffa M, Maartens A and Teichmann SA

    Nature methods 2023;20;12;1849-1851

    PUBMED: 38057509; DOI: 10.1038/s41592-023-02072-x

  • A signature of platelet reactivity in CBC scattergrams reveals genetic predictors of thrombotic disease risk.

    Verdier H, Thomas P, Batista J, Kempster C, McKinney H, Gleadall N, Danesh J, Mumford A, Heemskerk JWM, Ouwehand WH et al.

    Blood 2023;142;22;1895-1908

    PUBMED: 37647652; DOI: 10.1182/blood.2023021100

  • Integrated systems biology approach identifies gene targets for endothelial dysfunction.

    Pinheiro-de-Sousa I, Fonseca-Alaniz MH, Giudice G, Valadão IC, Modestia SM, Mattioli SV, Junior RR, Zalmas LP, Fang Y, Petsalaki E and Krieger JE

    Molecular systems biology 2023;e11462

    PUBMED: 38031960; DOI: 10.15252/msb.202211462

  • FastCAR: fast correction for ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets.

    Berg M, Petoukhov I, van den Ende I, Meyer KB, Guryev V, Vonk JM, Carpaij O, Banchero M, Hendriks RW, van den Berge M and Nawijn MC

    BMC genomics 2023;24;1;722

    PUBMED: 38030970; DOI: 10.1186/s12864-023-09822-3

  • Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants.

    Gaccioli F, Stephens K, Sovio U, Jessop F, Wong HS, Lager S, Cook E, de Goffau MC, Le Doare K, Peacock SJ et al.

    Nature microbiology 2023;8;12;2338-2348

    PUBMED: 38030897; DOI: 10.1038/s41564-023-01528-2

  • The value of genetic data from 665,460 individuals in managing iron deficiency anaemia and suitability to donate blood.

    Toivonen J, Allara E, FinnGen, Castrén J, di Angelantonio E and Arvas M

    Vox sanguinis 2023

    PUBMED: 38018286; DOI: 10.1111/vox.13564

  • EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

    Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M et al.

    Nucleic acids research 2023

    PUBMED: 38015445; DOI: 10.1093/nar/gkad1088

  • Ancient diversity in host-parasite interaction genes in a model parasitic nematode.

    Stevens L, Martínez-Ugalde I, King E, Wagah M, Absolon D, Bancroft R, Gonzalez de la Rosa P, Hall JL, Kieninger M, Kloch A et al.

    Nature communications 2023;14;1;7776

    PUBMED: 38012132; PMC: 10682056; DOI: 10.1038/s41467-023-43556-w

  • CIPSI: An open chemical intellectual property service for medicinal chemists.

    Martinez-Sevillano M, Falaguera MJ and Mestres J

    Molecular informatics 2023;e202300221

    PUBMED: 38010631; DOI: 10.1002/minf.202300221

  • Diverse macrophage populations contribute to distinct manifestations of human cutaneous graft-versus-host disease.

    Strobl J, Gail LM, Krecu L, Madad S, Kleissl L, Unterluggauer L, Redl A, Brazdilova K, Saluzzo S, Wohlfarth P et al.

    The British journal of dermatology 2023

    PUBMED: 38010706; DOI: 10.1093/bjd/ljad402

  • Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia.

    Kebede AM, Sutanto E, Trimarsanto H, Benavente ED, Barnes M, Pearson RD, Siegel SV, Erko B, Assefa A, Getachew S et al.

    Scientific reports 2023;13;1;20788

    PUBMED: 38012191; PMC: 10682486; DOI: 10.1038/s41598-023-47889-w

  • The genome sequence of a ground beetle, Pterostichus niger (Schaller, 1783).

    Barclay MVL, Geiser M, Vassiliades D, Bayfield Farrell W, Cristóvão J, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al.

    Wellcome open research 2023;8;544

    PUBMED: 38434746; PMC: 10907878; DOI: 10.12688/wellcomeopenres.20418.1

  • The genome sequence of a hoverfly, Pocota personata (Harris, 1780).

    Falk S, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;546

    PUBMED: 39036351; PMC: 11259775; DOI: 10.12688/wellcomeopenres.20501.1

  • The genome sequence of the Brown Rustic, Charanyca ferruginea (Esper, 1785).

    Boyes D, Hutchinson F, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;547

    PUBMED: 39129912; PMC: 11316178; DOI: 10.12688/wellcomeopenres.20137.1

  • The genome sequence of the bulrush Neoascia, Neoascia interrupta (Meigen, 1822).

    Falk S, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;549

    PUBMED: 38764967; PMC: 11101924; DOI: 10.12688/wellcomeopenres.20353.1

  • The genome sequence of the light-bulb sea squirt, Clavelina lepadiformis (Müller, 1776).

    Bishop J, Wood C, Mrowicki R, Harley J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team et al.

    Wellcome open research 2023;8;543

    PUBMED: 38404634; PMC: 10884593; DOI: 10.12688/wellcomeopenres.20417.1

  • The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis & Schiffermüller, 1775).

    Boyes D, Januszczak I, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;545

    PUBMED: 39295890; PMC: 11408916; DOI: 10.12688/wellcomeopenres.20148.1

  • Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana.

    Girgis ST, Adika E, Nenyewodey FE, Senoo Jnr DK, Ngoi JM, Bandoh K, Lorenz O, van de Steeg G, Harrott AJR, Nsoh S et al.

    Nature microbiology 2023;8;12;2365-2377

    PUBMED: 37996707; PMC: 10686832; DOI: 10.1038/s41564-023-01516-6

  • The genome sequence of the Gelatinous Scale Worm, Alentia gelatinosa (Sars, 1835).

    Adkins P, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;542

    PUBMED: 38558923; PMC: 10980856; DOI: 10.12688/wellcomeopenres.20176.1

  • Expression Atlas update: insights from sequencing data at both bulk and single cell level.

    George N, Fexova S, Fuentes AM, Madrigal P, Bi Y, Iqbal H, Kumbham U, Nolte NF, Zhao L, Thanki AS et al.

    Nucleic acids research 2023

    PUBMED: 37992296; DOI: 10.1093/nar/gkad1021

  • Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae.

    Henares D, Lo SW, Perez-Argüello A, Redin A, Ciruela P, Garcia-Garcia JJ, Brotons P, Yuste J, Sá-Leão R and Muñoz-Almagro C

    Journal of clinical microbiology 2023;e0074123

    PUBMED: 38092657; DOI: 10.1128/jcm.00741-23

  • How to estimate carbon footprint when training deep learning models? A guide and review.

    Bouza L, Bugeau A and Lannelongue L

    Environmental research communications 2023;5;11;115014

    PUBMED: 38022395; PMC: 10661046; DOI: 10.1088/2515-7620/acf81b

  • The genome sequence of an ichneumonid wasp, Heteropelma amictum (Fabricius, 1775).

    Crowley LM, Broad GR, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;537

    PUBMED: 38434733; PMC: 10905020; DOI: 10.12688/wellcomeopenres.20364.1

  • The genome sequence of the brown sea anemone, Metridium senile (Linnaeus, 1761).

    Adkins P, Bishop J, Mrowicki R, Blaxter ML, Modepalli V, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;536

    PUBMED: 39219858; PMC: 11362738; DOI: 10.12688/wellcomeopenres.20376.1

  • The genome sequence of the common buff snailkiller, Tetanocera ferruginea (Fallén, 1820).

    Crowley LM, Falk S, Williams CD, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;535

    PUBMED: 38434740; PMC: 10904942; DOI: 10.12688/wellcomeopenres.20366.1

  • The genome sequence of the flutter-wing fly, Palloptera scutellata (Macquart, 1835).

    Ashworth M, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;534

    PUBMED: 38798990; PMC: 11126900; DOI: 10.12688/wellcomeopenres.20381.1

  • The genome sequence of the Variegated Golden Tortrix, Archips xylosteana (Linnaeus, 1758).

    Boyes D, Gibbs M, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;538

    PUBMED: 38344693; PMC: 10853669; DOI: 10.12688/wellcomeopenres.20362.1

  • A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates.

    Stendahl AM, Sanghvi R, Peterson S, Ray K, Lima AC, Rahbari R and Conrad DF

    Genome research 2023

    PUBMED: 37984997; DOI: 10.1101/gr.277977.123

  • A primate nigrostriatal atlas of neuronal vulnerability and resilience in a model of Parkinson's disease.

    Tang L, Xu N, Huang M, Yi W, Sang X, Shao M, Li Y, Hao ZZ, Liu R, Shen Y et al.

    Nature communications 2023;14;1;7497

    PUBMED: 37980356; PMC: 10657376; DOI: 10.1038/s41467-023-43213-2

  • Adapting cardiovascular risk prediction models to different populations: the need for recalibration.

    Pennells L, Kaptoge S and Di Angelantonio E

    European heart journal 2023

    PUBMED: 37978887; DOI: 10.1093/eurheartj/ehad748

  • The genome sequence of the Chestnut, Conistra vaccinii (Linnaeus, 1761).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;532

    PUBMED: 38634068; PMC: 11021882; DOI: 10.12688/wellcomeopenres.20346.1

  • The genome sequence of the Large Longhorn, Nematopogon swammerdamella (Linnaeus, 1758).

    Langdon WBV, Baumberg C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;531

    PUBMED: 39233727; PMC: 11372353; DOI: 10.12688/wellcomeopenres.20186.1

  • Prevalence of Deleterious Variants in MC3R in Patients With Constitutional Delay of Growth and Puberty.

    Duckett K, Williamson A, Kincaid JWR, Rainbow K, Corbin LJ, Martin HC, Eberhardt RY, Huang QQ, Hurles ME, He W et al.

    The Journal of clinical endocrinology and metabolism 2023;108;12;e1580-e1587

    PUBMED: 37339320; PMC: 10655545; DOI: 10.1210/clinem/dgad373

  • Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale.

    Imaz-Rosshandler I, Rode C, Guibentif C, Harland LTG, Ton MN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J et al.

    Development (Cambridge, England) 2023

    PUBMED: 37982461; DOI: 10.1242/dev.201867

  • The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis & Schiffermüller, 1775).

    Boyes D, Blaxter ML, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;529

    PUBMED: 39309423; PMC: 11413856; DOI: 10.12688/wellcomeopenres.20351.1

  • Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease.

    Spencer Chapman M, Cull AH, Ciuculescu MF, Esrick EB, Mitchell E, Jung H, O'Neill L, Roberts K, Fabre MA, Williams N et al.

    Nature medicine 2023

    PUBMED: 37973947; DOI: 10.1038/s41591-023-02636-6

  • Towards robust clinical genome interpretation: developing a consistent terminology to characterize Mendelian disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms.

    Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2023;101029

    PUBMED: 37982373; DOI: 10.1016/j.gim.2023.101029

  • A cross-professional competency framework for communicating genomic results.

    Pichini A, Tatton-Brown K, Thomas E and Bishop M

    Journal of genetic counseling 2023

    PUBMED: 37965839; DOI: 10.1002/jgc4.1826

  • The genome sequence of the yellow-legged black legionnaire, Beris morrisii (Dale, 1841).

    McCulloch J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;527

    PUBMED: 38803349; PMC: 11128770; DOI: 10.12688/wellcomeopenres.20352.1

  • The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

    Murray GGR, Hossain ASMM, Miller EL, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li G et al.

    Proceedings of the National Academy of Sciences of the United States of America 2023;120;47;e2307773120

    PUBMED: 37963246; DOI: 10.1073/pnas.2307773120

  • The genome sequence of the Downland Villa bee-fly, Villa cingulata (Meigen, 1804).

    Taylor SC, Crowley LM, Luker S, Harvey M, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;526

    PUBMED: 39108663; PMC: 11301140; DOI: 10.12688/wellcomeopenres.20123.1

  • Genomics for public health and international surveillance of antimicrobial resistance.

    Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS et al.

    The Lancet. Microbe 2023

    PUBMED: 37977162; DOI: 10.1016/S2666-5247(23)00283-5

  • The genome sequence of a hoverfly, Epistrophe eligans (Harris, 1780).

    Sivell O, Sivell D, Crowley LM, Falk S, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;521

    PUBMED: 39219860; PMC: 11362734; DOI: 10.12688/wellcomeopenres.20336.1

  • The genome sequence of a rove beetle, Othius punctulatus (Goeze, 1777).

    McCulloch J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;519

    PUBMED: 38779053; PMC: 11109532; DOI: 10.12688/wellcomeopenres.20338.1

  • The genome sequence of Pycnococcus provasolii (CCAP190/2) (Guillard, 1991).

    Green DH, Rad-Menéndez C, Campbell C, Kilias ES, Culture Collection of Algae and Protozoa collective, University of Oxford and Wytham Woods Genome Acquisition Lab, Earlham Institute Genome Acquisition Lab and Protists Project, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective et al.

    Wellcome open research 2023;8;520

    PUBMED: 38808318; PMC: 11130579; DOI: 10.12688/wellcomeopenres.20345.1

  • The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis & Schiffermüller, 1775).

    Boyes D, Eljounaidi K, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;516

    PUBMED: 39086664; PMC: 11289590; DOI: 10.12688/wellcomeopenres.19923.1

  • The genome sequence of the Wasp Spider, Argiope bruennichi (Scopoli, 1772).

    Crowley LM, Hutchinson F, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;522

    PUBMED: 38434739; PMC: 10904950; DOI: 10.12688/wellcomeopenres.20339.1

  • Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas.

    Sutanto E, Pava Z, Echeverry DF, Lopera-Mesa TM, Montenegro LM, Yasnot-Acosta MF, Benavente ED, Pearson RD, Herrera S, Arévalo-Herrera M et al.

    Scientific reports 2023;13;1;19779

    PUBMED: 37957271; DOI: 10.1038/s41598-023-46076-1

  • Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson's disease mouse model.

    Fang TZ, Sun Y, Pearce AC, Eleuteri S, Kemp M, Luckhurst CA, Williams R, Mills R, Almond S, Burzynski L et al.

    Nature communications 2023;14;1;7295

    PUBMED: 37957154; DOI: 10.1038/s41467-023-42876-1

  • The genome sequence of the Brown-spot Pinion, Agrochola litura (Linnaeus, 1761).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;512

    PUBMED: 38798996; PMC: 11128041; DOI: 10.12688/wellcomeopenres.20347.1

  • The genome sequence of the hazel dormouse, Muscardinus avellanarius (Linnaeus, 1758).

    Böhne A, Thiel-Bender C, Kukowka S, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;514

    PUBMED: 38911281; PMC: 11190645; DOI: 10.12688/wellcomeopenres.20360.1

  • The genome sequence of the Heterolobosean amoeboflagellate, Tetramitus jugosus CCAP 1588/3C.

    Green DH, Rad-Menéndez C, Culture Collection of Algae and Protozoa collective, Earlham Institute Genome Acquisition Lab and Protists Project, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;513

    PUBMED: 38774489; PMC: 11106597; DOI: 10.12688/wellcomeopenres.20189.1

  • The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis & Schiffermüller, 1775).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;515

    PUBMED: 38813550; PMC: 11134158; DOI: 10.12688/wellcomeopenres.20279.1

  • The genome sequence of the Black Spongefly, Sisyra nigra (Retzius, 1783).

    Broad GR, Crowley LM, McCulloch J, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;511

    PUBMED: 38855724; PMC: 11162525; DOI: 10.12688/wellcomeopenres.20295.1

  • The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;509

    PUBMED: 39193090; PMC: 11347913; DOI: 10.12688/wellcomeopenres.20242.1

  • Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants.

    Wang A, Shen J, Rodriguez AA, Saunders EJ, Chen F, Janivara R, Darst BF, Sheng X, Xu Y, Chou AJ et al.

    Nature genetics 2023

    PUBMED: 37945903; DOI: 10.1038/s41588-023-01534-4

  • Test of the lateral angle method of sex estimation on Anglo-Saxon and medieval archaeological populations with genetically estimated sex

    Thompson, Jess E., Inskip, Sarah A., Scheib, Christiana L., Bates, Jessica, Ge, Xiangyu et al.

    Archaeometry 2023

    DOI: 10.1111/arcm.12927

  • A chromosomal reference genome sequence for the malaria mosquito, Anopheles moucheti, Evans, 1925.

    Nsango SN, Agbor JP, Ayala D, Johnson HF, Heaton H, Wagah MG, Collins JC, Krasheninnikova K, Pelan SE, Pointon DB et al.

    Wellcome open research 2023;8;507

    PUBMED: 38046191; PMC: 10690039; DOI: 10.12688/wellcomeopenres.20259.1

  • The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761).

    Boyes D, Eagles M, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;506

    PUBMED: 38404636; PMC: 10884592; DOI: 10.12688/wellcomeopenres.20187.1

  • A sensor histidine kinase from a plant-endosymbiont bacterium restores the virulence of a mammalian intracellular pathogen.

    Chaves-Olarte E, Meza-Torres J, Herrera-Rodríguez F, Lizano-González E, Suárez-Esquivel M, Baker KS, Rivas-Solano O, Ruiz-Villalobos N, Villalta-Romero F, Cheng HP et al.

    Microbial pathogenesis 2023;106442

    PUBMED: 37944675; DOI: 10.1016/j.micpath.2023.106442

  • The stage- and sex-specific transcriptome of the human parasite Schistosoma mansoni.

    Buddenborg SK, Lu Z, Sankaranarayan G, Doyle SR and Berriman M

    Scientific data 2023;10;1;775

    PUBMED: 37935722; PMC: 10630280; DOI: 10.1038/s41597-023-02674-2

  • An interpretable biological age.

    Zhang Q

    The lancet. Healthy longevity 2023

    PUBMED: 37944548; DOI: 10.1016/S2666-7568(23)00213-1

  • The Reactome Pathway Knowledgebase 2024.

    Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B et al.

    Nucleic acids research 2023

    PUBMED: 37941124; DOI: 10.1093/nar/gkad1025

  • Diagnosis and evaluation of prognosis of myelofibrosis: A British Society for Haematology Guideline.

    McLornan DP, Godfrey AL, Green A, Frewin R, Arami S, Brady J, Butt NM, Cargo C, Ewing J, Francis S et al.

    British journal of haematology 2023

    PUBMED: 37932932; DOI: 10.1111/bjh.19164

  • Microbial murmurs - decoding hidden conversations between bacteria.

    Kullberg RFJ, Rozday TJ and Haak BW

    Nature reviews. Microbiology 2023

    PUBMED: 37932604; DOI: 10.1038/s41579-023-00991-2

  • Characterizing Different Modes of Interplay between Rap1 and H3 using Inducible H3-depletion Yeast.

    Khamwachirapithak P, Guillaume-Schoepfer D, Chansongkrow P, Teichmann SA, Wigge PA and Charoenswan V

    Journal of molecular biology 2023;168355

    PUBMED: 37935256; DOI: 10.1016/j.jmb.2023.168355

  • Mutational spectra are associated with bacterial niche.

    Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA and Parkhill J

    Nature communications 2023;14;1;7091

    PUBMED: 37925514; PMC: 10625568; DOI: 10.1038/s41467-023-42916-w

  • Tissue-resident B cells orchestrate macrophage polarisation and function.

    Suchanek O, Ferdinand JR, Tuong ZK, Wijeyesinghe S, Chandra A, Clauder AK, Almeida LN, Clare S, Harcourt K, Ward CJ et al.

    Nature communications 2023;14;1;7081

    PUBMED: 37925420; PMC: 10625551; DOI: 10.1038/s41467-023-42625-4

  • Mendelian randomization for cardiovascular diseases: principles and applications.

    Larsson SC, Butterworth AS and Burgess S

    European heart journal 2023

    PUBMED: 37935836; DOI: 10.1093/eurheartj/ehad736

  • BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection.

    Angchagun K, Boonklang P, Chomkatekaew C, Pakdeerat S, Wongsuwan G, Amornchai P, Wuthiekanun V, Panapipat S, Ngernseng T, Waithira N et al.

    Wellcome open research 2023;8;347

    PUBMED: 37928212; PMC: 10624953; DOI: 10.12688/wellcomeopenres.19809.2

  • The genome sequence of a darkling beetle, Lagria hirta (Linnaeus, 1758).

    Sivell O, Levey B, Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;501

    PUBMED: 38434741; PMC: 10905005; DOI: 10.12688/wellcomeopenres.20232.1

  • Genetic support for FDA-approved drugs over the past decade.

    Rusina PV, Falaguera MJ, Romero JMR, McDonagh EM, Dunham I and Ochoa D

    Nature reviews. Drug discovery 2023;22;11;864

    PUBMED: 37803084; DOI: 10.1038/d41573-023-00158-x

  • Genomic epidemiology of Streptococcus pneumoniae serotype 16F lineages.

    Mokaya J, Mellor KC, Murray GGR, Kalizang'oma A, Lekhuleni C, Zar HJ, Nicol MP, McGee L, Bentley SD, Lo SW and Dube F

    Microbial genomics 2023;9;11

    PUBMED: 37917136; DOI: 10.1099/mgen.0.001123

  • Molecular epidemiology of Streptococcus agalactiae in non-pregnant populations: a systematic review.

    Founou LL, Khan UB, Medugu N, Pinto TCA, Darboe S, Chendi Z, Founou RC, To KN, Jamrozy D, Karampatsas K et al.

    Microbial genomics 2023;9;11

    PUBMED: 38019122; DOI: 10.1099/mgen.0.001140

  • CLICK-chemoproteomics and molecular dynamics simulation reveals pregnenolone targets and their binding conformations in Th2 cells.

    Roy S, Roy S, Mahata B, Pramanik J, Hennrich ML, Gavin AC and Teichmann SA

    Frontiers in immunology 2023;14;1229703

    PUBMED: 38022565; PMC: 10644475; DOI: 10.3389/fimmu.2023.1229703

  • The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758).

    Blaxter ML, Spurgeon D, Kille P, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;500

    PUBMED: 38249959; PMC: 10799228; DOI: 10.12688/wellcomeopenres.20178.1

  • Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis.

    Cuénod A, Agnetti J, Seth-Smith HMB, Roloff T, Wälchli D, Shcherbakov D, Akbergenov R, Tschudin-Sutter S, Bassetti S, Siegemund M et al.

    Genome medicine 2023;15;1;89

    PUBMED: 37904175; PMC: 10614358; DOI: 10.1186/s13073-023-01243-x

  • Epidemiology and Risk Factors for Diarrheagenic Escherichia coli Carriage among Children in Northern Ibadan, Nigeria.

    Akinlabi OC, Nwoko EQ, Dada RA, Ekpo S, Omotuyi A, Nwimo CC, Adepoju A, Popoola O, Dougan G, Thomson NR and Okeke IN

    The American journal of tropical medicine and hygiene 2023

    PUBMED: 37903436; DOI: 10.4269/ajtmh.22-0618

  • The genome sequence of the Saxon Wasp, Dolichovespula saxonica (Fabricius, 1793).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;498

    PUBMED: 38371738; PMC: 10873546; DOI: 10.12688/wellcomeopenres.20180.1

  • Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes.

    Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar MS, Sturgess KHM, Williams MJ et al.

    Cell genomics 2023;3;12;100426

    PUBMED: 38116120; PMC: 10726426; DOI: 10.1016/j.xgen.2023.100426

  • The genome sequence of Fabricius' Nomad Bee, Nomada fabriciana (Linne, 1767).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;497

    PUBMED: 38558924; PMC: 10980859; DOI: 10.12688/wellcomeopenres.20184.1

  • The genome sequence of the July Highflyer, Hydriomena furcata (Thunberg, 1784).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;496

    PUBMED: 38813548; PMC: 11134148; DOI: 10.12688/wellcomeopenres.20182.1

  • The genome sequence of the Rock Grayling, Hipparchia semele (Linnaeus, 1758).

    Macgregor CJ, Saccheri IJ, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;495

    PUBMED: 38292065; PMC: 10825418; DOI: 10.12688/wellcomeopenres.20183.1

  • Advancing intercontinental collaboration in human genetics: success story of the African and European Young Investigator Forum.

    Alimohamed MZ, Mnika K, Adadey SM, Barbosa-Matos R, Avram E, Nevondwe P, Akurugu WA, Mupfururirwa W, de Miranda Cerqueira JX, Dore R et al.

    European journal of human genetics : EJHG 2023

    PUBMED: 37880422; DOI: 10.1038/s41431-023-01487-6

  • Complete genome sequence of Paenibacillus sp. VCA1 isolated from crater lake of the El Chichón Volcano.

    Martínez-López NA, Peña-Ocaña BA, García-Contreras R, Maeda T, Rincón-Rosales R, Cazares A, Hoshiko Y and Ruíz-Valdiviezo VM

    Microbiology resource announcements 2023;e0058323

    PUBMED: 37882561; DOI: 10.1128/MRA.00583-23

  • Effects of psoriasis and psoralen exposure on the somatic mutation landscape of the skin.

    Olafsson S, Rodriguez E, Lawson ARJ, Abascal F, Huber AR, Suembuel M, Jones PH, Gerdes S, Martincorena I, Weidinger S et al.

    Nature genetics 2023

    PUBMED: 37884686; DOI: 10.1038/s41588-023-01545-1

  • Oral lactoferrin administration does not impact the diversity or composition of the infant gut microbiota in a Peruvian cohort.

    González L, Paredes Sosa JL, Mosquito S, Filio Y, Romero PE, Ochoa TJ and Tsukayama P

    Microbiology spectrum 2023;e0009623

    PUBMED: 37882571; DOI: 10.1128/spectrum.00096-23

  • Cold-driven hemoglobin evolution in Antarctic notothenioid fishes prior to hemoglobin gene loss in white-blooded icefishes.

    Desvignes T, Bista I, Herrera K, Landes A and Postlethwait JH

    Molecular biology and evolution 2023

    PUBMED: 37879119; DOI: 10.1093/molbev/msad236

  • Clinically relevant mutations in the PhoR sensor kinase of host-adapted Mycobacterium abscessus isolates impact response to acidic pH and virulence.

    Belardinelli JM, Arora D, Avanzi C, Wheat WH, Bryant JM, Spencer JS, Blundell TL, Parkhill J, Floto RA and Jackson M

    Microbiology spectrum 2023;e0158823

    PUBMED: 37874174; DOI: 10.1128/spectrum.01588-23

  • The genome sequence of the Northern Summer Mayfly, Siphlonurus alternatus (Say, 1824).

    Farr A, Macadam CR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;488

    PUBMED: 38707491; PMC: 11069044; DOI: 10.12688/wellcomeopenres.20172.1

  • The genome sequence of the Ruddy Flat-body, Agonopterix subpropinquella (Stainton, 1849).

    Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;487

    PUBMED: 38716048; PMC: 11074695; DOI: 10.12688/wellcomeopenres.20170.1

  • The genome sequence of the slender grass hoverfly, Melanostoma scalare (Fabricius, 1794).

    Hawkes WLS, Wotton KR, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;489

    PUBMED: 38798992; PMC: 11128046; DOI: 10.12688/wellcomeopenres.20171.1

  • A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa.

    Van Puyvelde S, de Block T, Sridhar S, Bawn M, Kingsley RA, Ingelbeen B, Beale MA, Barbé B, Jeon HJ, Mbuyi-Kalonji L et al.

    Nature communications 2023;14;1;6392

    PUBMED: 37872141; PMC: 10593746; DOI: 10.1038/s41467-023-41152-6

  • The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775).

    Boyes D, Phillips D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;485

    PUBMED: 38707490; PMC: 11066531; DOI: 10.12688/wellcomeopenres.20140.1

  • Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization.

    Willems SM, Ng NHJ, Fernandez J, Fine RS, Wheeler E, Wessel J, Kitajima H, Marenne G, Sim X, Yaghootkar H et al.

    Wellcome open research 2023;8;483

    PUBMED: 39280063; PMC: 11399760; DOI: 10.12688/wellcomeopenres.18754.1

  • Large-Scale Meta-GWAS Reveals Common Genetic Factors Linked to Radiation-Induced Acute Toxicities across Cancers.

    Naderi E, Aguado-Barrera ME, Schack LMH, Dorling L, Rattay T, Fachal L, Summersgill H, Martínez-Calvo L, Welsh C, Dudding T et al.

    JNCI cancer spectrum 2023

    PUBMED: 37862240; DOI: 10.1093/jncics/pkad088

  • Europe PMC annotated full-text corpus for gene/proteins, diseases and organisms.

    Yang X, Saha S, Venkatesan A, Tirunagari S, Vartak V and McEntyre J

    Scientific data 2023;10;1;722

    PUBMED: 37857688; DOI: 10.1038/s41597-023-02617-x

  • Nanopore sequencing for malaria molecular surveillance: opportunities and challenges.

    Hamilton WL, Ishengoma DS, Parr JB, Bridges DJ and Barry AE

    Trends in parasitology 2023

    PUBMED: 37865609; DOI: 10.1016/j.pt.2023.09.014

  • The genome sequence of a digger wasp, Ectemnius continuus (Fabricius, 1804).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;469

    PUBMED: 38533438; PMC: 10964002; DOI: 10.12688/wellcomeopenres.20138.1

  • The genome sequence of a drosophilid fruit fly, Chymomyza fuscimana (Drosophilidae) (Zetterstedt, 1838).

    Obbard DJ, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;477

    PUBMED: 39099645; PMC: 11294813; DOI: 10.12688/wellcomeopenres.20122.1

  • The genome sequence of a hoverfly, Sphaerophoria taeniata (Meigen, 1822).

    Falk S, Sudworth J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;474

    PUBMED: 38434738; PMC: 10905010; DOI: 10.12688/wellcomeopenres.19921.1

  • The genome sequence of a soldier beetle, Cantharis rufa (Linnaeus, 1758).

    Sivell O, Sivell D, Geiser M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;478

    PUBMED: 38549709; PMC: 10973763; DOI: 10.12688/wellcomeopenres.19986.1

  • The genome sequence of the Common Spotted Hoverfly, Eupeodes luniger (Meigen, 1822).

    Hawkes WLS, Wotton KR, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;472

    PUBMED: 38798994; PMC: 11128045; DOI: 10.12688/wellcomeopenres.20144.1

  • The genome sequence of the Fruity Milkcap, Lactarius evosmus (Kühner & Romagn., 1954).

    Cullington P, Douglas B, Woof K, Gaya E, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;471

    PUBMED: 38855723; PMC: 11157192; DOI: 10.12688/wellcomeopenres.19910.1

  • The genome sequence of the Large Brook Dun, Ecdyonurus torrentis (Kimmins, 1942).

    Farr A, Macadam C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;468

    PUBMED: 37997584; PMC: 10665603; DOI: 10.12688/wellcomeopenres.20149.1

  • The genome sequence of the Light Emerald, Campaea margaritaria (Linnaeus, 1761).

    Boyes D, Eagles M, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;476

    PUBMED: 38404638; PMC: 10891428; DOI: 10.12688/wellcomeopenres.20136.1

  • Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

    Lythgoe KA, Golubchik T, Hall M, House T, Cahuantzi R, MacIntyre-Cockett G, Fryer H, Thomson L, Nurtay A, Ghafani M et al.

    Proceedings. Biological sciences 2023;290;2009;20231284

    PUBMED: 37848057; PMC: 10581763; DOI: 10.1098/rspb.2023.1284

  • The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes.

    Bond DM, Ortega-Recalde O, Laird MK, Hayakawa T, Richardson KS, Reese FCB, Kyle B, McIsaac-Williams BE, Robertson BC, van Heezik Y et al.

    Nature communications 2023;14;1;6364

    PUBMED: 37848431; DOI: 10.1038/s41467-023-41784-8

  • Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract.

    Connor CH, Zucoloto AZ, Munnoch JT, Yu IL, Corander J, Hoskisson PA, McDonald B and McNally A

    PLoS biology 2023;21;10;e3002329

    PUBMED: 37847672; DOI: 10.1371/journal.pbio.3002329

  • Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study.

    Calland JK, Haukka K, Kpordze SW, Brusah A, Corbella M, Merla C, Samuelsen Ø, Feil EJ, Sassera D, Karikari AB et al.

    The Lancet. Microbe 2023

    PUBMED: 37858320; DOI: 10.1016/S2666-5247(23)00208-2

  • Cryptic susceptibility to penicillin/β-lactamase inhibitor combinations in emerging multidrug-resistant, hospital-adapted Staphylococcus epidermidis lineages.

    Ba X, Raisen CL, Restif O, Cavaco LM, Vingsbo Lundberg C, Lee JYH, Howden BP, Bartels MD, Strommenger B, Harrison EM et al.

    Nature communications 2023;14;1;6479

    PUBMED: 37838722; PMC: 10576800; DOI: 10.1038/s41467-023-42245-y

  • Metadata Improves Segmentation Through Multitasking Elicitation

    Plutenko, Iaroslav, Papkov, Mikhail, Palo, Kaupo, Parts, Leopold and Fishman, Dmytro

    Lecture Notes in Computer Science 2023;14293;147-155

    DOI: 10.1007/978-3-031-45857-6_15

  • The genome sequence of a leaf beetle, Cryptocephalus moraei (Linnaeus, 1758).

    Sivell O, Sivell D, Mitchell R, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;467

    PUBMED: 38680651; PMC: 11053346; DOI: 10.12688/wellcomeopenres.19522.1

  • The genome sequence of a tachinid fly, Cistogaster globosa (Fabricius, 1775).

    Falk S, Lennon R, University of Oxford Genome and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;462

    PUBMED: 39092424; PMC: 11292184; DOI: 10.12688/wellcomeopenres.19924.1

  • The genome sequence of the Common White Wave, Cabera pusaria (Linnaeus, 1758).

    Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;460

    PUBMED: 38868627; PMC: 11167327; DOI: 10.12688/wellcomeopenres.20135.1

  • The genome sequence of the Scarce Umber, Agriopis aurantiaria (Hübner, 1799).

    Boyes D, Mulhair PO, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;463

    PUBMED: 38779060; PMC: 11109570; DOI: 10.12688/wellcomeopenres.19922.1

  • The genome sequence of the silverweed cinquefoil, Potentilla anserina L., 1753.

    Christenhusz MJM, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;464

    PUBMED: 38855725; PMC: 11162522; DOI: 10.12688/wellcomeopenres.19908.1

  • The parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages.

    Cole R, Holroyd N, Tracey A, Berriman M and Viney M

    Nature communications 2023;14;1;6427

    PUBMED: 37833369; PMC: 10575991; DOI: 10.1038/s41467-023-42250-1

  • Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum.

    Kioko M, Pance A, Mwangi S, Goulding D, Kemp A, Rono M, Ochola-Oyier LI, Bull PC, Bejon P, Rayner JC and Abdi AI

    Nature communications 2023;14;1;6447

    PUBMED: 37833314; PMC: 10575976; DOI: 10.1038/s41467-023-42103-x

  • Genomic Heterogeneity of Cryptosporidium parvum Isolates From Children in Bangladesh: Implications for Parasite Biology and Human Infection.

    Carey M, Arju T, Cotton JA, Alam M, Kabir M, Faruque ASG, Haque R, Petri WA and Gilchrist CA

    The Journal of infectious diseases 2023

    PUBMED: 37832036; DOI: 10.1093/infdis/jiad257

  • Nr4a1 marks a distinctive ILC2 activation subset in the mouse inflammatory lung.

    Xu S, Zhang Y, Liu X, Liu H, Zou X, Zhang L, Wang J, Zhang Z, Xu X, Li M et al.

    BMC biology 2023;21;1;218

    PUBMED: 37833706; PMC: 10576290; DOI: 10.1186/s12915-023-01690-3

  • The genome sequence of a chalcid wasp, Gastracanthus pulcherrimus (Westwood, 1833).

    Broad GR, Fletcher C, Januszczak I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;440

    PUBMED: 39290573; PMC: 11406124; DOI: 10.12688/wellcomeopenres.19764.1

  • The genome sequence of black horehound, Ballota nigra L. subsp. foetida (Lam.) Hayek (Lamiaceae).

    Christenhusz MJM, Fay MF, Leitch IJ, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;439

    PUBMED: 39449984; PMC: 11499865; DOI: 10.12688/wellcomeopenres.19763.1

  • The genome sequence of common fleabane, Pulicaria dysenterica (L.) Bernh. (Asteraceae).

    Christenhusz MJM, Fay MF, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;447

    PUBMED: 38009086; PMC: 10674090; DOI: 10.12688/wellcomeopenres.20003.1

  • The genome sequence of the Feathered Ranunculus, Polymixis lichenea (Hübner, 1813).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;444

    PUBMED: 39114812; PMC: 11303942; DOI: 10.12688/wellcomeopenres.20007.1

  • The genome sequence of the Heart and Club moth, Agrotis clavis (Hufnagel, 1766).

    Wawman D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;446

    PUBMED: 39430044; PMC: 11489838; DOI: 10.12688/wellcomeopenres.20125.1

  • The genome sequence of the Ingrailed Clay, Diarsia mendica (Fabricius, 1775).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;448

    PUBMED: 38333733; PMC: 10850848; DOI: 10.12688/wellcomeopenres.20106.1

  • The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).

    Boyes D, Mulley JF, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;441

    PUBMED: 39224879; PMC: 11367073; DOI: 10.12688/wellcomeopenres.19999.1

  • The genome sequence of the small wasp-sawfly, Tenthredo distinguenda (R. Stein, 1885).

    Falk S, Green A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;459

    PUBMED: 38779059; PMC: 11109533; DOI: 10.12688/wellcomeopenres.19523.1

  • The genome sequence of the wood mouse, Apodemus sylvaticus (Linnaeus, 1758).

    Knowles SCL, Raulo A, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;442

    PUBMED: 39099644; PMC: 11294814; DOI: 10.12688/wellcomeopenres.20001.1

  • Precise identification of cell states altered in disease using healthy single-cell references.

    Dann E, Cujba AM, Oliver AJ, Meyer KB, Teichmann SA and Marioni JC

    Nature genetics 2023

    PUBMED: 37828140; DOI: 10.1038/s41588-023-01523-7

  • The genome sequence of a drosophilid fruit fly, Drosophila funebris (Fabricius, 1789).

    Obbard DJ, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;437

    PUBMED: 38798998; PMC: 11126897; DOI: 10.12688/wellcomeopenres.20035.1

  • Cardiovascular Disease Knowledge Portal: A Community Resource for Cardiovascular Disease Research.

    Costanzo MC, Roselli C, Brandes M, Duby M, Hoang Q, Jang D, Koesterer R, Kudtarkar P, Moriondo A, Nguyen T et al.

    Circulation. Genomic and precision medicine 2023;e004181

    PUBMED: 37814896; DOI: 10.1161/CIRCGEN.123.004181

  • The genome sequence of the Swift Louse Fly Crataerina pallida (Latreille, 1812).

    Wawman DC, Candelin G, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;434

    PUBMED: 37920844; PMC: 10618637; DOI: 10.12688/wellcomeopenres.20097.1

  • The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection.

    Chaguza C, Pöntinen AK, Top J, Arredondo-Alonso S, Freitas AR, Novais C, Torres C, Bentley SD, Peixe L, Coque TM et al.

    Microbiology spectrum 2023;e0020123

    PUBMED: 37811975; DOI: 10.1128/spectrum.00201-23

  • Age-dependent topic modeling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk.

    Jiang X, Zhang MJ, Zhang Y, Durvasula A, Inouye M, Holmes C, Price AL and McVean G

    Nature genetics 2023

    PUBMED: 37814053; DOI: 10.1038/s41588-023-01522-8

  • Population-level integration of single-cell datasets enables multi-scale analysis across samples.

    De Donno C, Hediyeh-Zadeh S, Moinfar AA, Wagenstetter M, Zappia L, Lotfollahi M and Theis FJ

    Nature methods 2023

    PUBMED: 37813989; DOI: 10.1038/s41592-023-02035-2

  • Systematic analyses identify modes of action of ten clinically relevant biocides and antibiotic antagonism in Acinetobacter baumannii.

    Li L, Short FL, Hassan KA, Naidu V, Pokhrel A, Nagy SS, Prity FT, Shah BS, Afrin N, Baker S et al.

    Nature microbiology 2023

    PUBMED: 37814070; DOI: 10.1038/s41564-023-01474-z

  • Dietary amino acids and risk of stroke subtypes: a prospective analysis of 356,000 participants in seven European countries.

    Tong TYN, Clarke R, Schmidt JA, Huybrechts I, Noor U, Forouhi NG, Imamura F, Travis RC, Weiderpass E, Aleksandrova K et al.

    European journal of nutrition 2023

    PUBMED: 37804448; DOI: 10.1007/s00394-023-03251-4

  • The genome sequence of a druid fly, Clusia tigrina (Fallén, 1820).

    Crowley LM, Akinmusola RY, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;430

    PUBMED: 38449716; PMC: 10915360; DOI: 10.12688/wellcomeopenres.20109.1

  • The genome sequence of the Crescent Plume, Marasmarcha lunaedactyla (Haworth, 1811).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;431

    PUBMED: 39359327; PMC: 11445637; DOI: 10.12688/wellcomeopenres.20107.1

  • The genome sequence of the Scalloped Oak, Crocallis elinguaria (Linneas, 1758).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;426

    PUBMED: 38644930; PMC: 11031643; DOI: 10.12688/wellcomeopenres.20081.1

  • Baseline TREM-1 Whole Blood Gene Expression Does Not Predict Response to Adalimumab Treatment in Patients with Ulcerative Colitis or Crohn's Disease in the SERENE Studies.

    Verstockt B, Pivorunas V, Mahi NA, Smaoui N, Guay H, Kennedy NA, Goodhand JR, Lin S, Bai BYH, Hanauer SB et al.

    Journal of Crohn's & colitis 2023

    PUBMED: 37801628; DOI: 10.1093/ecco-jcc/jjad170

  • Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection.

    Barmada A, Handfield LF, Godoy-Tena G, de la Calle-Fabregat C, Ciudad L, Arutyunyan A, Andrés-León E, Hoo R, Porter T, Oszlanczi A et al.

    European journal of immunology 2023;e2350633

    PUBMED: 37799110; DOI: 10.1002/eji.202350633

  • TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants.

    Wegert J, Fischer AK, Palhazi B, Treger TD, Hilgers C, Ziegler B, Jung H, Jüttner E, Waha A, Fuchs J et al.

    The Journal of pathology 2023

    PUBMED: 37792584; DOI: 10.1002/path.6206

  • Knowledge, attitudes and decision regret: a longitudinal survey study of participants offered genome sequencing in the 100,000 Genomes Project.

    Peter M, Hammond J, Sanderson SC, Gurasashvili J, Hunter A, Searle B, Patch C, Chitty LS, Hill M and Lewis C

    European journal of human genetics : EJHG 2023

    PUBMED: 37789083; DOI: 10.1038/s41431-023-01470-1

  • Multidrug resistance plasmids underlie clonal expansions and international spread of Salmonella enterica serotype 1,4,[5],12:i:- ST34 in Southeast Asia.

    Chung The H, Pham P, Ha Thanh T, Phuong LVK, Yen NP, Le SH, Vu Thuy D, Chau TTH, Le Phuc H, Ngoc NM et al.

    Communications biology 2023;6;1;1007

    PUBMED: 37789208; PMC: 10547704; DOI: 10.1038/s42003-023-05365-1

  • Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule.

    Bruzos AL, Santamarina M, García-Souto D, Díaz S, Rocha S, Zamora J, Lee Y, Viña-Feás A, Quail MA, Otero I et al.

    Nature cancer 2023

    PUBMED: 37783803; DOI: 10.1038/s43018-023-00641-9

  • The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom.

    Hamilton WL, Coscione S, Maes M, Warne B, Pike LJ, Khokhar FA, Blane B, Brown NM, Gouliouris T, Dougan G et al.

    Microbial genomics 2023;9;10

    PUBMED: 37902454; DOI: 10.1099/mgen.0.001122

  • Genomic, clinical and immunity data join forces for public health.

    Barton A and Colijn C

    Nature reviews. Microbiology 2023;21;10;639

    PUBMED: 37592055; DOI: 10.1038/s41579-023-00965-4

  • Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination.

    Aggarwal D, Rajan D, Bellis KL, Betteridge E, Brennan J, de Sousa C, Carriage Study Team, Parkhill J, Peacock SJ, de Goffau MC et al.

    Microbial genomics 2023;9;10

    PUBMED: 37843887; PMC: 10634443; DOI: 10.1099/mgen.0.001115

  • Baseline expression of immune gene modules in blood is associated with primary response to anti-TNF therapy in Crohn's disease patients.

    Bai BYH, Reppell M, Smaoui N, Waring JF, Pivorunas V, Guay H, Lin S, Chanchlani N, Bewshea C, Goodhand JR et al.

    Journal of Crohn's & colitis 2023

    PUBMED: 37776235; DOI: 10.1093/ecco-jcc/jjad166

  • Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids.

    Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA et al.

    Science (New York, N.Y.) 2023;381;6665;eade2833

    PUBMED: 37769075; DOI: 10.1126/science.ade2833

  • Epigenetic dynamics during capacitation of naïve human pluripotent stem cells.

    Agostinho de Sousa J, Wong CW, Dunkel I, Owens T, Voigt P, Hodgson A, Baker D, Schulz EG, Reik W, Smith A et al.

    Science advances 2023;9;39;eadg1936

    PUBMED: 37774033; PMC: 10541016; DOI: 10.1126/sciadv.adg1936

  • Prioritising cardiovascular disease risk assessment to high risk individuals based on primary care records.

    Chung R, Xu Z, Arnold M, Stevens D, Keogh R, Barrett J, Harrison H, Pennells L, Kim LG, DiAngelantonio E et al.

    PloS one 2023;18;9;e0292240

    PUBMED: 37773956; PMC: 10540947; DOI: 10.1371/journal.pone.0292240

  • Draft genomes of Aeromonas caviae from patients with cholera-like illness during the 2022-2023 cholera outbreak in Malawi.

    Jere KC, Chibwe I, Chaima D, Kasambala W, Mhango C, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Kamng'ona AW, Steele AD et al.

    Microbiology resource announcements 2023;e0058023

    PUBMED: 37768056; DOI: 10.1128/MRA.00580-23

  • Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen.

    Lassalle F, Al-Shalali S, Al-Hakimi M, Njamkepo E, Bashir IM, Dorman MJ, Rauzier J, Blackwell GA, Taylor-Brown A, Beale MA et al.

    Nature microbiology 2023;8;10;1787-1798

    PUBMED: 37770747; PMC: 10539172; DOI: 10.1038/s41564-023-01472-1

  • Single-cell RNA sequencing of human epidermis identifies Lunatic fringe as a novel regulator of the stem cell compartment.

    Negri VA, Louis B, Zijl S, Ganier C, Philippeos C, Ali S, Reynolds G, Haniffa M and Watt FM

    Stem cell reports 2023

    PUBMED: 37832539; DOI: 10.1016/j.stemcr.2023.09.007

  • Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae.

    Kwun MJ, Ion AV, Oggioni MR, Bentley SD and Croucher NJ

    Nucleic acids research 2023

    PUBMED: 37757859; DOI: 10.1093/nar/gkad760

  • Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map.

    Johansen M, Saenko S, Schilthuizen M, Wellcome Sanger Institute Tree of Life Programme, Blaxter M and Davison A

    Heredity 2023;131;5-6;327-337

    PUBMED: 37758900; PMC: 10673960; DOI: 10.1038/s41437-023-00648-z

  • Schistosoma mansoni excretory-secretory products induce protein kinase signalling, hyperkinesia, and stem cell proliferation in the opposite sex.

    Shakir EMN, Rinaldi G, Kirk RS and Walker AJ

    Communications biology 2023;6;1;985

    PUBMED: 37752334; PMC: 10522684; DOI: 10.1038/s42003-023-05333-9

  • Integrative GWAS and co-localisation analysis suggests novel genes associated with age-related multimorbidity.

    West CE, Karim M, Falaguera MJ, Speidel L, Green CJ, Logie L, Schwartzentruber J, Ochoa D, Lord JM, Ferguson MAJ et al.

    Scientific data 2023;10;1;655

    PUBMED: 37749083; PMC: 10520009; DOI: 10.1038/s41597-023-02513-4

  • Targetable NOTCH1 rearrangements in reninoma.

    Treger TD, Lawrence JEG, Anderson ND, Coorens THH, Letunovska A, Abby E, Lee-Six H, Oliver TRW, Al-Saadi R, Tullus K et al.

    Nature communications 2023;14;1;5826

    PUBMED: 37749094; PMC: 10519988; DOI: 10.1038/s41467-023-41118-8

  • Detecting value(s): Digital biomarkers for Alzheimer's disease and the valuation of new diagnostic technologies.

    Costa A and Milne R

    Sociology of health & illness 2023

    PUBMED: 37740673; DOI: 10.1111/1467-9566.13713

  • Genetically predicted androgenic profiles and adverse cardiac markers: a sex-specific Mendelian randomization study.

    Chen JY, Ardissino M, Reddy RK, Mason AM, Raisi-Estabragh Z, Di Angelantonio E, Burgess S and Ng FS

    ESC heart failure 2023

    PUBMED: 37736873; DOI: 10.1002/ehf2.14527

  • Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions.

    Pereira AP, Antunes P, Bierge P, Willems RJL, Corander J, Coque TM, Pich OQ, Peixe L, Freitas AR, Novais C and from the ESCMID Study Group on Food- and Water-borne Infections (EFWISG)

    Microbiology spectrum 2023;e0232423

    PUBMED: 37737589; DOI: 10.1128/spectrum.02324-23

  • The genome sequence of the centipede Strigamia acuminata (Leach, 1816).

    Edgecombe GD, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;420

    PUBMED: 37808388; PMC: 10556566; DOI: 10.12688/wellcomeopenres.19941.1

  • The genome sequence of the common limpet, Patella vulgata (Linnaeus, 1758).

    Hawkins SJ, Mieszkowska N, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;418

    PUBMED: 37994322; PMC: 10663661; DOI: 10.12688/wellcomeopenres.20008.1

  • Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells.

    Gayoso A, Weiler P, Lotfollahi M, Klein D, Hong J, Streets A, Theis FJ and Yosef N

    Nature methods 2023;21;1;50-59

    PUBMED: 37735568; PMC: 10776389; DOI: 10.1038/s41592-023-01994-w

  • The genome sequence of a ground beetle, Leistus spinibarbis (Fabricius, 1775).

    Barclay MVL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;412

    PUBMED: 37881256; PMC: 10594052; DOI: 10.12688/wellcomeopenres.19997.1

  • The genome sequence of a marine yeast, Metschnikowia zobellii (Uden & Cast.-Branco, 1961).

    Cunliffe M, Allen R, Chrismas N, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;411

    PUBMED: 39145284; PMC: 11322703; DOI: 10.12688/wellcomeopenres.19998.1

  • The genome sequence of bittersweet, Solanum dulcamara L. (Solanaceae).

    Christenhusz MJM, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;409

    PUBMED: 37869734; PMC: 10585204; DOI: 10.12688/wellcomeopenres.20004.1

  • The genome sequence of the Autumnal Rustic, Eugnorisma glareosa (Esper, 1788).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;410

    PUBMED: 38779049; PMC: 11109686; DOI: 10.12688/wellcomeopenres.19987.1

  • The genome sequence of the Grey Pine Carpet, Thera obeliscata (Hübner, 1787).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;408

    PUBMED: 38764975; PMC: 11099514; DOI: 10.12688/wellcomeopenres.20005.1

  • Predicting pathogenic protein variants.

    Marsh JA and Teichmann SA

    Science (New York, N.Y.) 2023;eadj8672

    PUBMED: 37725046; DOI: 10.1126/science.adj8672

  • SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

    Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM et al.

    Cell 2023

    PUBMED: 37738970; DOI: 10.1016/j.cell.2023.08.026

  • The genome sequence of the Diamondback Moth, Plutella xylostella (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;404

    PUBMED: 38779055; PMC: 11109710; DOI: 10.12688/wellcomeopenres.20006.1

  • eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs.

    Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ et al.

    PLoS genetics 2023;19;9;e1010932

    PUBMED: 37721944; DOI: 10.1371/journal.pgen.1010932

  • Genomic epidemiology of syphilis in England: a population-based study.

    Beale MA, Thorn L, Cole MJ, Pitt R, Charles H, Ewens M, French P, Guiver M, Page EE, Smit E et al.

    The Lancet. Microbe 2023

    PUBMED: 37722404; DOI: 10.1016/S2666-5247(23)00154-4

  • Genomics reveals complex population history and unexpected diversity of Eurasian otters (Lutra lutra) in Britain relative to genetic methods.

    du Plessis SJ, Blaxter M, Koepfli KP, Chadwick EA and Hailer F

    Molecular biology and evolution 2023

    PUBMED: 37713621; DOI: 10.1093/molbev/msad207

  • DMRT1 regulates human germline commitment.

    Irie N, Lee SM, Lorenzi V, Xu H, Chen J, Inoue M, Kobayashi T, Sancho-Serra C, Drousioti E, Dietmann S et al.

    Nature cell biology 2023;25;10;1439-1452

    PUBMED: 37709822; PMC: 10567552; DOI: 10.1038/s41556-023-01224-7

  • Mosaic BRAF fusions are a recurrent cause of congenital melanocytic naevi targetable by MEK inhibition.

    Martin SB, Polubothu S, Bruzos AL, Kelly G, Horswell S, Sauvadet A, Bryant D, Zecchin D, Riachi M, Michailidis F et al.

    The Journal of investigative dermatology 2023

    PUBMED: 37716647; DOI: 10.1016/j.jid.2023.06.213

  • Principles and challenges of modeling temporal and spatial omics data.

    Velten B and Stegle O

    Nature methods 2023;20;10;1462-1474

    PUBMED: 37710019; DOI: 10.1038/s41592-023-01992-y

  • Identification of genes required for Plasmodium gametocyte-to-sporozoite development in the mosquito vector.

    Ukegbu CV, Gomes AR, Giorgalli M, Campos M, Bailey AJ, Besson TRB, Billker O, Vlachou D and Christophides GK

    Cell host & microbe 2023;31;9;1539-1551.e6

    PUBMED: 37708854; DOI: 10.1016/j.chom.2023.08.010

  • Therapeutic blockade of ER stress and inflammation prevents NASH and progression to HCC.

    Boslem E, Reibe S, Carlessi R, Smeuninx B, Tegegne S, Egan CL, McLennan E, Terry LV, Nobis M, Mu A et al.

    Science advances 2023;9;37;eadh0831

    PUBMED: 37703359; DOI: 10.1126/sciadv.adh0831

  • Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

    Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP et al.

    eLife 2023;12

    PUBMED: 37697804; DOI: 10.7554/eLife.85867

  • Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India.

    Abrudan MI, Shamanna V, Prasanna A, Underwood A, Argimón S, Nagaraj G, Di Gregorio S, Govindan V, Vasanth A, Dharmavaram S et al.

    mSphere 2023;e0018523

    PUBMED: 37698417; DOI: 10.1128/msphere.00185-23

  • Life expectancy associated with different ages at diagnosis of type 2 diabetes in high-income countries: 23 million person-years of observation.

    Emerging Risk Factors Collaboration

    The lancet. Diabetes & endocrinology 2023;11;10;731-742

    PUBMED: 37708900; PMC: 7615299; DOI: 10.1016/S2213-8587(23)00223-1

  • Meeting report: Towards better risk stratification, prevention and therapy of invasive GBS disease, ESPID research meeting May 2022.

    Snoek L, Karampatsas K, Bijlsma MW, Henneke P, Jauneikaite E, Khan UB, Zadoks RN and Le Doare K

    Vaccine 2023

    PUBMED: 37699783; DOI: 10.1016/j.vaccine.2023.09.014

  • Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles.

    Xie X, Sun X, Wang Y, Lehner B and Li X

    Nature communications 2023;14;1;5551

    PUBMED: 37689712; PMC: 10492795; DOI: 10.1038/s41467-023-41188-8

  • The genome sequence of an ichneumon wasp, Ophion slaviceki (Kriechbaumer, 1892).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;397

    PUBMED: 38975568; PMC: 11224712; DOI: 10.12688/wellcomeopenres.19996.1

  • The genome sequence of the Orange-tailed Mining Bee, Andrena haemorrhoa (Fabricius, 1781).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;396

    PUBMED: 38813552; PMC: 11134145; DOI: 10.12688/wellcomeopenres.19982.1

  • The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).

    Boyes D, Mulley JF, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;399

    PUBMED: 38779048; PMC: 11109539; DOI: 10.12688/wellcomeopenres.19988.1

  • A novel mutation in EROS (CYBC1) causes chronic granulomatous disease.

    Mortimer PM, Nichols E, Thomas J, Shanbhag R, Singh N, Coomber EL, Malik TH, Pickering MC, Randzavola L, Rae W et al.

    Clinical immunology (Orlando, Fla.) 2023;255;109761

    PUBMED: 37673227; DOI: 10.1016/j.clim.2023.109761

  • Age at Menopause and the Risk of Stroke: Observational and Mendelian Randomization Analysis in 204 244 Postmenopausal Women.

    Tschiderer L, Peters SAE, van der Schouw YT, van Westing AC, Tong TYN, Willeit P, Seekircher L, Moreno-Iribas C, Huerta JM, Crous-Bou M et al.

    Journal of the American Heart Association 2023;e030280

    PUBMED: 37681566; DOI: 10.1161/JAHA.123.030280

  • Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings.

    Calderon Toledo C, von Mentzer A, Agramont J, Thorell K, Zhou Y, Szabó M, Colque P, Kuhn I, Gutiérrez-Cortez S and Joffré E

    mSystems 2023;e0014123

    PUBMED: 37681982; DOI: 10.1128/msystems.00141-23

  • Homeostatic role of B-1 cells in tissue immunity.

    Suchanek O and Clatworthy MR

    Frontiers in immunology 2023;14;1106294

    PUBMED: 37744333; PMC: 10515722; DOI: 10.3389/fimmu.2023.1106294

  • Tackling the lack of diversity in cancer research.

    Molina-Aguilar C and Robles-Espinoza CD

    Disease models & mechanisms 2023;16;9

    PUBMED: 37681401; DOI: 10.1242/dmm.050275

  • GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification.

    Lagou V, Jiang L, Ulrich A, Zudina L, González KSG, Balkhiyarova Z, Faggian A, Maina JG, Chen S, Todorov PV et al.

    Nature genetics 2023;55;9;1448-1461

    PUBMED: 37679419; PMC: 10484788; DOI: 10.1038/s41588-023-01462-3

  • The genome sequence of the fork-jawed nomad bee, Nomada ruficornis (Linnaeus, 1758).

    Falk S, Monks J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;394

    PUBMED: 38058536; PMC: 10697131; DOI: 10.12688/wellcomeopenres.19928.1

  • The genome sequence of the painted nomad bee, Nomada fucata (Panzer, 1798).

    Falk S, Monks J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;395

    PUBMED: 38385126; PMC: 10879756; DOI: 10.12688/wellcomeopenres.19927.1

  • A second update on mapping the human genetic architecture of COVID-19.

    COVID-19 Host Genetics Initiative

    Nature 2023;621;7977;E7-E26

    PUBMED: 37674002; PMC: 10482689; DOI: 10.1038/s41586-023-06355-3

  • Editorial: Challenges and progressions in herbal genomics.

    Cao Y, Ning Z and Zhao Y

    Frontiers in plant science 2023;14;1273769

    PUBMED: 37746010; PMC: 10513087; DOI: 10.3389/fpls.2023.1273769

  • A drug repurposing screen for whipworms informed by comparative genomics.

    Coghlan A, Partridge FA, Duque-Correa MA, Rinaldi G, Clare S, Seymour L, Brandt C, Mkandawire TT, McCarthy C, Holroyd N et al.

    PLoS neglected tropical diseases 2023;17;9;e0011205

    PUBMED: 37669291; DOI: 10.1371/journal.pntd.0011205

  • Genetically predicted plasma cortisol and common chronic diseases: A Mendelian randomization study.

    Lee WH, Larsson SC, Wood A, Di Angelantonio E, Butterworth AS, Burgess S and Allara E

    Clinical endocrinology 2023

    PUBMED: 37667866; DOI: 10.1111/cen.14966

  • Key attributes of successful research institutes.

    Bradke F, Maartens A and Teichmann SA

    PLoS biology 2023;21;9;e3002267

    PUBMED: 37669250; PMC: 10479891; DOI: 10.1371/journal.pbio.3002267

  • The genome sequence of a satellite fly, Leucophora obtusa (Zetterstedt, 1837).

    Falk S, Lennon R, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;392

    PUBMED: 38283326; PMC: 10811419; DOI: 10.12688/wellcomeopenres.19920.1

  • Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer.

    Dussex N, Tørresen OK, van der Valk T, Le Moullec M, Veiberg V, Tooming-Klunderud A, Skage M, Garmann-Aarhus B, Wood J, Rasmussen JA et al.

    iScience 2023;26;10;107811

    PUBMED: 37744038; PMC: 10514459; DOI: 10.1016/j.isci.2023.107811

  • The genome sequence of a heleomyzid fly, Suillia variegata (Loew, 1862).

    Falk S, Sivell D, Badham XR, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;382

    PUBMED: 39139764; PMC: 11319907; DOI: 10.12688/wellcomeopenres.19630.1

  • The genome sequence of the Common Darter, Sympetrum striolatum (Charpentier, 1840).

    Crowley LM, Price BW, Allan EL, Eagles M, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;389

    PUBMED: 38434743; PMC: 10904951; DOI: 10.12688/wellcomeopenres.19937.1

  • The genome sequence of the dark-edged bee fly, Bombylius major (Linnaeus, 1758).

    Lawniczak MKN, Crowley LM, McAlister E, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;379

    PUBMED: 38533437; PMC: 10964003; DOI: 10.12688/wellcomeopenres.19804.1

  • A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization.

    Almet AA, Yuan H, Annusver K, Ramos R, Liu Y, Wiedemann J, Sorkin DH, Landén NX, Sonkoly E, Haniffa M et al.

    The Journal of investigative dermatology 2023;143;9;1667-1677

    PUBMED: 37612031; DOI: 10.1016/j.jid.2023.03.1679

  • Molecular characterization of Streptococcus pneumoniae causing disease among children in Nigeria during the introduction of PCV10 (GSK).

    Lo SW, Hawkins PA, Jibir B, Hassan-Hanga F, Gambo M, Olaosebikan R, Olanipekun G, Munir H, Kocmich N, Rezac-Elgohary A et al.

    Microbial genomics 2023;9;9

    PUBMED: 37712828; DOI: 10.1099/mgen.0.001094

  • Scrubbing contaminated microbiomes.

    Shao Y

    Nature reviews. Microbiology 2023;21;9;554

    PUBMED: 37415041; DOI: 10.1038/s41579-023-00941-y

  • The legacy of language: What we say, and what people hear, when we talk about genomics.

    Middleton A, Costa A, Milne R, Patch C, Robarts L, Tomlin B, Danson M, Henriques S, Atutornu J, Aidid U et al.

    HGG advances 2023;4;4;100231

    PUBMED: 37869565; PMC: 10589723; DOI: 10.1016/j.xhgg.2023.100231

  • Viruses in Laboratory Drosophila and Their Impact on Host Gene Expression.

    Kuyateh O and Obbard DJ

    Viruses 2023;15;9

    PUBMED: 37766256; DOI: 10.3390/v15091849

  • The genome sequence of the Arctic Skipper, Carterocephalus palaemon (Pallas, 1771).

    Lohse K, Ebdon S, Mackintosh A, Martin S, Saccheri IJ, Bourn NAD, Vila R, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;369

    PUBMED: 39114815; PMC: 11303956; DOI: 10.12688/wellcomeopenres.19573.1

  • The genome sequence of the common toadflax, Linaria vulgaris Mill., 1768.

    Christenhusz MJM, Fisk B, Lu M, Royal Botanic Gardens Kew Genome Acquisition Lab, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;370

    PUBMED: 39257915; PMC: 11384191; DOI: 10.12688/wellcomeopenres.19661.1

  • The genome sequence of the European plaice, Pleuronectes platessa (Linnaeus, 1758).

    Brittain R, Brenen M, McTierney S, Adkins P, Mrowicki R, Harley J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective et al.

    Wellcome open research 2023;8;367

    PUBMED: 38586161; PMC: 10997986; DOI: 10.12688/wellcomeopenres.19397.1

  • The genome sequence of the Figwort Cheilosia, Cheilosia variabilis (Panzer, 1798).

    Crowley LM, Sivell O, Ashworth M, Poole O, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;377

    PUBMED: 37981983; PMC: 10654491; DOI: 10.12688/wellcomeopenres.19851.1

  • The genome sequence of the Notch-wing Button, Acleris emargana (Fabricius, 1775).

    Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;376

    PUBMED: 38873190; PMC: 11170068; DOI: 10.12688/wellcomeopenres.19843.1

  • The genome sequence of the short-fringed mining bee, Andrena dorsata (Kirby, 1802).

    Falk S, Mulley JF, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;373

    PUBMED: 39114811; PMC: 11305455; DOI: 10.12688/wellcomeopenres.19756.1

  • Editorial: Understanding the effects of metabolites and trace minerals on microbes during infection.

    Naderer T, Mu A, Monteith AJ and Wong Fok Lung T

    Frontiers in cellular and infection microbiology 2023;13;1276271

    PUBMED: 37712062; PMC: 10499517; DOI: 10.3389/fcimb.2023.1276271

  • Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma.

    Briest F, Noerenberg D, Hennch C, Yoshida K, Hablesreiter R, Nimo J, Sasca D, Kirchner M, Mansouri L, Inoue Y et al.

    Leukemia 2023;37;11;2237-2249

    PUBMED: 37648814; PMC: 10624633; DOI: 10.1038/s41375-023-02013-9

  • Genome structure and population genomics of the canine heartworm Dirofilaria immitis.

    Gandasegui J, Power RI, Curry E, Ching-Wai Lau D, O'Neill CM, Wolstenholme A, Prichard R, Šlapeta J and Doyle SR

    International journal for parasitology 2023

    PUBMED: 37652224; DOI: 10.1016/j.ijpara.2023.07.006

  • Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer.

    Wong K, Abascal F, Ludwig L, Aupperle-Lellbach H, Grassinger J, Wright CW, Allison SJ, Pinder E, Phillips RM, Romero LP et al.

    Genome biology 2023;24;1;191

    PUBMED: 37635261; PMC: 10464500; DOI: 10.1186/s13059-023-03026-4

  • VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.

    Rangel-Pineros G, Almeida A, Beracochea M, Sakharova E, Marz M, Reyes Muñoz A, Hölzer M and Finn RD

    PLoS computational biology 2023;19;8;e1011422

    PUBMED: 37639475; PMC: 10491390; DOI: 10.1371/journal.pcbi.1011422

  • Propensity of selecting mutant parasites for the antimalarial drug cabamiquine.

    Stadler E, Maiga M, Friedrich L, Thathy V, Demarta-Gatsi C, Dara A, Sogore F, Striepen J, Oeuvray C, Djimdé AA et al.

    Nature communications 2023;14;1;5205

    PUBMED: 37626093; PMC: 10457284; DOI: 10.1038/s41467-023-40974-8

  • Equity, diversity, and inclusion at the Global Alliance for Genomics and Health.

    Skantharajah N, Baichoo S, Boughtwood TF, Casas-Silva E, Chandrasekharan S, Dave SM, Fakhro KA, Falcon de Vargas AB, Gayle SS, Gupta VK et al.

    Cell genomics 2023;3;10;100386

    PUBMED: 37868041; PMC: 10589617; DOI: 10.1016/j.xgen.2023.100386

  • Assembly of 43 human Y chromosomes reveals extensive complexity and variation.

    Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K et al.

    Nature 2023;621;7978;355-364

    PUBMED: 37612510; PMC: 10726138; DOI: 10.1038/s41586-023-06425-6

  • The genome sequence of a drosophilid fruit fly, Hirtodrosophila cameraria (Haliday, 1833).

    Obbard DJ, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;361

    PUBMED: 38868628; PMC: 11167333; DOI: 10.12688/wellcomeopenres.19850.1

  • The genome sequence of the northern bat, Eptesicus nilssonii (Keyserling & Blasius, 1839).

    van der Kooij J, Vernes SC, Teeling EC, Mai M, Johannessen LE, Gundersen G, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;362

    PUBMED: 38774491; PMC: 11106602; DOI: 10.12688/wellcomeopenres.19896.1

  • Artificial intelligence for dementia genetics and omics.

    Bettencourt C, Skene N, Bandres-Ciga S, Anderson E, Winchester LM, Foote IF, Schwartzentruber J, Botia JA, Nalls M, Singleton A et al.

    Alzheimer's & dementia : the journal of the Alzheimer's Association 2023

    PUBMED: 37606627; DOI: 10.1002/alz.13427

  • Convergent somatic evolution commences in utero in a germline ribosomopathy.

    Machado HE, Øbro NF, Williams N, Tan S, Boukerrou AZ, Davies M, Belmonte M, Mitchell E, Baxter EJ, Mende N et al.

    Nature communications 2023;14;1;5092

    PUBMED: 37608017; PMC: 10444798; DOI: 10.1038/s41467-023-40896-5

  • Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum.

    Batugedara G, Lu XM, Hristov B, Abel S, Chahine Z, Hollin T, Williams D, Wang T, Cort A, Lenz T et al.

    Nature communications 2023;14;1;5086

    PUBMED: 37607941; PMC: 10444892; DOI: 10.1038/s41467-023-40883-w

  • The genome sequence of a conopid fly, Thecophora atra (Fabricius, 1775).

    Mitchell R, Falk S, Thomas S, Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective et al.

    Wellcome open research 2023;8;358

    PUBMED: 39139761; PMC: 11320186; DOI: 10.12688/wellcomeopenres.19902.1

  • The genome sequence of the Soprano Pipistrelle, Pipistrellus pygmaeus (Leach, 1825).

    Ruedi M, Vernes SC, Teeling EC, Mai M, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;360

    PUBMED: 38764969; PMC: 11101169; DOI: 10.12688/wellcomeopenres.19895.1

  • Topical repellents for malaria prevention.

    Gabaldón Figueira JC, Wagah MG, Adipo LB, Wanjiku C and Maia MF

    The Cochrane database of systematic reviews 2023;8;8;CD015422

    PUBMED: 37602418; PMC: 10440788; DOI: 10.1002/14651858.CD015422.pub2

  • The genome sequence of a click beetle, Agrypnus murinus (Linnaeus, 1758).

    Crowley LM, Sudworth J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;355

    PUBMED: 39139762; PMC: 11319899; DOI: 10.12688/wellcomeopenres.19847.1

  • The genome sequence of the Acer Sober, Anarsia innoxiella (Gregersen & Karsholt, 2017).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;357

    PUBMED: 39139763; PMC: 11320181; DOI: 10.12688/wellcomeopenres.19514.1

  • The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843).

    Short S, Green Etxabe A, Robinson A, Spurgeon D, Kille P, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;354

    PUBMED: 38618197; PMC: 11015115; DOI: 10.12688/wellcomeopenres.19834.1

  • A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.

    Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L et al.

    Nature communications 2023;14;1;5023

    PUBMED: 37596262; PMC: 10439125; DOI: 10.1038/s41467-023-40679-y

  • Yolk sac cell atlas reveals multiorgan functions during human early development.

    Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Quiroga Londoño M, Mather M, Mende N et al.

    Science (New York, N.Y.) 2023;381;6659;eadd7564

    PUBMED: 37590359; PMC: 7614978; DOI: 10.1126/science.add7564

  • A chromosome-level reference genome for the black-legged kittiwake (Rissa tridactyla), a declining circumpolar seabird.

    Sozzoni M, Ferrer Obiol J, Formenti G, Tigano A, Paris JR, Balacco JR, Jain N, Tilley T, Collins J, Sims Y et al.

    Genome biology and evolution 2023

    PUBMED: 37590950; DOI: 10.1093/gbe/evad153

  • The genome sequence of a ground beetle, Ophonus ardosiacus (Lutshnik, 1922).

    Crowley LM, Sudworth J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;353

    PUBMED: 39036352; PMC: 11259774; DOI: 10.12688/wellcomeopenres.19849.1

  • The genome sequence of the Mullein moth, Shargacucullia verbasci (Linnaeus, 1758).

    Lawniczak MKN, Holland PWH, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;346

    PUBMED: 39165692; PMC: 11333875; DOI: 10.12688/wellcomeopenres.19757.1

  • The genome sequence of the Thick-legged Hoverfly, Syritta pipiens (Linnaeus, 1758).

    Crowley LM, Ashworth M, Wawman DC, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;349

    PUBMED: 39114817; PMC: 11303951; DOI: 10.12688/wellcomeopenres.19848.1

  • Genetic insights into human cortical organization and development through genome-wide analyses of 2,347 neuroimaging phenotypes.

    Warrier V, Stauffer EM, Huang QQ, Wigdor EM, Slob EAW, Seidlitz J, Ronan L, Valk SL, Mallard TT, Grotzinger AD et al.

    Nature genetics 2023;55;9;1483-1493

    PUBMED: 37592024; PMC: 10600728; DOI: 10.1038/s41588-023-01475-y

  • Resolving the spatial architecture of myeloma and its microenvironment at the single-cell level.

    John L, Poos AM, Brobeil A, Schinke C, Huhn S, Prokoph N, Lutz R, Wagner B, Zangari M, Tirier SM et al.

    Nature communications 2023;14;1;5011

    PUBMED: 37591845; PMC: 10435504; DOI: 10.1038/s41467-023-40584-4

  • The genome sequence of the Whirlpool Ramshorn snail, Anisus vortex (Linnaeus, 1758).

    Skipp S, Ablett J, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;344

    PUBMED: 37674878; PMC: 10477736; DOI: 10.12688/wellcomeopenres.19836.1

  • Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly.

    Ferreira IATM, Lee CYC, Foster WS, Abdullahi A, Dratva LM, Tuong ZK, Stewart BJ, Ferdinand JR, Guillaume SM, Potts MOP et al.

    Cell reports 2023;42;8;112991

    PUBMED: 37590132; DOI: 10.1016/j.celrep.2023.112991

  • Discovering genes that affect cognitive ability.

    Young AS and Martin HC

    Trends in genetics : TIG 2023;39;11;810-812

    PUBMED: 37596117; DOI: 10.1016/j.tig.2023.08.001

  • Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii.

    Lucas ER, Nagi SC, Egyir-Yawson A, Essandoh J, Dadzie S, Chabi J, Djogbénou LS, Medjigbodo AA, Edi CV, Kétoh GK et al.

    Nature communications 2023;14;1;4946

    PUBMED: 37587104; PMC: 10432508; DOI: 10.1038/s41467-023-40693-0

  • Chromosomal deletions on 16p11.2 encompassing SH2B1 are associated with accelerated metabolic disease.

    Hanssen R, Auwerx C, Jõeloo M, Sadler MC, Estonian Biobank Research Team, Henning E, Keogh J, Bounds R, Smith M, Firth HV et al.

    Cell reports. Medicine 2023;4;8;101155

    PUBMED: 37586323; DOI: 10.1016/j.xcrm.2023.101155

  • Predicting the impact of sequence motifs on gene regulation using single-cell data.

    Hepkema J, Lee NK, Stewart BJ, Ruangroengkulrith S, Charoensawan V, Clatworthy MR and Hemberg M

    Genome biology 2023;24;1;189

    PUBMED: 37582793; DOI: 10.1186/s13059-023-03021-9

  • The genome sequence of an ichneumonid wasp, Tromatobia lineatoria (Villers, 1789).

    Price BW, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;339

    PUBMED: 39071794; PMC: 11282395; DOI: 10.12688/wellcomeopenres.19830.1

  • The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787).

    Boyes D, Skojec C, Kawahara AY, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;342

    PUBMED: 39145283; PMC: 11322702; DOI: 10.12688/wellcomeopenres.19808.1

  • The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;341

    PUBMED: 39015757; PMC: 11249514; DOI: 10.12688/wellcomeopenres.19837.1

  • The genome sequence of the Brown Argus, Aricia agestis (Denis & Schiffermüller, 1775).

    Hayward A, Lohse K, Vila R, Laetsch DR, Hedlund JSU, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;336

    PUBMED: 38404635; PMC: 10884594; DOI: 10.12688/wellcomeopenres.19784.1

  • Evaluation of interventions to prevent vasovagal reactions among whole blood donors: rationale and design of a large cluster randomised trial.

    McMahon A, Kaptoge S, Walker M, Mehenny S, Gilchrist PT, Sambrook J, Akhtar N, Sweeting M, Wood AM, Stirrups K et al.

    Trials 2023;24;1;512

    PUBMED: 37563721; PMC: 10413586; DOI: 10.1186/s13063-023-07473-z

  • Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.

    Zhao JH, Stacey D, Eriksson N, Macdonald-Dunlop E, Hedman ÅK, Kalnapenkis A, Enroth S, Cozzetto D, Digby-Bell J, Marten J et al.

    Nature immunology 2023;24;9;1540-1551

    PUBMED: 37563310; PMC: 10457199; DOI: 10.1038/s41590-023-01588-w

  • Pooled Genome-Scale CRISPR Screens in Single Cells.

    Schraivogel D, Steinmetz LM and Parts L

    Annual review of genetics 2023

    PUBMED: 37562410; DOI: 10.1146/annurev-genet-072920-013842

  • The Comparative Pathology Workbench: Interactive visual analytics for biomedical data.

    Wicks MN, Glinka M, Hill B, Houghton D, Sharghi M, Ferreira I, Adams D, Din S, Papatheodorou I, Kirkwood K et al.

    Journal of pathology informatics 2023;14;100328

    PUBMED: 37693862; PMC: 10491844; DOI: 10.1016/j.jpi.2023.100328

  • Distinct molecular profiles of skull bone marrow in health and neurological disorders.

    Kolabas ZI, Kuemmerle LB, Perneczky R, Förstera B, Ulukaya S, Ali M, Kapoor S, Bartos LM, Büttner M, Caliskan OS et al.

    Cell 2023;186;17;3706-3725.e29

    PUBMED: 37562402; PMC: 10443631; DOI: 10.1016/j.cell.2023.07.009

  • spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content.

    De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M et al.

    Nature communications 2023;14;1;4788

    PUBMED: 37553326; PMC: 10409775; DOI: 10.1038/s41467-023-40322-w

  • Whole blood DNA methylation changes are associated with anti-TNF drug concentration in patients with Crohn's disease.

    Lin S, Hannon E, Reppell M, Waring JF, Smaoui N, Pivorunas V, Guay H, Chanchlani N, Bewshea C, Bai BYH et al.

    Journal of Crohn's & colitis 2023

    PUBMED: 37551994; DOI: 10.1093/ecco-jcc/jjad133

  • Breathing in danger: how particulate matter pollution is putting the public at risk of lung cancer†.

    Balasubramanian A, John T and Adams DJ

    The Journal of pathology 2023;261;1;1-4

    PUBMED: 37550943; DOI: 10.1002/path.6160

  • High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae).

    Hundsdoerfer AK, Schell T, Patzold F, Wright CJ, Yoshido A, Marec F, Daneck H, Winkler S, Greve C, Podsiadlowski L et al.

    BMC genomics 2023;24;1;443

    PUBMED: 37550607; PMC: 10405479; DOI: 10.1186/s12864-023-09506-y

  • Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender.

    Fleming SJ, Chaffin MD, Arduini A, Akkad AD, Banks E, Marioni JC, Philippakis AA, Ellinor PT and Babadi M

    Nature methods 2023;20;9;1323-1335

    PUBMED: 37550580; DOI: 10.1038/s41592-023-01943-7

  • Time-resolved single-cell RNAseq profiling identifies a novel Fabp5+ subpopulation of inflammatory myeloid cells with delayed cytotoxic profile in chronic spinal cord injury.

    Hamel R, Peruzzotti-Jametti L, Ridley K, Testa V, Yu B, Rowitch D, Marioni JC and Pluchino S

    Heliyon 2023;9;8;e18339

    PUBMED: 37636454; PMC: 10450865; DOI: 10.1016/j.heliyon.2023.e18339

  • Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population.

    Rouskas K, Katsareli EA, Amerikanou C, Dimopoulos AC, Glentis S, Kalantzi A, Skoulakis A, Panousis N, Ongen H, Bielser D et al.

    BMC genomics 2023;24;1;442

    PUBMED: 37543566; PMC: 10403965; DOI: 10.1186/s12864-023-09532-w

  • Topography of mutational signatures in human cancer.

    Otlu B, Díaz-Gay M, Vermes I, Bergstrom EN, Zhivagui M, Barnes M and Alexandrov LB

    Cell reports 2023;42;8;112930

    PUBMED: 37540596; PMC: 10507738; DOI: 10.1016/j.celrep.2023.112930

  • Somatic mutations in facial skin from countries of contrasting skin cancer risk.

    King C, Fowler JC, Abnizova I, Sood RK, Hall MWJ, Szeverényi I, Tham M, Huang J, Young SM, Hall BA et al.

    Nature genetics 2023;55;9;1440-1447

    PUBMED: 37537257; PMC: 10484783; DOI: 10.1038/s41588-023-01468-x

  • Systematic benchmarking of single-cell ATAC-sequencing protocols.

    De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S et al.

    Nature biotechnology 2023;42;6;916-926

    PUBMED: 37537502; PMC: 11180611; DOI: 10.1038/s41587-023-01881-x

  • The genome sequence of the Locust Fly, Stomorhina lunata (Fabricius, 1805).

    Mitchell R, Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;330

    PUBMED: 38779051; PMC: 11109694; DOI: 10.12688/wellcomeopenres.19532.1

  • Africa-specific human genetic variation near CHD1L associates with HIV-1 load.

    McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW et al.

    Nature 2023;620;7976;1025-1030

    PUBMED: 37532928; DOI: 10.1038/s41586-023-06370-4

  • Direct inference and control of genetic population structure from RNA sequencing data.

    Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A et al.

    Communications biology 2023;6;1;804

    PUBMED: 37532769; PMC: 10397182; DOI: 10.1038/s42003-023-05171-9

  • The genome sequence of a stonefly, Nemoura dubitans (Morton, 1894).

    Farr A, Macadam CR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;329

    PUBMED: 39021512; PMC: 11252649; DOI: 10.12688/wellcomeopenres.19771.1

  • Concordance between culture, Molecular Culture and Illumina 16S rRNA gene amplicon sequencing of bone and ulcer bed biopsies in people with diabetic foot osteomyelitis.

    Gramberg MCTT, Knippers C, Lagrand RS, van Hattem JM, de Goffau MC, Budding Budding AE, Davids M, Matamoros S, Nieuwdorp M, de Groot V et al.

    BMC infectious diseases 2023;23;1;505

    PUBMED: 37525143; PMC: 10391922; DOI: 10.1186/s12879-023-08472-w

  • Democratizing knowledge representation with BioCypher.

    Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I et al.

    Nature biotechnology 2023;41;8;1056-1059

    PUBMED: 37337100; DOI: 10.1038/s41587-023-01848-y

  • Direct methylation sequencing.

    Abakir A and Reik W

    Nature chemical biology 2023;19;8;932-933

    PUBMED: 37322154; DOI: 10.1038/s41589-023-01356-9

  • Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya.

    Kigen C, Muraya A, Kyanya C, Kingwara L, Mmboyi O, Hamm T and Musila L

    Microbial genomics 2023;9;8

    PUBMED: 37646415; DOI: 10.1099/mgen.0.001098

  • Sequential roles for red blood cell binding proteins enable phased commitment to invasion for malaria parasites.

    Hart MN, Mohring F, DonVito SM, Thomas JA, Muller-Sienerth N, Wright GJ, Knuepfer E, Saibil HR and Moon RW

    Nature communications 2023;14;1;4619

    PUBMED: 37528099; PMC: 10393984; DOI: 10.1038/s41467-023-40357-z

  • Single-cell omics meets organoid cultures.

    Vento-Tormo R

    Nature reviews. Genetics 2023;24;8;492

    PUBMED: 37308608; DOI: 10.1038/s41576-023-00622-9

  • COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project.

    Shaw F, Minotto A, McTaggart S, Providence A, Harrison P, Paupério J, Rajan J, Burgin J, Cochrane G, Kilias E et al.

    Wellcome open research 2023;7;279

    PUBMED: 39091415; PMC: 11292180; DOI: 10.12688/wellcomeopenres.18499.2

  • Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i).

    Cerca J, Cotoras DD, Santander CG, Bieker VC, Hutchins L, Morin-Lagos J, Prada CF, Kennedy S, Krehenwinkel H, Rominger AJ et al.

    Molecular ecology 2023;32;18;4971-4985

    PUBMED: 37515430; DOI: 10.1111/mec.17082

  • Transposon delivery for CRISPR-based loss-of-function screen in mice identifies NF2 as a cooperating gene involved with the canonical WNT signaling molecular class of hepatocellular carcinoma.

    Keng VW, Chiu AP, To JC, Li XX, Linden MA, Amin K, Moriarity BS and Yusa K

    Heliyon 2023;9;8;e18774

    PUBMED: 37576222; PMC: 10412851; DOI: 10.1016/j.heliyon.2023.e18774

  • A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva.

    Shatilovich A, Gade VR, Pippel M, Hoffmeyer TT, Tchesunov AV, Stevens L, Winkler S, Hughes GM, Traikov S, Hiller M et al.

    PLoS genetics 2023;19;7;e1010798

    PUBMED: 37498820; DOI: 10.1371/journal.pgen.1010798

  • A Transcriptomic Approach to Understand Patient Susceptibility to Pneumonia After Abdominal Surgery.

    Torrance HD, Zhang P, Longbottom ER, Mi Y, Whalley JP, Allcock A, Kwok AJ, Cano-Gamez E, Geoghegan CG, Burnham KL et al.

    Annals of surgery 2023

    PUBMED: 37497667; DOI: 10.1097/SLA.0000000000006050

  • Ghost admixture in eastern gorillas.

    Pawar H, Rymbekova A, Cuadros-Espinoza S, Huang X, de Manuel M, van der Valk T, Lobon I, Alvarez-Estape M, Haber M, Dolgova O et al.

    Nature ecology & evolution 2023;7;9;1503-1514

    PUBMED: 37500909; PMC: 10482688; DOI: 10.1038/s41559-023-02145-2

  • The genome sequence of a riffle beetle, Elmis aenea (Müller, 1806).

    Findlay JDS, Foster G, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;322

    PUBMED: 37990650; PMC: 10660300; DOI: 10.12688/wellcomeopenres.19778.1

  • The genome sequence of common ivy, Hedera helix L., 1753.

    Christenhusz MJM, Bell D, Twyford AD, Royal Botanic Gardens Kew Genome Acquisition Lab, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Plant Genome Sizing collective, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;325

    PUBMED: 38046190; PMC: 10690035; DOI: 10.12688/wellcomeopenres.19662.1

  • The genome sequence of the Oak Hook-tip, Watsonalla binaria (Hufnagel, 1767).

    Boyes D, Chua P, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;324

    PUBMED: 37885811; PMC: 10598455; DOI: 10.12688/wellcomeopenres.19634.1

  • Association of Longer Leukocyte Telomere Length With Cardiac Size, Function, and Heart Failure.

    Aung N, Wang Q, van Duijvenboden S, Burns R, Stoma S, Raisi-Estabragh Z, Ahmet S, Allara E, Wood A, Di Angelantonio E et al.

    JAMA cardiology 2023

    PUBMED: 37494011; DOI: 10.1001/jamacardio.2023.2167

  • Single-cell reference mapping to construct and extend cell-type hierarchies.

    Michielsen L, Lotfollahi M, Strobl D, Sikkema L, Reinders MJT, Theis FJ and Mahfouz A

    NAR genomics and bioinformatics 2023;5;3;lqad070

    PUBMED: 37502708; PMC: 10370450; DOI: 10.1093/nargab/lqad070

  • The genome sequence of the tree of heaven, Ailanthus altissima (Mill.) Swingle, 1916.

    Schley RJ, Leitch IJ, Christenhusz MJM, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Plant Genome Sizing collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;321

    PUBMED: 37663793; PMC: 10472066; DOI: 10.12688/wellcomeopenres.19628.1

  • The genome sequence of the White-legged damselfly, Platycnemis pennipes (Pallas, 1771).

    Price BW, Allan EL, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;320

    PUBMED: 38764968; PMC: 11099507; DOI: 10.12688/wellcomeopenres.19772.1

  • Artificial Intelligence to Predict the BRAF V595E Mutation in Canine Urinary Bladder Urothelial Carcinomas.

    Küchler L, Posthaus C, Jäger K, Guscetti F, van der Weyden L, von Bomhard W, Schmidt JM, Farra D, Aupperle-Lellbach H, Kehl A et al.

    Animals : an open access journal from MDPI 2023;13;15

    PUBMED: 37570213; PMC: 10416820; DOI: 10.3390/ani13152404

  • Using Polygenic Risk Scores for Prioritizing Individuals at Greatest Need of a Cardiovascular Disease Risk Assessment.

    Chung R, Xu Z, Arnold M, Ip S, Harrison H, Barrett J, Pennells L, Kim LG, Di Angelantonio E, Paige E et al.

    Journal of the American Heart Association 2023;e029296

    PUBMED: 37489768; DOI: 10.1161/JAHA.122.029296

  • The human blood fluke, Schistosoma mansoni, harbours bacteria throughout the parasite's life cycle.

    Formenti F, Cortés A, Deiana M, Salter S, Parkhill J, Berriman M, Rinaldi G and Cantacessi C

    The Journal of infectious diseases 2023

    PUBMED: 37487539; DOI: 10.1093/infdis/jiad288

  • An integrated single-cell analysis of human adrenal cortex development.

    Del Valle I, Young MD, Kildisiute G, Ogunbiyi OK, Buonocore F, Simcock IC, Khabirova E, Crespo B, Moreno N, Brooks T et al.

    JCI insight 2023;8;14

    PUBMED: 37440461; DOI: 10.1172/jci.insight.168177

  • Highlights from the 1st European cancer dependency map symposium and workshop.

    Trastulla L, Savino A, Beltrao P, Ciriano IC, Fenici P, Garnett MJ, Guerini I, Bigas NL, Mattaj I, Petsalaki E et al.

    FEBS letters 2023

    PUBMED: 37487655; DOI: 10.1002/1873-3468.14699

  • Novel pneumococcal capsule type 33E results from the inactivation of glycosyltransferase WciE in vaccine type 33F.

    Ganaie FA, Saad JS, Lo SW, McGee L, van Tonder AJ, Hawkins PA, Calix JJ, Bentley SD and Nahm MH

    The Journal of biological chemistry 2023;105085

    PUBMED: 37495106; DOI: 10.1016/j.jbc.2023.105085

  • The genome sequence of the springtail Allacma fusca (Linnaeus, 1758).

    Jaron KS, Berg MP, Ellers J, Hodson CN, Ross L, University of Oxford and Wytham Woods Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;319

    PUBMED: 37593568; PMC: 10427803; DOI: 10.12688/wellcomeopenres.19690.1

  • The genome sequence of a scale worm, Harmothoe impar (Johnston, 1839).

    Adkins P, Mrowicki R, Harley J, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;315

    PUBMED: 37786780; PMC: 10541532; DOI: 10.12688/wellcomeopenres.19570.1

  • The genome sequence of an ichneumonid wasp, Campoletis raptor (Zetterstedt, 1838).

    Broad GR, Fletcher C, Januszczak I, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;313

    PUBMED: 38818412; PMC: 11137483; DOI: 10.12688/wellcomeopenres.19738.1

  • The genome sequence of the Pine Hawkmoth, Sphinx pinastri (Linneaus 1758).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;312

    PUBMED: 38173562; PMC: 10762287; DOI: 10.12688/wellcomeopenres.19731.1

  • Clonal origin of KMT2A wild-type lineage-switch leukemia following CAR-T cell and blinatumomab therapy.

    Coorens THH, Collord G, Treger TD, Adams S, Mitchell E, Newman B, Getz G, Godfrey AL, Bartram J and Behjati S

    Nature cancer 2023;4;8;1095-1101

    PUBMED: 37474833; PMC: 10447231; DOI: 10.1038/s43018-023-00604-0

  • Computational analysis of peripheral blood smears detects disease-associated cytomorphologies.

    de Almeida JG, Gudgin E, Besser M, Dunn WG, Cooper J, Haferlach T, Vassiliou GS and Gerstung M

    Nature communications 2023;14;1;4378

    PUBMED: 37474506; PMC: 10359268; DOI: 10.1038/s41467-023-39676-y

  • Radioactive contamination in feral dogs in the Chernobyl exclusion zone: Population body-burden survey and implications for human radiation exposure.

    Hecla J, Kambarian E, Tubbs R, McKinley C, Berliner AJ, Russell K, Spatola G, Chertok J, Braun W, Hank N et al.

    PloS one 2023;18;7;e0283206

    PUBMED: 37471331; PMC: 10358910; DOI: 10.1371/journal.pone.0283206

  • The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822).

    Falk S, Gorše I, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;311

    PUBMED: 39071792; PMC: 11282393; DOI: 10.12688/wellcomeopenres.19569.1

  • Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors.

    Campbell LI, Nwezeobi J, van Brunschot SL, Kaweesi T, Seal SE, Swamy RAR, Namuddu A, Maslen GL, Mugerwa H, Armean IM et al.

    BMC genomics 2023;24;1;408

    PUBMED: 37468834; PMC: 10357772; DOI: 10.1186/s12864-023-09474-3

  • Mutations observed in somatic evolution reveal underlying gene mechanisms.

    Hall MWJ, Shorthouse D, Alcraft R, Jones PH and Hall BA

    Communications biology 2023;6;1;753

    PUBMED: 37468606; PMC: 10356810; DOI: 10.1038/s42003-023-05136-y

  • Pharmacological inhibition of METTL3 impacts specific haematopoietic lineages.

    Sturgess K, Yankova E, Vijayabaskar MS, Isobe T, Rak J, Kucinski I, Barile M, Webster NA, Eleftheriou M, Hannah R et al.

    Leukemia 2023;37;10;2133-2137

    PUBMED: 37464070; PMC: 10539174; DOI: 10.1038/s41375-023-01965-2

  • Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters.

    Louis M, Korlević P, Nykänen M, Archer F, Berrow S, Brownlow A, Lorenzen ED, O'Brien J, Post K, Racimo F et al.

    Nature communications 2023;14;1;4020

    PUBMED: 37463880; PMC: 10354069; DOI: 10.1038/s41467-023-39532-z

  • A transcriptional and regulatory map of mouse somite maturation.

    Ibarra-Soria X, Thierion E, Mok GF, Münsterberg AE, Odom DT and Marioni JC

    Developmental cell 2023

    PUBMED: 37499658; DOI: 10.1016/j.devcel.2023.07.003

  • Seroprevalence of non-typhoidal Salmonella disease and associated factors in children in Mukuru settlement in Nairobi County, Kenya.

    Peter SK, Mutiso JM, Ngetich M, Mbae C and Kariuki S

    PloS one 2023;18;7;e0288015

    PUBMED: 37459317; PMC: 10351689; DOI: 10.1371/journal.pone.0288015

  • The genome sequence of the variegated scallop, Mimachlamys varia (Linnaeus, 1758).

    Fletcher C, Spencer Jones ME, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;307

    PUBMED: 39021514; PMC: 11252643; DOI: 10.12688/wellcomeopenres.19643.1

  • Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites.

    Lansink LIM, Skinner OP, Engel JA, Lee HJ, Soon MSF, Williams CG, SheelaNair A, Pernold CPS, Laohamonthonkul P, Akter J et al.

    mBio 2023;e0112923

    PUBMED: 37449844; DOI: 10.1128/mbio.01129-23

  • The human placenta exhibits a unique transcriptomic void.

    Gong S, Gaccioli F, Aye ILMH, Avellino G, Cook E, Lawson ARJ, Harvey LMR, Smith GCS and Charnock-Jones DS

    Cell reports 2023;42;7;112800

    PUBMED: 37453066; DOI: 10.1016/j.celrep.2023.112800

  • Inhibitory IL-10-producing CD4+ T cells are T-bet-dependent and facilitate cytomegalovirus persistence via coexpression of arginase-1.

    Clement M, Ladell K, Miners KL, Marsden M, Chapman L, Cardus Figueras A, Scott J, Andrews R, Clare S, Kriukova VV et al.

    eLife 2023;12

    PUBMED: 37440306; PMC: 10344424; DOI: 10.7554/eLife.79165

  • The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;303

    PUBMED: 39026607; PMC: 11255552; DOI: 10.12688/wellcomeopenres.19650.1

  • Models of KPTN-related disorder implicate mTOR signalling in cognitive and overgrowth phenotypes.

    Levitin MO, Rawlins LE, Sanchez-Andrade G, Arshad OA, Collins SC, Sawiak SJ, Iffland PH, Andersson MHL, Bupp C, Cambridge EL et al.

    Brain : a journal of neurology 2023

    PUBMED: 37437211; DOI: 10.1093/brain/awad231

  • The genome sequence of the Light Brocade, Lacanobia w-latinum (Hufnagel, 1766).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;299

    PUBMED: 37663789; PMC: 10472056; DOI: 10.12688/wellcomeopenres.19653.1

  • The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).

    Boyes D, Crowley LM, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;302

    PUBMED: 39026606; PMC: 11255550; DOI: 10.12688/wellcomeopenres.19646.1

  • The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).

    Boyes D, Sims I, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;298

    PUBMED: 37663792; PMC: 10472059; DOI: 10.12688/wellcomeopenres.19648.1

  • Genome sequence for the thick topshell, Phorcus lineatus (da Costa, 1778).

    Mieszkowska N, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;296

    PUBMED: 37621576; PMC: 10444997; DOI: 10.12688/wellcomeopenres.19485.1

  • Genome-wide association study of treatment-related toxicity two years following radiotherapy for breast cancer.

    Jandu HK, Veal CD, Fachal L, Luccarini C, Aguado-Barrera ME, Altabas M, Azria D, Baten A, Bourgier C, Bultijnck R et al.

    Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 2023;109806

    PUBMED: 37437607; DOI: 10.1016/j.radonc.2023.109806

  • Mge-cluster: a reference-free approach for typing bacterial plasmids.

    Arredondo-Alonso S, Gladstone RA, Pöntinen AK, Gama JA, Schürch AC, Lanza VF, Johnsen PJ, Samuelsen Ø, Tonkin-Hill G and Corander J

    NAR genomics and bioinformatics 2023;5;3;lqad066

    PUBMED: 37435357; PMC: 10331934; DOI: 10.1093/nargab/lqad066

  • OME-Zarr: a cloud-optimized bioimaging file format with international community support.

    Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE et al.

    Histochemistry and cell biology 2023

    PUBMED: 37428210; DOI: 10.1007/s00418-023-02209-1

  • Peptide location fingerprinting identifies structural alterations within basement membrane components in ageing kidney.

    Eckersley A, Morais MR, Ozols M and Lennon R

    Matrix biology : journal of the International Society for Matrix Biology 2023

    PUBMED: 37437747; DOI: 10.1016/j.matbio.2023.07.001

  • The genome sequence of a tachinid fly, Tachina lurida (Fabricius, 1781).

    Falk S, Smith MN, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;288

    PUBMED: 37635753; PMC: 10448141; DOI: 10.12688/wellcomeopenres.19635.1

  • The genome sequence of the Powdered Quaker, Orthosia gracilis (Schiffermüller, 1775).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;290

    PUBMED: 37635752; PMC: 10448147; DOI: 10.12688/wellcomeopenres.19644.1

  • SUNi mutagenesis: Scalable and uniform nicking for efficient generation of variant libraries.

    Mighell TL, Toledano I and Lehner B

    PloS one 2023;18;7;e0288158

    PUBMED: 37418460; PMC: 10328370; DOI: 10.1371/journal.pone.0288158

  • De novo detection of somatic mutations in high-throughput single-cell profiling data sets.

    Muyas F, Sauer CM, Valle-Inclán JE, Li R, Rahbari R, Mitchell TJ, Hormoz S and Cortés-Ciriano I

    Nature biotechnology 2023

    PUBMED: 37414936; DOI: 10.1038/s41587-023-01863-z

  • Investigation of the impact of clonal hematopoiesis on severity and pathophysiology of COVID-19 in rhesus macaques.

    Shin TH, Zhou Y, Lee BC, Hong SG, Andrew SF, Flynn BJ, Gagne M, Todd JM, Moore IN, Cook A et al.

    Frontiers in veterinary science 2023;10;1182197

    PUBMED: 37483285; PMC: 10358770; DOI: 10.3389/fvets.2023.1182197

  • Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia.

    Anderson ND, Birch J, Accogli T, Criado I, Khabirova E, Parks C, Wood Y, Young MD, Porter T, Richardson R et al.

    Nature medicine 2023;29;7;1700-1709

    PUBMED: 37407840; PMC: 10353931; DOI: 10.1038/s41591-023-02415-3

  • An Atlas of Variant Effects to understand the genome at nucleotide resolution.

    Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM and Hurles ME

    Genome biology 2023;24;1;147

    PUBMED: 37394429; PMC: 10316620; DOI: 10.1186/s13059-023-02986-x

  • Acetaldehyde and defective mismatch repair increase colonic tumours in a Lynch Syndrome model with Aldh1b1 inactivation.

    Cerretelli G, Zhou Y, Müller MF, Adams DJ and Arends MJ

    Disease models & mechanisms 2023

    PUBMED: 37395714; DOI: 10.1242/dmm.050240

  • Cell-level reference maps for the human body take shape.

    Vento-Tormo R and Vilarrasa-Blasi R

    Nature 2023;619;7970;467-468

    PUBMED: 37468591; DOI: 10.1038/d41586-023-01817-0

  • Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years.

    Roberts LW, Enoch DA, Khokhar F, Blackwell GA, Wilson H, Warne B, Gouliouris T, Iqbal Z and Török ME

    Microbial genomics 2023;9;7

    PUBMED: 37405394; DOI: 10.1099/mgen.0.001048

  • Nasopharyngeal competition dynamics are likely to be altered following vaccine introduction: bacteriocin prevalence and diversity among Icelandic and Kenyan pneumococci.

    Butler MEB, Jansen van Rensburg MJ, Karani A, Mvera B, Akech D, Akter A, Forrest C, van Tonder AJ, Quirk SJ, Haraldsson G et al.

    Microbial genomics 2023;9;7

    PUBMED: 37436819; DOI: 10.1099/mgen.0.001060

  • What Difference Can Public Engagement in Genome Editing Make, and for Whom?

    Milne R, Aidid U, Atutornu J, Bircan T, Boraschi D, Costa A, Henriques S, Patch C and Middleton A

    The American journal of bioethics : AJOB 2023;23;7;58-60

    PUBMED: 37339292; DOI: 10.1080/15265161.2023.2207545

  • Resolving therapy resistance mechanisms in multiple myeloma by multi-omics subclone analysis.

    Poos AM, Prokoph N, Przybilla MJ, Mallm JP, Steiger S, Seufert I, John L, Tirier SM, Bauer K, Baumann A et al.

    Blood 2023

    PUBMED: 37390336; DOI: 10.1182/blood.2023019758

  • A novel multifunctional radioprotective strategy using P7C3 as a countermeasure against ionizing radiation-induced bone loss.

    Wei F, Tuong ZK, Omer M, Ngo C, Asiatico J, Kinzel M, Pugazhendhi AS, Khaled AR, Ghosh R and Coathup M

    Bone research 2023;11;1;34

    PUBMED: 37385982; PMC: 10310858; DOI: 10.1038/s41413-023-00273-w

  • Biglycan and reduced glycolysis are associated with breast cancer cell dormancy in the brain.

    Sunderland A, Williams J, Andreou T, Rippaus N, Fife C, James F, Kartika YD, Speirs V, Carr I, Droop A and Lorger M

    Frontiers in oncology 2023;13;1191980

    PUBMED: 37456245; PMC: 10339804; DOI: 10.3389/fonc.2023.1191980

  • Clonal hematopoiesis with DNMT3A and PPM1D mutations impairs regeneration in autologous stem cell transplant recipients.

    Stelmach P, Richter S, Sauer S, Fabre MA, Gu M, Rohde C, Janssen M, Liebers N, Proynova R, Weinhold N et al.

    Haematologica 2023

    PUBMED: 37381752; DOI: 10.3324/haematol.2023.282992

  • The genome sequence of the Broken-barred Carpet, Electrophaes corylata (Thunberg, 1792).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;283

    PUBMED: 37766852; PMC: 10521117; DOI: 10.12688/wellcomeopenres.19627.1

  • The genome sequence of the Grey Poplar Bell, Epinotia nisella (Clerck, 1759).

    Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;281

    PUBMED: 38779050; PMC: 11109716; DOI: 10.12688/wellcomeopenres.19621.1

  • The genome sequence of the Orange Footman, Eilema sororcula (Hufnagel, 1766).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;282

    PUBMED: 38434736; PMC: 10905117; DOI: 10.12688/wellcomeopenres.19626.1

  • A landscape of response to drug combinations in non-small cell lung cancer.

    Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK et al.

    Nature communications 2023;14;1;3830

    PUBMED: 37380628; PMC: 10307832; DOI: 10.1038/s41467-023-39528-9

  • Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly.

    Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P et al.

    Nature 2023;619;7970;555-562

    PUBMED: 37380776; PMC: 7614783; DOI: 10.1038/s41586-023-06268-1

  • Transinteractome analysis reveals distinct niche requirements for isotype-based plasma cell subsets in the bone marrow.

    Bonaud A, Larraufie P, Khamyath M, Szachnowski U, Flint SM, Brunel-Meunier N, Delhommeau F, Munier A, Lönnberg T, Toffano-Nioche C et al.

    European journal of immunology 2023;e2250334

    PUBMED: 37377335; DOI: 10.1002/eji.202250334

  • The genome sequence of the Dark Spectacle, Abrostola triplasia (Linnaeus, 1758).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;278

    PUBMED: 37766851; PMC: 10521094; DOI: 10.12688/wellcomeopenres.19624.1

  • The genome sequence of the hoverfly, Epistrophella euchroma (Kowarz, 1885).

    Falk S, Woodcock KJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;279

    PUBMED: 38938786; PMC: 11208851; DOI: 10.12688/wellcomeopenres.19622.1

  • The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879).

    Saccheri IJ, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;280

    PUBMED: 37600587; PMC: 10439359; DOI: 10.12688/wellcomeopenres.19432.1

  • Computational workflow for investigating highly variable genes in single-cell RNA-seq across multiple time points and cell types.

    Arora JK, Opasawatchai A, Teichmann SA, Matangkasombut P and Charoensawan V

    STAR protocols 2023;4;3;102387

    PUBMED: 37379219; DOI: 10.1016/j.xpro.2023.102387

  • The genome sequence of the oyster mushroom, Pleurotus ostreatus ((Jacq.) P. Kummer, 1871).

    Wright R, Woof K, Royal Botanic Gardens Kew Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;277

    PUBMED: 38784713; PMC: 11112307; DOI: 10.12688/wellcomeopenres.19578.1

  • GREENER principles for environmentally sustainable computational science.

    Lannelongue L, Aronson HG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G and Inouye M

    Nature computational science 2023;3;6;514-521

    PUBMED: 38177425; DOI: 10.1038/s43588-023-00461-y

  • Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles.

    Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K et al.

    Nature neuroscience 2023;26;7;1208-1217

    PUBMED: 37365313; PMC: 10322709; DOI: 10.1038/s41593-023-01361-0

  • Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh.

    Taylor-Brown A, Afrad MH, Khan AI, Lassalle F, Islam MT, Tanvir NA, Thomson NR and Qadri F

    Nature communications 2023;14;1;3773

    PUBMED: 37355673; PMC: 10290697; DOI: 10.1038/s41467-023-39415-3

  • The genome sequence of a tachinid fly, Nowickia ferox (Panzer, 1809).

    Falk S, Raper C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;275

    PUBMED: 38919871; PMC: 11196934; DOI: 10.12688/wellcomeopenres.19575.1

  • The genome sequence of the greater pipefish, Syngnathus acus (Linnaeus, 1758).

    Scott-Somme K, McTierney S, Brittain R, Perry F, Brenen M, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;274

    PUBMED: 38868629; PMC: 11167339; DOI: 10.12688/wellcomeopenres.19528.1

  • Human 8-cell embryo-like cells from pluripotent stem cells.

    Taubenschmid-Stowers J and Reik W

    Current opinion in genetics & development 2023;81;102066

    PUBMED: 37356343; DOI: 10.1016/j.gde.2023.102066

  • Recent evolution of a maternally-acting sex-determining supergene in a fly with single-sex broods.

    Baird RB, Urban JM, Mongue AJ, Jaron KS, Hodson CN, Grewoldt M, Martin SH and Ross L

    Molecular biology and evolution 2023

    PUBMED: 37352554; DOI: 10.1093/molbev/msad148

  • What have we learned from a case of convalescent plasma treatment in a two-time kidney transplant recipient COVID-19 patient? A case report from the perspective of viral load evolution and immune response.

    Aldunate F, Fajardo A, Ibañez N, Rammauro F, Daghero H, Arce R, Ferla D, Pereira-Gomez M, Salazar C, Iraola G et al.

    Frontiers in nephrology 2023;3;1132763

    PUBMED: 37675346; PMC: 10479756; DOI: 10.3389/fneph.2023.1132763

  • The genome sequence of the spider, Parasteatoda lunata (Clerck, 1757).

    Oxford G, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;271

    PUBMED: 37766855; PMC: 10521088; DOI: 10.12688/wellcomeopenres.19585.1

  • Prevalence of NUDT15 genetic variants and incidence of thiopurine-induced leukopenia in Inflammatory Bowel Disease: A systematic review and meta-analysis.

    Yu N, Sriranganathan D, Walker GJ, Sazonovs A, Wilding H, Roberts C, Kennedy NA, Ahmad T, Boyapati RK, Ding NS and Segal JP

    Journal of Crohn's & colitis 2023

    PUBMED: 37346013; DOI: 10.1093/ecco-jcc/jjad107

  • The genome sequence of the Large Sharp-tail Bee, Coelioxys conoideus (Illiger,1806).

    Taylor SC, Luker S, Hawkes WLS, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;259

    PUBMED: 38938787; PMC: 11208850; DOI: 10.12688/wellcomeopenres.19507.1

  • The genome sequence of the Muslin moth, Diaphora mendica (Clerck, 1759).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;257

    PUBMED: 38268612; PMC: 10806365; DOI: 10.12688/wellcomeopenres.19540.1

  • What do you most hope spatial molecular profiling will help us understand? Part 1.

    Theis FJ, Dar D, Vento-Tormo R, Vicković S, Wang L, Kagohara LT, Rendeiro AF and Joyce JA

    Cell systems 2023;14;6;423-427

    PUBMED: 37348459; DOI: 10.1016/j.cels.2023.05.009

  • The relevance of competing risk adjustment in cardiovascular risk prediction models for clinical practice.

    Hageman SHJ, Dorresteijn JAN, Pennells L, van Smeden M, Bots ML, Di Angelantonio E and Visseren FLJ

    European journal of preventive cardiology 2023

    PUBMED: 37338108; DOI: 10.1093/eurjpc/zwad202

  • Activity of Ivermectin and Its Metabolites against Asexual Blood Stage Plasmodium falciparum and Its Interactions with Antimalarial Drugs.

    Yipsirimetee A, Tipthara P, Hanboonkunupakarn B, Tripura R, Lek D, Kümpornsin K, Lee MCS, Sattabongkot J, Dondorp AM, White NJ et al.

    Antimicrobial agents and chemotherapy 2023;e0173022

    PUBMED: 37338381; DOI: 10.1128/aac.01730-22

  • Imputation of ancient human genomes.

    Sousa da Mota B, Rubinacci S, Cruz Dávalos DI, G Amorim CE, Sikora M, Johannsen NN, Szmyt MH, Włodarczak P, Szczepanek A, Przybyła MM et al.

    Nature communications 2023;14;1;3660

    PUBMED: 37339987; PMC: 10282092; DOI: 10.1038/s41467-023-39202-0

  • Natural genetic variation in the pheromone production of C. elegans.

    Lee D, Fox BW, Palomino DF, Panda O, Tenjo FJ, Koury EJ, Evans KS, Stevens L, Rodrigues PR, Kolodziej AR et al.

    Proceedings of the National Academy of Sciences of the United States of America 2023;120;26;e2221150120

    PUBMED: 37339205; DOI: 10.1073/pnas.2221150120

  • Predicting Mutations Generated by Cas9, Base Editing, and Prime Editing in Mammalian Cells.

    Weller J, Pallaseni A, Koeppel J and Parts L

    The CRISPR journal 2023

    PUBMED: 37339457; DOI: 10.1089/crispr.2023.0016

  • Germline de novo mutations in families with Mendelian cancer syndromes caused by defects in DNA repair.

    Sherwood K, Ward JC, Soriano I, Martin L, Campbell A, Rahbari R, Kafetzopoulos I, Sproul D, Green A, Sampson JR et al.

    Nature communications 2023;14;1;3636

    PUBMED: 37336879; PMC: 10279637; DOI: 10.1038/s41467-023-39248-0

  • Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London.

    Bailey C, Sanderson T, Townsley H, Goldman J, Black JRM, Young G, Goldstone R, Fowler AS, Ward S, Jackson DJ et al.

    Lancet (London, England) 2023

    PUBMED: 37348521; DOI: 10.1016/S0140-6736(23)00917-0

  • The genome sequence of the Cloaked Minor, Mesoligia furuncula (Denis & Schiffermüller, 1775).

    Boyes D, Broad GR, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;251

    PUBMED: 38855721; PMC: 11162523; DOI: 10.12688/wellcomeopenres.19537.1

  • Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty.

    Ardern Z

    Journal of molecular evolution 2023

    PUBMED: 37326679; DOI: 10.1007/s00239-023-10122-3

  • Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58.

    Rutanga JP, de Block T, Cuypers WL, Cafmeyer J, Peeters M, Umumararungu E, Ngabonziza JCS, Rucogoza A, Vandenberg O, Martiny D et al.

    PLoS neglected tropical diseases 2023;17;6;e0011285

    PUBMED: 37327220; DOI: 10.1371/journal.pntd.0011285

  • An atlas of rabbit development as a model for single-cell comparative genomics.

    Ton MN, Keitley D, Theeuwes B, Guibentif C, Ahnfelt-Rønne J, Andreassen TK, Calero-Nieto FJ, Imaz-Rosshandler I, Pijuan-Sala B, Nichols J et al.

    Nature cell biology 2023;25;7;1061-1072

    PUBMED: 37322291; DOI: 10.1038/s41556-023-01174-0

  • Evolutionary and functional history of the Escherichia coli K1 capsule.

    Arredondo-Alonso S, Blundell-Hunter G, Fu Z, Gladstone RA, Fillol-Salom A, Loraine J, Cloutman-Green E, Johnsen PJ, Samuelsen Ø, Pöntinen AK et al.

    Nature communications 2023;14;1;3294

    PUBMED: 37322051; PMC: 10272209; DOI: 10.1038/s41467-023-39052-w

  • Genotoxic aldehyde stress prematurely ages hematopoietic stem cells in a p53-driven manner.

    Wang M, Brandt LTL, Wang X, Russell H, Mitchell E, Kamimae-Lanning AN, Brown JM, Dingler FA, Garaycoechea JI, Isobe T et al.

    Molecular cell 2023

    PUBMED: 37348497; DOI: 10.1016/j.molcel.2023.05.035

  • The genome sequence of a carabid beetle, Nebria salina (Fairmaire & Laboulbène, 1854).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;247

    PUBMED: 38196772; PMC: 10774627; DOI: 10.12688/wellcomeopenres.19372.1

  • The genome sequence of the Black-tipped Ermine, Yponomeuta plumbella (Denis & Schiffermüller, 1775).

    Boyes D, Sims I, Lees D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;246

    PUBMED: 38046192; PMC: 10690038; DOI: 10.12688/wellcomeopenres.19368.1

  • The genome sequence of the Common Emerald, Hemithea aestivaria (Hübner, 1789).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;243

    PUBMED: 38764972; PMC: 11099506; DOI: 10.12688/wellcomeopenres.19542.1

  • The genome sequence of the Coxcomb Prominent, Ptilodon capucinus (Linnaeus, 1758).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;242

    PUBMED: 38779054; PMC: 11109679; DOI: 10.12688/wellcomeopenres.19539.1

  • The genome sequence of the Minor Shoulder-knot, Brachylomia viminalis (Fabricius, 1777).

    Boyes D, Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;245

    PUBMED: 38434742; PMC: 10905140; DOI: 10.12688/wellcomeopenres.19538.1

  • A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.

    Cuypers WL, Meysman P, Weill FX, Hendriksen RS, Beyene G, Wain J, Nair S, Chattaway MA, Perez-Sepulveda BM, Ceyssens PJ et al.

    Nature communications 2023;14;1;3517

    PUBMED: 37316492; PMC: 10267216; DOI: 10.1038/s41467-023-38902-x

  • The genome sequence of a soldierfly, Nemotelus nigrinus (Fallén, 1817).

    Sivell O, Mitchell R, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;240

    PUBMED: 38798995; PMC: 11128052; DOI: 10.12688/wellcomeopenres.19534.1

  • The genome sequence of the Ashy Button, Acleris sparsana (Denis & Schiffermüller, 1775).

    Boyes D, Lees DC, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;241

    PUBMED: 38434745; PMC: 10907877; DOI: 10.12688/wellcomeopenres.19533.1

  • Mapping interindividual dynamics of innate immune response at single-cell resolution.

    Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI et al.

    Nature genetics 2023;55;6;1066-1075

    PUBMED: 37308670; PMC: 10260404; DOI: 10.1038/s41588-023-01421-y

  • Next Generation Sequencing Workshop at the Royal Society of Medicine (London, May 2022): How genomics is on the path to modernizing Genetic Toxicology.

    Lynch AM, Zanoni TB, Salk JJ, Martincorena I, Young RR, Kucab J, Valentine CC, Yauk C, Escobar PA, Witt KL et al.

    Mutagenesis 2023

    PUBMED: 37300447; DOI: 10.1093/mutage/gead012

  • Rare genetic variants impact muscle strength.

    Huang Y, Bodnar D, Chen CY, Sanchez-Andrade G, Sanderson M, Biogen Biobank Team, Shi J, Meilleur KG, Hurles ME, Gerety SS et al.

    Nature communications 2023;14;1;3449

    PUBMED: 37301943; PMC: 10257725; DOI: 10.1038/s41467-023-39247-1

  • Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

    Bista I, Wood JMD, Desvignes T, McCarthy SA, Matschiner M, Ning Z, Tracey A, Torrance J, Sims Y, Chow W et al.

    Nature communications 2023;14;1;3412

    PUBMED: 37296119; PMC: 10256766; DOI: 10.1038/s41467-023-38567-6

  • International genetic counseling: What do genetic counselors actually do?

    Ormond KE, Hayward L, Wessels TM, Patch C and Weil J

    Journal of genetic counseling 2023

    PUBMED: 37296526; DOI: 10.1002/jgc4.1735

  • Risk Factors of Secondary Cardiovascular Events in a Multi-Ethnic Asian Population with Acute Myocardial Infarction: A Retrospective Cohort Study from Malaysia.

    Ismail SR, Mohammad MSF, Butterworth AS, Chowdhury R, Danesh J, Di Angelantonio E, Griffin SJ, Pennells L, Wood AM, Md Noh MF and Shah SA

    Journal of cardiovascular development and disease 2023;10;6

    PUBMED: 37367415; DOI: 10.3390/jcdd10060250

  • Taurine deficiency as a driver of aging.

    Singh P, Gollapalli K, Mangiola S, Schranner D, Yusuf MA, Chamoli M, Shi SL, Lopes Bastos B, Nair T, Riermeier A et al.

    Science (New York, N.Y.) 2023;380;6649;eabn9257

    PUBMED: 37289866; DOI: 10.1126/science.abn9257

  • An integrated cell atlas of the lung in health and disease.

    Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M et al.

    Nature medicine 2023;29;6;1563-1577

    PUBMED: 37291214; PMC: 10287567; DOI: 10.1038/s41591-023-02327-2

  • South Asian medical cohorts reveal strong founder effects and high rates of homozygosity.

    Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J et al.

    Nature communications 2023;14;1;3377

    PUBMED: 37291107; PMC: 10250394; DOI: 10.1038/s41467-023-38766-1

  • The Promise of Single-Cell RNA Sequencing to Redefine the Understanding of Crohn's Disease Fibrosis Mechanisms.

    Campbell I, Glinka M, Shaban F, Kirkwood KJ, Nadalin F, Adams D, Papatheodorou I, Burger A, Baldock RA, Arends MJ and Din S

    Journal of clinical medicine 2023;12;12

    PUBMED: 37373578; DOI: 10.3390/jcm12123884

  • DECIPHER: Improving Genetic Diagnosis Through Dynamic Integration of Genomic and Clinical Data.

    Foreman J, Perrett D, Mazaika E, Hunt SE, Ware JS and Firth HV

    Annual review of genomics and human genetics 2023

    PUBMED: 37285546; DOI: 10.1146/annurev-genom-102822-100509

  • The genome sequence of the Lichen Button, Acleris literana (Linnaeus, 1758).

    Crowley LM, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;232

    PUBMED: 38249958; PMC: 10799227; DOI: 10.12688/wellcomeopenres.19481.1

  • The genome sequence of the variegated flesh fly, Sarcophaga variegata (Scopoli, 1763).

    Falk S, Mulley JF, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;234

    PUBMED: 38510269; PMC: 10951566; DOI: 10.12688/wellcomeopenres.19483.1

  • The genome sequence of the Willow Beauty, Peribatodes rhomboidaria (Denis & Schiffermüller, 1775).

    Boyes D, Eagles M, Holland PWH, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;233

    PUBMED: 38249957; PMC: 10799229; DOI: 10.12688/wellcomeopenres.19479.1

  • Improving 10-year cardiovascular risk prediction in apparently healthy people: flexible addition of risk modifiers on top of SCORE2.

    Hageman SH, Petitjean C, Pennells L, Kaptoge S, Pajouheshnia R, Tillmann T, Blaha MJ, McClelland RL, Matsushita K, Nambi V et al.

    European journal of preventive cardiology 2023

    PUBMED: 37264679; DOI: 10.1093/eurjpc/zwad187

  • Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization.

    Carey ME, Dyson ZA, Argimón S, Cerdeira L, Yeats C, Aanensen D, Mboowa G, Baker S, Tessema SK, Smith AM et al.

    Open forum infectious diseases 2023;10;Suppl 1;S38-S46

    PUBMED: 37274533; PMC: 10236510; DOI: 10.1093/ofid/ofad044

  • Early stage gastric adenocarcinoma: clinical and molecular landscapes.

    Hirata Y, Noorani A, Song S, Wang L and Ajani JA

    Nature reviews. Clinical oncology 2023;20;7;453-469

    PUBMED: 37264184; DOI: 10.1038/s41571-023-00767-w

  • Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity.

    Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Anscome C, Zuza A, Roberts AP, Heinz E, Thomson NR and Feasey NA

    Microbial genomics 2023;9;6

    PUBMED: 37314322; DOI: 10.1099/mgen.0.001035

  • Research software engineering accelerates the translation of biomedical research for health.

    Horsfall D, Cool J, Hettrick S, Pisco AO, Hong NC and Haniffa M

    Nature medicine 2023;29;6;1313-1316

    PUBMED: 37264207; DOI: 10.1038/s41591-023-02353-0

  • Trans-ethnic polygenic risk scores for body mass index: An international hundred K+ cohorts consortium study.

    Qu HQ, Connolly JJ, Kraft P, Long J, Pereira A, Flatley C, Turman C, Prins B, Mentch F, Lotufo PA et al.

    Clinical and translational medicine 2023;13;6;e1291

    PUBMED: 37337639; PMC: 10280047; DOI: 10.1002/ctm2.1291

  • Unexpected fishy microbiomes.

    Limborg MT, Chua PYS and Rasmussen JA

    Nature reviews. Microbiology 2023;21;6;346

    PUBMED: 36914757; DOI: 10.1038/s41579-023-00879-1

  • A Roadmap for the Human Gut Cell Atlas.

    Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F et al.

    Nature reviews. Gastroenterology & hepatology 2023;20;9;597-614

    PUBMED: 37258747; PMC: 10527367; DOI: 10.1038/s41575-023-00784-1

  • Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli.

    Miles SL, Torraca V, Dyson ZA, López-Jiménez AT, Foster-Nyarko E, Lobato-Márquez D, Jenkins C, Holt KE and Mostowy S

    mBio 2023;e0088223

    PUBMED: 37255304; DOI: 10.1128/mbio.00882-23

  • FIRRM/C1orf112 mediates resolution of homologous recombination intermediates in response to DNA interstrand crosslinks.

    Mazouzi A, Moser SC, Abascal F, van den Broek B, Del Castillo Velasco-Herrera M, van der Heijden I, Hekkelman M, Drenth AP, van der Burg E, Kroese LJ et al.

    Science advances 2023;9;22;eadf4409

    PUBMED: 37256941; DOI: 10.1126/sciadv.adf4409

  • PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production.

    Ebstein F, Küry S, Most V, Rosenfelt C, Scott-Boyer MP, van Woerden GM, Besnard T, Papendorf JJ, Studencka-Turski M, Wang T et al.

    Science translational medicine 2023;15;698;eabo3189

    PUBMED: 37256937; PMC: 10506367; DOI: 10.1126/scitranslmed.abo3189

  • HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion.

    Lin JQ, Khuperkar D, Pavlou S, Makarchuk S, Patikas N, Lee FC, Zbiegly JM, Kang J, Field SF, Bailey DM et al.

    The EMBO journal 2023;e113168

    PUBMED: 37248947; DOI: 10.15252/embj.2022113168

  • Trophic ecology of Octopus vulgaris paralarvae along the Iberian Canary current eastern boundary upwelling system.

    Roura Á, Doyle SR, Castro-Bugallo A, Hall NE, Gonzalez ÁF and Strugnell JM

    Scientific reports 2023;13;1;8744

    PUBMED: 37253926; PMC: 10229560; DOI: 10.1038/s41598-023-35206-4

  • Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation.

    Adlam D, Berrandou TE, Georges A, Nelson CP, Giannoulatou E, Henry J, Ma L, Blencowe M, Turley TN, Yang ML et al.

    Nature genetics 2023;55;6;964-972

    PUBMED: 37248441; PMC: 10260398; DOI: 10.1038/s41588-023-01410-1

  • Polygenic prediction of preeclampsia and gestational hypertension.

    Honigberg MC, Truong B, Khan RR, Xiao B, Bhatta L, Vy HMT, Guerrero RF, Schuermans A, Selvaraj MS, Patel AP et al.

    Nature medicine 2023;29;6;1540-1549

    PUBMED: 37248299; PMC: 10330886; DOI: 10.1038/s41591-023-02374-9

  • Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum.

    Kümpornsin K, Kochakarn T, Yeo T, Okombo J, Luth MR, Hoshizaki J, Rawat M, Pearson RD, Schindler KA, Mok S et al.

    Nature communications 2023;14;1;3059

    PUBMED: 37244916; PMC: 10224993; DOI: 10.1038/s41467-023-38774-1

  • The genome sequence of the fish leech, Piscicola geometra (Linnaeus, 1761).

    Doe J, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;229

    PUBMED: 38813549; PMC: 11134150; DOI: 10.12688/wellcomeopenres.19488.1

  • The impact of rare protein coding genetic variation on adult cognitive function.

    Chen CY, Tian R, Ge T, Lam M, Sanchez-Andrade G, Singh T, Urpa L, Liu JZ, Sanderson M, Rowley C et al.

    Nature genetics 2023;55;6;927-938

    PUBMED: 37231097; PMC: 10260403; DOI: 10.1038/s41588-023-01398-8

  • Stabilized mosaic single-cell data integration using unshared features.

    Ghazanfar S, Guibentif C and Marioni JC

    Nature biotechnology 2023

    PUBMED: 37231260; DOI: 10.1038/s41587-023-01766-z

  • The genome sequence of the surf clam, Spisula solida (Linnaeus, 1758).

    Holmes A, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;227

    PUBMED: 38764973; PMC: 11101916; DOI: 10.12688/wellcomeopenres.19486.1

  • Metagenomic analysis and antibacterial activity of kefir microorganisms.

    González-Orozco BD, García-Cano I, Escobar-Zepeda A, Jiménez-Flores R and Álvarez VB

    Journal of food science 2023

    PUBMED: 37222548; DOI: 10.1111/1750-3841.16614

  • Epitopes in the capsular polysaccharide and the porin OmpK36 receptors are required for bacteriophage infection of Klebsiella pneumoniae.

    Dunstan RA, Bamert RS, Tan KS, Imbulgoda U, Barlow CK, Taiaroa G, Pickard DJ, Schittenhelm RB, Dougan G, Short FL and Lithgow T

    Cell reports 2023;42;6;112551

    PUBMED: 37224021; DOI: 10.1016/j.celrep.2023.112551

  • Origin and segregation of the human germline.

    Castillo-Venzor A, Penfold CA, Morgan MD, Tang WW, Kobayashi T, Wong FC, Bergmann S, Slatery E, Boroviak TE, Marioni JC and Surani MA

    Life science alliance 2023;6;8

    PUBMED: 37217306; PMC: 10203729; DOI: 10.26508/lsa.202201706

  • The genome sequence of the Chevron, Eulithis testata (Linnaeus, 1761).

    Lees DC, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;223

    PUBMED: 38798991; PMC: 11128040; DOI: 10.12688/wellcomeopenres.19433.1

  • The genome sequence of the Large Scabious Mining Bee, Andrena hattorfiana (Fabricius, 1775).

    Falk S, Tan KT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;224

    PUBMED: 37744731; PMC: 10511852; DOI: 10.12688/wellcomeopenres.19438.1

  • Population genetics of group B Streptococcus from maternal carriage in an ethnically diverse community in London.

    Jamrozy D, Gopal Rao G, Feltwell T, Lamagni T, Khanna P, Efstratiou A, Parkhill J and Bentley SD

    Frontiers in microbiology 2023;14;1185753

    PUBMED: 37275158; PMC: 10233156; DOI: 10.3389/fmicb.2023.1185753

  • The genome sequence of a cockchafer, Melolontha melolontha (Linnaeus, 1758).

    Ashworth M, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;222

    PUBMED: 38618196; PMC: 11015117; DOI: 10.12688/wellcomeopenres.19434.1

  • Advances in malaria pharmacology and the online guide to MALARIA PHARMACOLOGY: IUPHAR review 38.

    Armstrong JF, Campo B, Alexander SPH, Arendse LB, Cheng X, Davenport AP, Faccenda E, Fidock DA, Godinez-Macias KP, Harding SD et al.

    British journal of pharmacology 2023

    PUBMED: 37197802; DOI: 10.1111/bph.16144

  • Between noise and function: Toward a taxonomy of the non-canonical translatome.

    Ardern Z and Uz-Zaman MH

    Cell systems 2023;14;5;343-345

    PUBMED: 37201506; DOI: 10.1016/j.cels.2023.04.004

  • Caecilian genomes reveal the molecular basis of adaptation, and convergent evolution of limblessness in snakes and caecilians.

    Ovchinnikov V, Uliano-Silva M, Wilkinson M, Wood J, Smith M, Oliver K, Sims Y, Torrance J, Suh A, McCarthy SA et al.

    Molecular biology and evolution 2023

    PUBMED: 37194566; DOI: 10.1093/molbev/msad102

  • Methods and Insights from Single-Cell Expression Quantitative Trait Loci.

    Kang JB, Raveane A, Nathan A, Soranzo N and Raychaudhuri S

    Annual review of genomics and human genetics 2023

    PUBMED: 37196361; DOI: 10.1146/annurev-genom-101422-100437

  • The genome sequence of the White-backed Marble, Hedya salicella (Linnaeus, 1758).

    Boyes D, Goate Z, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;219

    PUBMED: 38903245; PMC: 11187532; DOI: 10.12688/wellcomeopenres.19436.1

  • Integrative Genetic Manipulation of Plasmodium cynomolgi Reveals Multidrug Resistance-1 Y976F Associated With Increased In Vitro Susceptibility to Mefloquine.

    Ward KE, Christensen P, Racklyeft A, Dhingra SK, Chua ACY, Remmert C, Suwanarusk R, Matheson J, Blackman MJ, Kaneko O et al.

    The Journal of infectious diseases 2023;227;10;1121-1126

    PUBMED: 36478252; PMC: 10175063; DOI: 10.1093/infdis/jiac469

  • Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1.

    Amambua-Ngwa A, Button-Simons KA, Li X, Kumar S, Brenneman KV, Ferrari M, Checkley LA, Haile MT, Shoue DA, McDew-White M et al.

    Nature microbiology 2023;8;7;1213-1226

    PUBMED: 37169919; PMC: 10322710; DOI: 10.1038/s41564-023-01377-z

  • A draft human pangenome reference.

    Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ et al.

    Nature 2023;617;7960;312-324

    PUBMED: 37165242; PMC: 10172123; DOI: 10.1038/s41586-023-05896-x

  • The genome sequence of the Large Ear, Amphipoea lucens (Freyer, 1845).

    Lees D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;204

    PUBMED: 37469855; PMC: 10352624; DOI: 10.12688/wellcomeopenres.19287.1

  • The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758).

    Boyes D, Lewis OT, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;207

    PUBMED: 38764970; PMC: 11101918; DOI: 10.12688/wellcomeopenres.19213.1

  • The genome sequence of the Pinion-streaked Snout, Schrankia costaestrigalis (Stephens, 1834).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;203

    PUBMED: 38779056; PMC: 11109538; DOI: 10.12688/wellcomeopenres.19402.1

  • The genome sequence of the Red-green Carpet, Chloroclysta siterata (Hufnagel, 1767).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;206

    PUBMED: 38779046; PMC: 11109689; DOI: 10.12688/wellcomeopenres.19301.1

  • High-throughput deep learning variant effect prediction with Sequence UNET.

    Dunham AS, Beltrao P and AlQuraishi M

    Genome biology 2023;24;1;110

    PUBMED: 37161576; DOI: 10.1186/s13059-023-02948-3

  • Gut microbiome transitions across generations in different ethnicities in an urban setting-the HELIUS study.

    van der Vossen EWJ, Davids M, Bresser LRF, Galenkamp H, van den Born BH, Zwinderman AH, Levin E, Nieuwdorp M and de Goffau MC

    Microbiome 2023;11;1;99

    PUBMED: 37158898; DOI: 10.1186/s40168-023-01488-z

  • Predicting cellular responses to complex perturbations in high-throughput screens.

    Lotfollahi M, Klimovskaia Susmelj A, De Donno C, Hetzel L, Ji Y, Ibarra IL, Srivatsan SR, Naghipourfar M, Daza RM, Martin B et al.

    Molecular systems biology 2023;19;6;e11517

    PUBMED: 37154091; PMC: 10258562; DOI: 10.15252/msb.202211517

  • Risk factors for a serious adverse outcome in neonates: a retrospective cohort study of vaginal births.

    Jindal S, Steer PJ, Savvidou M, Draycott T, Dixon-Woods M, Wood A and Kim LG

    BJOG : an international journal of obstetrics and gynaecology 2023

    PUBMED: 37156754; DOI: 10.1111/1471-0528.17531

  • The genome sequence of Molossusnigricans (Chiroptera, Molossidae; Miller, 1902).

    Simmons NB, Ingala MR, Pieri M, Volkert TL, Singh LN, Philip P, Lindsey LL, Zhang N, Gray JL, O'Toole BP et al.

    Wellcome open research 2023;8;198

    PUBMED: 37600588; PMC: 10435916; DOI: 10.12688/wellcomeopenres.18724.1

  • The genome sequence of the Feathered Gothic, Tholera decimalis (Poda, 1761).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;200

    PUBMED: 37674876; PMC: 10477738; DOI: 10.12688/wellcomeopenres.19395.1

  • Functional heterogeneity of human skin-resident memory T cells in health and disease.

    Strobl J and Haniffa M

    Immunological reviews 2023

    PUBMED: 37144705; DOI: 10.1111/imr.13213

  • A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta).

    Squires TE, Rödin-Mörch P, Formenti G, Tracey A, Abueg L, Brajuka N, Jarvis E, Halapi EC, Melsted P, Höglund J and Magnússon KP

    G3 (Bethesda, Md.) 2023

    PUBMED: 37141262; DOI: 10.1093/g3journal/jkad099

  • Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs).

    Cocker D, Sammarro M, Chidziwisano K, Elviss N, Jacob ST, Kajumbula H, Mugisha L, Musoke D, Musicha P, Roberts AP et al.

    Wellcome open research 2023;7;55

    PUBMED: 38817338; PMC: 11137479; DOI: 10.12688/wellcomeopenres.17581.2

  • The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage.

    Snaith AE, Dunn SJ, Moran RA, Newton PN, Dance DAB, Davong V, Kuenzli E, Kantele A, Corander J and McNally A

    Microbial genomics 2023;9;5

    PUBMED: 37171860; DOI: 10.1099/mgen.0.001000

  • A novel resource to study endometriosis at the single-cell level.

    García-Alonso L, Zondervan KT and Vento-Tormo R

    Nature reviews. Endocrinology 2023;19;5;256-257

    PUBMED: 36864151; DOI: 10.1038/s41574-023-00814-7

  • The scverse project provides a computational ecosystem for single-cell omics data analysis.

    Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, Gayoso A, Kats I, Koutrouli M, Scverse Community, Berger B et al.

    Nature biotechnology 2023;41;5;604-606

    PUBMED: 37037904; DOI: 10.1038/s41587-023-01733-8

  • Bacteriophage discovery to advance biotechnology and biotherapeutics.

    Mu A and Lawley TD

    Nature reviews. Microbiology 2023;21;5;279

    PUBMED: 36807633; DOI: 10.1038/s41579-023-00870-w

  • Challenges in prokaryote pangenomics.

    Tonkin-Hill G, Corander J and Parkhill J

    Microbial genomics 2023;9;5

    PUBMED: 37227251; DOI: 10.1099/mgen.0.001021

  • Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates.

    Claessens A, Stewart LB, Drury E, Ahouidi AD, Amambua-Ngwa A, Diakite M, Kwiatkowski DP, Awandare GA and Conway DJ

    Microbial genomics 2023;9;5

    PUBMED: 37204422; DOI: 10.1099/mgen.0.001009

  • NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource.

    Dicks J, Fazal MA, Oliver K, Grayson NE, Turnbull JD, Bane E, Burnett E, Deheer-Graham A, Holroyd N, Kaushal D et al.

    Microbial genomics 2023;9;5

    PUBMED: 37194944; DOI: 10.1099/mgen.0.000976

  • Ruxolitinib Versus Best Available Therapy for Polycythemia Vera Intolerant or Resistant to Hydroxycarbamide in a Randomized Trial.

    Harrison CN, Nangalia J, Boucher R, Jackson A, Yap C, O'Sullivan J, Fox S, Ailts I, Dueck AC, Geyer HL et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2023;JCO2201935

    PUBMED: 37126762; DOI: 10.1200/JCO.22.01935

  • Screening for functional regulatory variants in open chromatin using GenIE-ATAC.

    Cooper S, Schwartzentruber J, Coomber EL, Wu Q and Bassett A

    Nucleic acids research 2023

    PUBMED: 37125635; DOI: 10.1093/nar/gkad332

  • A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants.

    Nishii K, Möller M, Foster RG, Forrest LL, Kelso N, Barber S, Howard C and Hart ML

    Plant methods 2023;19;1;41

    PUBMED: 37120601; PMC: 10148486; DOI: 10.1186/s13007-023-01009-x

  • The genome sequence of the Lesser Swallow Prominent, Pheosia gnoma (Fabricius, 1777).

    Boyes D, Goate Z, University of Oxford and Wytham Woods Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;192

    PUBMED: 37351546; PMC: 10282565; DOI: 10.12688/wellcomeopenres.19411.1

  • Mitigating age-related somatic mutation burden.

    Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY et al.

    Trends in molecular medicine 2023

    PUBMED: 37121869; DOI: 10.1016/j.molmed.2023.04.002

  • Using ChEMBL to Complement Schistosome Drug Discovery.

    Padalino G, Coghlan A, Pagliuca G, Forde-Thomas JE, Berriman M and Hoffmann KF

    Pharmaceutics 2023;15;5

    PUBMED: 37242601; PMC: 10220823; DOI: 10.3390/pharmaceutics15051359

  • The genome sequence of the Lesser Broad-bordered Yellow Underwing, Noctua janthe (Borkhausen, 1792).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;189

    PUBMED: 37840885; PMC: 10570690; DOI: 10.12688/wellcomeopenres.19412.1

  • A nutritional biomarker score of the Mediterranean diet and incident type 2 diabetes: Integrated analysis of data from the MedLey randomised controlled trial and the EPIC-InterAct case-cohort study.

    Sobiecki JG, Imamura F, Davis CR, Sharp SJ, Koulman A, Hodgson JM, Guevara M, Schulze MB, Zheng JS, Agnoli C et al.

    PLoS medicine 2023;20;4;e1004221

    PUBMED: 37104291; DOI: 10.1371/journal.pmed.1004221

  • The genome sequence of Clancy's Rustic, Caradrina kadenii (Freyer, 1836).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;187

    PUBMED: 37829675; PMC: 10565420; DOI: 10.12688/wellcomeopenres.19286.1

  • The genome sequence of the Diamond-back Marble, Eudemis profundana (Denis & Schiffermüller, 1775).

    Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;184

    PUBMED: 38434748; PMC: 10904960; DOI: 10.12688/wellcomeopenres.19370.1

  • The genome sequence of the orange ladybird, Halyzia sedecimguttata (Linnaeus, 1758).

    Crowley LM, Barclay M, Roy HE, Brown PMJ, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;186

    PUBMED: 37476650; PMC: 10354457; DOI: 10.12688/wellcomeopenres.19369.1

  • The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;185

    PUBMED: 38404637; PMC: 10891429; DOI: 10.12688/wellcomeopenres.19371.1

  • Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.

    Wijdeveld M, van Olst N, van der Vossen EWJ, de Brauw M, Acherman YIZ, de Goffau MC, Gerdes VEA and Nieuwdorp M

    Obesity surgery 2023

    PUBMED: 37093508; DOI: 10.1007/s11695-023-06610-6

  • Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis.

    Kwok AJ, Allcock A, Ferreira RC, Cano-Gamez E, Smee M, Burnham KL, Zurke YX, Emergency Medicine Research Oxford (EMROx), McKechnie S, Mentzer AJ et al.

    Nature immunology 2023;24;5;767-779

    PUBMED: 37095375; DOI: 10.1038/s41590-023-01490-5

  • Unraveling the genomic complexity of sylvatic mosquitoes in changing Neotropical environments.

    Loaiza JR, Bennett KL, Miller MJ and De León LF

    Current opinion in biotechnology 2023;81;102944

    PUBMED: 37099930; DOI: 10.1016/j.copbio.2023.102944

  • Single-cell RNA sequencing uncovers heterogeneous transcriptional signatures in tumor-infiltrated dendritic cells in prostate cancer.

    Feriz AM, Khosrojerdi A, Lotfollahi M, Shamsaki N, GhasemiGol M, HosseiniGol E, Fereidouni M, Rohban MH, Sebzari AR, Saghafi S et al.

    Heliyon 2023;9;5;e15694

    PUBMED: 37144199; PMC: 10151421; DOI: 10.1016/j.heliyon.2023.e15694

  • Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development.

    Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W et al.

    Genes 2023;14;5

    PUBMED: 37239317; PMC: 10218269; DOI: 10.3390/genes14050957

  • Distribution and molecular evolution of the anti-CRISPR family AcrIF7.

    Figueroa W, Cazares A, Cazares D, Wu Y, de la Cruz A, Welch M, Kameyama L, Nobrega FL and Guarneros G

    PLoS biology 2023;21;4;e3002072

    PUBMED: 37083687; DOI: 10.1371/journal.pbio.3002072

  • Putting hornets on the genomic map.

    Favreau E, Cini A, Taylor D, Câmara Ferreira F, Bentley MA, Cappa F, Cervo R, Privman E, Schneider J, Thiéry D et al.

    Scientific reports 2023;13;1;6232

    PUBMED: 37085574; PMC: 10121689; DOI: 10.1038/s41598-023-31932-x

  • The evolution of two transmissible cancers in Tasmanian devils.

    Stammnitz MR, Gori K, Kwon YM, Harry E, Martin FJ, Billis K, Cheng Y, Baez-Ortega A, Chow W, Comte S et al.

    Science (New York, N.Y.) 2023;380;6642;283-293

    PUBMED: 37079675; DOI: 10.1126/science.abq6453

  • Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta.

    Caron V, Chassaing N, Ragge N, Boschann F, Ngu AM, Meloche E, Chorfi S, Lakhani SA, Ji W, Steiner L et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2023;25;8;100856

    PUBMED: 37092537; PMC: 10757562; DOI: 10.1016/j.gim.2023.100856

  • pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls.

    Snajder R, Leger A, Stegle O and Bonder MJ

    Genome biology 2023;24;1;83

    PUBMED: 37081487; PMC: 10120131; DOI: 10.1186/s13059-023-02917-w

  • Applications to medical and surgical specialist training in the UK National Health Service, 2021-2022: a cross-sectional observational study to characterise the diversity of successful applicants.

    Aggarwal D, Roy-Chowdhury M, Xiang N and Peacock SJ

    BMJ open 2023;13;4;e069846

    PUBMED: 37076164; DOI: 10.1136/bmjopen-2022-069846

  • Identification of gametocyte-associated pir genes in the rodent malaria parasite, Plasmodium chabaudi chabaudi AS.

    Cunningham DA, Reid AJ, Hosking C, Deroost K, Tumwine-Downey I, Sanders M and Langhorne J

    BMC research notes 2023;16;1;56

    PUBMED: 37076932; DOI: 10.1186/s13104-023-06322-1

  • Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data.

    Li S, Schmid KT, de Vries DH, Korshevniuk M, Losert C, Oelen R, van Blokland IV, BIOS Consortium, sc-eQTLgen Consortium, Groot HE et al.

    Genome biology 2023;24;1;80

    PUBMED: 37072791; DOI: 10.1186/s13059-023-02897-x

  • Proximity-Induced Nucleic Acid Degrader (PINAD) Approach to Targeted RNA Degradation Using Small Molecules

    Mikutis, Sigitas, Rebelo, Maria, Yankova, Eliza, Gu, Muxin, Tang, Cong et al.

    ACS Central Science 2023;9;5;892-904

    PMC: 10214512; DOI: 10.1021/acscentsci.3c00015

  • The genome sequence of Philonthus cognatus (Stephens, 1832) (Coleoptera, Staphylinidae), a rove beetle.

    Crowley LM, Telfer M, Geiser M, University of Oxford and Wytham Woods Genome Acquisition Lab, Mulley JF, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;169

    PUBMED: 37440996; PMC: 10333781; DOI: 10.12688/wellcomeopenres.19336.1

  • Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.

    Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, Vento-Tormo R, Haniffa M, Meyer KB, Dratva LM, Tuong ZK et al.

    Nature biotechnology 2023;42;1;40-51

    PUBMED: 37055623; PMC: 10791579; DOI: 10.1038/s41587-023-01734-7

  • The genome sequence of the Buff-tailed Bumblebee, Bombus terrestris (Linnaeus, 1758).

    Crowley LM, Sivell O, Sivell D, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;161

    PUBMED: 38283327; PMC: 10818103; DOI: 10.12688/wellcomeopenres.19248.1

  • The genome sequence of the Chalkhill Blue, Lysandra coridon (Poda, 1761).

    Vila R, Lohse K, Hayward A, Laetsch DR, Wright C, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;162

    PUBMED: 38770266; PMC: 11103778; DOI: 10.12688/wellcomeopenres.19253.1

  • The genome sequence of the Crescent Bell, Epinotia bilunana (Haworth, 1811).

    Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;163

    PUBMED: 38680650; PMC: 11053349; DOI: 10.12688/wellcomeopenres.19334.1

  • The genome sequence of the Heath Knot-horn, Apomyelois bistriatella (Hulst, 1887).

    Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;164

    PUBMED: 38434735; PMC: 10905011; DOI: 10.12688/wellcomeopenres.19306.1

  • Low-dose IL-2 enhances the generation of IL-10-producing immunoregulatory B cells.

    Inaba A, Tuong ZK, Zhao TX, Stewart AP, Mathews R, Truman L, Sriranjan R, Kennet J, Saeb-Parsy K, Wicker L et al.

    Nature communications 2023;14;1;2071

    PUBMED: 37045832; PMC: 10097719; DOI: 10.1038/s41467-023-37424-w

  • FISHFactor: A Probabilistic Factor Model for Spatial Transcriptomics Data with Subcellular Resolution.

    Walter FC, Stegle O and Velten B

    Bioinformatics (Oxford, England) 2023

    PUBMED: 37039825; DOI: 10.1093/bioinformatics/btad183

  • Genetic factors predict hybrid formation in the British flora.

    Brown MR, Hollingsworth PM, Forrest LL, Hart ML, Leitch IJ, Jones L, Ford C, de Vere N and Twyford AD

    Proceedings of the National Academy of Sciences of the United States of America 2023;120;16;e2220261120

    PUBMED: 37040419; PMC: 10120012; DOI: 10.1073/pnas.2220261120

  • Trimming the genomic fat: minimising and re-functionalising genomes using synthetic biology.

    Xu X, Meier F, Blount BA, Pretorius IS, Ellis T, Paulsen IT and Williams TC

    Nature communications 2023;14;1;1984

    PUBMED: 37031253; PMC: 10082837; DOI: 10.1038/s41467-023-37748-7

  • The genome sequence of the Grey Chi, Antitype chi (Linnaeus, 1761).

    Lees D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;157

    PUBMED: 37674877; PMC: 10477731; DOI: 10.12688/wellcomeopenres.19288.1

  • The genome sequence of the Sulphur Tubic, Esperia sulphurella (Fabricius, 1775).

    Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;156

    PUBMED: 38046189; PMC: 10690030; DOI: 10.12688/wellcomeopenres.19212.1

  • First Report of OXA-181-Producing Enterobacterales Isolates in Latin America.

    Cuicapuza D, Alvarado L, Tocasca N, Aguilar D, Gómez-de-la-Torre JC, Salvatierra G, Tsukayama P and Tamariz J

    Microbiology spectrum 2023;e0458422

    PUBMED: 37022279; DOI: 10.1128/spectrum.04584-22

  • Identification of Protein-Protein Interaction Bridges for Multiple Sclerosis.

    Yazıcı G, Vatandaslar BK, Canturk IA, Aydinli FI, Arici Duz O, Karakoç E, Kerman BE and Alkan C

    Bioinformatics (Oxford, England) 2023

    PUBMED: 37018152; DOI: 10.1093/bioinformatics/btad175

  • Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease.

    Wang Z, Zhu S, Jia Y, Wang Y, Kubota N, Fujiwara N, Gordillo R, Lewis C, Zhu M, Sharma T et al.

    Cell 2023

    PUBMED: 37040760; DOI: 10.1016/j.cell.2023.03.014

  • RAF1 contributes to cell proliferation and STAT3 activation in colorectal cancer independently of microsatellite and KRAS status.

    Dorard C, Madry C, Buhard O, Toifl S, Didusch S, Ratovomanana T, Letourneur Q, Dolznig H, Garnett MJ, Duval A and Baccarini M

    Oncogene 2023;42;20;1649-1660

    PUBMED: 37020037; PMC: 10181936; DOI: 10.1038/s41388-023-02683-w

  • Childhood Cancer Treatment and Clonal Hematopoiesis.

    Collord G and Behjati S

    Cancer discovery 2023;13;4;811-813

    PUBMED: 37009705; DOI: 10.1158/2159-8290.CD-23-0090

  • A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction.

    Hawkins PA, Chochua S, Lo SW, Belman S, Antonio M, Kwambana-Adams B, von Gottberg A, du Plessis M, Cornick J, Beall B et al.

    Microbial genomics 2023;9;4

    PUBMED: 37083600; DOI: 10.1099/mgen.0.000998

  • Colonization and transmission of Staphylococcus aureus in schools: a citizen science project.

    van Tonder AJ, McCullagh F, McKeand H, Thaw S, Bellis K, Raisen C, Lay L, Aggarwal D, Holmes M, Parkhill J et al.

    Microbial genomics 2023;9;4

    PUBMED: 37074324; PMC: 10210949; DOI: 10.1099/mgen.0.000993

  • Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community.

    Rasmussen JA and Chua PYS

    Microbiological research 2023;271;127372

    PUBMED: 37018898; DOI: 10.1016/j.micres.2023.127372

  • Vibrio cholerae O37: one of the exceptions that prove the rule.

    Dorman MJ and Thomson NR

    Microbial genomics 2023;9;4

    PUBMED: 37043377; DOI: 10.1099/mgen.0.000980

  • Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov.

    Naranjo HD, Lebbe L, Cnockaert M, Lassalle F, Too CC and Willems A

    Systematic and applied microbiology 2023;46;3;126420

    PUBMED: 37031612; DOI: 10.1016/j.syapm.2023.126420

  • The genome sequence of a Tiger Cranefly, Nephrotoma flavescens (Linnaeus, 1758).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;148

    PUBMED: 37275324; PMC: 10238818; DOI: 10.12688/wellcomeopenres.19203.1

  • The genome sequence of the Dotted Border, Agriopis marginaria (Fabricius, 1776).

    Lees D, Boyes D, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;152

    PUBMED: 37600582; PMC: 10435923; DOI: 10.12688/wellcomeopenres.19284.1

  • The genome sequence of the Feathered Bright, Incurvaria masculella (Denis & Schiffermüller, 1775).

    Langdon WBV, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;144

    PUBMED: 38026731; PMC: 10682600; DOI: 10.12688/wellcomeopenres.19205.1

  • Analysis of genetic dominance in the UK Biobank.

    Palmer DS, Zhou W, Abbott L, Wigdor EM, Baya N, Churchhouse C, Seed C, Poterba T, King D, Kanai M et al.

    Science (New York, N.Y.) 2023;379;6639;1341-1348

    PUBMED: 36996212; DOI: 10.1126/science.abn8455

  • Low-temperature and circadian signals are integrated by the sigma factor SIG5.

    Cano-Ramirez DL, Panter PE, Takemura T, de Fraine TS, de Barros Dantas LL, Dekeya R, Barros-Galvão T, Paajanen P, Bellandi A, Batstone T et al.

    Nature plants 2023;9;4;661-672

    PUBMED: 36997687; PMC: 10119024; DOI: 10.1038/s41477-023-01377-1

  • Norepinephrine links astrocytic activity to regulation of cortical state.

    Reitman ME, Tse V, Mi X, Willoughby DD, Peinado A, Aivazidis A, Myagmar BE, Simpson PC, Bayraktar OA, Yu G and Poskanzer KE

    Nature neuroscience 2023;26;4;579-593

    PUBMED: 36997759; PMC: 10089924; DOI: 10.1038/s41593-023-01284-w

  • An atlas of genetic scores to predict multi-omic traits.

    Xu Y, Ritchie SC, Liang Y, Timmers PRHJ, Pietzner M, Lannelongue L, Lambert SA, Tahir UA, May-Wilson S, Foguet C et al.

    Nature 2023;616;7955;123-131

    PUBMED: 36991119; PMC: 10323211; DOI: 10.1038/s41586-023-05844-9

  • The genome sequence of the Early Bumblebee, Bombus pratorum (Linnaeus, 1761).

    Crowley LM, Sivell O, Sivell D, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;143

    PUBMED: 37954924; PMC: 10632595; DOI: 10.12688/wellcomeopenres.19250.1

  • A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution.

    Goodheart JA, Collins AG, Cummings MP, Egger B and Rawlinson KA

    Royal Society open science 2023;10;3;220939

    PUBMED: 36998763; PMC: 10049750; DOI: 10.1098/rsos.220939

  • Spatial multiomics map of trophoblast development in early pregnancy.

    Arutyunyan A, Roberts K, Troulé K, Wong FCK, Sheridan MA, Kats I, Garcia-Alonso L, Velten B, Hoo R, Ruiz-Morales ER et al.

    Nature 2023;616;7955;143-151

    PUBMED: 36991123; PMC: 10076224; DOI: 10.1038/s41586-023-05869-0

  • FBXO11 governs macrophage cell death and inflammation in response to bacterial toxins.

    Jeon Y, Chow SH, Stuart I, Weir A, Yeung AT, Hale C, Sridhar S, Dougan G, Vince JE and Naderer T

    Life science alliance 2023;6;6

    PUBMED: 36977592; DOI: 10.26508/lsa.202201735

  • YWHAE loss of function causes a rare neurodevelopmental disease with brain abnormalities in human and mouse.

    Denommé-Pichon AS, Collins SC, Bruel AL, Mikhaleva A, Wagner C, Vancollie VE, Thomas Q, Chevarin M, Weber M, Prada CE et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2023;100835

    PUBMED: 36999555; DOI: 10.1016/j.gim.2023.100835

  • Discovery and Characterization of Pneumococcal Serogroup 36 Capsule Subtypes, Serotypes 36A and 36B.

    Ganaie FA, Saad JS, Lo SW, McGee L, Bentley SD, van Tonder AJ, Hawkins P, Keenan JD, Calix JJ and Nahm MH

    Journal of clinical microbiology 2023;e0002423

    PUBMED: 36971549; DOI: 10.1128/jcm.00024-23

  • Optimized whole-genome CRISPR interference screens identify ARID1A-dependent growth regulators in human induced pluripotent stem cells.

    Usluer S, Hallast P, Crepaldi L, Zhou Y, Urgo K, Dincer C, Su J, Noell G, Alasoo K, El Garwany O et al.

    Stem cell reports 2023

    PUBMED: 37028423; DOI: 10.1016/j.stemcr.2023.03.008

  • Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq.

    Neikes HK, Kliza KW, Gräwe C, Wester RA, Jansen PWTC, Lamers LA, Baltissen MP, van Heeringen SJ, Logie C, Teichmann SA et al.

    Nature biotechnology 2023;41;12;1801-1809

    PUBMED: 36973556; DOI: 10.1038/s41587-023-01715-w

  • Spotlight on Feline Oncology.

    van der Weyden L

    Veterinary sciences 2023;10;4

    PUBMED: 37104401; DOI: 10.3390/vetsci10040246

  • The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).

    Boyes D, Mulley JF, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;129

    PUBMED: 38274410; PMC: 10808854; DOI: 10.12688/wellcomeopenres.19246.1

  • The genome sequence of the Oak-tree Pug, Eupithecia dodoneata (Guenée, 1858).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;133

    PUBMED: 37469857; PMC: 10352626; DOI: 10.12688/wellcomeopenres.19245.1

  • Somatic mutations alter the differentiation outcomes of iPSC-derived neurons.

    Puigdevall P, Jerber J, Danecek P, Castellano S and Kilpinen H

    Cell genomics 2023;3;4;100280

    PUBMED: 37082143; PMC: 10112289; DOI: 10.1016/j.xgen.2023.100280

  • The genome sequence of the White-shouldered Marble, Apotomis turbidana (Hübner, 1825).

    Boyes D, Hammond J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;127

    PUBMED: 37614677; PMC: 10442595; DOI: 10.12688/wellcomeopenres.19242.1

  • Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures.

    Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E et al.

    Cell genomics 2023;3;4;100281

    PUBMED: 37082141; PMC: 10112291; DOI: 10.1016/j.xgen.2023.100281

  • Re: Germline Variants Associated with Toxicity to Immune Checkpoint Blockade.

    Jones JO, Mitchell TJ and Stewart GD

    European urology 2023

    PUBMED: 36964039; DOI: 10.1016/j.eururo.2023.03.008

  • Toward novel treatment against filariasis: Insight into genome-wide co-evolutionary analysis of filarial nematodes and Wolbachia.

    Wangwiwatsin A, Kulwong S, Phetcharaburanin J, Namwat N, Klanrit P, Loilome W, Maleewong W and Reid AJ

    Frontiers in microbiology 2023;14;1052352

    PUBMED: 37032902; PMC: 10073474; DOI: 10.3389/fmicb.2023.1052352

  • Future prospects for human genetics and genomics in drug discovery.

    Ghoussaini M, Nelson MR and Dunham I

    Current opinion in structural biology 2023;80;102568

    PUBMED: 36963162; PMC: 7614359; DOI: 10.1016/j.sbi.2023.102568

  • A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

    Crowley L, Allen H, Barnes I, Boyes D, Broad GR, Fletcher C, Holland PWH, Januszczak I, Lawniczak M, Lewis OT et al.

    Wellcome open research 2023;8;123

    PUBMED: 37408610; PMC: 10318377; DOI: 10.12688/wellcomeopenres.18925.1

  • Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.

    Mu A, Klare WP, Baines SL, Ignatius Pang CN, Guérillot R, Harbison-Price N, Keller N, Wilksch J, Nhu NTK, Phan MD et al.

    Nature communications 2023;14;1;1530

    PUBMED: 36934086; PMC: 10024524; DOI: 10.1038/s41467-023-37200-w

  • Diagnostic classification of childhood cancer using multiscale transcriptomics.

    Comitani F, Nash JO, Cohen-Gogo S, Chang AI, Wen TT, Maheshwari A, Goyal B, Tio ES, Tabatabaei K, Mayoh C et al.

    Nature medicine 2023;29;3;656-666

    PUBMED: 36932241; PMC: 10033451; DOI: 10.1038/s41591-023-02221-x

  • An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.

    Timoshevskaya N, Eşkut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C et al.

    Cell reports 2023;42;3;112263

    PUBMED: 36930644; DOI: 10.1016/j.celrep.2023.112263

  • Inferring the heritability of bacterial traits in the era of machine learning.

    Mai TT, Lees JA, Gladstone RA and Corander J

    Bioinformatics advances 2023;3;1;vbad027

    PUBMED: 36974068; PMC: 10039732; DOI: 10.1093/bioadv/vbad027

  • TREs are still not about trust.

    Graham M, Milne R, Fitzsimmons P and Sheehan M

    Journal of medical ethics 2023

    PUBMED: 36918262; DOI: 10.1136/jme-2023-109031

  • The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions.

    Rahmioglu N, Mortlock S, Ghiasi M, Møller PL, Stefansdottir L, Galarneau G, Turman C, Danning R, Law MH, Sapkota Y et al.

    Nature genetics 2023;55;3;423-436

    PUBMED: 36914876; PMC: 10042257; DOI: 10.1038/s41588-023-01323-z

  • Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.

    Shrine N, Izquierdo AG, Chen J, Packer R, Hall RJ, Guyatt AL, Batini C, Thompson RJ, Pavuluri C, Malik V et al.

    Nature genetics 2023;55;3;410-422

    PUBMED: 36914875; PMC: 10011137; DOI: 10.1038/s41588-023-01314-0

  • Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations.

    Liu D, Meyer D, Fennessy B, Feng C, Cheng E, Johnson JS, Park YJ, Rieder MK, Ascolillo S, de Pins A et al.

    Nature genetics 2023;55;3;369-376

    PUBMED: 36914870; PMC: 10011128; DOI: 10.1038/s41588-023-01305-1

  • The genome sequence of the Spruce Carpet Moth, Thera britannica (Turner, 1925).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;114

    PUBMED: 37408609; PMC: 10318373; DOI: 10.12688/wellcomeopenres.19107.1

  • The genome sequence of the thick-headed fly,  Myopa tessellatipennis (Motschulsky, 1859).

    Ashworth M, Falk S, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Clements DK and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;115

    PUBMED: 37663791; PMC: 10468684; DOI: 10.12688/wellcomeopenres.19108.1

  • Advances in Understanding Spontaneously Occurring Melanoma in Animals.

    Blacklock KL and van der Weyden L

    Veterinary sciences 2023;10;3

    PUBMED: 36977249; DOI: 10.3390/vetsci10030210

  • Future of DNA-based insect monitoring.

    Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R and Lawniczak MKN

    Trends in genetics : TIG 2023;39;7;531-544

    PUBMED: 36907721; DOI: 10.1016/j.tig.2023.02.012

  • B lymphocyte responses in Parkinson's disease and their possible significance in disease progression.

    Scott KM, Chong YT, Park S, Wijeyekoon RS, Hayat S, Mathews RJ, Fitzpatrick Z, Tyers P, Wright G, Whitby J et al.

    Brain communications 2023;5;2;fcad060

    PUBMED: 36993946; PMC: 10042276; DOI: 10.1093/braincomms/fcad060

  • CRISPR-Cas9 genetic screen leads to the discovery of L-Moses, a KAT2B inhibitor that attenuates Tunicamycin-mediated neuronal cell death.

    Pavlou S, Foskolou S, Patikas N, Field SF, Papachristou EK, Santos C, Edwards AR, Kishore K, Ansari R, Rajan SS et al.

    Scientific reports 2023;13;1;3934

    PUBMED: 36894612; PMC: 9998435; DOI: 10.1038/s41598-023-31141-6

  • Genomic Analysis Reveals New Integrative Conjugal Elements and Transposons in GBS Conferring Antimicrobial Resistance.

    Khan UB, Portal EAR, Sands K, Lo S, Chalker VJ, Jauneikaite E and Spiller OB

    Antibiotics (Basel, Switzerland) 2023;12;3

    PUBMED: 36978411; PMC: 10044541; DOI: 10.3390/antibiotics12030544

  • Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients.

    Ashwin H, Milross L, Wilson J, Majo J, Hang Lee JT, Calder G, Hunter B, James S, Lagos D, Signoret N et al.

    Journal of clinical pathology 2023

    PUBMED: 36894313; DOI: 10.1136/jcp-2023-208771

  • The genome sequence of the Kite-tailed Robberfly, Machimus atricapillus (Fallén, 1814).

    Thomas S, Mitchell R, Crowley LM, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;113

    PUBMED: 37928207; PMC: 10622858; DOI: 10.12688/wellcomeopenres.19080.1

  • The genome sequence of the Vagrant Hoverfly, Eupeodes corollae (Fabricius, 1794).

    Sivell D, Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Hawkes WL, Wotton KR and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;112

    PUBMED: 37808390; PMC: 10556570; DOI: 10.12688/wellcomeopenres.19099.1

  • Cytoplasmic isoleucyl tRNA synthetase as an attractive multistage antimalarial drug target.

    Istvan ES, Guerra F, Abraham M, Huang KS, Rocamora F, Zhao H, Xu L, Pasaje C, Kumpornsin K, Luth MR et al.

    Science translational medicine 2023;15;686;eadc9249

    PUBMED: 36888694; DOI: 10.1126/scitranslmed.adc9249

  • Fumarate induces vesicular release of mtDNA to drive innate immunity.

    Zecchini V, Paupe V, Herranz-Montoya I, Janssen J, Wortel IMN, Morris JL, Ferguson A, Chowdury SR, Segarra-Mondejar M, Costa ASH et al.

    Nature 2023;615;7952;499-506

    PUBMED: 36890229; PMC: 10017517; DOI: 10.1038/s41586-023-05770-w

  • In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution.

    Fischer A, Lersch R, de Andrade Krätzig N, Strong A, Friedrich MJ, Weber J, Engleitner T, Öllinger R, Yen HY, Kohlhofer U et al.

    Cell genomics 2023;3;3;100276

    PUBMED: 36950387; PMC: 10025556; DOI: 10.1016/j.xgen.2023.100276

  • Targeting synthetic lethal paralogs in cancer.

    Ryan CJ, Mehta I, Kebabci N and Adams DJ

    Trends in cancer 2023

    PUBMED: 36890003; DOI: 10.1016/j.trecan.2023.02.002

  • Diagnostic utility of whole genome sequencing in adults with B-other acute lymphoblastic leukemia.

    Leongamornlert D, Gutiérrez-Abril J, Lee SW, Barretta E, Creasey T, Gundem G, Levine MF, Arango Ossa JE, Liosis K, Medina-Martinez JS et al.

    Blood advances 2023

    PUBMED: 36867579; DOI: 10.1182/bloodadvances.2022008992

  • Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons.

    Wu Q, Wu J, Karim K, Chen X, Wang T, Iwama S, Carobbio S, Keen P, Vidal-Puig A, Kotter MR and Bassett A

    Molecular cell 2023

    PUBMED: 36917981; DOI: 10.1016/j.molcel.2023.02.011

  • Screening for Clostridioides difficile colonization at admission to the hospital: a multi-centre study.

    Crobach MJT, Hornung BVH, Verduin C, Vos MC, Hopman J, Kumar N, Harmanus C, Sanders I, Terveer EM, Stares MD et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2023

    PUBMED: 36871826; DOI: 10.1016/j.cmi.2023.02.022

  • SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis.

    Mishra M, Barck L, Moreno P, Heger G, Song Y, Thornton JM and Papatheodorou I

    NAR genomics and bioinformatics 2023;5;1;lqad014

    PUBMED: 36879900; PMC: 9985330; DOI: 10.1093/nargab/lqad014

  • A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei.

    Gabrielli M, Benazzo A, Biello R, Ancona L, Fuselli S, Iannucci A, Balacco J, Mountcastle J, Tracey A, Ficetola GF et al.

    The Journal of heredity 2023

    PUBMED: 36866448; DOI: 10.1093/jhered/esad014

  • Cancer immune evasion through KRAS and PD-L1 and potential therapeutic interventions.

    Watterson A and Coelho MA

    Cell communication and signaling : CCS 2023;21;1;45

    PUBMED: 36864508; PMC: 9979509; DOI: 10.1186/s12964-023-01063-x

  • The genome sequence of the Lunar Hornet, Sesia bembeciformis (Hübner 1806).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Langdon WBV and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;109

    PUBMED: 37840882; PMC: 10568212; DOI: 10.12688/wellcomeopenres.19111.1

  • The genome sequence of the Mother Shipton moth , Euclidia mi (Clerck, 1759).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;108

    PUBMED: 37346819; PMC: 10280027; DOI: 10.12688/wellcomeopenres.19098.1

  • Chromosome Analysis and Sorting Using Conventional Flow Cytometers.

    Ng BL

    Current protocols 2023;3;3;e718

    PUBMED: 36920094; DOI: 10.1002/cpz1.718

  • Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017.

    Cleary DW, Lo SW, Kumar N, Bentley SD, Faust SN and Clarke SC

    Microbial genomics 2023;9;3

    PUBMED: 36867094; DOI: 10.1099/mgen.0.000945

  • Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study.

    Hadjirin NF, van Tonder AJ, Blane B, Lees JA, Kumar N, Delappe N, Brennan W, McGrath E, Parkhill J, Cormican M et al.

    Microbial genomics 2023;9;3

    PUBMED: 36916881; DOI: 10.1099/mgen.0.000924

  • Genomic attributes of Vibrio cholerae O1 responsible for 2022 massive cholera outbreak in Bangladesh.

    Monir MM, Islam MT, Mazumder R, Mondal D, Nahar KS, Sultana M, Morita M, Ohnishi M, Huq A, Watanabe H et al.

    Nature communications 2023;14;1;1154

    PUBMED: 36859426; PMC: 9977884; DOI: 10.1038/s41467-023-36687-7

  • Palidis: fast discovery of novel insertion sequences.

    Carr VR, Pissis SP, Mullany P, Shoaie S, Gomez-Cabrero D and Moyes DL

    Microbial genomics 2023;9;3

    PUBMED: 36897935; PMC: 10132078; DOI: 10.1099/mgen.0.000917

  • Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.

    Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G et al.

    Genes 2023;14;3

    PUBMED: 36980891; PMC: 10048373; DOI: 10.3390/genes14030619

  • The genome sequence of the Twin-spot Plume, Stenoptilia bipunctidactyla (Scopoli, 1763).

    Langdon WBV, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;103

    PUBMED: 37799508; PMC: 10548107; DOI: 10.12688/wellcomeopenres.19081.1

  • Large-scale single cell RNA sequencing atlases of human immune cells across lifespan: possibilities and challenges.

    Webb S and Haniffa M

    European journal of immunology 2023;e2250222

    PUBMED: 36826421; DOI: 10.1002/eji.202250222

  • The genome sequence of the Small Ranunculus, Hecatera dysodea (Denis & Schiffermüller, 1775).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;101

    PUBMED: 38046193; PMC: 10690034; DOI: 10.12688/wellcomeopenres.19067.1

  • Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases.

    de Klein N, Tsai EA, Vochteloo M, Baird D, Huang Y, Chen CY, van Dam S, Oelen R, Deelen P, Bakker OB et al.

    Nature genetics 2023;55;3;377-388

    PUBMED: 36823318; PMC: 10011140; DOI: 10.1038/s41588-023-01300-6

  • Network expansion of genetic associations defines a pleiotropy map of human cell biology.

    Barrio-Hernandez I, Schwartzentruber J, Shrivastava A, Del-Toro N, Gonzalez A, Zhang Q, Mountjoy E, Suveges D, Ochoa D, Ghoussaini M et al.

    Nature genetics 2023;55;3;389-398

    PUBMED: 36823319; PMC: 10011132; DOI: 10.1038/s41588-023-01327-9

  • The genome sequence of the black needle fly, Leuctra nigra (Olivier, 1811).

    Clifford C, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Macadam CR, Price BW and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;95

    PUBMED: 37346817; PMC: 10280035; DOI: 10.12688/wellcomeopenres.19082.1

  • The genome sequence of the Leopard Moth, Zeuzera pyrina (Linnaeus, 1761).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;94

    PUBMED: 37965283; PMC: 10643876; DOI: 10.12688/wellcomeopenres.19064.1

  • Hyperprogression of cutaneous T cell lymphoma after anti-PD-1 treatment.

    Gao Y, Hu S, Li R, Jin S, Liu F, Liu X, Li Y, Yan Y, Liu W, Gong J et al.

    JCI insight 2023;8;4

    PUBMED: 36649072; DOI: 10.1172/jci.insight.164793

  • The genome sequence of a bluebottle, Calliphora vomitoria (Linnaeus, 1758).

    Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;93

    PUBMED: 38173563; PMC: 10762291; DOI: 10.12688/wellcomeopenres.18891.1

  • The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;92

    PUBMED: 37621575; PMC: 10444995; DOI: 10.12688/wellcomeopenres.19065.1

  • The genome sequence of the Elbow-stripe Grass-veneer, Agriphila geniculea (Haworth, 1811).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Hammond J and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;86

    PUBMED: 37265476; PMC: 10230176; DOI: 10.12688/wellcomeopenres.18910.1

  • The genome sequence of the Turnip Sawfly, Athalia rosae (Linnaeus, 1758).

    Crowley LM, Broad GR, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Green A and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;87

    PUBMED: 38235342; PMC: 10792271; DOI: 10.12688/wellcomeopenres.18993.1

  • Heparan sulfate regulates IL-21 bioavailability and signal strength that control germinal center B cell selection and differentiation.

    Chen Z, Cui Y, Yao Y, Liu B, Yunis J, Gao X, Wang N, Cañete PF, Tuong ZK, Sun H et al.

    Science immunology 2023;8;80;eadd1728

    PUBMED: 36800411; DOI: 10.1126/sciimmunol.add1728

  • Decoding foreign antigen tolerance.

    Vento-Tormo R

    Science (New York, N.Y.) 2023;379;6633;655

    PUBMED: 36795842; DOI: 10.1126/science.adg6260

  • Evidence of widespread endemic populations of highly multidrug resistant Klebsiella pneumoniae in hospital settings in Hanoi, Vietnam: a prospective cohort study.

    Pham MH, Hoi LT, Beale MA, Khokhar FA, Hoa NT, Musicha P, Blackwell GA, Long HB, Huong DT, Binh NG et al.

    The Lancet. Microbe 2023

    PUBMED: 36801013; DOI: 10.1016/S2666-5247(22)00338-X

  • How genomics can help biodiversity conservation.

    Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA et al.

    Trends in genetics : TIG 2023

    PUBMED: 36801111; DOI: 10.1016/j.tig.2023.01.005

  • Impact of a post-donation hemoglobin testing strategy on efficiency and safety of whole blood donation in England: A modeling study.

    Kim LG, Bolton T, Sweeting MJ, Bell S, Fahle S, McMahon A, Walker M, Ferguson E, Miflin G, Robert DJ et al.

    Transfusion 2023

    PUBMED: 36794597; DOI: 10.1111/trf.17277

  • Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants.

    Koeppel J, Weller J, Peets EM, Pallaseni A, Kuzmin I, Raudvere U, Peterson H, Liberante FG and Parts L

    Nature biotechnology 2023;41;10;1446-1456

    PUBMED: 36797492; PMC: 10567557; DOI: 10.1038/s41587-023-01678-y

  • The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;82

    PUBMED: 37484482; PMC: 10357075; DOI: 10.12688/wellcomeopenres.18990.1

  • The genome sequence of the Field Cuckoo-bee, Bombus campestris (Panzer, 1801).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;77

    PUBMED: 37969482; PMC: 10646345; DOI: 10.12688/wellcomeopenres.18985.1

  • The genome sequence of the Forest Cuckoo Bee, Bombus sylvestris (Lepeletier, 1832).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;78

    PUBMED: 37881254; PMC: 10594053; DOI: 10.12688/wellcomeopenres.18986.1

  • The genome sequence of the Shuttle-shaped Dart, Agrotis puta (Hübner, 1803).

    Boyes D, Broad GR, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;84

    PUBMED: 38385124; PMC: 10879758; DOI: 10.12688/wellcomeopenres.18934.1

  • Rare genetic variants underlie outlying levels of DNA methylation and gene-expression.

    Chundru VK, Marioni RE, Pendergast JGD, Lin T, Beveridge AJ, Martin NG, Montgomery GW, Hume DA, Deary IJ, Visscher PM et al.

    Human molecular genetics 2023

    PUBMED: 36790133; DOI: 10.1093/hmg/ddad028

  • Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models.

    Burger A, Baldock RA, Adams DJ, Din S, Papatheodorou I, Glinka M, Hill B, Houghton D, Sharghi M, Wicks M and Arends MJ

    BMC medical informatics and decision making 2023;23;1;36

    PUBMED: 36793076; DOI: 10.1186/s12911-023-02111-9

  • The genome sequence of the Large Skipper, Ochlodes sylvanus, (Esper, 1777).

    Lohse K, Hayward A, Vila R, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Carvalho APS, Kawahara AY and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;75

    PUBMED: 37600586; PMC: 10435925; DOI: 10.12688/wellcomeopenres.18788.1

  • Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru.

    Quispe-Ricalde MA, Castelán-Sánchez HG, Meza-Rodríguez PM, Dávila-Ramos S, Sierra JL, Batista-Garcia R, Concha-Velasco F, Lucana SF, De Santa Cruz J, Zea V et al.

    Archives of virology 2023;168;3;88

    PUBMED: 36786950; DOI: 10.1007/s00705-022-05645-x

  • A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain.

    Habtewold T, Wagah M, Tambwe MM, Moore S, Windbichler N, Christophides G, Johnson H, Heaton H, Collins J, Krasheninnikova K et al.

    Wellcome open research 2023;8;74

    PUBMED: 37424773; PMC: 10326452; DOI: 10.12688/wellcomeopenres.18854.1

  • Coding-Complete Genome Sequences of 40 SARS-CoV-2 Omicron XBB, XBB.1, and XBB.2 Sublineage Strains in Bangladesh.

    Habib MT, Afrad MH, Rahman S, Khan MH, Hossain MM, Khanam F, Thomson NR, Shirin T and Qadri F

    Microbiology resource announcements 2023;e0000123

    PUBMED: 36779717; DOI: 10.1128/mra.00001-23

  • The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758).

    Crowley LM, Mitchell R, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Weston ST, Wotton KR and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;69

    PUBMED: 37928210; PMC: 10620480; DOI: 10.12688/wellcomeopenres.18897.1

  • What makes a good life: using theatrical performance to enhance communication about polygenic risk scores research in patient and public involvement.

    Mason AM, Obi I, Ayodele O, Lambert SA and Fahle S

    Journal of community genetics 2023

    PUBMED: 36763324; DOI: 10.1007/s12687-023-00635-1

  • The genome sequence of a bird blowfly, Protocalliphora azurea (Fallén,1817).

    Falk S, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Sivell O and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;67

    PUBMED: 37766849; PMC: 10521116; DOI: 10.12688/wellcomeopenres.18872.1

  • The genome sequence of the Birch Marble,  Apotomis betuletana (Haworth, 1811).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Mulley JF and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;66

    PUBMED: 37082718; PMC: 10111142; DOI: 10.12688/wellcomeopenres.18984.1

  • On predictive inference for intractable models via approximate Bayesian computation.

    Järvenpää M and Corander J

    Statistics and computing 2023;33;2;42

    PUBMED: 36785730; PMC: 9911513; DOI: 10.1007/s11222-022-10163-6

  • The genome sequence of the cinnamon sedge caddisfly, Limnephilus marmoratus (Curtis, 1834).

    Clifford C, Friend K, Skipp S, Wallace I, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Price BW and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;64

    PUBMED: 37736014; PMC: 10509604; DOI: 10.12688/wellcomeopenres.18753.1

  • The genome sequence of the lesser worm flesh fly, Sarcophaga ( Sarcophaga) subvicina (Baranov, 1937).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Mulley JF and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;65

    PUBMED: 37600583; PMC: 10435921; DOI: 10.12688/wellcomeopenres.18717.1

  • CBL/CAP Is Essential for Mitochondria Respiration Complex I Assembly and Bioenergetics Efficiency in Muscle Cells.

    Aye CC, Hammond DE, Rodriguez-Cuenca S, Doherty MK, Whitfield PD, Phelan MM, Yang C, Perez-Perez R, Li X, Diaz-Ramos A et al.

    International journal of molecular sciences 2023;24;4

    PUBMED: 36834818; PMC: 9964740; DOI: 10.3390/ijms24043399

  • Considerations for peripheral blood transport and storage during large-scale multicentre metabolome research.

    Alexander JL, Wyatt NJ, Camuzeaux S, Chekmeneva E, Jimenez B, Sands CJ, Fuller H, Takis P, Ahmad T, Doyle JA et al.

    Gut 2023

    PUBMED: 36754608; DOI: 10.1136/gutjnl-2022-329297

  • Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.

    Bentley BP, Carrasco-Valenzuela T, Ramos EKS, Pawar H, Souza Arantes L, Alexander A, Banerjee SM, Masterson P, Kuhlwilm M, Pippel M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2023;120;7;e2201076120

    PUBMED: 36749728; DOI: 10.1073/pnas.2201076120

  • Spatial and molecular profiling of the mononuclear phagocyte network in Classic Hodgkin lymphoma.

    Stewart BJ, Fergie M, Young M, Jones C, Sachdeva A, Blain AE, Bacon CM, Rand V, Ferdinand JR, James KR et al.

    Blood 2023

    PUBMED: 36758207; DOI: 10.1182/blood.2022015575

  • The genome sequence of an ichneumonid wasp, Amblyteles armatorius (Forster, 1771).

    Sivell O, Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;61

    PUBMED: 38037558; PMC: 10687389; DOI: 10.12688/wellcomeopenres.18920.1

  • The genome sequence of the pale Rhogogaster, Rhogogaster chlorosoma (Benson, 1943).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Green A and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;59

    PUBMED: 37781447; PMC: 10534084; DOI: 10.12688/wellcomeopenres.18924.1

  • Phenotypic and genetic alterations of Burkholderia pseudomallei in patients during relapse and persistent infections.

    Seng R, Phunpang R, Saiprom N, Dulsuk A, Chewapreecha C, Thaipadungpanit J, Batty EM, Chantratita W, West TE and Chantratita N

    Frontiers in microbiology 2023;14;1103297

    PUBMED: 36814569; PMC: 9939903; DOI: 10.3389/fmicb.2023.1103297

  • The genome sequence of a beetle-killing wasp, Tiphia femorata (Fabricius, 1775).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Pointon DL and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;57

    PUBMED: 38037557; PMC: 10687388; DOI: 10.12688/wellcomeopenres.18893.1

  • The genome sequence of a soldier beetle, Podabrus alpinus (Paykull, 1798).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Chua P, Kusy D and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;56

    PUBMED: 37346818; PMC: 10280036; DOI: 10.12688/wellcomeopenres.18890.1

  • The genome sequence of the Mouse Moth, Amphipyra tragopoginis (Clerck 1759).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;54

    PUBMED: 37363059; PMC: 10285349; DOI: 10.12688/wellcomeopenres.18946.1

  • Genome-wide screening reveals the genetic basis of mammalian embryonic eye development.

    Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE et al.

    BMC biology 2023;21;1;22

    PUBMED: 36737727; PMC: 9898963; DOI: 10.1186/s12915-022-01475-0

  • LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein.

    Shilts J, Crozier TWM, Teixeira-Silva A, Gabaev I, Gerber PP, Greenwood EJD, Watson SJ, Ortmann BM, Gawden-Bone CM, Pauzaite T et al.

    PLoS biology 2023;21;2;e3001959

    PUBMED: 36735681; PMC: 9897555; DOI: 10.1371/journal.pbio.3001959

  • The genome sequence of the Miller, Acronicta leporina (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;49

    PUBMED: 37954922; PMC: 10632593; DOI: 10.12688/wellcomeopenres.18889.1

  • The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;51

    PUBMED: 37736012; PMC: 10509607; DOI: 10.12688/wellcomeopenres.18712.1

  • Biologically informed deep learning to query gene programs in single-cell atlases.

    Lotfollahi M, Rybakov S, Hrovatin K, Hediyeh-Zadeh S, Talavera-López C, Misharin AV and Theis FJ

    Nature cell biology 2023;25;2;337-350

    PUBMED: 36732632; PMC: 9928587; DOI: 10.1038/s41556-022-01072-x

  • Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence.

    Ardern Z, Chakraborty S, Lenk F and Kaster AK

    FEMS microbiology reviews 2023

    PUBMED: 36725215; DOI: 10.1093/femsre/fuad003

  • Molecular evolution of classic Hodgkin lymphoma revealed through whole genome sequencing of Hodgkin and Reed Sternberg cells.

    Maura F, Ziccheddu B, Xiang JZ, Bhinder B, Rosiene J, Abascal F, Maclachlan KH, Eng KW, Uppal M, He F et al.

    Blood cancer discovery 2023

    PUBMED: 36723991; DOI: 10.1158/2643-3230.BCD-22-0128

  • The genome of Roselle's flesh fly Sarcophaga ( Helicophagella) rosellei (Böttcher, 1912).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Mulley JF and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;43

    PUBMED: 37766848; PMC: 10521103; DOI: 10.12688/wellcomeopenres.18874.1

  • The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Mulley JF and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;45

    PUBMED: 37484483; PMC: 10357074; DOI: 10.12688/wellcomeopenres.18899.1

  • Dementia prevention in memory clinics: recommendations from the European task force for brain health services.

    Frisoni GB, Altomare D, Ribaldi F, Villain N, Brayne C, Mukadam N, Abramowicz M, Barkhof F, Berthier M, Bieler-Aeschlimann M et al.

    The Lancet regional health. Europe 2023;26;100576

    PUBMED: 36895446; PMC: 9989648; DOI: 10.1016/j.lanepe.2022.100576

  • Quality control and removal of technical variation of NMR metabolic biomarker data in ~120,000 UK Biobank participants.

    Ritchie SC, Surendran P, Karthikeyan S, Lambert SA, Bolton T, Pennells L, Danesh J, Di Angelantonio E, Butterworth AS and Inouye M

    Scientific data 2023;10;1;64

    PUBMED: 36720882; PMC: 9887579; DOI: 10.1038/s41597-023-01949-y

  • Association of germline variants in telomere maintenance genes (POT1, TERF2IP, ACD, and TERT) with spitzoid morphology in familial melanoma: A multi-center case series.

    Goldstein AM, Qin R, Chu EY, Elder DE, Massi D, Adams DJ, Harms PW, Robles-Espinoza CD, Newton-Bishop JA, Bishop DT et al.

    JAAD international 2023;11;43-51

    PUBMED: 36876055; PMC: 9978843; DOI: 10.1016/j.jdin.2023.01.013

  • B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors.

    Kaemena DF, Yoshihara M, Beniazza M, Ashmore J, Zhao S, Bertenstam M, Olariu V, Katayama S, Okita K, Tomlinson SR et al.

    Nature communications 2023;14;1;488

    PUBMED: 36717582; PMC: 9887000; DOI: 10.1038/s41467-023-36097-9

  • The genome sequence of the Grey Dagger, Acronicta psi (Linnaeus, 1758).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;39

    PUBMED: 37363060; PMC: 10285329; DOI: 10.12688/wellcomeopenres.18711.1

  • The genome sequence of the plain dark bee, Stelis phaeoptera (Kirby, 1802).

    Boyes C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;42

    PUBMED: 37346821; PMC: 10280034; DOI: 10.12688/wellcomeopenres.18876.1

  • APOBEC mutagenesis is a common process in normal human small intestine.

    Wang Y, Robinson PS, Coorens THH, Moore L, Lee-Six H, Noorani A, Sanders MA, Jung H, Katainen R, Heuschkel R et al.

    Nature genetics 2023

    PUBMED: 36702998; DOI: 10.1038/s41588-022-01296-5

  • Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation.

    Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S and Pauklin S

    Nature communications 2023;14;1;405

    PUBMED: 36697417; PMC: 9876972; DOI: 10.1038/s41467-023-36116-9

  • Multiallelic Copy Number Variation in ORM1 is Associated with Plasma Cell-Free DNA Levels as an Intermediate Phenotype for Venous Thromboembolism.

    Martin-Fernandez L, Garcia-Martínez I, Lopez S, Martinez-Perez A, Vilalta N, Plaza M, Moret C, Viñuela A, Brown AA, Panousis NI et al.

    Thrombosis and haemostasis 2023

    PUBMED: 36696913; DOI: 10.1055/s-0043-1760844

  • Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.

    Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM et al.

    Nature 2023;613;7945;639-649

    PUBMED: 36697862; PMC: 11333990; DOI: 10.1038/s41586-022-05546-8

  • The genome sequence of the sea mat, Membranipora membranacea (Linnaeus, 1767).

    Bishop J, Adkins P, Wood C, Jenkins H, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;38

    PUBMED: 37363061; PMC: 10290214; DOI: 10.12688/wellcomeopenres.18855.1

  • scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection.

    Zhang Z, Sun H, Mariappan R, Chen X, Chen X, Jain MS, Efremova M, Teichmann SA, Rajan V and Zhang X

    Nature communications 2023;14;1;384

    PUBMED: 36693837; PMC: 9873790; DOI: 10.1038/s41467-023-36066-2

  • The genome sequence of the turban top shell, Gibbula magus (Linnaeus, 1758).

    Adkins P, Harley J, Darbyshire T, Holmes A, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Scott-Somme K et al.

    Wellcome open research 2023;8;35

    PUBMED: 37538380; PMC: 10394393; DOI: 10.12688/wellcomeopenres.18792.1

  • The swan genome and transcriptome, it is not all black and white.

    Karawita AC, Cheng Y, Chew KY, Challagulla A, Kraus R, Mueller RC, Tong MZW, Hulme KD, Bielefeldt-Ohmann H, Steele LE et al.

    Genome biology 2023;24;1;13

    PUBMED: 36683094; PMC: 9867998; DOI: 10.1186/s13059-022-02838-0

  • Causal effects of maternal circulating amino acids on offspring birthweight: a Mendelian randomisation study.

    Zhao J, Stewart ID, Baird D, Mason D, Wright J, Zheng J, Gaunt TR, Evans DM, Freathy RM, Langenberg C et al.

    EBioMedicine 2023;88;104441

    PUBMED: 36696816; DOI: 10.1016/j.ebiom.2023.104441

  • Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function.

    Lampersberger L, Conte F, Ghosh S, Xiao Y, Price J, Jordan D, Matus DQ, Sarkies P, Beli P, Miska EA and Burton NO

    Proceedings of the National Academy of Sciences of the United States of America 2023;120;5;e2217992120

    PUBMED: 36689659; DOI: 10.1073/pnas.2217992120

  • Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project.

    Vancaester E and Blaxter M

    PLoS biology 2023;21;1;e3001972

    PUBMED: 36689552; PMC: 9894559; DOI: 10.1371/journal.pbio.3001972

  • Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.

    Tonkin-Hill G, Gladstone RA, Pöntinen AK, Arredondo-Alonso S, Bentley SD and Corander J

    Genome research 2023

    PUBMED: 36669850; DOI: 10.1101/gr.277340.122

  • The genome sequence of a snail-killing fly, Pherbina coryleti (Scopoli, 1763).

    Sivell O, Mitchell R, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;30

    PUBMED: 37915954; PMC: 10616662; DOI: 10.12688/wellcomeopenres.18790.1

  • The genome sequence of the Pied Smudge, Ypsolopha sequella (Clerck, 1759).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Langdon WBV and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;32

    PUBMED: 37822564; PMC: 10562790; DOI: 10.12688/wellcomeopenres.18768.1

  • The genome sequence of the segmented worm, Sthenelais limicola (Ehlers, 1864).

    Darbyshire T, Brennan M, McTierney S, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;31

    PUBMED: 37469856; PMC: 10352628; DOI: 10.12688/wellcomeopenres.18856.1

  • A RUNX1-FPDMM rhesus macaque model reproduces the human phenotype and predicts challenges to curative gene therapies.

    Lee BC, Zhou Y, Bresciani E, Ozkaya N, Dulau-Florea A, Carrington B, Shin TH, Baena V, Syed ZA, Hong SG et al.

    Blood 2023;141;3;231-237

    PUBMED: 36322931; DOI: 10.1182/blood.2022018193

  • Base editing screens map mutations affecting interferon-γ signaling in cancer.

    Coelho MA, Cooper S, Strauss ME, Karakoc E, Bhosle S, Gonçalves E, Picco G, Burgold T, Cattaneo CM, Veninga V et al.

    Cancer cell 2023;41;2;288-303.e6

    PUBMED: 36669486; PMC: 9942875; DOI: 10.1016/j.ccell.2022.12.009

  • Notch1 mutations drive clonal expansion in normal esophageal epithelium but impair tumor growth.

    Abby E, Dentro SC, Hall MWJ, Fowler JC, Ong SH, Sood R, Herms A, Piedrafita G, Abnizova I, Siebel CW et al.

    Nature genetics 2023;55;2;232-245

    PUBMED: 36658434; PMC: 9925379; DOI: 10.1038/s41588-022-01280-z

  • A chromosome-level reference genome and pangenome for barn swallow population genomics.

    Secomandi S, Gallo GR, Sozzoni M, Iannucci A, Galati E, Abueg L, Balacco J, Caprioli M, Chow W, Ciofi C et al.

    Cell reports 2023;42;1;111992

    PUBMED: 36662619; DOI: 10.1016/j.celrep.2023.111992

  • The genome sequence of an erect bryozoan, Bugulina stolonifera (Ryland, 1960).

    Wood C, Bishop J, Adkins P, Jenkins H, Marine Biological Association Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;26

    PUBMED: 37251659; PMC: 10213821; DOI: 10.12688/wellcomeopenres.18775.1

  • Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition.

    Karin O, Miska EA and Simons BD

    Cell systems 2023;14;1;24-40.e11

    PUBMED: 36657390; DOI: 10.1016/j.cels.2022.12.003

  • The genome sequence of a caddisfly, Limnephilus lunatus (Curtis, 1834).

    Austin M, Clifford C, Rutt G, Price BW, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Wallace I and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;25

    PUBMED: 37408608; PMC: 10318372; DOI: 10.12688/wellcomeopenres.18752.1

  • Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life.

    Challis R, Kumar S, Sotero-Caio C, Brown M and Blaxter M

    Wellcome open research 2023;8;24

    PUBMED: 36864925; PMC: 9971660; DOI: 10.12688/wellcomeopenres.18658.1

  • Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples.

    MalariaGEN, Abdel Hamid MM, Abdelraheem MH, Acheampong DO, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amenga-Etego L et al.

    Wellcome open research 2023;8;22

    PUBMED: 36864926; PMC: 9971654; DOI: 10.12688/wellcomeopenres.18681.1

  • A genetic variant of the Wnt receptor LRP6 accelerates synapse degeneration during aging and in Alzheimer's disease.

    Jones ME, Büchler J, Dufor T, Palomer E, Teo S, Martin-Flores N, Boroviak K, Metzakopian E, Gibb A and Salinas PC

    Science advances 2023;9;2;eabo7421

    PUBMED: 36638182; DOI: 10.1126/sciadv.abo7421

  • The genome sequence of a ground beetle, Nebria brevicollis (Fabricius, 1792).

    Crowley L, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Garner B and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;20

    PUBMED: 37766846; PMC: 10521042; DOI: 10.12688/wellcomeopenres.18749.1

  • The genome sequence of the bluish flesh fly, Sarcophaga  ( Robineauella) caerulescens (Zetterstedt, 1838).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Mulley JF and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;17

    PUBMED: 37363063; PMC: 10288162; DOI: 10.12688/wellcomeopenres.18718.1

  • The genome sequence of the Festoon, Apoda limacodes (Hufnagel, 1766).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;19

    PUBMED: 37251660; PMC: 10213820; DOI: 10.12688/wellcomeopenres.18747.1

  • The genome sequence of the Four-dotted Footman, Cybosia mesomella (Linnaeus, 1758).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;18

    PUBMED: 37346820; PMC: 10280026; DOI: 10.12688/wellcomeopenres.18745.1

  • The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Lees D and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;16

    PUBMED: 37251658; PMC: 10220420; DOI: 10.12688/wellcomeopenres.18596.1

  • HERC1 deficiency causes osteopenia through transcriptional program dysregulation during bone remodeling.

    Pedrazza L, Martinez-Martinez A, Sánchez-de-Diego C, Valer JA, Pimenta-Lopes C, Sala-Gaston J, Szpak M, Tyler-Smith C, Ventura F and Rosa JL

    Cell death & disease 2023;14;1;17

    PUBMED: 36635269; PMC: 9837143; DOI: 10.1038/s41419-023-05549-x

  • PRC2 disruption in cerebellar progenitors produces cerebellar hypoplasia and aberrant myoid differentiation without blocking medulloblastoma growth.

    Cleveland AH, Malawsky D, Churiwal M, Rodriguez C, Reed F, Schniederjan M, Velazquez Vega JE, Davis I and Gershon TR

    Acta neuropathologica communications 2023;11;1;8

    PUBMED: 36635771; DOI: 10.1186/s40478-023-01508-x

  • The genome sequence of the Gold Triangle, Hypsopygia costalis (Fabricius, 1775).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Hammond J and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;15

    PUBMED: 38037560; PMC: 10687387; DOI: 10.12688/wellcomeopenres.18746.1

  • Evaluation of genome skimming to detect and characterise human and livestock helminths.

    Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Hall A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P et al.

    International journal for parasitology 2023

    PUBMED: 36641060; DOI: 10.1016/j.ijpara.2022.12.002

  • Prolidase Deficiency Causes Spontaneous T Cell Activation and Lupus-Like Autoimmunity.

    Hodgson R, Crockford TL, Bhandari A, Kepple JD, Back J, Cawthorne E, Abeler-Dörner L, Laing AG, Clare S, Speak A et al.

    Journal of immunology (Baltimore, Md. : 1950) 2023

    PUBMED: 36637239; DOI: 10.4049/jimmunol.2200212

  • Putting bacteria on the cancer map.

    Anderson ND and Behjati S

    Immunity 2023;56;1;11-13

    PUBMED: 36630910; DOI: 10.1016/j.immuni.2022.12.016

  • Genomic diagnosis and care co-ordination for monogenic inflammatory bowel disease in children and adults: consensus guideline on behalf of the British Society of Gastroenterology and British Society of Paediatric Gastroenterology, Hepatology and Nutrition.

    Kammermeier J, Lamb CA, Jones KDJ, Anderson CA, Baple EL, Bolton C, Braggins H, Coulter TI, Gilmour KC, Gregory V et al.

    The lancet. Gastroenterology & hepatology 2023

    PUBMED: 36634696; DOI: 10.1016/S2468-1253(22)00337-5

  • Mitochondrial and Endoplasmic Reticulum Stress Trigger Triglyceride Accumulation in Models of Parkinson's Disease Independent of Mutations in MAPT.

    Fernandes HJR, Kent JP, Bruntraeger M, Bassett AR, Koulman A, Metzakopian E and Snowden SG

    Metabolites 2023;13;1

    PUBMED: 36677037; PMC: 9861589; DOI: 10.3390/metabo13010112

  • The genome sequence of the ichneumon wasp Buathra laborator (Thunberg, 1822).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;7

    PUBMED: 37234744; PMC: 10206444; DOI: 10.12688/wellcomeopenres.18674.1

  • The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements.

    Botelho J, Cazares A and Schulenburg H

    Nucleic acids research 2023

    PUBMED: 36610752; DOI: 10.1093/nar/gkac1220

  • The genome sequence of the spotted kaleidoscope jellyfish, Haliclystus octoradiatus (James-Clark, 1863).

    Blaxter M, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;6

    PUBMED: 36875804; PMC: 9975415; DOI: 10.12688/wellcomeopenres.18669.1

  • The genome sequence of the White-barred Gold, Micropterix aruncella (Scopoli, 1763).

    Holland PWH, Hammond J, Holland AS, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2023;8;1

    PUBMED: 37363062; PMC: 10288161; DOI: 10.12688/wellcomeopenres.18714.1

  • Differentiation of human induced pluripotent stem cells into cortical neural stem cells.

    Neaverson A, Andersson MHL, Arshad OA, Foulser L, Goodwin-Trotman M, Hunter A, Newman B, Patel M, Roth C, Thwaites T et al.

    Frontiers in cell and developmental biology 2023;10;1023340

    PUBMED: 36684426; PMC: 9849742; DOI: 10.3389/fcell.2022.1023340

  • Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis.

    Light N, Layeghifard M, Attery A, Subasri V, Zatzman M, Anderson ND, Hatkar R, Blay S, Chen D, Novokmet A et al.

    Nature communications 2023;14;1;77

    PUBMED: 36604421; DOI: 10.1038/s41467-022-35727-y

  • Regulators of male and female sexual development are critical for the transmission of a malaria parasite.

    Russell AJC, Sanderson T, Bushell E, Talman AM, Anar B, Girling G, Hunziker M, Kent RS, Martin JS, Metcalf T et al.

    Cell host & microbe 2023

    PUBMED: 36634679; DOI: 10.1016/j.chom.2022.12.011

  • Cystic Fibrosis-Related Gut Dysbiosis: A Systematic Review.

    Caley LR, White H, de Goffau MC, Floto RA, Parkhill J, Marsland B and Peckham DG

    Digestive diseases and sciences 2023

    PUBMED: 36600119; DOI: 10.1007/s10620-022-07812-1

  • An interactive web application for processing, correcting, and visualizing genome-wide pooled CRISPR-Cas9 screens.

    Vinceti A, De Lucia RR, Cremaschi P, Perron U, Karakoc E, Mauri L, Fernandez C, Kluczynski KH, Anderson DS and Iorio F

    Cell reports methods 2023;3;1;100373

    PUBMED: 36814834; PMC: 9939378; DOI: 10.1016/j.crmeth.2022.100373

  • The genomic characterization of Salmonella Paratyphi A from an outbreak of enteric fever in Vadodara, India.

    Pereira-Dias J, Taneja N, Mahindroo J, Maheshwari G, Patel PJ, Thu TNH, Keane J, Dyson ZA, Baker S and Mylona E

    Microbial genomics 2023;9;1

    PUBMED: 36748526; DOI: 10.1099/mgen.0.000914

  • Assessing flower-visiting arthropod diversity in apple orchards through metabarcoding of environmental DNA from flowers and visual census

    Gomez, Nerea Gamonal, Sorensen, Didde Hedegaard, Chua, Physilia Ying Shi and Sigsgaard, Lene

    Environmental DNA 2023;5;1;117-131

    DOI: 10.1002/edn3.362

  • Dimensionality reduction under scrutiny.

    Yang Y, Tuong ZK and Yu D

    Nature computational science 2023;3;1;8-9

    PUBMED: 38177957; DOI: 10.1038/s43588-022-00383-1

  • Interrogation of Functional miRNA-Target Interactions by CRISPR/Cas9 Genome Engineering.

    Wu Q, Michaels YS and Fulga TA

    Methods in molecular biology (Clifton, N.J.) 2023;2630;243-264

    PUBMED: 36689187; DOI: 10.1007/978-1-0716-2982-6_16

  • MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

    Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle et al.

    BMC Bioinformatics 2023;24;1;1

    DOI: 10.1186/s12859-023-05385-y; URL: https://doi.org/10.1186/s12859-023-05385-y

  • Recording the ethical provenance of data and automating data stewardship

    Bernier, Alexander, Raven-Adams, Maili, Zaccagnini, Davide and Knoppers, Bartha M.

    Big Data & Society 2023;10;1

    DOI: 10.1177/20539517231163174

  • scRNA-seq for Microcephaly Research [III]: Computational Analysis of scRNA-seq Data.

    Babcock B and Malawsky D

    Methods in molecular biology (Clifton, N.J.) 2023;2583;105-121

    PUBMED: 36418729; DOI: 10.1007/978-1-0716-2752-5_10

  • scRNA-seq for Microcephaly Research [IV]: Dirichlet Regression for Single-Cell Population Differences.

    Malawsky D and Gershon TR

    Methods in molecular biology (Clifton, N.J.) 2023;2583;123-125

    PUBMED: 36418730; DOI: 10.1007/978-1-0716-2752-5_11

  • Spatial atlas reveals insight into lung immunity.

    No authors listed

    Nature genetics 2023;55;1;10-11

    PUBMED: 36609699; DOI: 10.1038/s41588-022-01244-3

  • Spatially resolved multiomics of human cardiac niches

    Kanemaru, Kazumasa, Cranley, James, Muraro, Daniele, Miranda, Antonio M. A., Ho, Siew Yen et al.

    Nature 2023;619;7971;801

    DOI: 10.1038/s41586-023-06311-1; URL: https://doi.org/10.1038/s41586-023-06311-1

  • Special considerations for studies of extracellular vesicles from parasitic helminths: A community-led roadmap to increase rigour and reproducibility.

    White R, Sotillo J, Ancarola ME, Borup A, Boysen AT, Brindley PJ, Buzás EI, Cavallero S, Chaiyadet S, Chalmers IW et al.

    Journal of extracellular vesicles 2023;12;1;e12298

    PUBMED: 36604533; DOI: 10.1002/jev2.12298

  • varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data.

    Kumar AA, Loeys B, Van De Beek G, Peeters N, Wuyts W, Van Laer L, Vandeweyer G and Alaerts M

    Bioinformatics (Oxford, England) 2023;39;1

    PUBMED: 36440912; PMC: 9805572; DOI: 10.1093/bioinformatics/btac756

2022

  • The gut microbiome is a significant risk factor for future chronic lung disease.

    Liu Y, Teo SM, Meric G, Tang HHF, Zhu Q, Sanders JG, Vazquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P et al.

    The Journal of allergy and clinical immunology 2022

    PUBMED: 36587850; DOI: 10.1016/j.jaci.2022.12.810

  • Metabolic Activation of Benzo[a]pyrene by Human Tissue Organoid Cultures.

    Caipa Garcia AL, Kucab JE, Al-Serori H, Beck RSS, Fischer F, Hufnagel M, Hartwig A, Floeder A, Balbo S, Francies H et al.

    International journal of molecular sciences 2022;24;1

    PUBMED: 36614051; PMC: 9820386; DOI: 10.3390/ijms24010606

  • Sex-Specific Survival Bias and Interaction Modeling in Coronary Artery Disease Risk Prediction.

    Surakka I, Wolford BN, Ritchie SC, Hornsby WE, Sutton NR, Elvenstad Gabrielsen M, Heidi Skogholt A, Thomas L, Inouye M, Hveem K and Willer CJ

    Circulation. Genomic and precision medicine 2022;e003542

    PUBMED: 36580301; DOI: 10.1161/CIRCGEN.121.003542

  • A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei).

    R N Ferreira JG, A Americo J, L A S do Amaral D, Sendim F, R da Cunha Y, Tree of Life Programme, Blaxter M, Uliano-Silva M and de F Rebelo M

    GigaScience 2022;12

    PUBMED: 37776366; DOI: 10.1093/gigascience/giad072

  • Integrated View of Baseline Protein Expression in Human Tissues.

    Prakash A, García-Seisdedos D, Wang S, Kundu DJ, Collins A, George N, Moreno P, Papatheodorou I, Jones AR and Vizcaíno JA

    Journal of proteome research 2022

    PUBMED: 36577097; DOI: 10.1021/acs.jproteome.2c00406

  • Predictive Utility of a Coronary Artery Disease Polygenic Risk Score in Primary Prevention.

    Marston NA, Pirruccello JP, Melloni GEM, Koyama S, Kamanu FK, Weng LC, Roselli C, Kamatani Y, Komuro I, Aragam KG et al.

    JAMA cardiology 2022

    PUBMED: 36576811; DOI: 10.1001/jamacardio.2022.4466

  • "Antigen Discovery for Next-Generation Pertussis Vaccines using Immunoproteomics and Transposon Directed Insertion Sequencing".

    Gregg KA, Wang Y, Warfel J, Schoenfeld E, Jankowska E, Cipollo JF, Mayho M, Boinett C, Prasad D, Brickman TJ et al.

    The Journal of infectious diseases 2022

    PUBMED: 36575950; DOI: 10.1093/infdis/jiac502

  • An empirical investigation into the impact of winner's curse on estimates from Mendelian randomization.

    Jiang T, Gill D, Butterworth AS and Burgess S

    International journal of epidemiology 2022

    PUBMED: 36573802; DOI: 10.1093/ije/dyac233

  • Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.

    Kanoni S, Graham SE, Wang Y, Surakka I, Ramdas S, Zhu X, Clarke SL, Bhatti KF, Vedantam S, Winkler TW et al.

    Genome biology 2022;23;1;268

    PUBMED: 36575460; PMC: 9793579; DOI: 10.1186/s13059-022-02837-1

  • Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19.

    Maher AK, Burnham KL, Jones EM, Tan MMH, Saputil RC, Baillon L, Selck C, Giang N, Argüello R, Pillay C et al.

    Nature communications 2022;13;1;7947

    PUBMED: 36572683; PMC: 9791976; DOI: 10.1038/s41467-022-35638-y

  • The genome sequence of the early grey, Xylocampa areola (Esper, 1789).

    Lees D, Boyes D, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;312

    PUBMED: 38037645; PMC: 10687390; DOI: 10.12688/wellcomeopenres.18663.1

  • The genome sequence of the northern brown argus, Aricia artaxerxes (Fabricius, 1793).

    Ebdon S, Lohse K, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Jansen Van Rensburg A and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;314

    PUBMED: 37389324; PMC: 10300502; DOI: 10.12688/wellcomeopenres.18664.1

  • The genome sequence of the Seraphim, Lobophora halterata (Hufnagel, 1767).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Holland PWH and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;313

    PUBMED: 36874578; PMC: 9975409; DOI: 10.12688/wellcomeopenres.18713.1

  • The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758).

    Hayward A, Lohse K, Laetsch DR, Vila R, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Taluy E and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;315

    PUBMED: 36874580; PMC: 9975408; DOI: 10.12688/wellcomeopenres.18607.1

  • A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

    Trimarsanto H, Amato R, Pearson RD, Sutanto E, Noviyanti R, Trianty L, Marfurt J, Pava Z, Echeverry DF, Lopera-Mesa TM et al.

    Communications biology 2022;5;1;1411

    PUBMED: 36564617; PMC: 9789135; DOI: 10.1038/s42003-022-04352-2

  • Assessing and removing the effect of unwanted technical variations in microbiome data.

    Fachrul M, Méric G, Inouye M, Pamp SJ and Salim A

    Scientific reports 2022;12;1;22236

    PUBMED: 36564466; PMC: 9789116; DOI: 10.1038/s41598-022-26141-x

  • Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity.

    Tanmoy AM, Hooda Y, Sajib MSI, da Silva KE, Iqbal J, Qamar FN, Luby SP, Dougan G, Dyson ZA, Baker S et al.

    Nature communications 2022;13;1;7912

    PUBMED: 36564386; PMC: 9782287; DOI: 10.1038/s41467-022-35587-6

  • Recurrent visceral leishmaniasis relapses in HIV co-infected patients are characterized by less efficient immune responses and higher parasite load.

    Takele Y, Mulaw T, Adem E, Womersley R, Kaforou M, Franssen SU, Levin M, Taylor GP, Müller I, Cotton JA and Kropf P

    iScience 2022;26;2;105867

    PUBMED: 36685039; PMC: 9845767; DOI: 10.1016/j.isci.2022.105867

  • The genome sequence of the cave orb-weaver, Meta bourneti (Simon, 1922).

    Henriques S, Sivell O, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;311

    PUBMED: 36874575; PMC: 9975426; DOI: 10.12688/wellcomeopenres.18638.1

  • The genome sequence of the Kent black arches, Meganola albula (Denis & Schiffermüller, 1775).

    Boyes D, Sims I, Lees D, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Dove A and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;310

    PUBMED: 37346773; PMC: 10280029; DOI: 10.12688/wellcomeopenres.18672.1

  • Molecular Epidemiology of Group B Streptococcus Colonization in Egyptian Women.

    Shabayek S, Vogel V, Jamrozy D, Bentley SD and Spellerberg B

    Microorganisms 2022;11;1

    PUBMED: 36677330; PMC: 9861799; DOI: 10.3390/microorganisms11010038

  • The genome sequence of the dotted bee-fly, Bombylius discolor (Mikan, 1796).

    Broad GR, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;306

    PUBMED: 37124844; PMC: 10133823; DOI: 10.12688/wellcomeopenres.18614.1

  • The genome sequence of the scale worm, Lepidonotus clava (Montagu, 1808).

    Darbyshire T, Bishop J, Mieszkowska N, Adkins P, Holmes A, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;307

    PUBMED: 37362008; PMC: 10288160; DOI: 10.12688/wellcomeopenres.18660.1

  • A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity.

    Knight-Schrijver VR, Davaapil H, Bayraktar S, Ross ADB, Kanemaru K, Cranley J, Dabrowska M, Patel M, Polanski K, He X et al.

    Nature cardiovascular research 2022;1;12;1215-1229

    PUBMED: 36938497; PMC: 7614330; DOI: 10.1038/s44161-022-00183-w

  • A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.

    Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, Richoz N, Ribeiro Orsi A, Mamanova L, Bolt L, Elmentaite R et al.

    Nature genetics 2022

    PUBMED: 36543915; DOI: 10.1038/s41588-022-01243-4

  • Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis.

    Carrasquilla M, Early AM, Taylor AR, Knudson Ospina A, Echeverry DF, Anderson TJC, Mancilla E, Aponte S, Cárdenas P, Buckee CO et al.

    PLoS pathogens 2022;18;12;e1010993

    PUBMED: 36542676; DOI: 10.1371/journal.ppat.1010993

  • Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort.

    Simonin-Wilmer I, Ossio R, Leddin EM, Harland M, Pooley KA, Martil de la Garza MG, Obolenski S, Hewinson J, Wong CC, Iyer V et al.

    Journal of medical genetics 2022

    PUBMED: 36539277; DOI: 10.1136/jmg-2022-108776

  • Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.

    Kwun MJ, Ion AV, Cheng HC, D'Aeth JC, Dougan S, Oggioni MR, Goulding DA, Bentley SD and Croucher NJ

    Genome medicine 2022;14;1;144

    PUBMED: 36539881; PMC: 9764711; DOI: 10.1186/s13073-022-01147-2

  • Single-cell transcriptomics for the assessment of cardiac disease.

    Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP and Noseda M

    Nature reviews. Cardiology 2022

    PUBMED: 36539452; DOI: 10.1038/s41569-022-00805-7

  • First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies.

    Gauthier J, Meier J, Legeai F, McClure M, Whibley A, Bretaudeau A, Boulain H, Parrinello H, Mugford ST, Durbin R et al.

    Molecular ecology resources 2022

    PUBMED: 36533297; DOI: 10.1111/1755-0998.13749

  • Genomic epidemiology on the move.

    Wilson CN, Musicha P and Beale MA

    Nature reviews. Microbiology 2022;1

    PUBMED: 36536144; PMC: 9762618; DOI: 10.1038/s41579-022-00836-4

  • Voicing the need to consider sex-specific differences in research.

    Miguel-Aliaga I, Vunjak-Novakovic G, Stephenson EJ, Gachon F, Milagre I, Mills E, Rubin JB and Kelava I

    Developmental cell 2022;57;24;2675-2678

    PUBMED: 36538892; DOI: 10.1016/j.devcel.2022.11.018

  • YaHS: yet another Hi-C scaffolding tool.

    Zhou C, McCarthy SA and Durbin R

    Bioinformatics (Oxford, England) 2022

    PUBMED: 36525368; DOI: 10.1093/bioinformatics/btac808

  • The genome sequence of the lesser treble-bar moth, Aplocera efformata (Guenée, 1857).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Palmada-Flores M and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;303

    PUBMED: 37942213; PMC: 10628359; DOI: 10.12688/wellcomeopenres.18595.1

  • Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis.

    Kalizang'oma A, Kwambana-Adams B, Chan JM, Viswanath A, Gori A, Richard D, Jolley KA, Lees J, Goldblatt D, Beleza S et al.

    Journal of clinical microbiology 2022;e0080222

    PUBMED: 36515506; DOI: 10.1128/jcm.00802-22

  • The genome sequence of the white admiral, Limenitis camilla (Linnaeus, 1764).

    Vila R, Lohse K, Hayward A, Laetsch DR, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Wahlberg N and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;301

    PUBMED: 37781634; PMC: 10539722; DOI: 10.12688/wellcomeopenres.18594.1

  • SC3s: efficient scaling of single cell consensus clustering to millions of cells.

    Quah FX and Hemberg M

    BMC bioinformatics 2022;23;1;536

    PUBMED: 36503522; PMC: 9743492; DOI: 10.1186/s12859-022-05085-z

  • The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis & Schiffermüller, 1775).

    Lohse K, Vila R, Hayward A, Laetsch DR, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Wahlberg N and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;298

    PUBMED: 37224319; PMC: 10186063; DOI: 10.12688/wellcomeopenres.18569.1

  • Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya.

    Obanda BA, Cook EAJ, Fèvre EM, Bebora L, Ogara W, Wang SH, Gebreyes W, Ngetich R, Wandede D, Muyodi J et al.

    Pathogens (Basel, Switzerland) 2022;11;12

    PUBMED: 36558838; PMC: 9781741; DOI: 10.3390/pathogens11121504

  • Emergence of Tropheryma whipplei detection in respiratory samples by next-generation sequencing: pathogen or innocent bystander?

    Xing F, Lo SW, Liu M, Deng C, Ye H, Sun L, Yang J, Lo SKF, Lau SKP and Woo PCY

    The Journal of infection 2022

    PUBMED: 36509359; DOI: 10.1016/j.jinf.2022.12.004

  • Spatial biology of cancer evolution.

    Seferbekova Z, Lomakin A, Yates LR and Gerstung M

    Nature reviews. Genetics 2022

    PUBMED: 36494509; DOI: 10.1038/s41576-022-00553-x

  • A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates.

    He P, Lim K, Sun D, Pett JP, Jeng Q, Polanski K, Dong Z, Bolt L, Richardson L, Mamanova L et al.

    Cell 2022;185;25;4841-4860.e25

    PUBMED: 36493756; DOI: 10.1016/j.cell.2022.11.005

  • Impact of the Human Cell Atlas on medicine.

    Rood JE, Maartens A, Hupalowska A, Teichmann SA and Regev A

    Nature medicine 2022

    PUBMED: 36482102; DOI: 10.1038/s41591-022-02104-7

  • The genome sequence of the European crab apple, Malus sylvestris  (L.) Mill., 1768.

    Ruhsam M, Bell D, Hart M, Hollingsworth P, Royal Botanic Garden Edinburgh Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;296

    PUBMED: 36874569; PMC: 9975420; DOI: 10.12688/wellcomeopenres.18645.1

  • A transcriptional switch controls sex determination in Plasmodium falciparum.

    Gomes AR, Marin-Menendez A, Adjalley SH, Bardy C, Cassan C, Lee MCS and Talman AM

    Nature 2022;612;7940;528-533

    PUBMED: 36477538; PMC: 9750867; DOI: 10.1038/s41586-022-05509-z

  • Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD.

    Faiz A, Pavlidis S, Kuo CH, Rowe A, Hiemstra PS, Timens W, Berg M, Wisman M, Guo YK, Djukanović R et al.

    Thorax 2022

    PUBMED: 36598042; DOI: 10.1136/thorax-2021-217736

  • The genome sequence of the setaceous Hebrew character, Xestia c-nigrum, (Linnaeus, 1758).

    Broad GR, Boyes D, Natural History Museum Genome Acquisition Lab, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;295

    PUBMED: 36865367; PMC: 9971640; DOI: 10.12688/wellcomeopenres.18608.1

  • Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants.

    Aragam KG, Jiang T, Goel A, Kanoni S, Wolford BN, Atri DS, Weeks EM, Wang M, Hindy G, Zhou W et al.

    Nature genetics 2022;54;12;1803-1815

    PUBMED: 36474045; DOI: 10.1038/s41588-022-01233-6

  • Genome Sequences of 23 SARS-CoV-2 Omicron-Lineage Strains from Bangladesh.

    Hossain M, Bin Manjur OH, Hasda L, Habib MT, Afrad MH, Khan MH, Banik N, Afreen N, Alam AN, Ayub M et al.

    Microbiology resource announcements 2022;e0095022

    PUBMED: 36472422; DOI: 10.1128/mra.00950-22

  • Identification of multiplicatively acting modulatory mutational signatures in cancer.

    Kičiatovas D, Guo Q, Kailas M, Pesonen H, Corander J, Kaski S, Pitkänen E and Mustonen V

    BMC bioinformatics 2022;23;1;522

    PUBMED: 36474143; DOI: 10.1186/s12859-022-05060-8

  • ER-associated RNA silencing promotes ER quality control.

    Efstathiou S, Ottens F, Schütter LS, Ravanelli S, Charmpilas N, Gutschmidt A, Le Pen J, Gehring NH, Miska EA, Bouças J and Hoppe T

    Nature cell biology 2022;24;12;1714-1725

    PUBMED: 36471127; DOI: 10.1038/s41556-022-01025-4

  • FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2.

    Brevini T, Maes M, Webb GJ, John BV, Fuchs CD, Buescher G, Wang L, Griffiths C, Brown ML, Scott WE et al.

    Nature 2022

    PUBMED: 36470304; DOI: 10.1038/s41586-022-05594-0

  • Mouse primordial germ-cell-like cells lack piRNAs.

    Ramakrishna NB, Battistoni G, Surani MA, Hannon GJ and Miska EA

    Developmental cell 2022;57;23;2661-2668.e5

    PUBMED: 36473462; DOI: 10.1016/j.devcel.2022.11.004

  • Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease.

    Lim K, Donovan APA, Tang W, Sun D, He P, Pett JP, Teichmann SA, Marioni JC, Meyer KB, Brand AH and Rawlins EL

    Cell stem cell 2022

    PUBMED: 36493780; DOI: 10.1016/j.stem.2022.11.013

  • Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.

    Salazar C, Giménez M, Riera N, Parada A, Puig J, Galiana A, Grill F, Vieytes M, Mason CE, Antelo V et al.

    Microbiome 2022;10;1;208

    PUBMED: 36457116; PMC: 9715416; DOI: 10.1186/s40168-022-01407-8

  • The heightened importance of the microbiome in cancer immunotherapy.

    Villemin C, Six A, Neville BA, Lawley TD, Robinson MJ and Bakdash G

    Trends in immunology 2022

    PUBMED: 36464584; DOI: 10.1016/j.it.2022.11.002

  • A minimal role for synonymous variation in human disease.

    Dhindsa RS, Wang Q, Vitsios D, Burren OS, Hu F, DiCarlo JE, Kruglyak L, MacArthur DG, Hurles ME and Petrovski S

    American journal of human genetics 2022;109;12;2105-2109

    PUBMED: 36459978; DOI: 10.1016/j.ajhg.2022.10.016

  • A reference human induced pluripotent stem cell line for large-scale collaborative studies.

    Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D et al.

    Cell stem cell 2022;29;12;1685-1702.e22

    PUBMED: 36459969; DOI: 10.1016/j.stem.2022.11.004

  • An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals.

    Afolayan AO, Aboderin AO, Oaikhena AO, Odih EE, Ogunleye VO, Adeyemo AT, Adeyemo AT, Bejide OS, Underwood A, Argimón S et al.

    Microbial genomics 2022;8;12

    PUBMED: 36748556; DOI: 10.1099/mgen.0.000863

  • Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes.

    Higgins K, Moore BA, Berberovic Z, Adissu HA, Eskandarian M, Flenniken AM, Shao A, Imai DM, Clary D, Lanoue L et al.

    Scientific reports 2022;12;1;20791

    PUBMED: 36456625; DOI: 10.1038/s41598-022-19710-7

  • Human gonadal development, cell by cell.

    Lorenzi V, Vento-Tormo R and Garcia-Alonso L

    Clinical and translational medicine 2022;12;12;e1123

    PUBMED: 36513876; PMC: 9747682; DOI: 10.1002/ctm2.1123

  • Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya.

    Obanda BA, Gibbons CL, Fèvre EM, Bebora L, Gitao G, Ogara W, Wang SH, Gebreyes W, Ngetich R, Blane B et al.

    Antibiotics (Basel, Switzerland) 2022;11;12

    PUBMED: 36551383; PMC: 9774130; DOI: 10.3390/antibiotics11121726

  • Reply to: When did mammoths go extinct?

    Wang Y, Prohaska A, Dong H, Alberti A, Alsos IG, Beilman DW, Bjørk AA, Cao J, Cherezova AA, Coissac E et al.

    Nature 2022;612;7938;E4-E6

    PUBMED: 36450908; PMC: 9712097; DOI: 10.1038/s41586-022-05417-2

  • Strong pathogen competition in neonatal gut colonisation.

    Mäklin T, Thorpe HA, Pöntinen AK, Gladstone RA, Shao Y, Pesonen M, McNally A, Johnsen PJ, Samuelsen Ø, Lawley TD et al.

    Nature communications 2022;13;1;7417

    PUBMED: 36456554; PMC: 9715557; DOI: 10.1038/s41467-022-35178-5

  • The genome sequence of the two-spot ladybird, Adalia bipunctata (Linnaeus, 1758).

    Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Goate Z and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;288

    PUBMED: 37767014; PMC: 10521051; DOI: 10.12688/wellcomeopenres.18610.1

  • A manually curated annotation characterises genomic features of P. falciparum lncRNAs.

    Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ and Lee MCS

    BMC genomics 2022;23;1;780

    PUBMED: 36451097; PMC: 9710153; DOI: 10.1186/s12864-022-09017-2

  • Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer.

    Webster ALH, Sanders MA, Patel K, Dietrich R, Noonan RJ, Lach FP, White RR, Goldfarb A, Hadi K, Edwards MM et al.

    Nature 2022;612;7940;495-502

    PUBMED: 36450981; DOI: 10.1038/s41586-022-05253-4

  • Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis.

    Wasakul V, Disratthakit A, Mayxay M, Chindavongsa K, Sengsavath V, Thuy-Nhien N, Pearson RD, Phalivong S, Xayvanghang S, Maude RJ et al.

    The Lancet. Infectious diseases 2022

    PUBMED: 36462526; DOI: 10.1016/S1473-3099(22)00697-1

  • Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales.

    Li NK, Corander J, Grad YH and Chang HH

    Virus evolution 2022;8;2;veac108

    PUBMED: 36601300; PMC: 9789396; DOI: 10.1093/ve/veac108

  • Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines.

    Godoy-Tena G, Barmada A, Morante-Palacios O, de la Calle-Fabregat C, Martins-Ferreira R, Ferreté-Bonastre AG, Ciudad L, Ruiz-Sanmartín A, Martínez-Gallo M, Ferrer R et al.

    Genome medicine 2022;14;1;134

    PUBMED: 36443794; PMC: 9706884; DOI: 10.1186/s13073-022-01137-4

  • Genetically personalised organ-specific metabolic models in health and disease.

    Foguet C, Xu Y, Ritchie SC, Lambert SA, Persyn E, Nath AP, Davenport EE, Roberts DJ, Paul DS, Di Angelantonio E et al.

    Nature communications 2022;13;1;7356

    PUBMED: 36446790; DOI: 10.1038/s41467-022-35017-7

  • Importance of adopting standardized MANE transcripts in clinical reporting.

    Wright CF, FitzPatrick DR, Ware JS, Rehm HL and Firth HV

    Genetics in medicine : official journal of the American College of Medical Genetics 2022

    PUBMED: 36441169; DOI: 10.1016/j.gim.2022.10.013

  • Population genomics reveal distinct and diverging populations of An. minimus in Cambodia.

    St Laurent B, Harding N, Deason N, Oy K, Sok Loeun C, Sary M, Sunly R, Nhep S, Drury E, Rockett K et al.

    Communications biology 2022;5;1;1308

    PUBMED: 36443434; DOI: 10.1038/s42003-022-04259-y

  • The genome sequence of the malaria mosquito, Anopheles funestus, Giles, 1900.

    Ayala D, Akone-Ella O, Kengne P, Johnson H, Heaton H, Collins J, Krasheninnikova K, Pelan S, Pointon DL, Sims Y et al.

    Wellcome open research 2022;7;287

    PUBMED: 36874567; PMC: 9975407; DOI: 10.12688/wellcomeopenres.18445.1

  • Recurrent FOSL1 rearrangements in desmoplastic fibroblastoma.

    De Noon S, Piggott R, Trotman J, Tadross JA, Fittall M, Hughes D, Ye H, Munasinghe E, Murray M, Tirabosco R et al.

    The Journal of pathology 2022

    PUBMED: 36426824; DOI: 10.1002/path.6038

  • EROS is a selective chaperone regulating the phagocyte NADPH oxidase and purinergic signalling.

    Randzavola LO, Mortimer PM, Garside E, Dufficy ER, Schejtman A, Roumelioti G, Yu L, Pardo M, Spirohn K, Tolley C et al.

    eLife 2022;11

    PUBMED: 36421765; DOI: 10.7554/eLife.76387

  • IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders.

    Aitken S, Firth HV, Wright CF, Hurles ME, FitzPatrick DR and Semple CA

    HGG advances 2022;4;1;100162

    PUBMED: 36561149; PMC: 9763511; DOI: 10.1016/j.xhgg.2022.100162

  • Longitudinal IgG antibody responses to Plasmodium vivax blood-stage antigens during and after acute vivax malaria in individuals living in the Brazilian Amazon.

    Tashi T, Upadhye A, Kundu P, Wu C, Menant S, Soares RR, Ferreira MU, Longley RJ, Mueller I, Hoang QQ et al.

    PLoS neglected tropical diseases 2022;16;11;e0010773

    PUBMED: 36417454; DOI: 10.1371/journal.pntd.0010773

  • Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer.

    Li R, Ferdinand JR, Loudon KW, Bowyer GS, Laidlaw S, Muyas F, Mamanova L, Neves JB, Bolt L, Fasouli ES et al.

    Cancer cell 2022;40;12;1583-1599.e10

    PUBMED: 36423636; PMC: 9767677; DOI: 10.1016/j.ccell.2022.11.001

  • Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila.

    Matute JD, Duan J, Flak MB, Griebel P, Tascon-Arcila JA, Doms S, Hanley T, Antanaviciute A, Gundrum J, Mark Welch JL et al.

    The Journal of experimental medicine 2022;220;1

    PUBMED: 36413219; PMC: 9683900; DOI: 10.1084/jem.20211938

  • Simultaneous depletion of RB, RBL1 and RBL2 affects endoderm differentiation of human embryonic stem cells.

    Nakanoh S, Kadiwala J, Pinte L, Morell CM, Lenaerts AS and Vallier L

    PloS one 2022;17;11;e0269122

    PUBMED: 36413521; DOI: 10.1371/journal.pone.0269122

  • A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings.

    Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S et al.

    Nature microbiology 2022

    PUBMED: 36411354; DOI: 10.1038/s41564-022-01263-0

  • Impact of Salmonella genome rearrangement on gene expression.

    Waters EV, Tucker LA, Ahmed JK, Wain J and Langridge GC

    Evolution letters 2022;6;6;426-437

    PUBMED: 36579163; PMC: 9783417; DOI: 10.1002/evl3.305

  • An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation.

    Seuma M, Lehner B and Bolognesi B

    Nature communications 2022;13;1;7084

    PUBMED: 36400770; PMC: 9674652; DOI: 10.1038/s41467-022-34742-3

  • The Cultural and Commercial Value of Tulsi (Ocimum tenuiflorum L.): Multidisciplinary Approaches Focusing on Species Authentication.

    Bhamra SK, Heinrich M, Johnson MRD, Howard C and Slater A

    Plants (Basel, Switzerland) 2022;11;22

    PUBMED: 36432888; DOI: 10.3390/plants11223160

  • The next-generation Open Targets Platform: reimagined, redesigned, rebuilt.

    Ochoa D, Hercules A, Carmona M, Suveges D, Baker J, Malangone C, Lopez I, Miranda A, Cruz-Castillo C, Fumis L et al.

    Nucleic acids research 2022

    PUBMED: 36399499; DOI: 10.1093/nar/gkac1046

  • Methylation Profiling in Diffuse Gliomas: Diagnostic Value and Considerations.

    Wenger A and Carén H

    Cancers 2022;14;22

    PUBMED: 36428772; DOI: 10.3390/cancers14225679

  • Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA.

    Navarro IC, Suen KM, Bensaddek D, Tanpure A, Lamond A, Balasubramanian S and Miska EA

    Wellcome open research 2022;7;282

    PUBMED: 37475875; PMC: 10354459; DOI: 10.12688/wellcomeopenres.17893.1

  • Tissue-Specific Human Extracellular Matrix Scaffolds Promote Pancreatic Tumour Progression and Chemotherapy Resistance.

    Al-Akkad W, Acedo P, Vilia MG, Frenguelli L, Ney A, Rodriguez-Hernandez I, Labib PL, Tamburrino D, Spoletini G, Hall AR et al.

    Cells 2022;11;22

    PUBMED: 36429078; DOI: 10.3390/cells11223652

  • Derivation of nociceptive sensory neurons from hiPSCs with early patterning and temporally controlled NEUROG2 overexpression.

    Plumbly W, Patikas N, Field SF, Foskolou S and Metzakopian E

    Cell reports methods 2022;2;11;100341

    PUBMED: 36452863; PMC: 9701618; DOI: 10.1016/j.crmeth.2022.100341

  • Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes.

    Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF and Genner MJ

    Molecular biology and evolution 2022

    PUBMED: 36376993; DOI: 10.1093/molbev/msac251

  • Chromosome painting and phylogenetic analysis suggest that the genus Lophostoma (Chiroptera, Phyllostomidae) is paraphyletic.

    da Silva NKN, Nagamachi CY, Rodrigues LRR, O'Brien PCM, Yang F, Ferguson-Smith MA and Pieczarka JC

    Scientific reports 2022;12;1;19514

    PUBMED: 36376355; DOI: 10.1038/s41598-022-21391-1

  • Single-cell transcriptomics defines an improved, validated monoculture protocol for differentiation of human iPSC to microglia.

    Washer SJ, Perez-Alcantara M, Chen Y, Steer J, James WS, Trynka G, Bassett AR and Cowley SA

    Scientific reports 2022;12;1;19454

    PUBMED: 36376339; PMC: 9663826; DOI: 10.1038/s41598-022-23477-2

  • Is there hybridisation between diploid and tetraploid Euphrasia in a secondary contact zone?

    Brown MR, Becher H, Williams S and Twyford AD

    American journal of botany 2022

    PUBMED: 36371731; DOI: 10.1002/ajb2.16100

  • A Multiplexed Cas13-Based Assay with Point-of-Care Attributes for Simultaneous COVID-19 Diagnosis and Variant Surveillance.

    Patchsung M, Homchan A, Aphicho K, Suraritdechachai S, Wanitchanon T, Pattama A, Sappakhaw K, Meesawat P, Wongsatit T, Athipanyasilp A et al.

    The CRISPR journal 2022

    PUBMED: 36367987; DOI: 10.1089/crispr.2022.0048

  • COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas.

    Wang D, Kumar V, Burnham KL, Mentzer AJ, Marsden BD and Knight JC

    Nucleic acids research 2022

    PUBMED: 36353986; DOI: 10.1093/nar/gkac1019

  • Rare and common genetic determinants of metabolic individuality and their effects on human health.

    Surendran P, Stewart ID, Au Yeung VPW, Pietzner M, Raffler J, Wörheide MA, Li C, Smith RF, Wittemans LBL, Bomba L et al.

    Nature medicine 2022

    PUBMED: 36357675; DOI: 10.1038/s41591-022-02046-0

  • Splitting up differentiation and cell cycle exit.

    Herms A and Jones PH

    Nature cell biology 2022

    PUBMED: 36357620; DOI: 10.1038/s41556-022-01022-7

  • The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.

    Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Güneş O, Hall P, Hayhurst J et al.

    Nucleic acids research 2022

    PUBMED: 36350656; DOI: 10.1093/nar/gkac1010

  • Detailed characterizations of cranial nerve anatomy in E14.5 mouse embryos/fetuses and their use as reference for diagnosing subtle, but potentially lethal malformations in mutants.

    Reissig LF, Geyer SH, Winkler V, Preineder E, Prin F, Wilson R, Galli A, Tudor C, White JK, Mohun TJ and Weninger WJ

    Frontiers in cell and developmental biology 2022;10;1006620

    PUBMED: 36438572; PMC: 9682249; DOI: 10.3389/fcell.2022.1006620

  • Primary hypertension, anti-hypertensive medications and the risk of severe COVID-19 in UK Biobank.

    Pavey H, Kulkarni S, Wood A, Ben-Shlomo Y, Sever P, McEniery C and Wilkinson I

    PloS one 2022;17;11;e0276781

    PUBMED: 36350810; DOI: 10.1371/journal.pone.0276781

  • Screening for Obstructive Sleep Apnea Risk by Using Machine Learning Approaches and Anthropometric Features.

    Tsai CY, Huang HT, Cheng HC, Wang J, Duh PJ, Hsu WH, Stettler M, Kuan YC, Lin YT, Hsu CR et al.

    Sensors (Basel, Switzerland) 2022;22;22

    PUBMED: 36433227; DOI: 10.3390/s22228630

  • Spatial genomics maps the structure, nature and evolution of cancer clones.

    Lomakin A, Svedlund J, Strell C, Gataric M, Shmatko A, Rukhovich G, Park JS, Ju YS, Dentro S, Kleshchevnikov V et al.

    Nature 2022;611;7936;594-602

    PUBMED: 36352222; PMC: 9668746; DOI: 10.1038/s41586-022-05425-2

  • Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor.

    Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW et al.

    Cell genomics 2022;2;11;None

    PUBMED: 36388765; PMC: 9646490; DOI: 10.1016/j.xgen.2022.100179

  • A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.

    Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G et al.

    BMC biology 2022;20;1;245

    PUBMED: 36344967; DOI: 10.1186/s12915-022-01427-8

  • Distinct pathogenic roles for resident and monocyte-derived macrophages in lupus nephritis.

    Richoz N, Tuong ZK, Loudon KW, Patiño-Martínez E, Ferdinand JR, Portet A, Bashant KR, Thevenon E, Rucci F, Hoyler T et al.

    JCI insight 2022;7;21

    PUBMED: 36345939; DOI: 10.1172/jci.insight.159751

  • Molecular subclusters of follicular lymphoma: a report from the United Kingdom's Haematological Malignancy Research Network.

    Crouch S, Painter D, Barrans SL, Roman E, Beer PA, Cooke SL, Glover P, Van Hoppe SJL, Webster N, Lacy SE et al.

    Blood advances 2022;6;21;5716-5731

    PUBMED: 35363872; PMC: 9619185; DOI: 10.1182/bloodadvances.2021005284

  • Origins and evolution of human tandem duplicated exon substitution events.

    Martinez-Gomez L, Cerdán-Vélez D, Abascal F and Tress ML

    Genome biology and evolution 2022

    PUBMED: 36346145; DOI: 10.1093/gbe/evac162

  • A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. 'Hillquist').

    Brůna T, Aryal R, Dudchenko O, Sargent DJ, Mead D, Buti M, Cavallini A, Hytönen T, Andrés J, Pham M et al.

    G3 (Bethesda, Md.) 2022

    PUBMED: 36331334; DOI: 10.1093/g3journal/jkac289

  • Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context.

    Rosso AD, Aguilera P, Quesada S, Mascardi F, Mascuka SN, Cimolai MC, Cerezo J, Spiazzi R, Conlon C, Milano C et al.

    Microorganisms 2022;10;11

    PUBMED: 36363782; DOI: 10.3390/microorganisms10112190

  • Prevalence and risk factors of bacterial enteric pathogens in men who have sex with men: a cross-sectional study at the UK's largest sexual health service.

    Mitchell HD, Whitlock G, Zdravkov J, Olsson J, Silalang P, Bardsley M, Blomquist PB, Jenkins C, Thomson NR, Field N and Hughes G

    The Journal of infection 2022

    PUBMED: 36343788; DOI: 10.1016/j.jinf.2022.10.033

  • The Childhood Acute Illness and Nutrition (CHAIN) network nested case-cohort study protocol: a multi-omics approach to understanding mortality among children in sub-Saharan Africa and South Asia.

    Njunge JM, Tickell K, Diallo AH, Sayeem Bin Shahid ASM, Gazi MA, Saleem A, Kazi Z, Ali S, Tigoi C, Mupere E et al.

    Gates open research 2022;6;77

    PUBMED: 36415883; PMC: 9646488; DOI: 10.12688/gatesopenres.13635.2

  • Demystifying the black box: from ignorance to observation to mechanism in cancer research.

    Campbell PJ

    European journal of epidemiology 2022

    PUBMED: 36326980; DOI: 10.1007/s10654-022-00935-9

  • Effect of resistance to third-generation cephalosporins on morbidity and mortality from bloodstream infections in Blantyre, Malawi: a prospective cohort study.

    Lester R, Musicha P, Kawaza K, Langton J, Mango J, Mangochi H, Bakali W, Pearse O, Mallewa J, Denis B et al.

    The Lancet. Microbe 2022;3;12;e922-e930

    PUBMED: 36335953; PMC: 9712123; DOI: 10.1016/S2666-5247(22)00282-8

  • Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.

    Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U et al.

    PLoS genetics 2022;18;11;e1010367

    PUBMED: 36327219; DOI: 10.1371/journal.pgen.1010367

  • An immune dysfunction score for stratification of patients with acute infection based on whole-blood gene expression.

    Cano-Gamez E, Burnham KL, Goh C, Allcock A, Malick ZH, Overend L, Kwok A, Smith DA, Peters-Sengers H, Antcliffe D et al.

    Science translational medicine 2022;14;669;eabq4433

    PUBMED: 36322631; DOI: 10.1126/scitranslmed.abq4433

  • The genetic counsellor role in the United Kingdom : Position on behalf of the Association of Genetic Nurses and Counsellors (AGNC), Endorsed by the Genetic Counsellor Registration Board (GCRB) and Academy for Healthcare Science (AHCS).

    Middleton A, Taverner N, Moreton N, Rizzo R, Houghton C, Watt C, Horton E, Levene S, Leonard P, Melville A et al.

    European journal of human genetics : EJHG 2022

    PUBMED: 36316491; DOI: 10.1038/s41431-022-01212-9

  • CO-CONNECT: A hybrid architecture to facilitate rapid discovery and access to UK wide data in the response to the COVID-19 pandemic.

    Jefferson E, Cole C, Mumtaz S, Cox S, Giles T, Adejumo S, Urwin E, Lea D, McDonald C, Best J et al.

    Journal of medical Internet research 2022

    PUBMED: 36322788; DOI: 10.2196/40035

  • Scope of professional roles for genetic counsellors and clinical geneticists in the United Kingdom : Position on behalf of the Association of Genetic Nurses and Counsellors and the Clinical Genetics Society.

    Middleton A, Taverner N, Houghton C, Smithson S, Balasubramanian M and Elmslie F

    European journal of human genetics : EJHG 2022

    PUBMED: 36316490; DOI: 10.1038/s41431-022-01214-7

  • Sequence-Based Identification of Metronidazole-Resistant Clostridioides difficile Isolates.

    Smits WK, Harmanus C, Sanders IMJG, Bry L, Blackwell GA, Ducarmon QR, de Oliveira Ferreira E and Kuijper EJ

    Emerging infectious diseases 2022;28;11;2308-2311

    PUBMED: 36286226; PMC: 9622256; DOI: 10.3201/eid2811.220615

  • Mild-to-Moderate Kidney Dysfunction and Cardiovascular Disease: Observational and Mendelian Randomization Analyses.

    Gaziano L, Sun L, Arnold M, Bell S, Cho K, Kaptoge SK, Song RJ, Burgess S, Posner DC, Mosconi K et al.

    Circulation 2022

    PUBMED: 36314129; DOI: 10.1161/CIRCULATIONAHA.122.060700

  • Chromosomal instability (CIN) in HAP1 cell lines revealed by multiplex fluorescence in situ hybridisation (M-FISH).

    Banerjee R, Sotero-Caio CG, Fu B and Yang F

    Molecular cytogenetics 2022;15;1;46

    PUBMED: 36289492; PMC: 9609465; DOI: 10.1186/s13039-022-00625-x

  • Large-Scale Evaluation of a Rapid Fully Automated Analysis Platform to Detect and Refute Outbreaks Based on MRSA Genome Comparisons.

    Raven KE, Bragin E, Blane B, Leek D, Kumar N, Rhodes PA, Enoch DA, Thaxter R, Brown NM, Parkhill J and Peacock SJ

    mSphere 2022;e0028322

    PUBMED: 36286527; DOI: 10.1128/msphere.00283-22

  • Small non-coding RNA sequencing reveals global dysregulation of piwi-interacting RNA (piRNA) expression in gonadal malignant germ cell tumours.

    Laidlaw S, Alonso-Crisostomo L, Bailey S, Saini HK, Molnár A, Nicholson JC, Enright AJ, Scarpini CG, Rahbari R, Coleman N et al.

    Andrology 2022;11;4;738-755

    PUBMED: 36254403; DOI: 10.1111/andr.13312

  • The gut microbial metabolic capacity of microbiome-humanized vs. wild type rodents reveals a likely dual role of intestinal bacteria in hepato-intestinal schistosomiasis.

    Cortés A, Martin J, Rosa BA, Stark KA, Clare S, McCarthy C, Harcourt K, Brandt C, Tolley C, Lawley TD et al.

    PLoS neglected tropical diseases 2022;16;10;e0010878

    PUBMED: 36279280; DOI: 10.1371/journal.pntd.0010878

  • HIRA loss transforms FH-deficient cells.

    Valcarcel-Jimenez L, Rogerson C, Yong C, Schmidt C, Yang M, Cremades-Rodelgo M, Harle V, Offord V, Wong K, Mora A et al.

    Science advances 2022;8;42;eabq8297

    PUBMED: 36269833; PMC: 9586478; DOI: 10.1126/sciadv.abq8297

  • Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish.

    Vernaz G, Hudson AG, Santos ME, Fischer B, Carruthers M, Shechonge AH, Gabagambi NP, Tyers AM, Ngatunga BP, Malinsky M et al.

    Nature ecology & evolution 2022

    PUBMED: 36266459; DOI: 10.1038/s41559-022-01894-w

  • p53 mutation in normal esophagus promotes multiple stages of carcinogenesis but is constrained by clonal competition.

    Murai K, Dentro S, Ong SH, Sood R, Fernandez-Antoran D, Herms A, Kostiou V, Abnizova I, Hall BA, Gerstung M and Jones PH

    Nature communications 2022;13;1;6206

    PUBMED: 36266286; PMC: 9584949; DOI: 10.1038/s41467-022-33945-y

  • An assembly line for an improved human reference genome.

    No authors listed

    Nature 2022

    PUBMED: 36261717; DOI: 10.1038/d41586-022-03151-3

  • Genetic insights into the social organization of Neanderthals.

    Skov L, Peyrégne S, Popli D, Iasi LNM, Devièse T, Slon V, Zavala EI, Hajdinjak M, Sümer AP, Grote S et al.

    Nature 2022;610;7932;519-525

    PUBMED: 36261548; DOI: 10.1038/s41586-022-05283-y

  • Identifying the transcriptional drivers of metastasis embedded within localized melanoma.

    Suresh S, Rabbie R, Garg M, Lumaquin D, Huang TH, Montal E, Ma Y, Cruz NM, Tang X, Nsengimana J et al.

    Cancer discovery 2022

    PUBMED: 36259947; DOI: 10.1158/2159-8290.CD-22-0427

  • Semi-automated assembly of high-quality diploid human reference genomes.

    Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D et al.

    Nature 2022

    PUBMED: 36261518; DOI: 10.1038/s41586-022-05325-5

  • Genomic landscape of drug response reveals mediators of anthelmintic resistance.

    Doyle SR, Laing R, Bartley D, Morrison A, Holroyd N, Maitland K, Antonopoulos A, Chaudhry U, Flis I, Howell S et al.

    Cell reports 2022;41;3;111522

    PUBMED: 36261007; DOI: 10.1016/j.celrep.2022.111522

  • ABC of the future

    Pesonen, Henri, Simola, Umberto, Kohn-Luque, Alvaro, Vuollekoski, Henri, Lai, Xiaoran et al.

    International Statistical Review 2022

    DOI: 10.1111/insr.12522

  • Defining the origin, evolution, and immune composition of SDH-deficient renal cell carcinoma.

    Neves JB, Roberts K, Nguyen JS, El Sheikh S, Tran-Dang MA, Horsfield C, Mumtaz F, Campbell P, Stauss H, Tran MGB and Mitchell T

    iScience 2022;25;11;105389

    PUBMED: 36345344; PMC: 9636038; DOI: 10.1016/j.isci.2022.105389

  • Isolation and Genomic Analysis of an Intracellular Mycobacterium gordonae from a Free-Living Acanthamoeba sp. in a Hospital Environment in Lima, Peru.

    Cabello-Vílchez AM, Dávila-Barclay A and Tsukayama P

    Microbiology resource announcements 2022;e0078422

    PUBMED: 36250863; DOI: 10.1128/mra.00784-22

  • Systematic Mendelian randomization using the human plasma proteome to discover potential therapeutic targets for stroke.

    Chen L, Peters JE, Prins B, Persyn E, Traylor M, Surendran P, Karthikeyan S, Yonova-Doing E, Di Angelantonio E, Roberts DJ et al.

    Nature communications 2022;13;1;6143

    PUBMED: 36253349; DOI: 10.1038/s41467-022-33675-1

  • Analyses of circRNA Expression throughout the Light-Dark Cycle Reveal a Strong Regulation of Cdr1as, Associated with Light Entrainment in the SCN.

    Ivanov A, Mattei D, Radscheit K, Compagnion AC, Pett JP, Herzel H, Paolicelli RC, Piwecka M, Meyer U and Beule D

    International journal of molecular sciences 2022;23;20

    PUBMED: 36293208; PMC: 9604060; DOI: 10.3390/ijms232012347

  • Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells.

    Lynall ME, Soskic B, Hayhurst J, Schwartzentruber J, Levey DF, Pathak GA, Polimanti R, Gelernter J, Stein MB, Trynka G et al.

    Nature communications 2022;13;1;6102

    PUBMED: 36243721; DOI: 10.1038/s41467-022-33885-7

  • AKT-mTORC1 reactivation is the dominant resistance driver for PI3Kβ/AKT inhibitors in PTEN-null breast cancer and can be overcome by combining with Mcl-1 inhibitors.

    Dunn S, Eberlein C, Yu J, Gris-Oliver A, Ong SH, Yelland U, Cureton N, Staniszewska A, McEwen R, Fox M et al.

    Oncogene 2022;41;46;5046-5060

    PUBMED: 36241868; PMC: 9652152; DOI: 10.1038/s41388-022-02482-9

  • Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids.

    Rebelo A, Duarte B, Ferreira C, Mourão J, Ribeiro S, Freitas AR, Coque TM, Willems R, Corander J, Peixe L et al.

    International journal of food microbiology 2022;384;109981

    PUBMED: 36306546; DOI: 10.1016/j.ijfoodmicro.2022.109981

  • The genome sequence of the orange-tip butterfly, Anthocharis cardamines (Linnaeus, 1758).

    Ebdon S, Bisschop G, Lohse K, Saccheri I, Davies J, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;260

    PUBMED: 36408293; PMC: 9643846; DOI: 10.12688/wellcomeopenres.18117.1

  • Aetiology and Potential Animal Exposure in Central Nervous System Infections in Vietnam.

    Brindle HE, Nadjm B, Choisy M, Christley R, Griffiths M, Baker S, Bryant JE, Campbell JI, Nguyen VVC, Nguyen TND et al.

    EcoHealth 2022

    PUBMED: 36227390; DOI: 10.1007/s10393-022-01611-w

  • Diving into the complexity of the spirochetal endoflagellum.

    San Martin F, Fule L, Iraola G, Buschiazzo A and Picardeau M

    Trends in microbiology 2022

    PUBMED: 36244923; DOI: 10.1016/j.tim.2022.09.010

  • Schistosomes go single cell.

    Rinaldi G, Attenborough T, Rawlinson KA and Berriman M

    Nature reviews. Microbiology 2022

    PUBMED: 36229520; DOI: 10.1038/s41579-022-00810-0

  • The genome sequence of the Adonis blue, Lysandra bellargus (Rottemburg, 1775).

    Lohse K, Hayward A, Vila R, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Howe C and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;255

    PUBMED: 37065725; PMC: 10090861; DOI: 10.12688/wellcomeopenres.18330.1

  • The genome sequence of the meadow field syrph, Eupeodes latifasciatus (Macquart, 1829).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Chua P and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;253

    PUBMED: 36938120; PMC: 10015120; DOI: 10.12688/wellcomeopenres.18113.1

  • The genome sequence of the wood white butterfly, Leptidea sinapis (Linnaeus, 1758).

    Lohse K, Höök L, Näsvall K, Backström N, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;254

    PUBMED: 37025368; PMC: 10071140; DOI: 10.12688/wellcomeopenres.18118.1

  • A saturated map of common genetic variants associated with human height.

    Yengo L, Vedantam S, Marouli E, Sidorenko J, Bartell E, Sakaue S, Graff M, Eliasen AU, Jiang Y, Raghavan S et al.

    Nature 2022

    PUBMED: 36224396; DOI: 10.1038/s41586-022-05275-y

  • Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease.

    Zhou W, Kanai M, Wu KH, Rasheed H, Tsuo K, Hirbo JB, Wang Y, Bhattacharya A, Zhao H, Namba S et al.

    Cell genomics 2022;2;10;100192

    PUBMED: 36777996; PMC: 9903716; DOI: 10.1016/j.xgen.2022.100192

  • High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences.

    Boddé M, Makunin A, Ayala D, Bouafou L, Diabaté A, Ekpo UF, Kientega M, Le Goff G, Makanga BK, Ngangue MF et al.

    eLife 2022;11

    PUBMED: 36222650; PMC: 9648975; DOI: 10.7554/eLife.78775

  • Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma.

    Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles-Espinoza CD et al.

    The Journal of pathology 2022

    PUBMED: 36219477; DOI: 10.1002/path.6019

  • Gene Sequencing Identifies Perturbation in Nitric Oxide Signaling as a Nonlipid Molecular Subtype of Coronary Artery Disease.

    Khera AV, Wang M, Chaffin M, Emdin CA, Samani NJ, Schunkert H, Watkins H, McPherson R, Elosua R, Boerwinkle E et al.

    Circulation. Genomic and precision medicine 2022;101161CIRCGEN121003598

    PUBMED: 36215124; DOI: 10.1161/CIRCGEN.121.003598

  • Pneumococcal within-host diversity during colonization, transmission and treatment.

    Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C et al.

    Nature microbiology 2022

    PUBMED: 36216891; DOI: 10.1038/s41564-022-01238-1

  • Importance of Aspartyl Protease 5 in the establishment of the intracellular niche during acute and chronic infection of Toxoplasma gondii.

    Dogga SK, Lunghi M, Maco B, Li J, Claudi B, Marq JB, Chicherova N, Kockmann T, Bumann D, Hehl AB et al.

    Molecular microbiology 2022

    PUBMED: 36210525; DOI: 10.1111/mmi.14987

  • The genome sequence of the killer whale, Orcinus orca (Linnaeus, 1758).

    Foote A, Bunskoek P, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;250

    PUBMED: 36974126; PMC: 10039322; DOI: 10.12688/wellcomeopenres.18278.1

  • Development and validation of a quantitative PCR for the detection of Guinea worm (Dracunculus medinensis).

    Coker SM, Box EK, Stilwell N, Thiele EA, Cotton JA, Haynes E, Yabsley MJ and Cleveland CA

    PLoS neglected tropical diseases 2022;16;10;e0010830

    PUBMED: 36206300; DOI: 10.1371/journal.pntd.0010830

  • Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal Disease.

    Kwambana-Adams BA, Clark SA, Tay N, Agbla S, Chaguza C, Kagucia EW, Borrow R and Heyderman RS

    International journal of molecular sciences 2022;23;19

    PUBMED: 36233182; DOI: 10.3390/ijms231911879

  • The genome sequence of the garden grass-veneer, Chrysoteuchia culmella (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Parkerson L and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;248

    PUBMED: 36926380; PMC: 10011750; DOI: 10.12688/wellcomeopenres.18107.1

  • Faecal egg counts and nemabiome metabarcoding highlight the genomic complexity of equine cyathostomin communities and provide insight into their dynamics in a Scottish native pony herd.

    Sargison N, Chambers A, Chaudhry U, Costa L, Doyle SR, Ehimiyein A, Evans M, Jennings A, Kelly R, Sargison F et al.

    International journal for parasitology 2022

    PUBMED: 36208676; DOI: 10.1016/j.ijpara.2022.08.002

  • Robust Genetic Analysis of the X-Linked Anophthalmic (Ie) Mouse.

    Hernandez-Moran BA, Papanastasiou AS, Parry D, Meynert A, Gautier P, Grimes G, Adams IR, Trejo-Reveles V, Bengani H, Keighren M et al.

    Genes 2022;13;10

    PUBMED: 36292683; PMC: 9601528; DOI: 10.3390/genes13101797

  • The genome sequence of the merveille du jour, Griposia aprilina (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Lees D and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;247

    PUBMED: 36865376; PMC: 9971638; DOI: 10.12688/wellcomeopenres.18122.1

  • Feline Oncogenomics: What Do We Know about the Genetics of Cancer in Domestic Cats?

    Ludwig L, Dobromylskyj M, Wood GA and van der Weyden L

    Veterinary sciences 2022;9;10

    PUBMED: 36288160; PMC: 9609674; DOI: 10.3390/vetsci9100547

  • Gain-of-function mutations in KCNK3 cause a developmental disorder with sleep apnea.

    Sörmann J, Schewe M, Proks P, Jouen-Tachoire T, Rao S, Riel EB, Agre KE, Begtrup A, Dean J, Descartes M et al.

    Nature genetics 2022;54;10;1534-1543

    PUBMED: 36195757; PMC: 9534757; DOI: 10.1038/s41588-022-01185-x

  • A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin.

    Qiu D, Pei JV, Rosling JEO, Thathy V, Li D, Xue Y, Tanner JD, Penington JS, Aw YTV, Aw JYH et al.

    Nature communications 2022;13;1;5746

    PUBMED: 36180431; PMC: 9525273; DOI: 10.1038/s41467-022-33403-9

  • Stroke genetics informs drug discovery and risk prediction across ancestries.

    Mishra A, Malik R, Hachiya T, Jürgenson T, Namba S, Posner DC, Kamanu FK, Koido M, Le Grand Q, Shi M et al.

    Nature 2022

    PUBMED: 36180795; PMC: 9524349; DOI: 10.1038/s41586-022-05165-3

  • Characterization of Two Mouse Chd7 Heterozygous Loss-of-Function Models Shows Dysgenesis of the Corpus Callosum and Previously Unreported Features of CHARGE Syndrome.

    Collins SC, Vancollie VE, Mikhaleva A, Wagner C, Balz R, Lelliott CJ and Yalcin B

    International journal of molecular sciences 2022;23;19

    PUBMED: 36232804; DOI: 10.3390/ijms231911509

  • Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework.

    Rossi SH, Newsham I, Pita S, Brennan K, Park G, Smith CG, Lach RP, Mitchell T, Huang J, Babbage A et al.

    Science advances 2022;8;39;eabn9828

    PUBMED: 36170366; DOI: 10.1126/sciadv.abn9828

  • False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.

    Kim J, Lee C, Ko BJ, Yoo DA, Won S, Phillippy AM, Fedrigo O, Zhang G, Howe K, Wood J et al.

    Genome biology 2022;23;1;204

    PUBMED: 36167554; DOI: 10.1186/s13059-022-02765-0

  • Effect of long-lasting insecticidal nets with and without piperonyl butoxide on malaria indicators in Uganda (LLINEUP): final results of a cluster-randomised trial embedded in a national distribution campaign.

    Maiteki-Sebuguzi C, Gonahasa S, Kamya MR, Katureebe A, Bagala I, Lynd A, Mutungi P, Kigozi SP, Opigo J, Hemingway J et al.

    The Lancet. Infectious diseases 2022

    PUBMED: 36174592; DOI: 10.1016/S1473-3099(22)00469-8

  • Evolution of the ancestral mammalian karyotype and syntenic regions.

    Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, Ryder OA, Steiner C, Houck ML, Hall S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;40;e2209139119

    PUBMED: 36161960; DOI: 10.1073/pnas.2209139119

  • Myeloid cell interferon secretion restricts Zika flavivirus infection of developing and malignant human neural progenitor cells.

    Bulstrode H, Girdler GC, Gracia T, Aivazidis A, Moutsopoulos I, Young AMH, Hancock J, He X, Ridley K, Xu Z et al.

    Neuron 2022

    PUBMED: 36174572; DOI: 10.1016/j.neuron.2022.09.002

  • Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis.

    Clark SJ, Argelaguet R, Lohoff T, Krueger F, Drage D, Göttgens B, Marioni JC, Nichols J and Reik W

    Genome biology 2022;23;1;202

    PUBMED: 36163261; DOI: 10.1186/s13059-022-02762-3

  • Altered Plasma, Urine, and Tissue Profiles of Sulfatides and Sphingomyelins in Patients with Renal Cell Carcinoma.

    Jirásko R, Idkowiak J, Wolrab D, Kvasnička A, Friedecký D, Polański K, Študentová H, Študent V, Melichar B and Holčapek M

    Cancers 2022;14;19

    PUBMED: 36230546; DOI: 10.3390/cancers14194622

  • Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate.

    Ijaz UZ, Gundogdu O, Keating C, van Eekert M, Gibson W, Parkhill J, Abilahi F, Liseki B, Nguyen VA, Sudgen S et al.

    Frontiers in microbiology 2022;13;960747

    PUBMED: 36212864; PMC: 9539666; DOI: 10.3389/fmicb.2022.960747

  • Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass.

    Duffy MF, Tonkin-Hill GQ, Trianty L, Noviyanti R, Nguyen HHT, Rambhatla JS, McConville MJ, Rogerson SJ, Brown GV, Price RN et al.

    Nature communications 2022;13;1;5557

    PUBMED: 36151085; PMC: 9508081; DOI: 10.1038/s41467-022-32996-5

  • The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates.

    Buhigas C, Warren AY, Leung WK, Whitaker HC, Luxton HJ, Hawkins S, Kay J, Butler A, Xu Y, Woodcock DJ et al.

    Molecular cancer 2022;21;1;183

    PUBMED: 36131292; PMC: 9494848; DOI: 10.1186/s12943-022-01644-3

  • GWAS of genetic factors affecting white blood cell morphological parameters in Sardinians uncovers influence of chromosome 11 innate immunity gene cluster on eosinophil morphology.

    Marongiu M, Pérez-Mejías G, Orrù V, Steri M, Sidore C, Díaz-Quintana A, Mulas A, Busonero F, Maschio A, Walter K et al.

    Human molecular genetics 2022

    PUBMED: 36136759; DOI: 10.1093/hmg/ddac238

  • The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life.

    Rivas-Solano O, Van der Henst M, Castillo-Zeledón A, Suárez-Esquivel M, Muñoz-Vargas L, Capitan-Barrios Z, Thomson NR, Chaves-Olarte E, Moreno E, De Bolle X and Guzmán-Verri C

    PloS one 2022;17;9;e0274397

    PUBMED: 36129877; DOI: 10.1371/journal.pone.0274397

  • Causal discovery for the microbiome.

    Corander J, Hanage WP and Pensar J

    The Lancet. Microbe 2022

    PUBMED: 36152674; DOI: 10.1016/S2666-5247(22)00186-0

  • Somatic Mutational Landscape in Mexican Patients: CDH1 Mutations and chr20q13.33 Amplifications Are Associated with Diffuse-Type Gastric Adenocarcinoma.

    Cerrato-Izaguirre D, Chirino YI, Prada D, Quezada-Maldonado EM, Herrera LA, Hernández-Guerrero A, Alonso-Larraga JO, Herrera-Goepfert R, Oñate-Ocaña LF, Cantú-de-León D et al.

    International journal of molecular sciences 2022;23;19

    PUBMED: 36232418; DOI: 10.3390/ijms231911116

  • Vivaxin genes encode highly immunogenic, non-variant antigens on the Trypanosoma vivax cell-surface.

    Romero-Ramirez A, Casas-Sánchez A, Autheman D, Duffy CW, Brandt C, Clare S, Harcourt K, André MR, de Almeida Castilho Neto KJG, Teixeira MMG et al.

    PLoS neglected tropical diseases 2022;16;9;e0010791

    PUBMED: 36129968; DOI: 10.1371/journal.pntd.0010791

  • An in situ analysis pipeline for initial host-pathogen interactions reveals signatures of human colorectal HIV transmission.

    Baharlou H, Canete N, Vine EE, Hu K, Yuan D, Sandgren KJ, Bertram KM, Nasr N, Rhodes JW, Gosselink MP et al.

    Cell reports 2022;40;12;111385

    PUBMED: 36130503; DOI: 10.1016/j.celrep.2022.111385

  • Association of COVID-19 With Major Arterial and Venous Thrombotic Diseases: A Population-Wide Cohort Study of 48 Million Adults in England and Wales.

    Knight R, Walker V, Ip S, Cooper JA, Bolton T, Keene S, Denholm R, Akbari A, Abbasizanjani H, Torabi F et al.

    Circulation 2022;146;12;892-906

    PUBMED: 36121907; DOI: 10.1161/CIRCULATIONAHA.122.060785

  • SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling.

    Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA et al.

    The EMBO journal 2022;e111338

    PUBMED: 36121125; DOI: 10.15252/embj.2022111338

  • Treatment time and circadian genotype interact to influence radiotherapy side-effects. A prospective European validation study using the REQUITE cohort.

    Webb AJ, Harper E, Rattay T, Aguado-Barrera ME, Azria D, Bourgier C, Brengues M, Briers E, Bultijnck R, Chang-Claude J et al.

    EBioMedicine 2022;84;104269

    PUBMED: 36130474; DOI: 10.1016/j.ebiom.2022.104269

  • Efficient generation of mNeonGreen Plasmodium falciparum reporter lines enables quantitative fitness analysis.

    Hoshizaki J, Jagoe H and Lee MCS

    Frontiers in cellular and infection microbiology 2022;12;981432

    PUBMED: 36189342; PMC: 9523114; DOI: 10.3389/fcimb.2022.981432

  • Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis.

    Vaishnavi A, Juan J, Jacob M, Stehn C, Gardner EE, Scherzer MT, Schuman S, van Veen JE, Murphy B, Hackett CS et al.

    Cancer research 2022

    PUBMED: 36112789; DOI: 10.1158/0008-5472.CAN-21-3214

  • The genome sequence of the yellow-legged clearwing, Synanthedon vespiformis (Linnaeus, 1761).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Lees D and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;233

    PUBMED: 36895518; PMC: 9989545; DOI: 10.12688/wellcomeopenres.18109.1

  • Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study.

    Stirrup O, Blackstone J, Mapp F, MacNeil A, Panca M, Holmes A, Machin N, Shin GY, Mahungu T, Saeed K et al.

    eLife 2022;11

    PUBMED: 36098502; DOI: 10.7554/eLife.78427

  • Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations.

    Wit J, Workentine ML, Redman E, Laing R, Stevens L, Cotton JA, Chaudhry U, Ali Q, Andersen EC, Yeaman S et al.

    International journal for parasitology 2022

    PUBMED: 36113620; DOI: 10.1016/j.ijpara.2022.07.004

  • Linking transcriptomes with morphological and functional phenotypes in mammalian retinal ganglion cells.

    Huang W, Xu Q, Su J, Tang L, Hao ZZ, Xu C, Liu R, Shen Y, Sang X, Xu N et al.

    Cell reports 2022;40;11;111322

    PUBMED: 36103830; DOI: 10.1016/j.celrep.2022.111322

  • The genome sequence of the brimstone moth, Opisthograptis luteolata (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Phillips D and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;227

    PUBMED: 36226159; PMC: 9523282; DOI: 10.12688/wellcomeopenres.18101.1

  • The genome sequence of the pale mottled willow, Caradrina clavipalpis (Scopoli, 1763).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Boyes C and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;225

    PUBMED: 36998243; PMC: 10043633; DOI: 10.12688/wellcomeopenres.18103.1

  • The genome sequence of the peacock moth, Macaria notata (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Couch C, Plotkin D, Kawahara AY and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;228

    PUBMED: 37767015; PMC: 10521120; DOI: 10.12688/wellcomeopenres.18108.1

  • The genome sequence of the sallow kitten, Furcula furcula (Clerck, 1759).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Parker B, Plotkin D, Kawahara AY and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;229

    PUBMED: 36879919; PMC: 9984736; DOI: 10.12688/wellcomeopenres.18112.1

  • The pathophysiology of bilateral and multifocal Wilms tumors: What we can learn from the study of predisposition syndromes.

    Welter N, Brzezinski J, Treece A, Chintagumpala M, Young MD, Perotti D, Kieran K, Jongmans MCJ and Murphy AJ

    Pediatric blood & cancer 2022;e29984

    PUBMED: 36094328; DOI: 10.1002/pbc.29984

  • Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.

    Njoroge SM, Madé LF, von Mentzer A, Kulohoma BW, Kamanu TK, Ouko TT, Kiiru J, Ward MJ, Thomson NR, Fèvre EM et al.

    Microbiology resource announcements 2022;e0041622

    PUBMED: 36094211; DOI: 10.1128/mra.00416-22

  • Obesity Is Associated with Attenuated Tissue Immunity in COVID-19.

    Guo SA, Bowyer GS, Ferdinand JR, Maes M, Tuong ZK, Gillman E, Liao M, Lindeboom RGH, Yoshida M, Worlock K et al.

    American journal of respiratory and critical care medicine 2022

    PUBMED: 36095143; DOI: 10.1164/rccm.202204-0751OC

  • Spatial transcriptomics.

    Anderson AC, Yanai I, Yates LR, Wang L, Swarbrick A, Sorger P, Santagata S, Fridman WH, Gao Q, Jerby L et al.

    Cancer cell 2022;40;9;895-900

    PUBMED: 36099884; DOI: 10.1016/j.ccell.2022.08.021

  • Endocarditis Caused by Nontypeable Streptococcus pneumoniae.

    Henriet SSV, Langereis JD, Lo SW, Bentley S, Mesman RJ, Fejzic Z, van Niftrik L, van Sorge NM, Wertheim HFL, de Jonge MI and Cremers AJH

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022;75;4;719-722

    PUBMED: 35134152; PMC: 9464071; DOI: 10.1093/cid/ciac079

  • Epidemiology of Renal Cell Carcinoma: 2022 Update.

    Bukavina L, Bensalah K, Bray F, Carlo M, Challacombe B, Karam J, Kassouf W, Mitchell T, Montironi R, O'Brien T et al.

    European urology 2022

    PUBMED: 36100483; DOI: 10.1016/j.eururo.2022.08.019

  • Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays.

    Flynn R, Washer S, Jeffries AR, Andrayas A, Shireby G, Kumari M, Schalkwyk LC, Mill J and Hannon E

    Human molecular genetics 2022;31;18;3181-3190

    PUBMED: 35567415; PMC: 9476619; DOI: 10.1093/hmg/ddac112

  • Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity.

    Huyghe A, Furlan G, Schroeder J, Cascales E, Trajkova A, Ruel M, Stüder F, Larcombe M, Yang Sun YB, Mugnier F et al.

    Nature cell biology 2022;24;9;1350-1363

    PUBMED: 36075976; PMC: 9481462; DOI: 10.1038/s41556-022-00986-w

  • IFITM3 restricts virus-induced inflammatory cytokine production by limiting Nogo-B mediated TLR responses.

    Clement M, Forbester JL, Marsden M, Sabberwal P, Sommerville MS, Wellington D, Dimonte S, Clare S, Harcourt K, Yin Z et al.

    Nature communications 2022;13;1;5294

    PUBMED: 36075894; DOI: 10.1038/s41467-022-32587-4

  • Defence mitigation by predators of chemically defended prey integrated over the predation sequence and across biological levels with a focus on cardiotonic steroids.

    Mohammadi S, Yang L, Bulbert M and Rowland HM

    Royal Society open science 2022;9;9;220363

    PUBMED: 36133149; PMC: 9449480; DOI: 10.1098/rsos.220363

  • Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.

    Wang Z, Emmerich A, Pillon NJ, Moore T, Hemerich D, Cornelis MC, Mazzaferro E, Broos S, Ahluwalia TS, Bartz TM et al.

    Nature genetics 2022

    PUBMED: 36071172; DOI: 10.1038/s41588-022-01165-1

  • Novel antigen presenting cell imparts Treg-dependent tolerance to gut microbiota.

    Akagbosu B, Tayyebi Z, Shibu G, Paucar Iza YA, Deep D, Parisotto YF, Fisher L, Pasolli HA, Thevin V, Elmentaite R et al.

    Nature 2022

    PUBMED: 36070798; DOI: 10.1038/s41586-022-05309-5

  • Precise identification of cancer cells from allelic imbalances in single cell transcriptomes.

    Trinh MK, Pacyna CN, Kildisiute G, Thevanesan C, Piapi A, Ambridge K, Anderson ND, Khabirova E, Prigmore E, Straathof K et al.

    Communications biology 2022;5;1;884

    PUBMED: 36071103; PMC: 9452529; DOI: 10.1038/s42003-022-03808-9

  • Vibrio cholerae O1 El Tor strains linked to global cholera show region-specific patterns by pulsed-field gel electrophoresis.

    Johura FT, Biswas SR, Rashed SM, Islam MT, Islam S, Sultana M, Watanabe H, Huq A, Thomson NR, Colwell RR and Alam M

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2022;105363

    PUBMED: 36087684; DOI: 10.1016/j.meegid.2022.105363

  • EpiBeds: Data informed modelling of the COVID-19 hospital burden in England.

    Overton CE, Pellis L, Stage HB, Scarabel F, Burton J, Fraser C, Hall I, House TA, Jewell C, Nurtay A et al.

    PLoS computational biology 2022;18;9;e1010406

    PUBMED: 36067224; DOI: 10.1371/journal.pcbi.1010406

  • Colonization dynamics of extended-spectrum beta-lactamase-producing Enterobacterales in the gut of Malawian adults.

    Lewis JM, Mphasa M, Banda R, Beale MA, Heinz E, Mallewa J, Jewell C, Faragher B, Thomson NR and Feasey NA

    Nature microbiology 2022

    PUBMED: 36065064; DOI: 10.1038/s41564-022-01216-7

  • One step closer to quantifying 'clinical likelihood' in pre-test probability.

    Weir-McCall JR, Williams MC and Wood A

    European heart journal. Quality of care & clinical outcomes 2022;8;6;597-599

    PUBMED: 35776955; PMC: 9442847; DOI: 10.1093/ehjqcco/qcac039

  • The genus Serratia revisited by genomics.

    Williams DJ, Grimont PAD, Cazares A, Grimont F, Ageron E, Pettigrew KA, Cazares D, Njamkepo E, Weill FX, Heinz E et al.

    Nature communications 2022;13;1;5195

    PUBMED: 36057639; DOI: 10.1038/s41467-022-32929-2

  • Clinical and laboratory factors associated with neonatal sepsis mortality at a major Vietnamese children's hospital.

    Toan ND, Darton TC, Huong NHT, Nhat LTH, Nguyen TNT, Tuyen HT, Thinh LQ, Mau NK, Tam PTT, Phuong CN et al.

    PLOS global public health 2022;2;9;e0000875

    PUBMED: 36962870; PMC: 10021837; DOI: 10.1371/journal.pgph.0000875

  • Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011-2018 determined through whole-genome sequencing.

    Egorova E, Kumar N, Gladstone RA, Urban Y, Voropaeva E, Chaplin AV, Rumiantseva E, Svistunova TS, Hawkins PA, Klugman KP et al.

    Microbial genomics 2022;8;9

    PUBMED: 36112007; DOI: 10.1099/mgen.0.000851

  • Neurocognitive trajectory and proteomic signature of inherited risk for Alzheimer's disease.

    Paranjpe MD, Chaffin M, Zahid S, Ritchie S, Rotter JI, Rich SS, Gerszten R, Guo X, Heckbert S, Tracy R et al.

    PLoS genetics 2022;18;9;e1010294

    PUBMED: 36048760; DOI: 10.1371/journal.pgen.1010294

  • Ribosomal MLST nucleotide identity (rMLST-NI), a rapid bacterial species identification method: application to Klebsiella and Raoultella genomic species validation.

    Bray JE, Correia A, Varga M, Jolley KA, Maiden MCJ and Rodrigues CMC

    Microbial genomics 2022;8;9

    PUBMED: 36098501; DOI: 10.1099/mgen.0.000849

  • Contribution of Common Genetic Variants to Risk of Early Onset Ischemic Stroke.

    Jaworek T, Xu H, Gaynor BJ, Cole JW, Rannikmae K, Stanne TM, Tomppo L, Abedi V, Amouyel P, Armstrong ND et al.

    Neurology 2022

    PUBMED: 36240095; DOI: 10.1212/WNL.0000000000201006

  • Physiological robustness of model Gram-negative bacteria in response to genome rewiring.

    Dorman CJ and Dorman MJ

    Microbial physiology 2022

    PUBMED: 36041419; DOI: 10.1159/000526651

  • Processive and distributive non-equilibrium networks discriminate in alternate limits

    Venkataraman, G.G., Miska, E.A. and Jordan, D.J.

    Journal of Statistical Mechanics-Theory and Experiment 2022;083206

    DOI: 10.1088/1742-5468/ac85e8

  • Self-organization of plasticity and specialization in a primitively social insect.

    Patalano S, Alsina A, Gregorio-Rodríguez C, Bachman M, Dreier S, Hernando-Herraez I, Nana P, Balasubramanian S, Sumner S, Reik W and Rulands S

    Cell systems 2022;13;9;768-779.e4

    PUBMED: 36044898; DOI: 10.1016/j.cels.2022.08.002

  • Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a.

    Wongpalee SP, Thananchai H, Chewapreecha C, Roslund HB, Chomkatekaew C, Tananupak W, Boonklang P, Pakdeerat S, Seng R, Chantratita N et al.

    PLoS neglected tropical diseases 2022;16;8;e0010659

    PUBMED: 36037185; PMC: 9423629; DOI: 10.1371/journal.pntd.0010659

  • Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility.

    Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G et al.

    Nature genetics 2022

    PUBMED: 36038634; DOI: 10.1038/s41588-022-01156-2

  • The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK.

    Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, Ellaby N, Gallagher E, Groves N, Jackson B et al.

    Virus evolution 2022;8;2;veac080

    PUBMED: 36533153; PMC: 9752794; DOI: 10.1093/ve/veac080

  • Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19.

    Kotanidis CP, Xie C, Alexander D, Rodrigues JCL, Burnham K, Mentzer A, O'Connor D, Knight J, Siddique M, Lockstone H et al.

    The Lancet. Digital health 2022

    PUBMED: 36038496; DOI: 10.1016/S2589-7500(22)00132-7

  • Mycobacterium abscessus pathogenesis identified by phenogenomic analyses.

    Boeck L, Burbaud S, Skwark M, Pearson WH, Sangen J, Wuest AW, Marshall EKP, Weimann A, Everall I, Bryant JM et al.

    Nature microbiology 2022

    PUBMED: 36008617; DOI: 10.1038/s41564-022-01204-x

  • Sinonasal Meningioma in a Siberian Tiger (Panthera tigris altaica).

    van der Weyden L, Caldwell P, Steyrer C, O'Dell N and Henning A

    Veterinary sciences 2022;9;9

    PUBMED: 36136673; DOI: 10.3390/vetsci9090457

  • Trust and the Goldacre Review: why trusted research environments are not about trust.

    Graham M, Milne R, Fitzsimmons P and Sheehan M

    Journal of medical ethics 2022

    PUBMED: 35999038; DOI: 10.1136/jme-2022-108435

  • Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation.

    Lees JA, Tonkin-Hill G, Yang Z and Corander J

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2022;377;1861;20210237

    PUBMED: 35989601; DOI: 10.1098/rstb.2021.0237

  • The genome sequence of the scotch argus butterfly, Erebia aethiops (Esper, 1777).

    Lohse O, Lohse K, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Augustijnen H, Lucek K and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;217

    PUBMED: 36105557; PMC: 9445563; DOI: 10.12688/wellcomeopenres.17927.1

  • The association between early-life gut microbiota and childhood respiratory diseases: a systematic review.

    Alcazar CG, Paes VM, Shao Y, Oesser C, Miltz A, Lawley TD, Brocklehurst P, Rodger A and Field N

    The Lancet. Microbe 2022;3;11;e867-e880

    PUBMED: 35988549; PMC: 10499762; DOI: 10.1016/S2666-5247(22)00184-7

  • Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities.

    Vianney TJ, Berger DJ, Doyle SR, Sankaranarayanan G, Serubanja J, Nakawungu PK, Besigye F, Sanya RE, Holroyd N, Allan F et al.

    PLoS neglected tropical diseases 2022;16;8;e0010188

    PUBMED: 35981002; PMC: 9426917; DOI: 10.1371/journal.pntd.0010188

  • Barcoding Genetically Distinct Plasmodium falciparum Strains for Comparative Assessment of Fitness and Antimalarial Drug Resistance.

    Carrasquilla M, Drammeh NF, Rawat M, Sanderson T, Zenonos Z, Rayner JC and Lee MCS

    mBio 2022;13;5;e0093722

    PUBMED: 35972144; PMC: 9600763; DOI: 10.1128/mbio.00937-22

  • Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study.

    Lo SW, Mellor K, Cohen R, Alonso AR, Belman S, Kumar N, Hawkins PA, Gladstone RA, von Gottberg A, Veeraraghavan B et al.

    The Lancet. Microbe 2022

    PUBMED: 35985351; DOI: 10.1016/S2666-5247(22)00158-6

  • Following successful anti-leishmanial treatment, neutrophil counts, CD10 expression and phagocytic capacity remain reduced in visceral leishmaniasis patients co-infected with HIV.

    Takele Y, Adem E, Mulaw T, Müller I, Cotton JA and Kropf P

    PLoS neglected tropical diseases 2022;16;8;e0010681

    PUBMED: 35969625; DOI: 10.1371/journal.pntd.0010681

  • Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming.

    Bergmann T, Liu Y, Skov J, Mogus L, Lee J, Pfisterer U, Handfield LF, Asenjo-Martinez A, Lisa-Vargas I, Seemann SE et al.

    Frontiers in cell and developmental biology 2022;10;976549

    PUBMED: 36046338; PMC: 9420913; DOI: 10.3389/fcell.2022.976549

  • Author Correction: Comparative and demographic analysis of orang-utan genomes.

    Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al.

    Nature 2022

    PUBMED: 35962045; DOI: 10.1038/s41586-022-04799-7

  • Generation of functional hepatocytes by forward programming with nuclear receptors.

    Tomaz RA, Zacharis ED, Bachinger F, Wurmser A, Yamamoto D, Petrus-Reurer S, Morell CM, Dziedzicka D, Wesley BT, Geti I et al.

    eLife 2022;11

    PUBMED: 35959725; PMC: 9374437; DOI: 10.7554/eLife.71591

  • Immunodeficiency, autoimmunity, and increased risk of B cell malignancy in humans with TRAF3 mutations.

    Rae W, Sowerby JM, Verhoeven D, Youssef M, Kotagiri P, Savinykh N, Coomber EL, Boneparth A, Chan A, Gong C et al.

    Science immunology 2022;7;74;eabn3800

    PUBMED: 35960817; DOI: 10.1126/sciimmunol.abn3800

  • Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers.

    Aghakhanian F, Hoh BP, Yew CW, Kumar Subbiah V, Xue Y, Tyler-Smith C, Ayub Q and Phipps ME

    Scientific reports 2022;12;1;13743

    PUBMED: 35962005; PMC: 9374673; DOI: 10.1038/s41598-022-17884-8

  • Clonal diversification and histogenesis of malignant germ cell tumours.

    Oliver TRW, Chappell L, Sanghvi R, Deighton L, Ansari-Pour N, Dentro SC, Young MD, Coorens THH, Jung H, Butler T et al.

    Nature communications 2022;13;1;4272

    PUBMED: 35953478; PMC: 9372159; DOI: 10.1038/s41467-022-31375-4

  • Context-specific emergence and growth of the SARS-CoV-2 Delta variant.

    McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S et al.

    Nature 2022

    PUBMED: 35952712; DOI: 10.1038/s41586-022-05200-3

  • Detection of early seeding of Richter transformation in chronic lymphocytic leukemia.

    Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N et al.

    Nature medicine 2022;28;8;1662-1671

    PUBMED: 35953718; PMC: 9388377; DOI: 10.1038/s41591-022-01927-8

  • Highly Variable Expression of Merozoite Surface Protein MSPDBL2 in Diverse Plasmodium falciparum Clinical Isolates and Transcriptome Scans for Correlating Genes.

    Hocking SE, Stewart LB, Freville A, Reid AJ, Tarr SJ, Tetteh KKA, Flueck C, Ahouidi AD, Amambua-Ngwa A, Diakite M et al.

    mBio 2022;e0194822

    PUBMED: 35950755; DOI: 10.1128/mbio.01948-22

  • Phylogenetic and Multiple-Locus Variable number tandem repeat analysis of Mycobacterium avium subsp. paratuberculosis isolates from Argentina.

    Vasini B, Farace P, Ariel A, Cirone K, Mendez L, Morsella C, Fresia P, Iraola G, Gioffré A and Paolicchi F

    Veterinary research communications 2022

    PUBMED: 35948855; DOI: 10.1007/s11259-022-09983-8

  • Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells.

    Rouhani FJ, Zou X, Danecek P, Badja C, Amarante TD, Koh G, Wu Q, Memari Y, Durbin R, Martincorena I et al.

    Nature genetics 2022;54;9;1406-1416

    PUBMED: 35953586; PMC: 9470532; DOI: 10.1038/s41588-022-01147-3

  • Allele specific PCR for a major marker of levamisole resistance in Haemonchus contortus.

    Antonopoulos A, Doyle SR, Bartley DJ, Morrison AA, Kaplan R, Howell S, Neveu C, Busin V, Devaney E and Laing R

    International journal for parasitology. Drugs and drug resistance 2022;20;17-26

    PUBMED: 35970104; DOI: 10.1016/j.ijpddr.2022.08.001

  • Autophagy-mediated NCOR1 degradation is required for brown fat maturation and thermogenesis.

    Sabaté-Pérez A, Romero M, Sànchez-Fernàndez-de-Landa P, Carobbio S, Mouratidis M, Sala D, Engel P, Villena JA, Virtue S, Vidal-Puig A et al.

    Autophagy 2022

    PUBMED: 35947488; DOI: 10.1080/15548627.2022.2111081

  • Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing.

    Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M et al.

    GigaScience 2022;11

    PUBMED: 35946988; PMC: 9364683; DOI: 10.1093/gigascience/giac068

  • Chromosomal painting in Charadrius collaris Vieillot, 1818 and Vanellus chilensis Molina, 1782 and an analysis of chromosomal signatures in Charadriiformes.

    Pinheiro MLS, Nagamachi CY, Ribas TFA, Diniz CG, O Brien PCM, Ferguson-Smith MA, Yang F and Pieczarka JC

    PloS one 2022;17;8;e0272836

    PUBMED: 35947613; DOI: 10.1371/journal.pone.0272836

  • Diverse mutational landscapes in human lymphocytes.

    Machado HE, Mitchell E, Øbro NF, Kübler K, Davies M, Leongamornlert D, Cull A, Maura F, Sanders MA, Cagan ATJ et al.

    Nature 2022;608;7924;724-732

    PUBMED: 35948631; PMC: 9402440; DOI: 10.1038/s41586-022-05072-7

  • Single-cell multi-omics of human preimplantation embryos demonstrates susceptibility to glucocorticoids.

    Zhao C, Biondic S, Vandal K, Bjorklund AK, Hagemann-Jensen M, Sommer TM, Canizo J, Clark S, Raymond P, Zenklusen D et al.

    Genome research 2022

    PUBMED: 35948369; DOI: 10.1101/gr.276665.122

  • First detection and origin of multi-drug resistant Klebsiella pneumoniae ST15 harboring OXA-48 in South America.

    Salazar C, Antelo V, Vieytes M, Dávila C, Grill F, Galiana A and Iraola G

    Journal of global antimicrobial resistance 2022;30;480-484

    PUBMED: 35961584; DOI: 10.1016/j.jgar.2022.08.005

  • Transferability of genetic loci and polygenic scores for cardiometabolic traits in British Pakistani and Bangladeshi individuals.

    Huang QQ, Sallah N, Dunca D, Trivedi B, Hunt KA, Hodgson S, Lambert SA, Arciero E, Wright J, Griffiths C et al.

    Nature communications 2022;13;1;4664

    PUBMED: 35945198; PMC: 9363492; DOI: 10.1038/s41467-022-32095-5

  • Genomic evidence of contemporary hybridization between Schistosoma species.

    Berger DJ, Léger E, Sankaranarayanan G, Sène M, Diouf ND, Rabone M, Emery A, Allan F, Cotton JA, Berriman M and Webster JP

    PLoS pathogens 2022;18;8;e1010706

    PUBMED: 35939508; DOI: 10.1371/journal.ppat.1010706

  • SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing.

    Nelson ME, Riva SG and Cvejic A

    BMC bioinformatics 2022;23;1;328

    PUBMED: 35941549; DOI: 10.1186/s12859-022-04860-2

  • Unified classification and risk-stratification in Acute Myeloid Leukemia.

    Tazi Y, Arango-Ossa JE, Zhou Y, Bernard E, Thomas I, Gilkes A, Freeman S, Pradat Y, Johnson SJ, Hills R et al.

    Nature communications 2022;13;1;4622

    PUBMED: 35941135; PMC: 9360033; DOI: 10.1038/s41467-022-32103-8

  • Poor correlation between preclinical and patient efficacy data for tumor targeted monotherapies in glioblastoma: the results of a systematic review.

    Gunjur A, Balasubramanian A, Hafeez U, Menon S, Cher L, Parakh S and Gan HK

    Journal of neuro-oncology 2022;159;3;539-549

    PUBMED: 35933567; DOI: 10.1007/s11060-022-04092-7

  • Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.

    Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K et al.

    Science (New York, N.Y.) 2022;377;6606;eabo1984

    PUBMED: 35926050; DOI: 10.1126/science.abo1984

  • A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.

    Ramdas S, Judd J, Graham SE, Kanoni S, Wang Y, Surakka I, Wenz B, Clarke SL, Chesi A, Wells A et al.

    American journal of human genetics 2022;109;8;1366-1387

    PUBMED: 35931049; PMC: 9388392; DOI: 10.1016/j.ajhg.2022.06.012

  • Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries.

    Carvalho MJ, Sands K, Thomson K, Portal E, Mathias J, Milton R, Gillespie D, Dyer C, Akpulu C, Boostrom I et al.

    Nature microbiology 2022

    PUBMED: 35927336; DOI: 10.1038/s41564-022-01184-y

  • A chromoanagenesis-driven ultra-complex t(5;7;21)dn truncates neurodevelopmental genes in a disabled boy as revealed by whole-genome sequencing.

    Córdova-Fletes C, Rivera H, Aguayo-Orozco TA, Martínez-Jacobo LA, Garza-González E, Robles-Espinoza CD, Basurto-Lozada P, Avalos-Gómez HG, Esparza-García E and Domínguez-Quezada MG

    European journal of medical genetics 2022;104579

    PUBMED: 35933106; DOI: 10.1016/j.ejmg.2022.104579

  • A first update on mapping the human genetic architecture of COVID-19.

    COVID-19 Host Genetics Initiative

    Nature 2022;608;7921;E1-E10

    PUBMED: 35922517; PMC: 9352569; DOI: 10.1038/s41586-022-04826-7

  • A physical wiring diagram for the human immune system.

    Shilts J, Severin Y, Galaway F, Müller-Sienerth N, Chong ZS, Pritchard S, Teichmann S, Vento-Tormo R, Snijder B and Wright GJ

    Nature 2022;608;7922;397-404

    PUBMED: 35922511; DOI: 10.1038/s41586-022-05028-x

  • A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.

    Malaka De Silva P, Stenhouse GE, Blackwell GA, Bengtsson RJ, Jenkins C, Hall JPJ and Baker KS

    Proceedings. Biological sciences 2022;289;1980;20220581

    PUBMED: 35919999; PMC: 9346365; DOI: 10.1098/rspb.2022.0581

  • Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018.

    Cleary DW, Jones J, Gladstone RA, Osman KL, Devine VT, Jefferies JM, Bentley SD, Faust SN and Clarke SC

    Scientific reports 2022;12;1;13332

    PUBMED: 35922536; PMC: 9349173; DOI: 10.1038/s41598-022-17600-6

  • Transcriptional variability accelerates preleukemia by cell diversification and perturbation of protein synthesis.

    Gupta S, Dovey OM, Domingues AF, Cyran OW, Cash CM, Giotopoulos G, Rak J, Cooper J, Gozdecka M, Dijkhuis L et al.

    Science advances 2022;8;31;eabn4886

    PUBMED: 35921412; DOI: 10.1126/sciadv.abn4886

  • Impact of the COVID-19 pandemic on time to diagnosis and treatment in children with cancer at tertiary care level.

    Dufour L, Simon A, Murray MJ and Behjati S

    Archives of disease in childhood 2022;107;9;851

    PUBMED: 35918139; DOI: 10.1136/archdischild-2022-324246

  • Integrated analyses of growth differentiation factor-15 concentration and cardiometabolic diseases in humans.

    Lemmelä S, Wigmore EM, Benner C, Havulinna AS, Ong RMY, Kempf T, Wollert KC, Blankenberg S, Zeller T, Peters JE et al.

    eLife 2022;11

    PUBMED: 35916366; PMC: 9391041; DOI: 10.7554/eLife.76272

  • A cross-disorder dosage sensitivity map of the human genome.

    Collins RL, Glessner JT, Porcu E, Lepamets M, Brandon R, Lauricella C, Han L, Morley T, Niestroj LM, Ulirsch J et al.

    Cell 2022;185;16;3041-3055.e25

    PUBMED: 35917817; DOI: 10.1016/j.cell.2022.06.036

  • The Effects of Cucumber Mosaic Virus and Its 2a and 2b Proteins on Interactions of Tomato Plants with the Aphid Vectors Myzus persicae and Macrosiphum euphorbiae.

    Arinaitwe W, Guyon A, Tungadi TD, Cunniffe NJ, Rhee SJ, Khalaf A, Mhlanga NM, Pate AE, Murphy AM and Carr JP

    Viruses 2022;14;8

    PUBMED: 36016326; PMC: 9416248; DOI: 10.3390/v14081703

  • CellRegMap: a statistical framework for mapping context-specific regulatory variants using scRNA-seq.

    Cuomo ASE, Heinen T, Vagiaki D, Horta D, Marioni JC and Stegle O

    Molecular systems biology 2022;18;8;e10663

    PUBMED: 35972065; DOI: 10.15252/msb.202110663

  • Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals.

    Mellor KC, Blackwell GA, Cawthraw SA, Mensah NE, Reid SWJ, Thomson NR, Petrovska L and Mather AE

    Microbial genomics 2022;8;8

    PUBMED: 35997596; DOI: 10.1099/mgen.0.000826

  • Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience.

    Okeke IN, Aboderin AO, Egwuenu A, Underwood A, Afolayan AO, Kekre M, Oaikhena AO, Odih EE, Omotayo HT, Dada-Adegbola H et al.

    Microbiology (Reading, England) 2022;168;8

    PUBMED: 35980376; DOI: 10.1099/mic.0.001208

  • Genomic dissection of the Vibrio cholerae O-serogroup global reference strains: reassessing our view of diversity and plasticity between two chromosomes.

    Murase K, Arakawa E, Izumiya H, Iguchi A, Takemura T, Kikuchi T, Nakagawa I, Thomson NR, Ohnishi M and Morita M

    Microbial genomics 2022;8;8

    PUBMED: 35930328; DOI: 10.1099/mgen.0.000860

  • Human genetics evidence supports two-thirds of the 2021 FDA-approved drugs.

    Ochoa D, Karim M, Ghoussaini M, Hulcoop DG, McDonagh EM and Dunham I

    Nature reviews. Drug discovery 2022;21;8;551

    PUBMED: 35804044; DOI: 10.1038/d41573-022-00120-3

  • Taking metagenomics under the wings.

    Chua PYS and Rasmussen JA

    Nature reviews. Microbiology 2022;20;8;447

    PUBMED: 35546350; DOI: 10.1038/s41579-022-00746-5

  • A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages.

    Tran M, Yoon S, Teoh M, Andersen S, Lam PY, Purdue BW, Raghubar A, Hanson SJ, Devitt K, Jones K et al.

    Frontiers in immunology 2022;13;911873

    PUBMED: 35967449; PMC: 9373800; DOI: 10.3389/fimmu.2022.911873

  • Assessing Trustworthy AI in Times of COVID-19: Deep Learning for Predicting a Multiregional Score Conveying the Degree of Lung Compromise in COVID-19 Patients.

    Allahabadi H, Amann J, Balot I, Beretta A, Binkley C, Bozenhard J, Bruneault F, Brusseau J, Candemir S, Cappellini LA et al.

    IEEE transactions on technology and society 2022;3;4;272-289

    PUBMED: 36573115; PMC: 9762021; DOI: 10.1109/TTS.2022.3195114

  • De novo putative loss-of-function variants in TAF4 are associated with a neuro-developmental disorder.

    Janssen BDE, van den Boogaard MH, Lichtenbelt K, Seaby EG, Stals K, Ellard S, Newbury-Ecob R, Dixit A, Roht L, Pajusalu S et al.

    Human mutation 2022

    PUBMED: 35904126; DOI: 10.1002/humu.24444

  • Global analysis of cytosine and adenine DNA modifications across the tree of life.

    Varma SJ, Calvani E, Grüning NM, Messner CB, Grayson N, Capuano F, Mülleder M and Ralser M

    eLife 2022;11

    PUBMED: 35900202; DOI: 10.7554/eLife.81002

  • Putting a twist in syphilis vaccine development.

    Grillová L

    Nature reviews. Microbiology 2022

    PUBMED: 35902764; PMC: 9332037; DOI: 10.1038/s41579-022-00784-z

  • The Relationship of Maternal Gestational Mass Spectrometry-Derived Metabolites with Offspring Congenital Heart Disease: Results from Multivariable and Mendelian Randomization Analyses.

    Taylor K, McBride N, Zhao J, Oddie S, Azad R, Wright J, Andreassen OA, Stewart ID, Langenberg C, Magnus MC et al.

    Journal of cardiovascular development and disease 2022;9;8

    PUBMED: 36005401; DOI: 10.3390/jcdd9080237

  • Pneumococcal genetic variability in age-dependent bacterial carriage.

    Kremer PHC, Ferwerda B, Bootsma HJ, Rots NY, Wijmenga-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Turner P, van der Ende A et al.

    eLife 2022;11

    PUBMED: 35881438; DOI: 10.7554/eLife.69244

  • Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens.

    Vinceti A, Perron U, Trastulla L and Iorio F

    Cell reports 2022;40;4;111145

    PUBMED: 35905712; DOI: 10.1016/j.celrep.2022.111145

  • MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia.

    Reid KM, Spaull R, Salian S, Barwick K, Meyer E, Zhen J, Hirata H, Sheipouri D, Benkerroum H, Gorman KM et al.

    Movement disorders : official journal of the Movement Disorder Society 2022;37;10;2139-2146

    PUBMED: 35876425; PMC: 9796674; DOI: 10.1002/mds.29147

  • Telomere length and risk of incident fracture and arthroplasty: findings from UK Biobank.

    Curtis EM, Codd V, Nelson C, D'Angelo S, Wang Q, Allara E, Kaptoge S, Matthews P, Tobias J, Danesh J et al.

    Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2022

    PUBMED: 35880304; DOI: 10.1002/jbmr.4664

  • Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests.

    Sloat SA, Noble LM, Paaby AB, Bernstein M, Chang A, Kaur T, Yuen J, Tintori SC, Jackson JL, Martel A et al.

    Ecology and evolution 2022;12;7;e9124

    PUBMED: 35898425; PMC: 9309040; DOI: 10.1002/ece3.9124

  • BIRC6 modifies risk of invasive bacterial infection in Kenyan children.

    Gilchrist JJ, Kariuki SN, Watson JA, Band G, Uyoga S, Ndila CM, Mturi N, Mwarumba S, Mohammed S, Mosobo M et al.

    eLife 2022;11

    PUBMED: 35866869; PMC: 9391038; DOI: 10.7554/eLife.77461

  • Multiplex PCR assay to detect high risk lineages of Salmonella Typhi and Paratyphi A.

    Khokhar F, Pickard D, Dyson Z, Iqbal J, Pragasam A, John JJ, Veeraraghavan B, Qamar F, Dougan G, MacQueen H et al.

    PloS one 2022;17;7;e0267805

    PUBMED: 35867662; PMC: 9307194; DOI: 10.1371/journal.pone.0267805

  • Mechanisms of APOBEC3 mutagenesis in human cancer cells.

    Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J, von Morgen P, Chen Y, Shah H, Sale JE, Alexandrov LB et al.

    Nature 2022;607;7920;799-807

    PUBMED: 35859169; PMC: 9329121; DOI: 10.1038/s41586-022-04972-y

  • A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours.

    Hamed AA, Kunz DJ, El-Hamamy I, Trinh QM, Subedar OD, Richards LM, Foltz W, Bullivant G, Ware M, Vladoiu MC et al.

    Nature communications 2022;13;1;4178

    PUBMED: 35853870; DOI: 10.1038/s41467-022-31408-y

  • Identification of anti-schistosomal, anthelmintic and anti-parasitic compounds curated and text-mined from the scientific literature.

    Coghlan A, Padalino G, O'Boyle NM, Hoffmann KF and Berriman M

    Wellcome open research 2022;7;193

    PUBMED: 36003342; PMC: 9363976; DOI: 10.12688/wellcomeopenres.17987.1

  • Recommendations for clinical interpretation of variants found in non-coding regions of the genome.

    Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR et al.

    Genome medicine 2022;14;1;73

    PUBMED: 35850704; PMC: 9295495; DOI: 10.1186/s13073-022-01073-3

  • Genetic and Structural Variation in the O-Antigen of Salmonella enterica Serovar Typhimurium Isolates Causing Bloodstream Infections in the Democratic Republic of the Congo.

    Van Puyvelde S, Gasperini G, Biggel M, Phoba MF, Raso MM, de Block T, Vanheer LN, Deborggraeve S, Vandenberg O, Thomson N et al.

    mBio 2022;e0037422

    PUBMED: 35862803; DOI: 10.1128/mbio.00374-22

  • An international report on bacterial communities in esophageal squamous cell carcinoma.

    Nomburg J, Bullman S, Nasrollahzadeh D, Collisson EA, Abedi-Ardekani B, Akoko LO, Atkins JR, Buckle GC, Gopal S, Hu N et al.

    International journal of cancer 2022

    PUBMED: 35837755; DOI: 10.1002/ijc.34212

  • Clonal Hematopoiesis Is Not Significantly Associated with Covid-19 Disease Severity.

    Zhou Y, Shalhoub RN, Rogers SN, Yu S, Gu M, Fabre MA, Quiros PM, Diangson A, Deng W, Anand S et al.

    Blood 2022

    PUBMED: 35839449; PMC: 9293387; DOI: 10.1182/blood.2022015721

  • Ivermectin and albendazole coadministration: opportunities for strongyloidiasis control.

    Gandasegui J, Onwuchekwa C, Krolewiecki AJ, Doyle SR, Pullan RL, Enbiale W, Kepha S, Hatherell HA, van Lieshout L, Cambra-Pellejà M et al.

    The Lancet. Infectious diseases 2022

    PUBMED: 35850127; DOI: 10.1016/S1473-3099(22)00369-3

  • Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis.

    Kar SP, Quiros PM, Gu M, Jiang T, Mitchell J, Langdon R, Iyer V, Barcena C, Vijayabaskar MS, Fabre MA et al.

    Nature genetics 2022

    PUBMED: 35835912; DOI: 10.1038/s41588-022-01121-z

  • Pan-cancer proteomic map of 949 human cell lines.

    Gonçalves E, Poulos RC, Cai Z, Barthorpe S, Manda SS, Lucas N, Beck A, Bucio-Noble D, Dausmann M, Hall C et al.

    Cancer cell 2022;40;8;835-849.e8

    PUBMED: 35839778; PMC: 9387775; DOI: 10.1016/j.ccell.2022.06.010

  • Community voices: policy proposals to promote inclusion in academia through the lens of women in science.

    Teichmann SA, Haniffa M and Fisher J

    Nature communications 2022;13;1;4068

    PUBMED: 35831416; PMC: 9279379; DOI: 10.1038/s41467-022-31616-6

  • Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.

    Hardt U, Carlberg K, Af Klint E, Sahlström P, Larsson L, van Vollenhoven A, Hernandez Machado S, Israelsson L, Amara K, Chemin K et al.

    Scientific reports 2022;12;1;11876

    PUBMED: 35831338; DOI: 10.1038/s41598-022-15293-5

  • Venetoclax synergizes with Gilteritinib in FLT3 wildtype high-risk Acute Myeloid Leukemia by suppressing MCL-1.

    Janssen M, Schmidt C, Bruch PM, Blank MF, Rohde C, Waclawiczek A, Heid D, Renders S, Göllner S, Vierbaum L et al.

    Blood 2022

    PUBMED: 35857899; DOI: 10.1182/blood.2021014241

  • Alternative splicing as a source of phenotypic diversity.

    Wright CJ, Smith CWJ and Jiggins CD

    Nature reviews. Genetics 2022;23;11;697-710

    PUBMED: 35821097; DOI: 10.1038/s41576-022-00514-4

  • Fracture hematoma micro-architecture influences transcriptional profile and plays a crucial role in determining bone healing outcomes.

    Woloszyk A, Tuong ZK, Perez L, Aguilar L, Bankole AI, Evans CH and Glatt V

    Biomaterials advances 2022;139;213027

    PUBMED: 35882120; DOI: 10.1016/j.bioadv.2022.213027

  • No association between polygenic risk scores for cancer and development of radiotherapy toxicity.

    Barnett GC, Kerns SL, Dorling L, Fachal L, Aguado-Barrera ME, Martínez-Calvo L, Jandu HK, Welsh C, Tyrer J, Coles CE et al.

    International journal of radiation oncology, biology, physics 2022

    PUBMED: 35840111; DOI: 10.1016/j.ijrobp.2022.06.098

  • Variants of Streptococcus pneumoniae Serotype 14 from Papua New Guinea with the Potential to Be Mistyped and Escape Vaccine-Induced Protection.

    Manna S, Spry L, Wee-Hee A, Ortika BD, Boelsen LK, Batinovic S, Mazarakis N, Ford RL, Lo SW, Bentley SD et al.

    Microbiology spectrum 2022;10;4;e0152422

    PUBMED: 35862970; PMC: 9431120; DOI: 10.1128/spectrum.01524-22

  • Dynamics of Host Immune Response Development During Schistosoma mansoni Infection.

    Costain AH, Phythian-Adams AT, Colombo SAP, Marley AK, Owusu C, Cook PC, Brown SL, Webb LM, Lundie RJ, Smits HH et al.

    Frontiers in immunology 2022;13;906338

    PUBMED: 35958580; PMC: 9362740; DOI: 10.3389/fimmu.2022.906338

  • Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells.

    Robinson PS, Thomas LE, Abascal F, Jung H, Harvey LMR, West HD, Olafsson S, Lee BCH, Coorens THH, Lee-Six H et al.

    Nature communications 2022;13;1;3949

    PUBMED: 35803914; PMC: 9270427; DOI: 10.1038/s41467-022-31341-0

  • Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans.

    Pereira AP, Antunes P, Willems R, Corander J, Coque TM, Peixe L, Freitas AR and Novais C

    Microbiology spectrum 2022;10;4;e0117622

    PUBMED: 35862993; PMC: 9430118; DOI: 10.1128/spectrum.01176-22

  • ArtSeg-Artifact segmentation and removal in brightfield cell microscopy images without manual pixel-level annotations.

    Ali MAS, Hollo K, Laasfeld T, Torp J, Tahk MJ, Rinken A, Palo K, Parts L and Fishman D

    Scientific reports 2022;12;1;11404

    PUBMED: 35794119; DOI: 10.1038/s41598-022-14703-y

  • flashfm-ivis: interactive visualisation for fine-mapping of multiple quantitative traits.

    Zhou F, Butterworth AS and Asimit JL

    Bioinformatics (Oxford, England) 2022

    PUBMED: 35792838; DOI: 10.1093/bioinformatics/btac453

  • Improving helminth genome resources in the post-genomic era.

    Doyle SR

    Trends in parasitology 2022;38;10;831-840

    PUBMED: 35810065; DOI: 10.1016/j.pt.2022.06.002

  • Population genomics of ancient and modern Trichuris trichiura.

    Doyle SR, Søe MJ, Nejsum P, Betson M, Cooper PJ, Peng L, Zhu XQ, Sanchez A, Matamoros G, Sandoval GAF et al.

    Nature communications 2022;13;1;3888

    PUBMED: 35794092; DOI: 10.1038/s41467-022-31487-x

  • Single-cell roadmap of human gonadal development.

    Garcia-Alonso L, Lorenzi V, Mazzeo CI, Alves-Lopes JP, Roberts K, Sancho-Serra C, Engelbert J, Marečková M, Gruhn WH, Botting RA et al.

    Nature 2022

    PUBMED: 35794482; DOI: 10.1038/s41586-022-04918-4

  • Somatic Mutation: What Shapes the Mutational Landscape of Normal Epithelia?

    Fowler JC and Jones PH

    Cancer discovery 2022;12;7;1642-1655

    PUBMED: 35397477; PMC: 7613026; DOI: 10.1158/2159-8290.CD-22-0145

  • The genome sequence of the hawthorn shieldbug, Acanthosoma haemorrhoidale (Linnaeus, 1758).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Mulley J and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;178

    PUBMED: 36865370; PMC: 9971695; DOI: 10.12688/wellcomeopenres.17926.1

  • Equity in recruitment to Combined Infection Training, 2021: Diversity & Inclusion considerations.

    Aggarwal D, Roy-Chowdhury M, Xiang N and Peacock SJ

    The Journal of infection 2022;85;4;436-480

    PUBMED: 35803385; DOI: 10.1016/j.jinf.2022.06.031

  • Interrogating breast cancer heterogeneity using single and pooled circulating tumor cell analysis.

    Rothé F, Venet D, Peeters D, Rouas G, Rediti M, Smeets D, Dupont F, Campbell P, Lambrechts D, Dirix L et al.

    NPJ breast cancer 2022;8;1;79

    PUBMED: 35790747; PMC: 9256697; DOI: 10.1038/s41523-022-00445-7

  • Vibrio cholerae O139 genomes provide a clue to why it may have failed to usher in the eighth cholera pandemic.

    Ramamurthy T, Pragasam AK, Taylor-Brown A, Will RC, Vasudevan K, Das B, Srivastava SK, Chowdhury G, Mukhopadhyay AK, Dutta S et al.

    Nature communications 2022;13;1;3864

    PUBMED: 35790755; DOI: 10.1038/s41467-022-31391-4

  • The genome sequence of the clay, Mythimna ferrago (Fabricius, 1787).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Gibbs M and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;177

    PUBMED: 36051895; PMC: 9382153; DOI: 10.12688/wellcomeopenres.17923.1

  • Metastatic Uterine Adenocarcinoma in a Sable Antelope (Hippotragus niger).

    van der Weyden L, Bezuidenhout A, van Wilpe E and O'Dell N

    Veterinary sciences 2022;9;7

    PUBMED: 35878356; DOI: 10.3390/vetsci9070339

  • Combinatorial genetics reveals the Dock1-Rac2 axis as a potential target for the treatment of NPM1;Cohesin mutated AML.

    Meyer AE, Stelloh C, Pulakanti K, Burns R, Fisher JB, Heimbruch KE, Tarima S, Furumo Q, Brennan J, Zheng Y et al.

    Leukemia 2022

    PUBMED: 35778533; DOI: 10.1038/s41375-022-01632-y

  • Distinct Streptococcus pneumoniae cause invasive disease in Papua New Guinea.

    Mellor KC, Lo S, Yoannes M, Michael A, Orami T, Greenhill AR, Breiman RF, Hawkins P, McGee L, Bentley SD et al.

    Microbial genomics 2022;8;7

    PUBMED: 35816442; PMC: 9455700; DOI: 10.1099/mgen.0.000835

  • Identification of a rapidly-spreading triple mutant for high-level metabolic insecticide resistance in Anopheles gambiae provides a real-time molecular diagnostic for anti-malarial intervention deployment.

    Njoroge H, Van't Hof A, Oruni A, Pipini D, Nagi SC, Lynd A, Lucas ER, Tomlinson S, Grau-Bove X, McDermott D et al.

    Molecular ecology 2022

    PUBMED: 35775282; DOI: 10.1111/mec.16591

  • Incremental value of risk factor variability for cardiovascular risk prediction in individuals with type 2 diabetes: results from UK primary care electronic health records.

    Xu Z, Arnold M, Sun L, Stevens D, Chung R, Ip S, Barrett J, Kaptoge S, Pennells L, Di Angelantonio E and Wood AM

    International journal of epidemiology 2022

    PUBMED: 35776101; DOI: 10.1093/ije/dyac140

  • Mother-infant transmission of human microbiota.

    Browne HP, Shao Y and Lawley TD

    Current opinion in microbiology 2022;69;102173

    PUBMED: 35785616; DOI: 10.1016/j.mib.2022.102173

  • Simultaneously screening for methicillin-resistant Staphylococcus aureus and its susceptibility to potentiated penicillins.

    Ba X, Raisen CL, Zhou ZC, Harrison EM, Peacock SJ and Holmes MA

    Journal of medical microbiology 2022;71;7

    PUBMED: 35867942; DOI: 10.1099/jmm.0.001562

  • STAT1 is essential for HSC function and maintains MHCIIhi stem cells that resists myeloablation and neoplastic expansion.

    Li J, Williams MJ, Park HJ, Bastos HP, Wang X, Prins DP, Wilson NK, Johnson C, Sham K, Wantoch M et al.

    Blood 2022

    PUBMED: 35767701; DOI: 10.1182/blood.2021014009

  • Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago, Chile in the 1980s and 2010-2016.

    Maes M, Sikorski MJ, Carey ME, Higginson EE, Dyson ZA, Fernandez A, Araya P, Tennant SM, Baker S, Lagos R et al.

    PLoS neglected tropical diseases 2022;16;6;e0010178

    PUBMED: 35767580; DOI: 10.1371/journal.pntd.0010178

  • SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination.

    Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ et al.

    Nature communications 2022;13;1;3707

    PUBMED: 35764636; DOI: 10.1038/s41467-022-31287-3

  • An introduction to spatial transcriptomics for biomedical research.

    Williams CG, Lee HJ, Asatsuma T, Vento-Tormo R and Haque A

    Genome medicine 2022;14;1;68

    PUBMED: 35761361; DOI: 10.1186/s13073-022-01075-1

  • High-throughput total RNA sequencing in single cells using VASA-seq.

    Salmen F, De Jonghe J, Kaminski TS, Alemany A, Parada GE, Verity-Legg J, Yanagida A, Kohler TN, Battich N, van den Brekel F et al.

    Nature biotechnology 2022

    PUBMED: 35760914; DOI: 10.1038/s41587-022-01361-8

  • Multi-ancestry Mendelian randomization of omics traits revealing drug targets of COVID-19 severity.

    Zheng J, Zhang Y, Zhao H, Liu Y, Baird D, Karim MA, Ghoussaini M, Schwartzentruber J, Dunham I, Elsworth B et al.

    EBioMedicine 2022;81;104112

    PUBMED: 35772218; DOI: 10.1016/j.ebiom.2022.104112

  • Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.

    Kilpatrick AM, Rahman F, Anjum A, Shome S, Andalib KMS, Banik S, Chowdhury SF, Coombe P, Astroz YC, Douglas JM et al.

    Bioinformatics (Oxford, England) 2022;38;Supplement_1;i19-i27

    PUBMED: 35758800; DOI: 10.1093/bioinformatics/btac236

  • Impaired in vitro Interferon-γ production in patients with visceral leishmaniasis is improved by inhibition of PD1/PDL-1 ligation.

    Takele Y, Adem E, Franssen SU, Womersley R, Kaforou M, Levin M, Müller I, Cotton JA and Kropf P

    PLoS neglected tropical diseases 2022;16;6;e0010544

    PUBMED: 35749568; DOI: 10.1371/journal.pntd.0010544

  • Replacement of Leishmania (Leishmania) infantum Populations in an Endemic Focus of Visceral Leishmaniasis in Brazil.

    Valdivia HO, Roatt BM, Baptista RP, Ottino J, Coqueiro-Dos-Santos A, Sanders MJ, Reis AB, Cotton JA and Bartholomeu DC

    Frontiers in cellular and infection microbiology 2022;12;900084

    PUBMED: 35811682; PMC: 9263273; DOI: 10.3389/fcimb.2022.900084

  • A Phase II study of neoadjuvant axitinib for reducing the extent of venous tumour thrombus in clear cell renal cell cancer with venous invasion (NAXIVA).

    Stewart GD, Welsh SJ, Ursprung S, Gallagher FA, Jones JO, Shields J, Smith CG, Mitchell TJ, Warren AY, Bex A et al.

    British journal of cancer 2022

    PUBMED: 35739300; DOI: 10.1038/s41416-022-01883-7

  • Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease.

    Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A et al.

    Genome medicine 2022;14;1;67

    PUBMED: 35739588; PMC: 9219160; DOI: 10.1186/s13073-022-01071-5

  • Conjunctival epithelial cells resist productive SARS-CoV-2 infection.

    Jackson RM, Hatton CF, Spegarova JS, Georgiou M, Collin J, Stephenson E, Verdon B, Haq IJ, Hussain R, Coxhead JM et al.

    Stem cell reports 2022;17;7;1699-1713

    PUBMED: 35750043; PMC: 9222349; DOI: 10.1016/j.stemcr.2022.05.017

  • Geographical distribution and genetic diversity of Plasmodium vivax reticulocyte binding protein 1a correlates with patient antigenicity.

    Park JH, Kim MH, Sutanto E, Na SW, Kim MJ, Yeom JS, Nyunt MH, Abbas Elfaki MM, Abdel Hamid MM, Cha SH et al.

    PLoS neglected tropical diseases 2022;16;6;e0010492

    PUBMED: 35737709; DOI: 10.1371/journal.pntd.0010492

  • OLIG2 Is a Determinant for the Relapse of MYC-Amplified Medulloblastoma.

    Xu Z, Murad N, Malawsky D, Tao R, Rivero-Hinojosa S, Holdhof D, Schüller U, Zhang P, Lazarski C, Rood BR et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2022;OF1-OF14

    PUBMED: 35736214; DOI: 10.1158/1078-0432.CCR-22-0527

  • Genomic analysis provides novel insights into diversification and taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis).

    Kuzmanović N, Biondi E, Overmann J, Puławska J, Verbarg S, Smalla K and Lassalle F

    BMC genomics 2022;23;1;462

    PUBMED: 35733110; DOI: 10.1186/s12864-022-08662-x

  • Group 3 innate lymphocytes make a distinct contribution to type 17 immunity in bladder defence.

    Riding AM, Loudon KW, Guo A, Ferdinand JR, Lok LSC, Richoz N, Stewart A, Castro-Dopico T, Tuong ZK, Fiancette R et al.

    iScience 2022;25;7;104660

    PUBMED: 35845169; PMC: 9283510; DOI: 10.1016/j.isci.2022.104660

  • Pharmacogenomics research in Africa: A promising but underexplored prospect.

    Okereke M, Olumoh-Abdul HA, Pius M, David KB, Ekpenyong A and Okoya F

    Pharmacological research 2022;182;106317

    PUBMED: 35750300; DOI: 10.1016/j.phrs.2022.106317

  • Profiling gut microbiota and bile acid metabolism in critically ill children.

    Kean IRL, Wagner J, Wijeyesekera A, De Goffau M, Thurston S, Clark JA, White DK, Ridout J, Agrawal S, Kayani R et al.

    Scientific reports 2022;12;1;10432

    PUBMED: 35729169; DOI: 10.1038/s41598-022-13640-0

  • Functional characterization of the schizophrenia associated gene AS3MT identifies a role in neuronal development.

    Washer SJ, Flynn R, Oguro-Ando A, Hannon E, Burrage J, Jeffries A, Mill J and Dempster EL

    American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2022;189;5;151-162

    PUBMED: 35719055; PMC: 9546433; DOI: 10.1002/ajmg.b.32905

  • Nonalcoholic steatohepatitis and mechanisms by which it is ameliorated by activation of the CNC-bZIP transcription factor Nrf2.

    Bathish B, Robertson H, Dillon JF, Dinkova-Kostova AT and Hayes JD

    Free radical biology & medicine 2022

    PUBMED: 35728768; DOI: 10.1016/j.freeradbiomed.2022.06.226

  • Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues.

    Wang S, García-Seisdedos D, Prakash A, Kundu DJ, Collins A, George N, Fexova S, Moreno P, Papatheodorou I, Jones AR and Vizcaíno JA

    PLoS computational biology 2022;18;6;e1010174

    PUBMED: 35714157; DOI: 10.1371/journal.pcbi.1010174

  • Macaque Clonal Hematopoiesis Model Demonstrates Expansion of TET2-Disrupted Clones and Utility for Testing Interventions.

    Shin TH, Zhou Y, Chen S, Cordes S, Grice MZ, Fan X, Lee BC, AlJanahi AA, Hong SG, Vaughan KL et al.

    Blood 2022

    PUBMED: 35714307; DOI: 10.1182/blood.2021014875

  • Cas9-induced large deletions and small indels are controlled in a convergent fashion.

    Kosicki M, Allen F, Steward F, Tomberg K, Pan Y and Bradley A

    Nature communications 2022;13;1;3422

    PUBMED: 35701408; DOI: 10.1038/s41467-022-30480-8

  • Genome-enabled discovery of candidate virulence loci in Striga hermonthica, a devastating parasite of African cereal crops.

    Qiu S, Bradley JM, Zhang P, Chaudhuri R, Blaxter M, Butlin RK and Scholes JD

    The New phytologist 2022

    PUBMED: 35699626; DOI: 10.1111/nph.18305

  • Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels.

    Uniken Venema WTC, Ramírez-Sánchez AD, Bigaeva E, Withoff S, Jonkers I, McIntyre RE, Ghouraba M, Raine T, Weersma RK, Franke L et al.

    Scientific reports 2022;12;1;9897

    PUBMED: 35701452; PMC: 9197976; DOI: 10.1038/s41598-022-13812-y

  • Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.

    Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J et al.

    Nature biotechnology 2022;40;11;1624-1633

    PUBMED: 35697807; PMC: 9646498; DOI: 10.1038/s41587-022-01342-x

  • Transcriptomic analyses implicate neuronal plasticity and chloride homeostasis in ivermectin resistance and response to treatment in a parasitic nematode.

    Laing R, Doyle SR, McIntyre J, Maitland K, Morrison A, Bartley DJ, Kaplan R, Chaudhry U, Sargison N, Tait A et al.

    PLoS pathogens 2022;18;6;e1010545

    PUBMED: 35696434; DOI: 10.1371/journal.ppat.1010545

  • Plant-microbe interactions in the rhizosphere via a circular metabolic economy.

    Korenblum E, Massalha H and Aharoni A

    The Plant cell 2022

    PUBMED: 35678568; DOI: 10.1093/plcell/koac163

  • The female protective effect against autism spectrum disorder.

    Wigdor EM, Weiner DJ, Grove J, Fu JM, Thompson WK, Carey CE, Baya N, van der Merwe C, Walters RK, Satterstrom FK et al.

    Cell genomics 2022;2;6;100134

    PUBMED: 36778135; PMC: 9903803; DOI: 10.1016/j.xgen.2022.100134

  • Live-cell microscopy or fluorescence anisotropy with budded baculoviruses-which way to go with measuring ligand binding to M4 muscarinic receptors?

    Tahk MJ, Torp J, Ali MAS, Fishman D, Parts L, Grätz L, Müller C, Keller M, Veiksina S, Laasfeld T and Rinken A

    Open biology 2022;12;6;220019

    PUBMED: 35674179; DOI: 10.1098/rsob.220019

  • A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago.

    Catania T, Li Y, Winzer T, Harvey D, Meade F, Caridi A, Leech A, Larson TR, Ning Z, Chang J et al.

    Nature communications 2022;13;1;3150

    PUBMED: 35672295; DOI: 10.1038/s41467-022-30856-w

  • Mapping the developing human immune system across organs.

    Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK et al.

    Science (New York, N.Y.) 2022;376;6597;eabo0510

    PUBMED: 35549310; PMC: 7612819; DOI: 10.1126/science.abo0510

  • Genetic correlates of phenotypic heterogeneity in autism.

    Warrier V, Zhang X, Reed P, Havdahl A, Moore TM, Cliquet F, Leblond CS, Rolland T, Rosengren A, EU-AIMS LEAP et al.

    Nature genetics 2022;54;9;1293-1304

    PUBMED: 35654973; PMC: 9470531; DOI: 10.1038/s41588-022-01072-5

  • Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy.

    Xie SC, Metcalfe RD, Dunn E, Morton CJ, Huang SC, Puhalovich T, Du Y, Wittlin S, Nie S, Luth MR et al.

    Science (New York, N.Y.) 2022;376;6597;1074-1079

    PUBMED: 35653481; PMC: 7613620; DOI: 10.1126/science.abn0611

  • The genome that fuelled a Mexican scientific revolution.

    Robles-Espinoza CD

    Nature reviews. Genetics 2022;23;6;322-323

    PUBMED: 35301488; DOI: 10.1038/s41576-022-00472-x

  • The longitudinal dynamics and natural history of clonal haematopoiesis.

    Fabre MA, de Almeida JG, Fiorillo E, Mitchell E, Damaskou A, Rak J, Orrù V, Marongiu M, Chapman MS, Vijayabaskar MS et al.

    Nature 2022;606;7913;335-342

    PUBMED: 35650444; PMC: 9177423; DOI: 10.1038/s41586-022-04785-z

  • A molecular map of T cell activation gives insights into immune disease.

    No authors listed

    Nature genetics 2022;54;6;752-753

    PUBMED: 35637385; DOI: 10.1038/s41588-022-01067-2

  • Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield.

    Liao B, Shen X, Xiang L, Guo S, Chen S, Meng Y, Liang Y, Ding D, Bai J, Zhang D et al.

    Molecular plant 2022;15;8;1310-1328

    PUBMED: 35655434; DOI: 10.1016/j.molp.2022.05.013

  • Can Drug Repurposing Accelerate Precision Oncology?

    Schipper LJ, Zeverijn LJ, Garnett MJ and Voest EE

    Cancer discovery 2022;OF1-OF8

    PUBMED: 35642948; DOI: 10.1158/2159-8290.CD-21-0612

  • Clonal dynamics of haematopoiesis across the human lifespan.

    Mitchell E, Spencer Chapman M, Williams N, Dawson KJ, Mende N, Calderbank EF, Jung H, Mitchell T, Coorens THH, Spencer DH et al.

    Nature 2022;606;7913;343-350

    PUBMED: 35650442; PMC: 9177428; DOI: 10.1038/s41586-022-04786-y

  • Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13.

    Belman S, Soeng S, Soputhy C, Gladstone R, Hawkins PA, Breiman RF, McGee L, Bentley SD, Lo SW and Turner P

    Microbial genomics 2022;8;6

    PUBMED: 35763412; PMC: 9455705; DOI: 10.1099/mgen.0.000837

  • Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization.

    Javaid N, Olwagen C, Nzenze S, Hawkins P, Gladstone R, McGee L, Breiman RF, Bentley SD, Madhi SA and Lo S

    Microbial genomics 2022;8;6

    PUBMED: 35737523; PMC: 9455715; DOI: 10.1099/mgen.0.000831

  • Widespread metastasis of a spermatocytic seminoma with concomitant hepatic peliosis in a Southern African hedgehog (Atelerix frontalis).

    O'Dell N, O'Dell JH and Van der Weyden L

    Journal of the South African Veterinary Association 2022;93;1;41-44

    PUBMED: 35950811

  • Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen.

    Gorrie CL, Mirčeta M, Wick RR, Judd LM, Lam MMC, Gomi R, Abbott IJ, Thomson NR, Strugnell RA, Pratt NF et al.

    Nature communications 2022;13;1;3017

    PUBMED: 35641522; DOI: 10.1038/s41467-022-30717-6

  • Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study.

    Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J et al.

    European urology 2022

    PUBMED: 35659150; DOI: 10.1016/j.eururo.2022.05.007

  • Developing a National Newborn Genomes Program: An Approach Driven by Ethics, Engagement and Co-design.

    Pichini A, Ahmed A, Patch C, Bick D, Leblond M, Kasperaviciute D, Deen D, Wilde S, Garcia Noriega S, Matoko C et al.

    Frontiers in genetics 2022;13;866168

    PUBMED: 35711926; PMC: 9195613; DOI: 10.3389/fgene.2022.866168

  • The erythrocyte membrane properties of beta thalassaemia heterozygotes and their consequences for Plasmodium falciparum invasion.

    Introini V, Marin-Menendez A, Nettesheim G, Lin YC, Kariuki SN, Smith AL, Jean L, Brewin JN, Rees DC, Cicuta P et al.

    Scientific reports 2022;12;1;8934

    PUBMED: 35624125; DOI: 10.1038/s41598-022-12060-4

  • Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation.

    Soskic B, Cano-Gamez E, Smyth DJ, Ambridge K, Ke Z, Matte JC, Bossini-Castillo L, Kaplanis J, Ramirez-Navarro L, Lorenc A et al.

    Nature genetics 2022

    PUBMED: 35618845; DOI: 10.1038/s41588-022-01066-3

  • Characterising genome architectures using genome decomposition analysis.

    Aunin E, Berriman M and Reid AJ

    BMC genomics 2022;23;1;398

    PUBMED: 35610562; DOI: 10.1186/s12864-022-08616-3

  • Patients With Inflammatory Bowel Disease Show IgG Immune Responses Towards Specific Intestinal Bacterial Genera.

    Bourgonje AR, Roo-Brand G, Lisotto P, Sadaghian Sadabad M, Reitsema RD, de Goffau MC, Faber KN, Dijkstra G and Harmsen HJM

    Frontiers in immunology 2022;13;842911

    PUBMED: 35693832; PMC: 9174456; DOI: 10.3389/fimmu.2022.842911

  • Robust temporal map of human in vitro myelopoiesis using single-cell genomics.

    Alsinet C, Primo MN, Lorenzi V, Bello E, Kelava I, Jones CP, Vilarrasa-Blasi R, Sancho-Serra C, Knights AJ, Park JE et al.

    Nature communications 2022;13;1;2885

    PUBMED: 35610203; DOI: 10.1038/s41467-022-30557-4

  • Systematic Analysis of Kaposi's Sarcoma-associated Herpesvirus Genomes from a Kaposi's Sarcoma (KS) Case-Control Study in Cameroon: Evidence of Dual Infections but No Association Between Viral Sequence Variation and KS Risk.

    Marshall VA, Fisher NC, Goodman CA, Cornejo Castro EM, Liu I, Khanal S, Holdridge BM, Thorpe AL, Labo N, Stolka KB et al.

    International journal of cancer 2022

    PUBMED: 35608873; DOI: 10.1002/ijc.34136

  • Transcriptional profiling of human Vδ1 T cells reveals a pathogen-driven adaptive differentiation program.

    McMurray JL, von Borstel A, Taher TE, Syrimi E, Taylor GS, Sharif M, Rossjohn J, Remmerswaal EBM, Bemelman FJ, Vieira Braga FA et al.

    Cell reports 2022;39;8;110858

    PUBMED: 35613583; DOI: 10.1016/j.celrep.2022.110858

  • The 17-gene stemness score associates with relapse risk and long-term outcomes following allogeneic haematopoietic cell transplantation in acute myeloid leukaemia.

    Kim DDH, Novitzky Basso I, Kim TS, Yi SY, Kim KH, Murphy T, Chan S, Minden M, Pasic I, Lam W et al.

    EJHaem 2022;3;3;873-884

    PUBMED: 36051057; PMC: 9422016; DOI: 10.1002/jha2.466

  • Peptide location fingerprinting identifies species- and tissue-conserved structural remodelling of proteins as a consequence of ageing and disease.

    Eckersley A, Ozols M, Chen P, Tam V, Ward LJ, Hoyland JA, Trafford A, Yuan XM, Schiller HB, Chan D and Sherratt MJ

    Matrix biology : journal of the International Society for Matrix Biology 2022

    PUBMED: 35618217; DOI: 10.1016/j.matbio.2022.05.007

  • 'Know thyself' - host factors influencing cancer response to immune checkpoint inhibitors.

    Gunjur A, Manrique-Rincón AJ, Klein O, Behren A, Lawley TD, Welsh SJ and Adams DJ

    The Journal of pathology 2022;257;4;513-525

    PUBMED: 35394069; PMC: 9320825; DOI: 10.1002/path.5907

  • Genomic analysis of qnr-harbouring IncX plasmids and their transferability within different hosts under induced stress.

    Nohejl T, Valcek A, Papousek I, Palkovicova J, Wailan AM, Pratova H, Minoia M and Dolejska M

    BMC microbiology 2022;22;1;136

    PUBMED: 35590235; DOI: 10.1186/s12866-022-02546-6

  • Integrating polygenic risk scores in the prediction of type 2 diabetes risk and subtypes in British Pakistanis and Bangladeshis: A population-based cohort study.

    Hodgson S, Huang QQ, Sallah N, Genes & Health Research Team, Griffiths CJ, Newman WG, Trembath RC, Wright J, Lumbers RT, Kuchenbaecker K et al.

    PLoS medicine 2022;19;5;e1003981

    PUBMED: 35587468; PMC: 9119501; DOI: 10.1371/journal.pmed.1003981

  • A nationally agreed cross-professional competency framework to facilitate genomic testing.

    Pichini A and Bishop M

    Genetics in medicine : official journal of the American College of Medical Genetics 2022;24;8;1743-1752

    PUBMED: 35583551; DOI: 10.1016/j.gim.2022.04.023

  • A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos.

    Demeter F, Zanolli C, Westaway KE, Joannes-Boyau R, Duringer P, Morley MW, Welker F, Rüther PL, Skinner MM, McColl H et al.

    Nature communications 2022;13;1;2557

    PUBMED: 35581187; DOI: 10.1038/s41467-022-29923-z

  • Mutational landscape of normal epithelial cells in Lynch Syndrome patients.

    Lee BCH, Robinson PS, Coorens THH, Yan HHN, Olafsson S, Lee-Six H, Sanders MA, Siu HC, Hewinson J, Yue SSK et al.

    Nature communications 2022;13;1;2710

    PUBMED: 35581206; PMC: 9114395; DOI: 10.1038/s41467-022-29920-2

  • The NaHCO3-Responsive Phenotype in Methicillin-Resistant Staphylococcus aureus (MRSA) Is Influenced by mecA Genotype.

    Ersoy SC, Manna AC, Proctor RA, Chambers HF, Harrison EM, Bayer AS and Cheung A

    Antimicrobial agents and chemotherapy 2022;66;6;e0025222

    PUBMED: 35575577; PMC: 9211399; DOI: 10.1128/aac.00252-22

  • Inducible apelin receptor knockdown reduces differentiation efficiency and contractility of hESC-derived cardiomyocytes.

    Macrae RGC, Colzani MT, Williams TL, Bayraktar S, Kuc RE, Pullinger AL, Bernard WG, Robinson EL, Davenport EE, Maguire JJ et al.

    Cardiovascular research 2022

    PUBMED: 36239923; DOI: 10.1093/cvr/cvac065

  • Cross-tissue immune cell analysis reveals tissue-specific features in humans.

    Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Wells SB, Gomes T, Howlett SK, Suchanek O, Polanski K, King HW et al.

    Science (New York, N.Y.) 2022;376;6594;eabl5197

    PUBMED: 35549406; PMC: 7612735; DOI: 10.1126/science.abl5197

  • GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans.

    Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR et al.

    The Journal of experimental medicine 2022;219;6

    PUBMED: 35551368; DOI: 10.1084/jem.20201405

  • Mapping Human Reproduction with Single-Cell Genomics.

    Marečková M, Massalha H, Lorenzi V and Vento-Tormo R

    Annual review of genomics and human genetics 2022

    PUBMED: 35567278; DOI: 10.1146/annurev-genom-120121-114415

  • Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites.

    Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J et al.

    American journal of human genetics 2022;109;6;1038-1054

    PUBMED: 35568032; PMC: 9247822; DOI: 10.1016/j.ajhg.2022.04.009

  • Humoral immunity at the brain borders in homeostasis.

    Posner DA, Lee CY, Portet A and Clatworthy MR

    Current opinion in immunology 2022;76;102188

    PUBMED: 35569417; DOI: 10.1016/j.coi.2022.102188

  • Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation.

    Mahajan A, Spracklen CN, Zhang W, Ng MCY, Petty LE, Kitajima H, Yu GZ, Rüeger S, Speidel L, Kim YJ et al.

    Nature genetics 2022

    PUBMED: 35551307; DOI: 10.1038/s41588-022-01058-3

  • Genetic and chemotherapeutic influences on germline hypermutation.

    Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J et al.

    Nature 2022;605;7910;503-508

    PUBMED: 35545669; PMC: 9117138; DOI: 10.1038/s41586-022-04712-2

  • Bromodomain Inhibitors Modulate FcγR-Mediated Mononuclear Phagocyte Activation and Chemotaxis.

    Banham GD, Lee CYC, Ferdinand JR, Matthews RJ, Jing C, Smithers N, Prinjha RK and Clatworthy MR

    Frontiers in immunology 2022;13;885101

    PUBMED: 35619690; PMC: 9127238; DOI: 10.3389/fimmu.2022.885101

  • Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study.

    Sánchez-Busó L, Cole MJ, Spiteri G, Day M, Jacobsson S, Golparian D, Sajedi N, Yeats CA, Abudahab K, Underwood A et al.

    The Lancet. Microbe 2022;3;6;e452-e463

    PUBMED: 35659907; DOI: 10.1016/S2666-5247(22)00044-1

  • Should we modulate the neonatal microbiome and what should be the goal?

    van Best N, Dominguez-Bello MG, Hornef MW, Jašarević E, Korpela K and Lawley TD

    Microbiome 2022;10;1;74

    PUBMED: 35538552; PMC: 9087991; DOI: 10.1186/s40168-022-01281-4

  • Effect of childhood vaccination and antibiotic use on pneumococcal populations and genome-wide associations with disease among children in Nepal: an observational study.

    Kandasamy R, Lo S, Gurung M, Carter MJ, Gladstone R, Lees J, Shrestha S, Thorson S, Bijukchhe S, Gautam MC et al.

    The Lancet. Microbe 2022;3;7;e503-e511

    PUBMED: 35779566; PMC: 9242864; DOI: 10.1016/S2666-5247(22)00066-0

  • Co-designing models for the communication of genomic results for rare diseases: a comparative study in the Czech Republic and the United Kingdom.

    Costa A, Franková V, Robert G, Macek M, Patch C, Alexander E, Arellanesova A, Clayton-Smith J, Hunter A, Havlovicová M et al.

    Journal of community genetics 2022

    PUBMED: 35523996; DOI: 10.1007/s12687-022-00589-w

  • DNA methylation can alter CRISPR/Cas9 editing frequency and DNA repair outcome in a target-specific manner.

    Přibylová A, Fischer L, Pyott DE, Bassett A and Molnar A

    The New phytologist 2022

    PUBMED: 35524464; DOI: 10.1111/nph.18212

  • An adaptive phase II/III safety and efficacy randomized controlled trial of single day or three-day fixed-dose albendazole-ivermectin co-formulation versus albendazole for the treatment of Trichuris trichiura and other STH infections. ALIVE trial protocol.

    Krolewiecki A, Enbiale W, Gandasegui J, van Lieshout L, Kepha S, Messa Junior A, Bengtson M, Gelaye W, Escola V, Martinez-Valladares M et al.

    Gates open research 2022;6;62

    PUBMED: 36540062; PMC: 9714317; DOI: 10.12688/gatesopenres.13615.1

  • Human branching cholangiocyte organoids recapitulate functional bile duct formation.

    Roos FJM, van Tienderen GS, Wu H, Bordeu I, Vinke D, Albarinos LM, Monfils K, Niesten S, Smits R, Willemse J et al.

    Cell stem cell 2022;29;5;776-794.e13

    PUBMED: 35523140; DOI: 10.1016/j.stem.2022.04.011

  • The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources.

    DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2022

    PUBMED: 35507016; DOI: 10.1016/j.gim.2022.04.017

  • Outcomes of SARS-CoV-2 omicron infection in residents of long-term care facilities in England (VIVALDI): a prospective, cohort study.

    Krutikov M, Stirrup O, Nacer-Laidi H, Azmi B, Fuller C, Tut G, Palmer T, Shrotri M, Irwin-Singer A, Baynton V et al.

    The Lancet. Healthy longevity 2022;3;5;e347-e355

    PUBMED: 35531432; PMC: 9067940; DOI: 10.1016/S2666-7568(22)00093-9

  • Alternative splicing modulation by G-quadruplexes.

    Georgakopoulos-Soares I, Parada GE, Wong HY, Medhi R, Furlan G, Munita R, Miska EA, Kwok CK and Hemberg M

    Nature communications 2022;13;1;2404

    PUBMED: 35504902; DOI: 10.1038/s41467-022-30071-7

  • Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.

    Fernández-Justel D, Marcos-Alcalde Í, Abascal F, Vidaña N, Gómez-Puertas P, Jiménez A, Revuelta JL and Buey RM

    Protein science : a publication of the Protein Society 2022;31;5;e4314

    PUBMED: 35481629; DOI: 10.1002/pro.4314

  • Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam.

    Bloomfield S, Duong VT, Tuyen HT, Campbell JI, Thomson NR, Parkhill J, Le Phuc H, Chau TTH, Maskell DJ, Perron GG et al.

    Microbial genomics 2022;8;5

    PUBMED: 35511231; DOI: 10.1099/mgen.0.000798

  • Modifiable traits, healthy behaviours, and leukocyte telomere length: a population-based study in UK Biobank.

    Bountziouka V, Musicha C, Allara E, Kaptoge S, Wang Q, Angelantonio ED, Butterworth AS, Thompson JR, Danesh JN, Wood AM et al.

    The Lancet. Healthy longevity 2022;3;5;e321-e331

    PUBMED: 35685390; PMC: 9068584; DOI: 10.1016/S2666-7568(22)00072-1

  • Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes.

    Lobon I, Solís-Moruno M, Juan D, Muhaisen A, Abascal F, Esteller-Cucala P, García-Pérez R, Martí MJ, Tolosa E, Ávila J et al.

    Frontiers in aging 2022;3;851039

    PUBMED: 35821807; PMC: 9261316; DOI: 10.3389/fragi.2022.851039

  • ETS transcription factor ELF3 (ESE-1) is a cell cycle regulator in benign and malignant prostate.

    Archer LK, Frame FM, Walker HF, Droop AP, McDonald GLK, Kucko S, Berney DM, Mann VM, Simms MS and Maitland NJ

    FEBS open bio 2022

    PUBMED: 35472129; DOI: 10.1002/2211-5463.13417

  • In vivo labeling reveals continuous trafficking of TCF-1+ T cells between tumor and lymphoid tissue.

    Li Z, Tuong ZK, Dean I, Willis C, Gaspal F, Fiancette R, Idris S, Kennedy B, Ferdinand JR, Peñalver A et al.

    The Journal of experimental medicine 2022;219;6

    PUBMED: 35472220; DOI: 10.1084/jem.20210749

  • Tissue Immunity in the Bladder.

    Bowyer GS, Loudon KW, Suchanek O and Clatworthy MR

    Annual review of immunology 2022;40;499-523

    PUBMED: 35471839; DOI: 10.1146/annurev-immunol-101220-032117

  • A Phase 1 Study of ADI-PEG20 (Pegargiminase) Combined with Cisplatin and Pemetrexed in ASS1-Negative Metastatic Uveal Melanoma.

    Chan PY, Phillips MM, Ellis S, Johnston A, Feng X, Arora A, Hay G, Cohen VML, Sagoo M, Bomalaski JS et al.

    Pigment cell & melanoma research 2022

    PUBMED: 35466524; DOI: 10.1111/pcmr.13042

  • Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors.

    Herpers B, Eppink B, James MI, Cortina C, Cañellas-Socias A, Boj SF, Hernando-Momblona X, Glodzik D, Roovers RC, van de Wetering M et al.

    Nature cancer 2022

    PUBMED: 35469014; DOI: 10.1038/s43018-022-00359-0

  • Npm1 Haploinsufficiency in collaboration with MEIS1 is sufficient to induce AML in mice.

    Muranyi A, Ammer T, Kechter A, Rawat VPS, Sinha AU, Gonzalez-Menendez I, Quintanilla-Martinez L, Azoitei A, Günes C, Mupo A et al.

    Blood advances 2022

    PUBMED: 35468619; DOI: 10.1182/bloodadvances.2022007015

  • The NHS England 100,000 Genomes Project: feasibility and utility of centralised genome sequencing for children with cancer.

    Trotman J, Armstrong R, Firth H, Trayers C, Watkins J, Allinson K, Jacques TS, Nicholson JC, Burke GAA, Genomics England Research Consortium et al.

    British journal of cancer 2022

    PUBMED: 35449451; DOI: 10.1038/s41416-022-01788-5

  • Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.

    Attwood SW, Hill SC, Aanensen DM, Connor TR and Pybus OG

    Nature reviews. Genetics 2022

    PUBMED: 35459859; DOI: 10.1038/s41576-022-00483-8

  • Smallpox vaccination induces a substantial increase in commensal skin bacteria that promote pathology and influence the host response.

    Shmeleva EV, Gomez de Agüero M, Wagner J, Enright AJ, Macpherson AJ, Ferguson BJ and Smith GL

    PLoS pathogens 2022;18;4;e1009854

    PUBMED: 35446919; DOI: 10.1371/journal.ppat.1009854

  • The Human Pangenome Project: a global resource to map genomic diversity.

    Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP et al.

    Nature 2022;604;7906;437-446

    PUBMED: 35444317; DOI: 10.1038/s41586-022-04601-8

  • Characterisation of Treponema pallidum lineages within the contemporary syphilis outbreak in Australia: a genomic epidemiological analysis.

    Taouk ML, Taiaroa G, Pasricha S, Herman S, Chow EPF, Azzatto F, Zhang B, Sia CM, Duchene S, Lee A et al.

    The Lancet. Microbe 2022;3;6;e417-e426

    PUBMED: 35659903; DOI: 10.1016/S2666-5247(22)00035-0

  • Germline MBD4 deficiency causes a multi-tumor predisposition syndrome.

    Palles C, West HD, Chew E, Galavotti S, Flensburg C, Grolleman JE, Jansen EAM, Curley H, Chegwidden L, Arbe-Barnes EH et al.

    American journal of human genetics 2022

    PUBMED: 35460607; DOI: 10.1016/j.ajhg.2022.03.018

  • Comparative genomics of disease and carriage serotype 1 pneumococci.

    Chaguza C, Ebruke C, Senghore M, Lo SW, Tientcheu PE, Gladstone RA, Tonkin-Hill G, Cornick JE, Yang M, Worwui A et al.

    Genome biology and evolution 2022

    PUBMED: 35439297; PMC: 9048925; DOI: 10.1093/gbe/evac052

  • Amniogenesis occurs in two independent waves in primates.

    Rostovskaya M, Andrews S, Reik W and Rugg-Gunn PJ

    Cell stem cell 2022;29;5;744-759.e6

    PUBMED: 35439430; DOI: 10.1016/j.stem.2022.03.014

  • The Leishmania donovani Ortholog of the Glycosylphosphatidylinositol Anchor Biosynthesis Cofactor PBN1 Is Essential for Host Infection.

    Roberts A, Nagar R, Brandt C, Harcourt K, Clare S, Ferguson MAJ and Wright GJ

    mBio 2022;e0043322

    PUBMED: 35420475; DOI: 10.1128/mbio.00433-22

  • An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples.

    MalariaGEN, Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, Andrianaranjaka V, Anstey NM, Aseffa A, Ashley E et al.

    Wellcome open research 2022;7;136

    PUBMED: 35651694; PMC: 9127374; DOI: 10.12688/wellcomeopenres.17795.1

  • BTBBCL6 dimers as building blocks for reversible drug-induced protein oligomerization.

    Nitsch L, Jensen P, Yoon H, Koeppel J, Burman SSR, Fischer ES, Scholl C, Fröhling S and Słabicki M

    Cell reports methods 2022;2;4;100193

    PUBMED: 35497498; PMC: 9046236; DOI: 10.1016/j.crmeth.2022.100193

  • Immune disease variants modulate gene expression in regulatory CD4+ T cells.

    Bossini-Castillo L, Glinos DA, Kunowska N, Golda G, Lamikanra AA, Spitzer M, Soskic B, Cano-Gamez E, Smyth DJ, Cattermole C et al.

    Cell genomics 2022;2;4;None

    PUBMED: 35591976; PMC: 9010307; DOI: 10.1016/j.xgen.2022.100117

  • Cooperation in Countering Artemisinin Resistance in Africa: Learning from COVID-19.

    Rosenthal PJ, Björkman A, Dhorda M, Djimde A, Dondorp AM, Gaye O, Guerin PJ, Juma E, Kwiatkowski DP, Merson L et al.

    The American journal of tropical medicine and hygiene 2022

    PUBMED: 35413688; PMC: 9209939; DOI: 10.4269/ajtmh.22-0148

  • G protein-coupled receptor kinase 5 regulates thrombin signaling in platelets via PAR-1.

    Downes K, Zhao X, Gleadall NS, McKinney H, Kempster C, Batista J, Thomas PL, Cooper M, Michael JV, Kreuzhuber R et al.

    Blood advances 2022;6;7;2319-2330

    PUBMED: 34581777; DOI: 10.1182/bloodadvances.2021005453

  • Narrowing the chromosome 22q11.2 locus duplicated in bladder exstrophy-epispadias complex.

    Beaman GM, Woolf AS, Lopes FM, Guo SA, Harkness JR, Cervellione RM, Keene D, Mushtaq I, Clatworthy MR and Newman WG

    Journal of pediatric urology 2022

    PUBMED: 35491304; DOI: 10.1016/j.jpurol.2022.04.006

  • NPM1 gene mutations can be confidently identified in blood DNA months before de novo AML onset.

    Quiros PM, Gu M, Barcena C, Iyer V and Vassiliou GS

    Blood advances 2022;6;7;2409-2413

    PUBMED: 34920452; PMC: 9006299; DOI: 10.1182/bloodadvances.2021005927

  • Fetal central nervous system anomalies: When should we offer exome sequencing?

    Baptiste C, Mellis R, Aggarwal V, Lord J, Eberhardt R, Kilby MD, Maher ER, Wapner R, Giordano J and Chitty LS

    Prenatal diagnosis 2022

    PUBMED: 35411553; DOI: 10.1002/pd.6145

  • Physical activity attenuates but does not eliminate coronary heart disease risk amongst adults with risk factors: EPIC-CVD case-cohort study.

    Fortuin-de Smidt MC, Sewe MO, Lassale C, Weiderpass E, Andersson J, Huerta JM, Ekelund U, Aleksandrova K, Tong TY, Dahm CC et al.

    European journal of preventive cardiology 2022

    PUBMED: 35403197; DOI: 10.1093/eurjpc/zwac055

  • Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae.

    Lu J, Gao D, Sims Y, Fang W, Collins J, Torrance J, Lin G, Xie J, Liu J and Howe K

    Marine biotechnology (New York, N.Y.) 2022

    PUBMED: 35394576; DOI: 10.1007/s10126-022-10119-x

  • Multi-omic rejuvenation of human cells by maturation phase transient reprogramming.

    Gill D, Parry A, Santos F, Okkenhaug H, Todd CD, Hernando-Herraez I, Stubbs TM, Milagre I and Reik W

    eLife 2022;11

    PUBMED: 35390271; PMC: 9023058; DOI: 10.7554/eLife.71624

  • Genetic Landscape of the ACE2 Coronavirus Receptor.

    Yang Z, MacDonald-Dunlop E, Chen J, Zhai R, Li T, Richmond A, Klaric L, Pirastu N, Ning Z, Zheng C et al.

    Circulation 2022

    PUBMED: 35387486; DOI: 10.1161/CIRCULATIONAHA.121.057888

  • Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential.

    Nakao T, Bick AG, Taub MA, Zekavat SM, Uddin MM, Niroula A, Carty CL, Lane J, Honigberg MC, Weinstock JS et al.

    Science advances 2022;8;14;eabl6579

    PUBMED: 35385311; DOI: 10.1126/sciadv.abl6579

  • Analyzing human knockouts to validate GPR151 as a therapeutic target for reduction of body mass index.

    Gurtan A, Dominy J, Khalid S, Vong L, Caplan S, Currie T, Richards S, Lamarche L, Denning D, Shpektor D et al.

    PLoS genetics 2022;18;4;e1010093

    PUBMED: 35381001; DOI: 10.1371/journal.pgen.1010093

  • Panakeia - a universal tool for bacterial pangenome analysis.

    Beier S and Thomson NR

    BMC genomics 2022;23;1;265

    PUBMED: 35382730; DOI: 10.1186/s12864-022-08303-3

  • Reproducible disease phenotyping at scale: Example of coronary artery disease in UK Biobank.

    Patel RS, Denaxas S, Howe LJ, Eggo RM, Shah AD, Allen NE, Danesh J, Hingorani A, Sudlow C and Hemingway H

    PloS one 2022;17;4;e0264828

    PUBMED: 35381005; DOI: 10.1371/journal.pone.0264828

  • The genome sequence of the blue-rayed limpet, Patella pellucida Linnaeus, 1758.

    Lawniczak MKN, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;126

    PUBMED: 36874573; PMC: 9975397; DOI: 10.12688/wellcomeopenres.17825.1

  • The genome sequence of the marbled white butterfly, Melanargia galathea (Linnaeus, 1758).

    Vila R, Lohse K, Hayward A, Laetsch D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;123

    PUBMED: 36874572; PMC: 9975406; DOI: 10.12688/wellcomeopenres.17807.1

  • The genome sequence of the northern goshawk, Accipiter gentilis (Linnaeus, 1758).

    August K, Davison M, Bortoluzzi C, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;122

    PUBMED: 35493200; PMC: 9020535; DOI: 10.12688/wellcomeopenres.17821.1

  • Bayesian networks elucidate complex genomic landscapes in cancer.

    Angelopoulos N, Chatzipli A, Nangalia J, Maura F and Campbell PJ

    Communications biology 2022;5;1;306

    PUBMED: 35379892; PMC: 8980036; DOI: 10.1038/s42003-022-03243-w

  • SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time.

    Ashford F, Best A, Dunn SJ, Ahmed Z, Siddiqui H, Melville J, Wilkinson S, Mirza J, Cumley N, Stockton J et al.

    Journal of clinical microbiology 2022;e0240821

    PUBMED: 35369709; DOI: 10.1128/jcm.02408-21

  • WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans.

    Davis P, Zarowiecki M, Arnaboldi V, Becerra A, Cain S, Chan J, Chen WJ, Cho J, da Veiga Beltrame E, Diamantakis S et al.

    Genetics 2022;220;4

    PUBMED: 35134929; PMC: 8982018; DOI: 10.1093/genetics/iyac003

  • Individualised prediction of drug response and rational combination therapy in NSCLC using artificial intelligence enabled studies of acute phosphoproteomic changes.

    Coker EA, Stewart A, Ozer B, Minchom AR, Pickard L, Ruddle R, Carreira S, Popat S, O'Brien ME, Raynaud FI et al.

    Molecular cancer therapeutics 2022

    PUBMED: 35368084; DOI: 10.1158/1535-7163.MCT-21-0442

  • A suspension technique for efficient large-scale cancer organoid culturing and perturbation screens.

    Price S, Bhosle S, Gonçalves E, Li X, McClurg DP, Barthorpe S, Beck A, Hall C, Lightfoot H, Farrow L et al.

    Scientific reports 2022;12;1;5571

    PUBMED: 35368031; PMC: 8976852; DOI: 10.1038/s41598-022-09508-y

  • Isolation and Characterisation of Bacteriophage Selective for Key Acinetobacter baumannii Capsule Chemotypes.

    Soontarach R, Srimanote P, Enright MC, Blundell-Hunter G, Dorman MJ, Thomson NR, Taylor PW and Voravuthikunchai SP

    Pharmaceuticals (Basel, Switzerland) 2022;15;4

    PUBMED: 35455440; DOI: 10.3390/ph15040443

  • A distinct hematopoietic differentiation state characterizes aggressive infant leukemia.

    No authors listed

    Nature medicine 2022;28;4;641-642

    PUBMED: 35288696; DOI: 10.1038/s41591-022-01719-0

  • The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;119

    PUBMED: 36874564; PMC: 9975414; DOI: 10.12688/wellcomeopenres.17747.1

  • A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV.

    Ndlangisa KM, du Plessis M, Lo S, de Gouveia L, Chaguza C, Antonio M, Kwambana-Adams B, Cornick J, Everett DB, Dagan R et al.

    Microbial genomics 2022;8;4

    PUBMED: 35384831; PMC: 9453074; DOI: 10.1099/mgen.0.000746

  • Design and Husbandry Considerations for a Containment Level 2 Aquatic Facility.

    Goodwin N and Westall L

    Zebrafish 2022;19;2;56-66

    PUBMED: 35439044; DOI: 10.1089/zeb.2021.0086

  • Diversity of microbial defence systems.

    Cazares A, Figueroa W and Cazares D

    Nature reviews. Microbiology 2022;20;4;191

    PUBMED: 35149840; DOI: 10.1038/s41579-022-00702-3

  • Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399.

    Ledda A, Cummins M, Shaw LP, Jauneikaite E, Cole K, Lasalle F, Barry D, Turton J, Rosmarin C, Anaraki S et al.

    Microbial genomics 2022;8;4

    PUBMED: 35442183; DOI: 10.1099/mgen.0.000675

  • Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis.

    Forster SC, Clare S, Beresford-Jones BS, Harcourt K, Notley G, Stares MD, Kumar N, Soderholm AT, Adoum A, Wong H et al.

    Nature microbiology 2022;7;4;590-599

    PUBMED: 35365791; DOI: 10.1038/s41564-022-01094-z

  • Linear plasmids in Klebsiella and other Enterobacteriaceae.

    Hawkey J, Cottingham H, Tokolyi A, Wick RR, Judd LM, Cerdeira L, de Oliveira Garcia D, Wyres KL and Holt KE

    Microbial genomics 2022;8;4

    PUBMED: 35416146; PMC: 9453081; DOI: 10.1099/mgen.0.000807

  • Matrikines as mediators of tissue remodelling.

    Jariwala N, Ozols M, Bell M, Bradley E, Gilmore A, Debelle L and Sherratt MJ

    Advanced drug delivery reviews 2022;185;114240

    PUBMED: 35378216; DOI: 10.1016/j.addr.2022.114240

  • miR-374a-5p regulates inflammatory genes and monocyte function in patients with inflammatory bowel disease.

    Perez-Sanchez C, Barbera Betancourt A, Lyons PA, Zhang Z, Suo C, Lee JC, McKinney EF, Modis LK, Ellson C and Smith KGC

    The Journal of experimental medicine 2022;219;5

    PUBMED: 35363256; PMC: 8980842; DOI: 10.1084/jem.20211366

  • Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types.

    Edwards T, Heinz E, van Aartsen J, Howard A, Roberts P, Corless C, Fraser AJ, Williams CT, Bulgasim I, Cuevas LE et al.

    Microbial genomics 2022;8;4

    PUBMED: 35404783; DOI: 10.1099/mgen.0.000789

  • Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses.

    Rodríguez-Ubreva J, Arutyunyan A, Bonder MJ, Del Pino-Molina L, Clark SJ, de la Calle-Fabregat C, Garcia-Alonso L, Handfield LF, Ciudad L, Andrés-León E et al.

    Nature communications 2022;13;1;1779

    PUBMED: 35365635; DOI: 10.1038/s41467-022-29450-x

  • Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae.

    Stevens EJ, Morse DJ, Bonini D, Duggan S, Brignoli T, Recker M, Lees JA, Croucher NJ, Bentley S, Wilson DJ et al.

    Microbial genomics 2022;8;4

    PUBMED: 35416147; DOI: 10.1099/mgen.0.000784

  • Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics.

    Papaiakovou M, Littlewood DTJ, Doyle SR, Gasser RB and Cantacessi C

    Parasites & vectors 2022;15;1;118

    PUBMED: 35365192; DOI: 10.1186/s13071-022-05225-7

  • A blood-based miRNA signature with prognostic value for overall survival in advanced stage non-small cell lung cancer treated with immunotherapy.

    Rajakumar T, Horos R, Jehn J, Schenz J, Muley T, Pelea O, Hofmann S, Kittner P, Kahraman M, Heuvelman M et al.

    NPJ precision oncology 2022;6;1;19

    PUBMED: 35361874; PMC: 8971493; DOI: 10.1038/s41698-022-00262-y

  • The complete sequence of a human genome.

    Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A et al.

    Science (New York, N.Y.) 2022;376;6588;44-53

    PUBMED: 35357919; DOI: 10.1126/science.abj6987

  • The genome sequence of the Atlantic horse mackerel, Trachurus trachurus (Linnaeus 1758).

    Genner M, Collins R, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;118

    PUBMED: 36874570; PMC: 9975430; DOI: 10.12688/wellcomeopenres.17813.1

  • Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.

    Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA et al.

    Nature methods 2022

    PUBMED: 35361931; DOI: 10.1038/s41592-022-01440-3

  • Defining novel causal SNPs and linked phenotypes at melanoma-associated loci.

    Castaneda-Garcia C, Iyer V, Nsengimana J, Trower A, Droop A, Brown KM, Choi J, Zhang T, Harland M, Newton-Bishop JA et al.

    Human molecular genetics 2022

    PUBMED: 35357426; DOI: 10.1093/hmg/ddac074

  • The genome sequence of the box-headed blood bee, Sphecodes monilicornis (Kirby, 1802).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Monks J and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;115

    PUBMED: 36969718; PMC: 10034205; DOI: 10.12688/wellcomeopenres.17786.1

  • The genome sequence of the grizzled skipper, Pyrgus malvae (Linnaeus, 1758).

    Hayward A, Vila R, Lohse K, Laetsch D, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;114

    PUBMED: 35673393; PMC: 9156896; DOI: 10.12688/wellcomeopenres.17806.1

  • Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting.

    Liu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K et al.

    Cell metabolism 2022;34;5;719-730.e4

    PUBMED: 35354069; PMC: 9097589; DOI: 10.1016/j.cmet.2022.03.002

  • The genome sequence of the tree wasp, Dolichovespula sylvestris Scopoli, 1763.

    Falk S, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Broad GR and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;113

    PUBMED: 36451628; PMC: 9672531; DOI: 10.12688/wellcomeopenres.17783.1

  • Artemisinin resistance in the malaria parasite, Plasmodium falciparum, originates from its initial transcriptional response.

    Zhu L, van der Pluijm RW, Kucharski M, Nayak S, Tripathi J, White NJ, Day NPJ, Faiz A, Phyo AP, Amaratunga C et al.

    Communications biology 2022;5;1;274

    PUBMED: 35347215; DOI: 10.1038/s42003-022-03215-0

  • Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics.

    Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJM, Baugh LR and Andersen EC

    Genome biology and evolution 2022

    PUBMED: 35348662; DOI: 10.1093/gbe/evac042

  • Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials.

    Dyson ZA, Malau E, Horwood PF, Ford R, Siba V, Yoannes M, Pomat W, Passey M, Judd LM, Ingle DJ et al.

    PLoS neglected tropical diseases 2022;16;3;e0010306

    PUBMED: 35344544; DOI: 10.1371/journal.pntd.0010306

  • The genome sequence of the pebble prominent, Notodonta ziczac (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Lewin T and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;111

    PUBMED: 35694197; PMC: 9171288; DOI: 10.12688/wellcomeopenres.17789.1

  • A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic.

    Aguilera P, Mascardi MF, Belforte FS, Rosso AD, Quesada S, Llovet I, Iraola G, Trinks J and Penas-Steinhardt A

    Frontiers in microbiology 2022;13;803121

    PUBMED: 35401432; PMC: 8988235; DOI: 10.3389/fmicb.2022.803121

  • Genome Sequences of 25 SARS-CoV-2 Sublineage B.1.1.529 Omicron Strains in Bangladesh.

    Bin Manjur OH, Afrad MH, Khan MH, Hossain M, Kawser Z, Alam AN, Banik N, Alam S, Billah MM, Afreen N et al.

    Microbiology resource announcements 2022;11;4;e0011922

    PUBMED: 35323016; PMC: 9022525; DOI: 10.1128/mra.00119-22

  • eIF6 rebinding dynamically couples ribosome maturation and translation.

    Jaako P, Faille A, Tan S, Wong CC, Escudero-Urquijo N, Castro-Hartmann P, Wright P, Hilcenko C, Adams DJ and Warren AJ

    Nature communications 2022;13;1;1562

    PUBMED: 35322020; DOI: 10.1038/s41467-022-29214-7

  • Reduced reproductive success is associated with selective constraint on human genes.

    Gardner EJ, Neville MDC, Samocha KE, Barclay K, Kolk M, Niemi MEK, Kirov G, Martin HC and Hurles ME

    Nature 2022;603;7903;858-863

    PUBMED: 35322230; DOI: 10.1038/s41586-022-04549-9

  • A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell.

    Ruiz Tejada Segura ML, Abou Moussa E, Garabello E, Nakahara TS, Makhlouf M, Mathew LS, Wang L, Valle F, Huang SSY, Mainland JD et al.

    Cell reports 2022;38;12;110547

    PUBMED: 35320714; PMC: 8995392; DOI: 10.1016/j.celrep.2022.110547

  • The genome sequence of Aplidium turbinatum (Savigny 1816), a colonial sea squirt.

    Bishop J, Harley J, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;106

    PUBMED: 35694195; PMC: 9171297; DOI: 10.12688/wellcomeopenres.17785.1

  • Genomic Characteristics of Recently Recognized Vibrio cholerae El Tor Lineages Associated with Cholera in Bangladesh, 1991 to 2017.

    Monir MM, Hossain T, Morita M, Ohnishi M, Johura FT, Sultana M, Monira S, Ahmed T, Thomson N, Watanabe H et al.

    Microbiology spectrum 2022;10;2;e0039122

    PUBMED: 35315699; PMC: 9045249; DOI: 10.1128/spectrum.00391-22

  • The genome sequence of Gymnosoma rotundatum (Linnaeus, 1758), a parasitoid ladybird fly.

    Smith M, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;104

    PUBMED: 35419492; PMC: 8987346; DOI: 10.12688/wellcomeopenres.17782.1

  • Defining the Protease and Protease Inhibitor (P/PI) Proteomes of Healthy and Diseased Human Skin by Modified Systematic Review.

    Stewart-McGuinness C, Platt CI, Ozols M, Goh B, Griffiths TW and Sherratt MJ

    Biomolecules 2022;12;3

    PUBMED: 35327667; DOI: 10.3390/biom12030475

  • Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.

    Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun R, Jackson B, Orton R, Nielsen M, Hsu NS et al.

    Virus evolution 2022;8;1;veac023

    PUBMED: 35502202; PMC: 9037374; DOI: 10.1093/ve/veac023

  • The genome sequence of the peppered moth, Biston betularia Linnaeus, 1758.

    Boyes D, Wright C, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;97

    PUBMED: 37008251; PMC: 10061035; DOI: 10.12688/wellcomeopenres.17578.1

  • Association of shorter leucocyte telomere length with risk of frailty.

    Bountziouka V, Nelson CP, Codd V, Wang Q, Musicha C, Allara E, Kaptoge S, Di Angelantonio E, Butterworth AS, Thompson JR et al.

    Journal of cachexia, sarcopenia and muscle 2022

    PUBMED: 35297226; DOI: 10.1002/jcsm.12971

  • Biallelic variants in TRAPPC10 cause a microcephalic TRAPPopathy disorder in humans and mice.

    Rawlins LE, Almousa H, Khan S, Collins SC, Milev MP, Leslie J, Saint-Dic D, Khan V, Hincapie AM, Day JO et al.

    PLoS genetics 2022;18;3;e1010114

    PUBMED: 35298461; DOI: 10.1371/journal.pgen.1010114

  • Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme.

    Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V et al.

    BMC biology 2022;20;1;67

    PUBMED: 35296311; DOI: 10.1186/s12915-022-01257-8

  • Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome.

    Forster SC, Liu J, Kumar N, Gulliver EL, Gould JA, Escobar-Zepeda A, Mkandawire T, Pike LJ, Shao Y, Stares MD et al.

    Nature communications 2022;13;1;1445

    PUBMED: 35301310; PMC: 8931123; DOI: 10.1038/s41467-022-29096-9

  • Taming transposable elements in vertebrates: from epigenetic silencing to domestication.

    Almeida MV, Vernaz G, Putman ALK and Miska EA

    Trends in genetics : TIG 2022;38;6;529-553

    PUBMED: 35307201; DOI: 10.1016/j.tig.2022.02.009

  • Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.

    Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J et al.

    Virus evolution 2022;8;1;veac022

    PUBMED: 35402002; PMC: 8986633; DOI: 10.1093/ve/veac022

  • The genome sequence of the orange-striped anemone, Diadumene lineata (Verrill, 1869).

    Wood C, Bishop J, Harley J, Mrowicki R, Marine Biological Association Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;93

    PUBMED: 36874574; PMC: 9975403; DOI: 10.12688/wellcomeopenres.17763.1

  • High-throughput characterization of the role of non-B DNA motifs on promoter function.

    Georgakopoulos-Soares I, Victorino J, Parada GE, Agarwal V, Zhao J, Wong HY, Umar MI, Elor O, Muhwezi A, An JY et al.

    Cell genomics 2022;2;4

    PUBMED: 35573091; PMC: 9105345; DOI: 10.1016/j.xgen.2022.100111

  • The genome sequence of the angle shades moth, Phlogophora meticulosa (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;89

    PUBMED: 36324701; PMC: 9608255; DOI: 10.12688/wellcomeopenres.17757.1

  • A public backlash towards genomics is a risk all of us working in genomics must share.

    Middleton A, Parry V, Borra J and Orviss K

    The Lancet regional health. Europe 2022;15;100347

    PUBMED: 35309760; PMC: 8927847; DOI: 10.1016/j.lanepe.2022.100347

  • Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases.

    Kundu K, Tardaguila M, Mann AL, Watt S, Ponstingl H, Vasquez L, Von Schiller D, Morrell NW, Stegle O, Pastinen T et al.

    Nature genetics 2022;54;3;251-262

    PUBMED: 35288711; DOI: 10.1038/s41588-022-01025-y

  • Predicting base editing outcomes using position-specific sequence determinants.

    Pallaseni A, Peets EM, Koeppel J, Weller J, Vanderstichele T, Ho UL, Crepaldi L, van Leeuwen J, Allen F and Parts L

    Nucleic acids research 2022

    PUBMED: 35286377; DOI: 10.1093/nar/gkac161

  • Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia.

    Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A et al.

    Nature medicine 2022

    PUBMED: 35288693; DOI: 10.1038/s41591-022-01720-7

  • Colocalization analysis of pancreas eQTLs with risk loci from alcoholic and novel non-alcoholic chronic pancreatitis GWAS suggests potential disease causing mechanisms.

    Schmidt AW, Kühnapfel A, Kirsten H, Grallert H, Hellerbrand C, Kiefer F, Mann K, Mueller S, Nöthen MM, Peters A et al.

    Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.] 2022

    PUBMED: 35331647; DOI: 10.1016/j.pan.2022.03.007

  • A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae.

    Sim CK, Kashaf SS, Stacy A, Proctor DM, Almeida A, Bouladoux N, Chen M, NISC Comparative Sequencing Program, Finn RD, Belkaid Y et al.

    Microbiome 2022;10;1;43

    PUBMED: 35272717; DOI: 10.1186/s40168-021-01207-6

  • Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular epidemiological study.

    Jauneikaite E, Honeyford K, Blandy O, Mosavie M, Pearson M, Ramzan FA, Ellington MJ, Parkhill J, Costelloe CE, Woodford N and Sriskandan S

    The Journal of antimicrobial chemotherapy 2022

    PUBMED: 35265995; DOI: 10.1093/jac/dkac071

  • Evaluation of antithrombotic use and COVID-19 outcomes in a nationwide atrial fibrillation cohort.

    Handy A, Banerjee A, Wood AM, Dale C, Sudlow CLM, Tomlinson C, Bean D, Thygesen JH, Mizani MA, Katsoulis M et al.

    Heart (British Cardiac Society) 2022

    PUBMED: 35273122; DOI: 10.1136/heartjnl-2021-320325

  • Integrated GWAS and Gene Expression Suggest ORM1 as a Potential Regulator of Plasma Levels of Cell-Free DNA and Thrombosis Risk.

    Lopez S, Martinez-Perez A, Rodriguez-Rius A, Viñuela A, Brown AA, Martin-Fernandez L, Vilalta N, Arús M, Panousis NI, Buil A et al.

    Thrombosis and haemostasis 2022

    PUBMED: 35272364; DOI: 10.1055/s-0041-1742169

  • Elucidating mechanisms of genetic cross-disease associations at the PROCR vascular disease locus.

    Stacey D, Chen L, Stanczyk PJ, Howson JMM, Mason AM, Burgess S, MacDonald S, Langdown J, McKinney H, Downes K et al.

    Nature communications 2022;13;1;1222

    PUBMED: 35264566; DOI: 10.1038/s41467-022-28729-3

  • Genomic consequences of domestication of the Siamese fighting fish.

    Kwon YM, Vranken N, Hoge C, Lichak MR, Norovich AL, Francis KX, Camacho-Garcia J, Bista I, Wood J, McCarthy S et al.

    Science advances 2022;8;10;eabm4950

    PUBMED: 35263139; DOI: 10.1126/sciadv.abm4950

  • The genome sequence of the small elephant hawk moth, Deilephila porcellus (Linnaeus, 1758).

    Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Sivess L and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;80

    PUBMED: 35505773; PMC: 9021678; DOI: 10.12688/wellcomeopenres.17740.1

  • Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain.

    Marsh SE, Walker AJ, Kamath T, Dissing-Olesen L, Hammond TR, de Soysa TY, Young AMH, Murphy S, Abdulraouf A, Nadaf N et al.

    Nature neuroscience 2022;25;3;306-316

    PUBMED: 35260865; DOI: 10.1038/s41593-022-01022-8

  • Genomic and antimicrobial resistance analyses of Neisseria gonorrhoeae isolates, Burkina Faso, 2018-2019.

    Congo-Ouedraogo M, Poncin T, Sangaré L, Mérimèche M, Braille A, Jacquier H, Ouedraogo AS, Dah E, Traore I, Corander J et al.

    Journal of the European Academy of Dermatology and Venereology : JEADV 2022;36;7;e565-e568

    PUBMED: 35224783; DOI: 10.1111/jdv.18037

  • Triple therapy with artemether-lumefantrine plus amodiaquine versus artemether-lumefantrine alone for artemisinin-resistant, uncomplicated falciparum malaria: an open-label, randomised, multicentre trial.

    Peto TJ, Tripura R, Callery JJ, Lek D, Nghia HDT, Nguon C, Thuong NTH, van der Pluijm RW, Dung NTP, Sokha M et al.

    The Lancet. Infectious diseases 2022

    PUBMED: 35276064; DOI: 10.1016/S1473-3099(21)00692-7

  • Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria.

    Odih EE, Irek EO, Obadare TO, Oaikhena AO, Afolayan AO, Underwood A, Adenekan AT, Ogunleye VO, Argimon S, Dalsgaard A et al.

    Frontiers in medicine 2022;9;846051

    PUBMED: 35321470; PMC: 8936076; DOI: 10.3389/fmed.2022.846051

  • Single-cell transcriptomics reveals expression profiles of Trypanosoma brucei sexual stages.

    Howick VM, Peacock L, Kay C, Collett C, Gibson W and Lawniczak MKN

    PLoS pathogens 2022;18;3;e1010346

    PUBMED: 35255094; DOI: 10.1371/journal.ppat.1010346

  • Single-cell temporal analysis of natural dengue infection reveals skin-homing lymphocyte expansion one day before defervescence.

    Arora JK, Opasawatchai A, Poonpanichakul T, Jiravejchakul N, Sungnak W, DENFREE Thailand, Matangkasombut O, Teichmann SA, Matangkasombut P and Charoensawan V

    iScience 2022;25;4;104034

    PUBMED: 35345453; PMC: 8957021; DOI: 10.1016/j.isci.2022.104034

  • The genome sequence of the small pearl-bordered fritillary butterfly, Boloria selene (Schiffermüller, 1775).

    Lohse K, Setter D, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;76

    PUBMED: 36507315; PMC: 9713055; DOI: 10.12688/wellcomeopenres.17734.1

  • CRAM 3.1: advances in the CRAM file format.

    Bonfield JK

    Bioinformatics (Oxford, England) 2022;38;6;1497-1503

    PUBMED: 34999766; PMC: 8896640; DOI: 10.1093/bioinformatics/btac010

  • Metastatic urothelial carcinoma of the urinary bladder in a Sumatran tiger (Panthera tigris sondaica).

    van der Weyden L, Tibbs C, Knott C and Dobromylskyj M

    Veterinary medicine and science 2022

    PUBMED: 35239258; DOI: 10.1002/vms3.771

  • Single-cell transcriptomics links malignant T cells to the tumor immune landscape in cutaneous T cell lymphoma.

    Liu X, Jin S, Hu S, Li R, Pan H, Liu Y, Lai P, Xu D, Sun J, Liu Z et al.

    Nature communications 2022;13;1;1158

    PUBMED: 35241665; DOI: 10.1038/s41467-022-28799-3

  • Covid-19 Vaccine Effectiveness against the Omicron (B.1.1.529) Variant.

    Andrews N, Stowe J, Kirsebom F, Toffa S, Rickeard T, Gallagher E, Gower C, Kall M, Groves N, O'Connell AM et al.

    The New England journal of medicine 2022

    PUBMED: 35249272; DOI: 10.1056/NEJMoa2119451

  • Grxcr1 regulates hair bundle morphogenesis and is required for normal mechanoelectrical transduction in mouse cochlear hair cells.

    Lorente-Cánovas B, Eckrich S, Lewis MA, Johnson SL, Marcotti W and Steel KP

    PloS one 2022;17;3;e0261530

    PUBMED: 35235570; DOI: 10.1371/journal.pone.0261530

  • Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming.

    Chondronasiou D, Gill D, Mosteiro L, Urdinguio RG, Berenguer-Llergo A, Aguilera M, Durand S, Aprahamian F, Nirmalathasan N, Abad M et al.

    Aging cell 2022;e13578

    PUBMED: 35235716; DOI: 10.1111/acel.13578

  • TransposonUltimate: software for transposon classification, annotation and detection.

    Riehl K, Riccio C, Miska EA and Hemberg M

    Nucleic acids research 2022

    PUBMED: 35234904; DOI: 10.1093/nar/gkac136

  • A genetic TRP down the channel to praziquantel resistance.

    Cotton JA and Doyle SR

    Trends in parasitology 2022;38;5;351-352

    PUBMED: 35246385; DOI: 10.1016/j.pt.2022.02.006

  • Africa: sequence 100,000 species to safeguard biodiversity.

    Ebenezer TE, Muigai AWT, Nouala S, Badaoui B, Blaxter M, Buddie AG, Jarvis ED, Korlach J, Kuja JO, Lewin HA et al.

    Nature 2022;603;7901;388-392

    PUBMED: 35292740; DOI: 10.1038/d41586-022-00712-4

  • Cancer-Associated SF3B1 Mutations Confer a BRCA-Like Cellular Phenotype and Synthetic Lethality to PARP Inhibitors.

    Lappin KM, Barros EM, Jhujh SS, Irwin GW, McMillan H, Liberante FG, Latimer C, La Bonte MJ, Mills KI, Harkin DP et al.

    Cancer research 2022;82;5;819-830

    PUBMED: 35027467; PMC: 7612475; DOI: 10.1158/0008-5472.CAN-21-1843

  • Dose-response relationships for vitamin D and all-cause mortality - Authors' reply.

    Burgess S and Butterworth AS

    The lancet. Diabetes & endocrinology 2022;10;3;158-159

    PUBMED: 35202588; DOI: 10.1016/S2213-8587(22)00015-8

  • Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi.

    Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Heinz E, Thomson NR and Feasey NA

    Microbial genomics 2022;8;3

    PUBMED: 35302438; DOI: 10.1099/mgen.0.000778

  • Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation.

    Kuzmanović N, Fagorzi C, Mengoni A, Lassalle F and diCenzo GC

    International journal of systematic and evolutionary microbiology 2022;72;3

    PUBMED: 35238735; DOI: 10.1099/ijsem.0.005243

  • The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900.

    Macadam C, Clifford C, Price BW, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;56

    PUBMED: 35592548; PMC: 9086528; DOI: 10.12688/wellcomeopenres.17684.2

  • Mechanistic study of the effect of Endothelin SNPs in microvascular angina - Protocol of the PRIZE Endothelin Sub-Study.

    Abraham GR, Morrow AJ, Oliveira J, Weir-McCall JR, Davenport EE, Berry C, Davenport AP and Hoole SP

    International journal of cardiology. Heart & vasculature 2022;39;100980

    PUBMED: 35242999; PMC: 8885580; DOI: 10.1016/j.ijcha.2022.100980

  • Phylogeography of ancient and modern brown bears from eastern Eurasia.

    Molodtseva AS, Makunin AI, Salomashkina VV, Kichigin IG, Vorobieva NV, Vasiliev SK, Shunkov MV, Tishkin AA, Grushin SP, Anijalg P et al.

    Biological journal of the Linnean Society. Linnean Society of London 2022;135;4;722-733

    PUBMED: 35359699; PMC: 8943912; DOI: 10.1093/biolinnean/blac009

  • Single-cell atlases: shared and tissue-specific cell types across human organs.

    Elmentaite R, Domínguez Conde C, Yang L and Teichmann SA

    Nature reviews. Genetics 2022

    PUBMED: 35217821; DOI: 10.1038/s41576-022-00449-w

  • 8C-like cells capture the human zygotic genome activation program in vitro.

    Taubenschmid-Stowers J, Rostovskaya M, Santos F, Ljung S, Argelaguet R, Krueger F, Nichols J and Reik W

    Cell stem cell 2022;29;3;449-459.e6

    PUBMED: 35216671; PMC: 8901440; DOI: 10.1016/j.stem.2022.01.014

  • Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model.

    Bierzynska A, Bull K, Miellet S, Dean P, Neal C, Colby E, McCarthy HJ, Hegde S, Sinha MD, Bugarin Diz C et al.

    Pediatric nephrology (Berlin, Germany) 2022

    PUBMED: 35211795; DOI: 10.1007/s00467-022-05440-5

  • Systematic identification of genes encoding cell surface and secreted proteins that are essential for in vitro growth and infection in Leishmania donovani.

    Roberts AJ, Ong HB, Clare S, Brandt C, Harcourt K, Franssen SU, Cotton JA, Müller-Sienerth N and Wright GJ

    PLoS pathogens 2022;18;2;e1010364

    PUBMED: 35202447; DOI: 10.1371/journal.ppat.1010364

  • The gut-meningeal immune axis: Priming brain defense against the most likely invaders.

    Di Marco Barros R, Fitzpatrick Z and Clatworthy MR

    The Journal of experimental medicine 2022;219;3

    PUBMED: 35195681; DOI: 10.1084/jem.20211520

  • Effective drug combinations in breast, colon and pancreatic cancer cells.

    Jaaks P, Coker EA, Vis DJ, Edwards O, Carpenter EF, Leto SM, Dwane L, Sassi F, Lightfoot H, Barthorpe S et al.

    Nature 2022;603;7899;166-173

    PUBMED: 35197630; PMC: 8891012; DOI: 10.1038/s41586-022-04437-2

  • Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission.

    Aggarwal D, Page AJ, Schaefer U, Savva GM, Myers R, Volz E, Ellaby N, Platt S, Groves N, Gallagher E et al.

    Nature communications 2022;13;1;1012

    PUBMED: 35197443; PMC: 8866425; DOI: 10.1038/s41467-022-28371-z

  • Multilateral benefit-sharing from digital sequence information will support both science and biodiversity conservation.

    Scholz AH, Freitag J, Lyal CHC, Sara R, Cepeda ML, Cancio I, Sett S, Hufton AL, Abebaw Y, Bansal K et al.

    Nature communications 2022;13;1;1086

    PUBMED: 35197464; PMC: 8866420; DOI: 10.1038/s41467-022-28594-0

  • The genome sequence of the blue-tailed damselfly, Ischnura elegans (Vander Linden, 1820).

    Price BW, Winter M, Brooks SJ, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;66

    PUBMED: 36874565; PMC: 9975421; DOI: 10.12688/wellcomeopenres.17691.1

  • Coagulation factor V is a T-cell inhibitor expressed by leukocytes in COVID-19.

    Wang J, Kotagiri P, Lyons PA, Al-Lamki RS, Mescia F, Bergamaschi L, Turner L, Morgan MD, Calero-Nieto FJ, Bach K et al.

    iScience 2022;25;3;103971

    PUBMED: 35224470; PMC: 8863325; DOI: 10.1016/j.isci.2022.103971

  • Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae.

    Mallawaarachchi S, Tonkin-Hill G, Croucher NJ, Turner P, Speed D, Corander J and Balding D

    NAR genomics and bioinformatics 2022;4;1;lqac011

    PUBMED: 35211669; PMC: 8862724; DOI: 10.1093/nargab/lqac011

  • Multiple genetic paths including massive gene amplification allow Mycobacterium tuberculosis to overcome loss of ESX-3 secretion system substrates.

    Wang L, Asare E, Shetty AC, Sanchez-Tumbaco F, Edwards MR, Saranathan R, Weinrick B, Xu J, Chen B, Bénard A et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;8

    PUBMED: 35193958; DOI: 10.1073/pnas.2112608119

  • Heat inactivation of clinical COVID-19 samples on an industrial scale for low risk and efficient high-throughput qRT-PCR diagnostic testing.

    Delpuech O, Douthwaite JA, Hill T, Niranjan D, Malintan NT, Duvoisin H, Elliott J, Goodfellow I, Hosmillo M, Orton AL et al.

    Scientific reports 2022;12;1;2883

    PUBMED: 35190592; DOI: 10.1038/s41598-022-06888-z

  • Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity.

    Uzzan M, Martin JC, Mesin L, Livanos AE, Castro-Dopico T, Huang R, Petralia F, Magri G, Kumar S, Zhao Q et al.

    Nature medicine 2022;28;4;766-779

    PUBMED: 35190725; PMC: 9107072; DOI: 10.1038/s41591-022-01680-y

  • The impact of hypoxia on B cells in COVID-19.

    Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ et al.

    EBioMedicine 2022;77;103878

    PUBMED: 35189575; DOI: 10.1016/j.ebiom.2022.103878

  • Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy.

    Spielmann N, Miller G, Oprea TI, Hsu CW, Fobo G, Frishman G, Montrone C, Haseli Mashhadi H, Mason J, Munoz Fuentes V et al.

    Nature cardiovascular research 2022;1;2;157-173

    PUBMED: 39195995; DOI: 10.1038/s44161-022-00018-8

  • Exploiting genomics to mitigate the public health impact of antimicrobial resistance.

    Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B and Baker S

    Genome medicine 2022;14;1;15

    PUBMED: 35172877; DOI: 10.1186/s13073-022-01020-2

  • Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

    Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB et al.

    GigaScience 2022;11

    PUBMED: 35169842; PMC: 8847733; DOI: 10.1093/gigascience/giac003

  • Molecular Composition of Serum Exosomes Could Discriminate Rectal Cancer Patients with Different Responses to Neoadjuvant Radiotherapy.

    Strybel U, Marczak L, Zeman M, Polanski K, Mielańczyk Ł, Klymenko O, Samelak-Czajka A, Jackowiak P, Smolarz M, Chekan M et al.

    Cancers 2022;14;4

    PUBMED: 35205741; DOI: 10.3390/cancers14040993

  • Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.

    Gardner PP, Paterson JM, McGimpsey S, Ashari-Ghomi F, Umu SU, Pawlik A, Gavryushkin A and Black MA

    Genome biology 2022;23;1;56

    PUBMED: 35172880; DOI: 10.1186/s13059-022-02625-x

  • The genome sequence of the dumpy grass hoverfly, Melanostoma mellinum (Linnaeus, 1758).

    Hawkes W, Wotton K, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;59

    PUBMED: 36874577; PMC: 9975431; DOI: 10.12688/wellcomeopenres.17615.1

  • The genome sequence of the furry-claspered furrow bee, Lasioglossum lativentre (Schenck, 1853).

    Falk S, Monks J, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;57

    PUBMED: 36865377; PMC: 9971656; DOI: 10.12688/wellcomeopenres.17706.1

  • The genome sequence of the German wasp, Vespula germanica (Fabricius, 1793).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;60

    PUBMED: 36128012; PMC: 9471221; DOI: 10.12688/wellcomeopenres.17703.1

  • CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.

    Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD et al.

    Nature reviews. Chemistry 2022;6;4;287-295

    PUBMED: 35783295; PMC: 9246350; DOI: 10.1038/s41570-022-00363-z

  • Open Data in the Era of the GDPR: Lessons from the Human Cell Atlas.

    Knoppers BM, Bernier A, Bowers S and Kirby E

    Annual review of genomics and human genetics 2022

    PUBMED: 36791787; DOI: 10.1146/annurev-genom-101322-113255

  • Towards equitable and trustworthy genomics research.

    Atutornu J, Milne R, Costa A, Patch C and Middleton A

    EBioMedicine 2022;76;103879

    PUBMED: 35158310; PMC: 8850759; DOI: 10.1016/j.ebiom.2022.103879

  • THE CARBON FOOTPRINT OF BIOINFORMATICS.

    Grealey J, Lannelongue L, Saw WY, Marten J, Méric G, Ruiz-Carmona S and Inouye M

    Molecular biology and evolution 2022

    PUBMED: 35143670; DOI: 10.1093/molbev/msac034

  • The genome sequence of a parasitoid wasp, Ichneumon xanthorius Forster, 1771.

    University of Oxford and Wytham Woods Genome Acquisition Lab, Broad G, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;47

    PUBMED: 35419493; PMC: 8984213; DOI: 10.12688/wellcomeopenres.17683.1

  • Biallelic mutations in cancer genomes reveal local mutational determinants.

    Demeulemeester J, Dentro SC, Gerstung M and Van Loo P

    Nature genetics 2022;54;2;128-133

    PUBMED: 35145300; DOI: 10.1038/s41588-021-01005-8

  • Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages.

    Demirci Y, Heger G, Katkat E, Papatheodorou I, Brazma A and Ozhan G

    Frontiers in cell and developmental biology 2022;10;813314

    PUBMED: 35223842; PMC: 8868567; DOI: 10.3389/fcell.2022.813314

  • DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research.

    Foreman J, Brent S, Perrett D, Bevan AP, Hunt SE, Cunningham F, Hurles ME and Firth HV

    Human mutation 2022

    PUBMED: 35143074; DOI: 10.1002/humu.24340

  • High-content CRISPR screening.

    Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B et al.

    Nature reviews. Methods primers 2022;2;1

    PUBMED: 37214176; PMC: 10200264; DOI: 10.1038/s43586-022-00098-7

  • Investigating Genetic and Other Determinants of First-Onset Myocardial Infarction in Malaysia: Protocol for the Malaysian Acute Vascular Events Risk Study.

    Chowdhury R, Noh MFM, Ismail SR, van Daalen KR, Kamaruddin PSNM, Zulkiply SH, Azizul NH, Khalid NM, Ali A, Idris IM et al.

    JMIR research protocols 2022;11;2;e31885

    PUBMED: 35142634; DOI: 10.2196/31885

  • The eternal quest for self-improvement of somatic cells.

    Campbell PJ

    Cell genomics 2022;2;2;100094

    PUBMED: 36778659; PMC: 9903819; DOI: 10.1016/j.xgen.2022.100094

  • Known allosteric proteins have central roles in genetic disease.

    Abrusán G, Ascher DB and Inouye M

    PLoS computational biology 2022;18;2;e1009806

    PUBMED: 35139069; DOI: 10.1371/journal.pcbi.1009806

  • Transcriptome-wide association study in UK biobank Europeans identifies associations with blood cell traits.

    Rowland B, Venkatesh S, Tardaguila M, Wen J, Rosen JD, Tapia AL, Sun Q, Graff M, Vuckovic D, Lettre G et al.

    Human molecular genetics 2022

    PUBMED: 35138379; DOI: 10.1093/hmg/ddac011

  • Genetic load: genomic estimates and applications in non-model animals.

    Bertorelle G, Raffini F, Bosse M, Bortoluzzi C, Iannucci A, Trucchi E, Morales HE and van Oosterhout C

    Nature reviews. Genetics 2022

    PUBMED: 35136196; DOI: 10.1038/s41576-022-00448-x

  • Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission.

    Aggarwal D, Warne B, Jahun AS, Hamilton WL, Fieldman T, du Plessis L, Hill V, Blane B, Watkins E, Wright E et al.

    Nature communications 2022;13;1;751

    PUBMED: 35136068; PMC: 8826310; DOI: 10.1038/s41467-021-27942-w

  • Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency.

    McGlacken-Byrne SM, Del Valle I, Le Quesne Stabej P, Bellutti L, Garcia-Alonso L, Ocaka LA, Ishida M, Suntharalingham JP, Gagunashvili A, Ogunbiyi OK et al.

    JCI insight 2022

    PUBMED: 35138268; DOI: 10.1172/jci.insight.154671

  • Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.

    Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM et al.

    Nature medicine 2022

    PUBMED: 35130561; DOI: 10.1038/s41591-022-01734-1

  • 10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity.

    Addy JWG, Bediako Y, Ndungu FM, Valetta JJ, Reid AJ, Mwacharo J, Ngoi JM, Wambua J, Otieno E, Musyoki J et al.

    Wellcome open research 2022;6;79

    PUBMED: 35141425; PMC: 8822141; DOI: 10.12688/wellcomeopenres.16562.3

  • A highly virulent variant of HIV-1 circulating in the Netherlands.

    Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L et al.

    Science (New York, N.Y.) 2022;375;6580;540-545

    PUBMED: 35113714; DOI: 10.1126/science.abk1688

  • Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.

    Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brożyńska M, Zhu Q et al.

    Nature genetics 2022;54;2;134-142

    PUBMED: 35115689; PMC: 9883041; DOI: 10.1038/s41588-021-00991-z

  • Complete mitochondrial genome of the greater round-eared bat, Tonatia bidens (Chiroptera: Phyllostomidae) from Brazil and phylogenetic relationships within the family.

    Farias JC, Vasconcelos S, Oliveira G, Santos N and Sotero-Caio CG

    Mitochondrial DNA. Part B, Resources 2022;7;2;323-325

    PUBMED: 35141410; PMC: 8820812; DOI: 10.1080/23802359.2022.2030820

  • Return of genomic results does not motivate intent to participate in research for all: Perspectives across 22 countries.

    Milne R, Morley KI, Almarri MA, Atutornu J, Baranova EE, Bevan P, Cerezo M, Cong Y, Costa A, Feijao C et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2022;24;5;1120-1129

    PUBMED: 35125311; DOI: 10.1016/j.gim.2022.01.002

  • The genome sequence of a hoverfly, Xanthogramma pedissequum (Harris, 1776).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;38

    PUBMED: 35224214; PMC: 8831851; DOI: 10.12688/wellcomeopenres.17559.1

  • The genome sequence of the square-spot rustic, Xestia xanthographa (Schiffermuller, 1775).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2022;7;37

    PUBMED: 36447758; PMC: 9664021; DOI: 10.12688/wellcomeopenres.17538.1

  • A2B-COVID: A tool for rapidly evaluating potential SARS-CoV-2 transmission events.

    Illingworth CJR, Hamilton WL, Jackson C, Warne B, Popay A, Meredith L, Hosmillo M, Jahun A, Fieldman T, Routledge M et al.

    Molecular biology and evolution 2022

    PUBMED: 35106603; DOI: 10.1093/molbev/msac025

  • Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens.

    Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D et al.

    PLoS computational biology 2022;18;2;e1009801

    PUBMED: 35108259; DOI: 10.1371/journal.pcbi.1009801

  • The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis.

    van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Pinholt M, Howden BP, Malhotra-Kumar S et al.

    The Lancet. Microbe 2022;3;2;e133-e141

    PUBMED: 35146465; PMC: 8810393; DOI: 10.1016/S2666-5247(21)00236-6

  • A new perspective on ancient Mitis group streptococcal genetics.

    Belman S, Chaguza C, Kumar N, Lo S and Bentley SD

    Microbial genomics 2022;8;2

    PUBMED: 35225216; PMC: 8942026; DOI: 10.1099/mgen.0.000753

  • A Python library for probabilistic analysis of single-cell omics data.

    Gayoso A, Lopez R, Xing G, Boyeau P, Valiollah Pour Amiri V, Hong J, Wu K, Jayasuriya M, Mehlman E, Langevin M et al.

    Nature biotechnology 2022;40;2;163-166

    PUBMED: 35132262; DOI: 10.1038/s41587-021-01206-w

  • Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity.

    Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S et al.

    Nature 2022

    PUBMED: 35104837; DOI: 10.1038/s41586-022-04474-x

  • Antibiotic Use and Resistance Knowledge Assessment of Personnel on Chicken Farms with High Levels of Antimicrobial Resistance: A Cross-Sectional Survey in Ica, Peru.

    Dávalos-Almeyda M, Guerrero A, Medina G, Dávila-Barclay A, Salvatierra G, Calderón M, Gilman RH and Tsukayama P

    Antibiotics (Basel, Switzerland) 2022;11;2

    PUBMED: 35203794; DOI: 10.3390/antibiotics11020190

  • Depression and genetic susceptibility to cardiometabolic diseases.

    Ritchie SC and Inouye M

    Nature cardiovascular research 2022;1;2;102-103

    PUBMED: 39195987; DOI: 10.1038/s44161-021-00012-6

  • MUON: multimodal omics analysis framework.

    Bredikhin D, Kats I and Stegle O

    Genome biology 2022;23;1;42

    PUBMED: 35105358; DOI: 10.1186/s13059-021-02577-8

  • Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence.

    Pozdeev G, Beckett MC, Mogre A, Thomson NR and Dorman CJ

    Microbial genomics 2022;8;2

    PUBMED: 35166652; DOI: 10.1099/mgen.0.000768

  • Small proteins: overcoming size restrictions.

    Ardern Z

    Nature reviews. Microbiology 2022;20;2;65

    PUBMED: 34848872; DOI: 10.1038/s41579-021-00672-y

  • Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection.

    Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S and Neuhaus K

    iScience 2022;25;2;103844

    PUBMED: 35198897; PMC: 8850804; DOI: 10.1016/j.isci.2022.103844

  • Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints.

    Senghore M, Chaguza C, Bojang E, Tientcheu PE, Bancroft RE, Lo SW, Gladstone RA, McGee L, Worwui A, Foster-Nyarko E et al.

    Microbial genomics 2022;8;2

    PUBMED: 35119356; PMC: 8942022; DOI: 10.1099/mgen.0.000732

  • B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination.

    Kotagiri P, Mescia F, Rae WM, Bergamaschi L, Tuong ZK, Turner L, Hunter K, Gerber PP, Hosmillo M, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID BioResource Collaboration et al.

    Cell reports 2022;38;7;110393

    PUBMED: 35143756; PMC: 8801326; DOI: 10.1016/j.celrep.2022.110393

  • Chromosome Painting in Lonchorhina aurita Sheds Light onto the Controversial Phylogenetic Position of Sword-Nosed Bats (Chiroptera, Phyllostomidae).

    Farias JC, Santos N, Bezerra DP and Sotero-Caio CG

    Cytogenetic and genome research 2022;1-9

    PUBMED: 35093945; DOI: 10.1159/000520969

  • The discovAIR project: a roadmap towards the Human Lung Cell Atlas.

    Luecken MD, Zaragozi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA et al.

    The European respiratory journal 2022

    PUBMED: 35086829; DOI: 10.1183/13993003.02057-2021

  • Functional genomic identification of predictors of sensitivity and mechanisms of resistance to multivalent 2nd generation TRAIL-R2 agonists.

    Grinkevich V, Wappett M, Crawford N, Price S, Lees A, McCann C, McAllister KA, Prehn JH, Young J, Bateson JH et al.

    Molecular cancer therapeutics 2022

    PUBMED: 35086954; DOI: 10.1158/1535-7163.MCT-21-0532

  • Placing ancient DNA sequences into reference phylogenies.

    Martiniano R, De Sanctis B, Hallast P and Durbin R

    Molecular biology and evolution 2022

    PUBMED: 35084493; DOI: 10.1093/molbev/msac017

  • Enhancing CDK4/6 inhibitor therapy for medulloblastoma using nanoparticle delivery and scRNA-seq-guided combination with sapanisertib.

    Lim C, Dismuke T, Malawsky D, Ramsey JD, Hwang D, Godfrey VL, Kabanov AV, Gershon TR and Sokolsky-Papkov M

    Science advances 2022;8;4;eabl5838

    PUBMED: 35080986; DOI: 10.1126/sciadv.abl5838

  • The Earth BioGenome Project 2020: Starting the clock.

    Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;4

    PUBMED: 35042800; DOI: 10.1073/pnas.2115635118

  • Association between hypertensive disorders of pregnancy and later risk of cardiovascular outcomes.

    Oliver-Williams C, Stevens D, Payne RA, Wilkinson IB, Smith GCS and Wood A

    BMC medicine 2022;20;1;19

    PUBMED: 35073907; DOI: 10.1186/s12916-021-02218-8

  • Coding and regulatory variants are associated with serum protein levels and disease.

    Emilsson V, Gudmundsdottir V, Gudjonsson A, Jonmundsson T, Jonsson BG, Karim MA, Ilkov M, Staley JR, Gudmundsson EF, Launer LJ et al.

    Nature communications 2022;13;1;481

    PUBMED: 35079000; DOI: 10.1038/s41467-022-28081-6

  • Ethical, legal, and social issues in the Earth BioGenome Project.

    Sherkow JS, Barker KB, Braverman I, Cook-Deegan R, Durbin R, Easter CL, Goldstein MM, Hudson M, Kress WJ, Lewin HA et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;4

    PUBMED: 35042809; DOI: 10.1073/pnas.2115859119

  • Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.

    Kanagaraj R, Mitter R, Kantidakis T, Edwards MM, Benitez A, Chakravarty P, Fu B, Becherel O, Yang F, Lavin MF et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;4

    PUBMED: 35042798; DOI: 10.1073/pnas.2114314119

  • Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin.

    Krueger A, Zaugg J, Chisholm S, Linedale R, Lachner N, Teoh SM, Tuong ZK, Lukowski SW, Morrison M, Soyer HP et al.

    Frontiers in microbiology 2022;12;789042

    PUBMED: 35145494; PMC: 8822148; DOI: 10.3389/fmicb.2021.789042

  • Sequence locally, think globally: The Darwin Tree of Life Project.

    Darwin Tree of Life Project Consortium

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;4

    PUBMED: 35042805; PMC: 8797607; DOI: 10.1073/pnas.2115642118

  • Standards recommendations for the Earth BioGenome Project.

    Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;4

    PUBMED: 35042802; PMC: 8795494; DOI: 10.1073/pnas.2115639118

  • Why sequence all eukaryotes?

    Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2022;119;4

    PUBMED: 35042801; DOI: 10.1073/pnas.2115636118

  • The era of reference genomes in conservation genomics.

    Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J et al.

    Trends in ecology & evolution 2022;37;3;197-202

    PUBMED: 35086739; DOI: 10.1016/j.tree.2021.11.008

  • The MITRE trial protocol: a study to evaluate the microbiome as a biomarker of efficacy and toxicity in cancer patients receiving immune checkpoint inhibitor therapy.

    Thompson NA, Stewart GD, Welsh SJ, Doherty GJ, Robinson MJ, Neville BA, Vervier K, Harris SR, Adams DJ, Dalchau K et al.

    BMC cancer 2022;22;1;99

    PUBMED: 35073853; DOI: 10.1186/s12885-021-09156-x

  • Higher body mass index raises immature platelet count: potential contribution to obesity-related thrombosis.

    Goudswaard LJ, Corbin LJ, Burley KL, Mumford A, Akbari P, Soranzo N, Butterworth AS, Watkins NA, Pournaras DJ, Harris J et al.

    Platelets 2022;1-10

    PUBMED: 35068290; DOI: 10.1080/09537104.2021.2003317

  • Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans.

    Mende N, Bastos HP, Santoro A, Mahbubani KT, Ciaurro V, Calderbank EF, Quiroga Londoño M, Sham K, Mantica G, Morishima T et al.

    Blood 2022

    PUBMED: 35073399; DOI: 10.1182/blood.2021013450

  • Babies of South Asian and European Ancestry Show Similar Associations with Genetic Risk Score for Birth Weight Despite the Smaller Size of South Asian Newborns.

    Nongmaithem SS, Beaumont RN, Dedaniya A, Wood AR, Ogunkolade BW, Hassan Z, Krishnaveni GV, Kumaran K, Potdar RD, Sahariah SA et al.

    Diabetes 2022

    PUBMED: 35061033; DOI: 10.2337/db21-0479

  • Insights into the genetic architecture of haematological traits from deep phenotyping and whole-genome sequencing for two Mediterranean isolated populations.

    Kuchenbaecker K, Gilly A, Suveges D, Southam L, Giannakopoulou O, Kilian B, Tsafantakis E, Karaleftheri M, Farmaki AE, Gurdasani D et al.

    Scientific reports 2022;12;1;1131

    PUBMED: 35064169; DOI: 10.1038/s41598-021-04436-9

  • Associations Between Glycemic Traits and Colorectal Cancer: A Mendelian Randomization Analysis.

    Murphy N, Song M, Papadimitriou N, Carreras-Torres R, Langenberg C, Martin RM, Tsilidis KK, Barroso I, Chen J, Frayling T et al.

    Journal of the National Cancer Institute 2022

    PUBMED: 35048991; DOI: 10.1093/jnci/djac011

  • CRLF3 plays a key role in the final stage of platelet genesis and is a potential therapeutic target for thrombocythaemia.

    Bennett C, Lawrence M, Guerrero JA, Stritt S, Waller AK, Yan Y, Mifsud RW, Ballester-Beltran J, Baig AA, Mueller A et al.

    Blood 2022

    PUBMED: 35051265; DOI: 10.1182/blood.2021013113

  • Life histories of myeloproliferative neoplasms inferred from phylogenies.

    Williams N, Lee J, Mitchell E, Moore L, Baxter EJ, Hewinson J, Dawson KJ, Menzies A, Godfrey AL, Green AR et al.

    Nature 2022;602;7895;162-168

    PUBMED: 35058638; DOI: 10.1038/s41586-021-04312-6

  • Voices on technology: The molecular biologists' ever-expanding toy box.

    McCord RP, Taipale M, Teichmann S, Vorhees R, Wan Y, Dekker C and Sanjana NE

    Molecular cell 2022;82;2;221-226

    PUBMED: 35063087; DOI: 10.1016/j.molcel.2021.12.025

  • Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis.

    Antimicrobial Resistance Collaborators

    Lancet (London, England) 2022;399;10325;629-655

    PUBMED: 35065702; PMC: 8841637; DOI: 10.1016/S0140-6736(21)02724-0

  • Fine-Scale Reconstruction of the Evolution of FII-33 Multidrug Resistance Plasmids Enables High-Resolution Genomic Surveillance.

    Hu Y, Moran RA, Blackwell GA, McNally A and Zong Z

    mSystems 2022;e0083121

    PUBMED: 35040701; DOI: 10.1128/msystems.00831-21

  • Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe.

    Garcia-Souto D, Bruzos AL, Diaz S, Rocha S, Pequeño-Valtierra A, Roman-Lewis CF, Alonso J, Rodriguez R, Costas D, Rodriguez-Castro J et al.

    eLife 2022;11

    PUBMED: 35040778; DOI: 10.7554/eLife.66946

  • A genome-wide association study of radiotherapy induced toxicity in head and neck cancer patients identifies a susceptibility locus associated with mucositis.

    Schack LMH, Naderi E, Fachal L, Dorling L, Luccarini C, Dunning AM, Head and Neck Group of the Radiogenomics Consortium, Danish Head and Neck Cancer Group (DAHANCA), Ong EHW, Chua MLK et al.

    British journal of cancer 2022

    PUBMED: 35039627; DOI: 10.1038/s41416-021-01670-w

  • RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.

    Belenguer G, Mastrogiovanni G, Pacini C, Hall Z, Dowbaj AM, Arnes-Benito R, Sljukic A, Prior N, Kakava S, Bradshaw CR et al.

    Nature communications 2022;13;1;334

    PUBMED: 35039505; DOI: 10.1038/s41467-021-27923-z

  • Innovative vaccine approaches-a Keystone Symposia report.

    Cable J, Rappuoli R, Klemm EJ, Kang G, Mutreja A, Wright GJ, Pizza M, Castro SA, Hoffmann JP, Alter G et al.

    Annals of the New York Academy of Sciences 2022

    PUBMED: 35029310; DOI: 10.1111/nyas.14739

  • Stem cell-derived porcine macrophages as a new platform for studying host-pathogen interactions.

    Meek S, Watson T, Eory L, McFarlane G, Wynne FJ, McCleary S, Dunn LEM, Charlton EM, Craig C, Shih B et al.

    BMC biology 2022;20;1;14

    PUBMED: 35027054; DOI: 10.1186/s12915-021-01217-8

  • An accurate method for identifying recent recombinants from unaligned sequences.

    Feng Q, Tiedje KE, Ruybal-Pesántez S, Tonkin-Hill G, Duffy MF, Day KP, Shim H and Chan YB

    Bioinformatics (Oxford, England) 2022

    PUBMED: 35025988; DOI: 10.1093/bioinformatics/btac012

  • Cell2location maps fine-grained cell types in spatial transcriptomics.

    Kleshchevnikov V, Shmatko A, Dann E, Aivazidis A, King HW, Li T, Elmentaite R, Lomakin A, Kedlian V, Gayoso A et al.

    Nature biotechnology 2022

    PUBMED: 35027729; DOI: 10.1038/s41587-021-01139-4

  • Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO.

    Velten B, Braunger JM, Argelaguet R, Arnol D, Wirbel J, Bredikhin D, Zeller G and Stegle O

    Nature methods 2022

    PUBMED: 35027765; DOI: 10.1038/s41592-021-01343-9

  • Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific.

    Shahdadi A, von Wyschetzki K, Liu HC, Chu KH and Schubart CD

    PloS one 2022;17;1;e0262122

    PUBMED: 35025933; DOI: 10.1371/journal.pone.0262122

  • An Overview of Transcriptional Responses of Schistosome-Susceptible (M line) or -Resistant (BS-90) Biomphalaria glabrata Exposed or Not to Schistosoma mansoni Infection.

    Lu L, Bu L, Zhang SM, Buddenborg SK and Loker ES

    Frontiers in immunology 2022;12;805882

    PUBMED: 35095891; PMC: 8791074; DOI: 10.3389/fimmu.2021.805882

  • Machine learning optimized polygenic scores for blood cell traits identify sex-specific trajectories and genetic correlations with disease.

    Xu Y, Vuckovic D, Ritchie SC, Akbari P, Jiang T, Grealey J, Butterworth AS, Ouwehand WH, Roberts DJ, Di Angelantonio E et al.

    Cell genomics 2022;2;1;None

    PUBMED: 35072137; PMC: 8758502; DOI: 10.1016/j.xgen.2021.100086

  • Genomic and Phenotypic Characterization of Experimentally Selected Resistant Leishmania donovani Reveals a Role for Dynamin-1-Like Protein in the Mechanism of Resistance to a Novel Antileishmanial Compound.

    Hefnawy A, Negreira G, Jara M, Cotton JA, Maes I, D'Haenens E, Imamura H, Cuypers B, Monsieurs P, Mouchtoglou C et al.

    mBio 2022;e0326421

    PUBMED: 35012338; PMC: 8749414; DOI: 10.1128/mbio.03264-21

  • Hyperpolarized 13C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell Carcinoma-A Proof of Principle Study.

    Ursprung S, Woitek R, McLean MA, Priest AN, Crispin-Ortuzar M, Brodie CR, Gill AB, Gehrung M, Beer L, Riddick ACP et al.

    Cancers 2022;14;2

    PUBMED: 35053497; PMC: 8773685; DOI: 10.3390/cancers14020335

  • PDZD8 Disruption Causes Cognitive Impairment in Humans, Mice, and Fruit Flies.

    Al-Amri AH, Armstrong P, Amici M, Ligneul C, Rouse J, El-Asrag ME, Pantiru A, Vancollie VE, Ng HWY, Ogbeta JA et al.

    Biological psychiatry 2022

    PUBMED: 35227461; DOI: 10.1016/j.biopsych.2021.12.017

  • Clinical findings and a DNA methylation signature in kindreds with alterations in ZNF711.

    Wang J, Foroutan A, Richardson E, Skinner SA, Reilly J, Kerkhof J, Curry CJ, Tarpey PS, Robertson SP, Maystadt I et al.

    European journal of human genetics : EJHG 2022

    PUBMED: 34992252; DOI: 10.1038/s41431-021-01018-1

  • Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment.

    Chewapreecha C, Pensar J, Chattagul S, Pesonen M, Sangphukieo A, Boonklang P, Potisap C, Koosakulnirand S, Feil EJ, Dunachie S et al.

    Molecular biology and evolution 2022;39;1

    PUBMED: 34662416; PMC: 8760936; DOI: 10.1093/molbev/msab306

  • Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

    Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M et al.

    Nucleic acids research 2022;50;D1;D996-D1003

    PUBMED: 34791415; PMC: 8728113; DOI: 10.1093/nar/gkab1007

  • Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya.

    Phan MVT, Agoti CN, Munywoki PK, Otieno GP, Ngama M, Kellam P, Cotten M and Nokes DJ

    Scientific reports 2022;12;1;202

    PUBMED: 34997042; PMC: 8742071; DOI: 10.1038/s41598-021-03987-1

  • Identification of Putative β-Galactosidase Genes in the Genome of Lactobacillus helveticus OSU-PECh-4A.

    García-Cano I, Escobar-Zepeda A, Ruiz-Ramírez S, Rocha-Mendoza D and Jiménez-Flores R

    Microbiology resource announcements 2022;e0076621

    PUBMED: 34989615; DOI: 10.1128/MRA.00766-21

  • Trial of Three Rounds of Mass Azithromycin Administration for Yaws Eradication.

    John LN, Beiras CG, Houinei W, Medappa M, Sabok M, Kolmau R, Jonathan E, Maika E, Wangi JK, Pospíšilová P et al.

    The New England journal of medicine 2022;386;1;47-56

    PUBMED: 34986286; PMC: 7612200; DOI: 10.1056/NEJMoa2109449

  • The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity.

    Zhang H, Perez-Garcia P, Dierkes RF, Applegate V, Schumacher J, Chibani CM, Sternagel S, Preuss L, Weigert S, Schmeisser C et al.

    Frontiers in microbiology 2022;12;803896

    PUBMED: 35069509; PMC: 8767016; DOI: 10.3389/fmicb.2021.803896

  • Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae.

    Nazar N, Howard C, Slater A and Sgamma T

    Plants (Basel, Switzerland) 2022;11;1

    PUBMED: 35009140; DOI: 10.3390/plants11010137

  • Emergence of methicillin resistance predates the clinical use of antibiotics.

    Larsen J, Raisen CL, Ba X, Sadgrove NJ, Padilla-González GF, Simmonds MSJ, Loncaric I, Kerschner H, Apfalter P, Hartl R et al.

    Nature 2022;602;7895;135-141

    PUBMED: 34987223; PMC: 8810379; DOI: 10.1038/s41586-021-04265-w

  • A purine metabolic checkpoint that prevents autoimmunity and autoinflammation.

    Saveljeva S, Sewell GW, Ramshorn K, Cader MZ, West JA, Clare S, Haag LM, de Almeida Rodrigues RP, Unger LW, Iglesias-Romero AB et al.

    Cell metabolism 2022;34;1;106-124.e10

    PUBMED: 34986329; DOI: 10.1016/j.cmet.2021.12.009

  • International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease.

    Gladstone RA, Siira L, Brynildsrud OB, Vestrheim DF, Turner P, Clarke SC, Srifuengfung S, Ford R, Lehmann D, Egorova E et al.

    Vaccine 2022

    PUBMED: 34996643; DOI: 10.1016/j.vaccine.2021.10.046

  • B Cell Class-Switching in Intestinal Immunity in Health and Disease.

    Fleming A, Castro-Dopico T and Clatworthy MR

    Scandinavian journal of immunology 2022;e13139

    PUBMED: 34978077; DOI: 10.1111/sji.13139

  • CRISPR/Cas9 Editing of the Plasmodium falciparum Genome.

    Adjalley S and Lee MCS

    Methods in molecular biology (Clifton, N.J.) 2022;2470;221-239

    PUBMED: 35881349; DOI: 10.1007/978-1-0716-2189-9_17

  • Defining the early stages of intestinal colonisation by whipworms

    Duque-Correa, María A., Goulding, David, Rodgers, Faye H., Gillis, J. Andrew, Cormie, Claire et al.

    Nature Communications 2022;13;1;1

    DOI: 10.1038/s41467-022-29334-0; URL: https://doi.org/10.1038/s41467-022-29334-0

  • Guideline for feedback of individual genetic research findings for genomics research in Africa.

    Matimba A, Ali S, Littler K, Madden E, Marshall P, McCurdy S, Nembaware V, Rodriguez L, Seeley J, Tindana P et al.

    BMJ global health 2022;7;1

    PUBMED: 35017180; DOI: 10.1136/bmjgh-2021-007184

  • Identification and Quantification of Microexons Using Bulk and Single-Cell RNA-Seq Data.

    Parada GE and Hemberg M

    Methods in molecular biology (Clifton, N.J.) 2022;2537;129-147

    PUBMED: 35895262; DOI: 10.1007/978-1-0716-2521-7_8

  • Primary de-differentiated, trans-differentiated and undifferentiated melanomas: overview of the clinicopathological, immunohistochemical and molecular spectrum.

    Ferreira I, Arends MJ, van der Weyden L, Adams DJ and Brenn T

    Histopathology 2022;80;1;135-149

    PUBMED: 34958502; DOI: 10.1111/his.14545

  • Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI.

    Degasperi A, Nguyen LK, Fey D and Kholodenko BN

    Methods in molecular biology (Clifton, N.J.) 2022;2385;91-115

    PUBMED: 34888717; DOI: 10.1007/978-1-0716-1767-0_5

  • SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs.

    Belman S, Saha S and Beale MA

    Nature reviews. Microbiology 2022;20;1;3

    PUBMED: 34799703; PMC: 8603645; DOI: 10.1038/s41579-021-00664-y

  • When to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome.

    Bihl S, de Goffau M, Podlesny D, Segata N, Shanahan F, Walter J and Fricke WF

    Gut microbes 2022;14;1;2005751

    PUBMED: 34923897; PMC: 8726709; DOI: 10.1080/19490976.2021.2005751

2021

  • Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network.

    de Goffau MC, Jallow AT, Sanyang C, Prentice AM, Meagher N, Price DJ, Revill PA, Parkhill J, Pereira DIA and Wagner J

    Nature microbiology 2021

    PUBMED: 34972822; DOI: 10.1038/s41564-021-01023-6

  • A catalogue of 1,167 genomes from the human gut archaeome.

    Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère JF, Gribaldo S, Finn RD, Schmitz RA and Moissl-Eichinger C

    Nature microbiology 2021

    PUBMED: 34969981; DOI: 10.1038/s41564-021-01020-9

  • The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping.

    Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K et al.

    Cell host & microbe 2021;30;1;124-138.e8

    PUBMED: 34971560; PMC: 8763404; DOI: 10.1016/j.chom.2021.12.003

  • Immunological factors, but not clinical features, predict visceral leishmaniasis relapse in patients co-infected with HIV.

    Takele Y, Mulaw T, Adem E, Shaw CJ, Franssen SU, Womersley R, Kaforou M, Taylor GP, Levin M, Müller I et al.

    Cell reports. Medicine 2021;3;1;100487

    PUBMED: 35106507; PMC: 8784791; DOI: 10.1016/j.xcrm.2021.100487

  • Transcriptional analysis identifies potential novel biomarkers associated with successful ex-vivo perfusion of human donor lungs.

    Ferdinand JR, Morrison MI, Andreasson A, Charlton C, Chhatwal AK, Scott WE, Borthwick LA, Clatworthy MR and Fisher AJ

    Clinical transplantation 2021;e14570

    PUBMED: 34954872; DOI: 10.1111/ctr.14570

  • Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.

    Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA, Almeida A and Finn RD

    Nature microbiology 2021;7;1;169-179

    PUBMED: 34952941; PMC: 8732310; DOI: 10.1038/s41564-021-01011-w

  • Genome-wide analysis of the response to ivermectin treatment by a Swedish field population of Haemonchus contortus.

    Baltrušis P, Doyle SR, Halvarsson P and Höglund J

    International journal for parasitology. Drugs and drug resistance 2021;18;12-19

    PUBMED: 34959200; DOI: 10.1016/j.ijpddr.2021.12.002

  • Morphological and genomic characterisation of the Schistosoma hybrid infecting humans in Europe reveals admixture between Schistosoma haematobium and Schistosoma bovis.

    Kincaid-Smith J, Tracey A, de Carvalho Augusto R, Bulla I, Holroyd N, Rognon A, Rey O, Chaparro C, Oleaga A, Mas-Coma S et al.

    PLoS neglected tropical diseases 2021;15;12;e0010062

    PUBMED: 34941866; DOI: 10.1371/journal.pntd.0010062

  • Local and systemic responses to SARS-CoV-2 infection in children and adults.

    Yoshida M, Worlock KB, Huang N, Lindeboom RGH, Butler CR, Kumasaka N, Conde CD, Mamanova L, Bolt L, Richardson L et al.

    Nature 2021

    PUBMED: 34937051; DOI: 10.1038/s41586-021-04345-x

  • A customised target capture sequencing tool for molecular identification of Aloe vera and relatives.

    Woudstra Y, Viruel J, Fritzsche M, Bleazard T, Mate R, Howard C, Rønsted N and Grace OM

    Scientific reports 2021;11;1;24347

    PUBMED: 34934068; PMC: 8692607; DOI: 10.1038/s41598-021-03300-0

  • Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival.

    Kubinyecz O, Santos F, Drage D, Reik W and Eckersley-Maslin MA

    Development (Cambridge, England) 2021;148;24

    PUBMED: 34931676; DOI: 10.1242/dev.200191

  • Resolving the immune landscape of human prostate at a single-cell level in health and cancer.

    Tuong ZK, Loudon KW, Berry B, Richoz N, Jones J, Tan X, Nguyen Q, George A, Hori S, Field S et al.

    Cell reports 2021;37;12;110132

    PUBMED: 34936871; DOI: 10.1016/j.celrep.2021.110132

  • Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

    Hurst CD, Cheng G, Platt FM, Castro MAA, Marzouka NS, Eriksson P, Black EVI, Alder O, Lawson ARJ, Lindskrog SV et al.

    Cell reports. Medicine 2021;2;12;100472

    PUBMED: 35028613; PMC: 8714941; DOI: 10.1016/j.xcrm.2021.100472

  • A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).

    Mueller RC, Ellström P, Howe K, Uliano-Silva M, Kuo RI, Miedzinska K, Warr A, Fedrigo O, Haase B, Mountcastle J et al.

    GigaScience 2021;10;12

    PUBMED: 34927191; PMC: 8685854; DOI: 10.1093/gigascience/giab081

  • Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework.

    Dyson ZA and Holt KE

    The Journal of infectious diseases 2021;224;12 Suppl 2;S775-S780

    PUBMED: 34453548; PMC: 8687072; DOI: 10.1093/infdis/jiab414

  • MultiMAP: dimensionality reduction and integration of multimodal data.

    Jain MS, Polanski K, Conde CD, Chen X, Park J, Mamanova L, Knights A, Botting RA, Stephenson E, Haniffa M et al.

    Genome biology 2021;22;1;346

    PUBMED: 34930412; PMC: 8686224; DOI: 10.1186/s13059-021-02565-y

  • Peru - Progress in health and sciences in 200 years of independence

    Carrillo-Larco,Rodrigo M., Cristobal Guzman-Vilca,Wilmer, Leon-Velarde,Fabiola, Bernabe-Ortiz,Antonio, Michelle Jimenez,M., Penny,Mary E., Gianella,Camila, Leguia,Mariana, Tsukayama,Pablo, Hartinger,Stella M. et al.

    The Lancet Regional Health - Americas 2021;7;100148

    DOI: 10.1016/j.lana.2021.100148

  • Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms.

    Chaguza C, Yang M, Jacques LC, Bentley SD and Kadioglu A

    Trends in microbiology 2021;30;6;581-592

    PUBMED: 34949516; PMC: 7613904; DOI: 10.1016/j.tim.2021.11.007

  • Prioritising positively selected variants in whole-genome sequencing data using FineMAV.

    Wahyudi F, Aghakhanian F, Rahman S, Teo YY, Szpak M, Dhaliwal J and Ayub Q

    BMC bioinformatics 2021;22;1;604

    PUBMED: 34922440; DOI: 10.1186/s12859-021-04506-9

  • The genome sequence of the large burdock Cheilosia, Cheilosia vulpina (Meigen, 1822).

    Falk S, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;351

    PUBMED: 36415321; PMC: 9652505; DOI: 10.12688/wellcomeopenres.17491.1

  • Searching for transmissible cancers among the mussels of Europe.

    Baez-Ortega A and Murchison EP

    Molecular ecology 2021

    PUBMED: 34918407; DOI: 10.1111/mec.16330

  • Trends in the molecular epidemiology and population genetics of emerging Sporothrix species.

    de Carvalho JA, Beale MA, Hagen F, Fisher MC, Kano R, Bonifaz A, Toriello C, Negroni R, Rego RSM, Gremião IDF et al.

    Studies in mycology 2021;100;100129

    PUBMED: 35027980; PMC: 8693333; DOI: 10.1016/j.simyco.2021.100129

  • β2-spectrin (SPTBN1) as a therapeutic target for diet-induced liver disease and preventing cancer development.

    Rao S, Yang X, Ohshiro K, Zaidi S, Wang Z, Shetty K, Xiang X, Hassan MI, Mohammad T, Latham PS et al.

    Science translational medicine 2021;13;624;eabk2267

    PUBMED: 34910547; DOI: 10.1126/scitranslmed.abk2267

  • COMPARISON OF WHOLE GENOME SEQUENCE-BASED METHODS AND PCR RIBOTYPING FOR SUBTYPING OF Clostridioides difficile.

    Baktash A, Corver J, Harmanus C, Smits WK, Fawley W, Wilcox MH, Kumar N, Eyre DW, Indra A, Mellmann A and Kuijper EJ

    Journal of clinical microbiology 2021;JCM0173721

    PUBMED: 34911367; DOI: 10.1128/JCM.01737-21

  • Linkage of Whole Genome Sequencing, Epidemiological, and Clinical Data to Understand the Genetic Diversity and Clinical Outcomes of Shigella flexneri among Men Who Have Sex with Men in England.

    Mitchell HD, Thomson NR, Jenkins C, Dallman TJ, Painset A, Kirwan P, Delpech V, Mikhail AFW, Field N and Hughes G

    Microbiology spectrum 2021;e0121321

    PUBMED: 34908501; DOI: 10.1128/Spectrum.01213-21

  • The genome sequence of the holly blue, Celastrina argiolus (Linnaeus, 1758).

    Hayward A, Wright C, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;340

    PUBMED: 35028429; PMC: 8729184; DOI: 10.12688/wellcomeopenres.17478.1

  • The meninges-a cradle and school for nurturing and educating developing B cells.

    Clatworthy MR

    Immunity 2021;54;12;2688-2690

    PUBMED: 34910935; DOI: 10.1016/j.immuni.2021.11.010

  • The genome sequence of a snail-killing fly,  Coremacera marginata (Fabricius, 1775).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;338

    PUBMED: 36415322; PMC: 9647149; DOI: 10.12688/wellcomeopenres.17482.1

  • The genome sequence of the ornate tailed digger wasp, Cerceris rybyensis (Linnaeus, 1771).

    Crowley L, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;337

    PUBMED: 35425864; PMC: 8980675; DOI: 10.12688/wellcomeopenres.17483.1

  • Biological factors in the synthetic construction of overlapping genes.

    Wichmann S, Scherer S and Ardern Z

    BMC genomics 2021;22;1;888

    PUBMED: 34895142; PMC: 8665328; DOI: 10.1186/s12864-021-08181-1

  • Fine-scale population structure and demographic history of British Pakistanis.

    Arciero E, Dogra SA, Malawsky DS, Mezzavilla M, Tsismentzoglou T, Huang QQ, Hunt KA, Mason D, Sharif SM, van Heel DA et al.

    Nature communications 2021;12;1;7189

    PUBMED: 34893604; PMC: 8664933; DOI: 10.1038/s41467-021-27394-2

  • A high-throughput multiplexing and selection strategy to complete bacterial genomes.

    Arredondo-Alonso S, Pöntinen AK, Cléon F, Gladstone RA, Schürch AC, Johnsen PJ, Samuelsen Ø and Corander J

    GigaScience 2021;10;12

    PUBMED: 34891160; PMC: 8673558; DOI: 10.1093/gigascience/giab079

  • The power of genetic diversity in genome-wide association studies of lipids.

    Graham SE, Clarke SL, Wu KH, Kanoni S, Zajac GJM, Ramdas S, Surakka I, Ntalla I, Vedantam S, Winkler TW et al.

    Nature 2021;600;7890;675-679

    PUBMED: 34887591; PMC: 8730582; DOI: 10.1038/s41586-021-04064-3

  • Malaria protection due to sickle haemoglobin depends on parasite genotype.

    Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T et al.

    Nature 2021

    PUBMED: 34883497; DOI: 10.1038/s41586-021-04288-3

  • The genome sequence of the yellow-tail moth, Euproctis similis (Fuessly, 1775).

    Boyes DH, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;227

    PUBMED: 34632092; PMC: 8474102; DOI: 10.12688/wellcomeopenres.17188.2

  • Controlled human malaria infection with a clone of Plasmodium vivax with high-quality genome assembly.

    Minassian AM, Themistocleous Y, Silk SE, Barrett JR, Kemp A, Quinkert D, Nielsen CM, Edwards NJ, Rawlinson TA, Ramos Lopez F et al.

    JCI insight 2021;6;23

    PUBMED: 34609964; PMC: 8675201; DOI: 10.1172/jci.insight.152465

  • Embryonal sarcoma of the liver in a girl with Cockayne syndrome.

    Thorbinson C, Penn A, Nicola P, Hardcastle C, Waller S, Ramsden S, Coorens THH, Tang V, Cheesman E, Douzgou S and Meyer S

    Clinical genetics 2021;101;3;375-376

    PUBMED: 34878179; DOI: 10.1111/cge.14094

  • The genome sequence of the European nightjar, Caprimulgus europaeus (Linnaeus, 1758).

    Secomandi S, Spina F, Formenti G, Gallo GR, Caprioli M, Ambrosini R, Riello S, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;332

    PUBMED: 35028428; PMC: 8729189; DOI: 10.12688/wellcomeopenres.17451.1

  • Delayed induction of type I and III interferons mediates nasal epithelial cell permissiveness to SARS-CoV-2.

    Hatton CF, Botting RA, Dueñas ME, Haq IJ, Verdon B, Thompson BJ, Spegarova JS, Gothe F, Stephenson E, Gardner AI et al.

    Nature communications 2021;12;1;7092

    PUBMED: 34876592; DOI: 10.1038/s41467-021-27318-0

  • A Nationwide Outbreak of Invasive Pneumococcal Disease in Israel Caused by Streptococcus pneumoniae Serotype 2.

    Dagan R, Ben-Shimol S, Benisty R, Regev-Yochay G, Lo SW, Bentley SD, Hawkins PA, McGee L, Ron M, Givon-Lavi N et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;11;e3768-e3777

    PUBMED: 33197932; DOI: 10.1093/cid/ciaa1720

  • Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

    Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, Lassalle F and Venkateswaran K

    Frontiers in microbiology 2021;12;765943

    PUBMED: 34938279; PMC: 8685578; DOI: 10.3389/fmicb.2021.765943

  • geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

    Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M et al.

    Genome biology 2021;22;1;333

    PUBMED: 34872616; DOI: 10.1186/s13059-021-02548-z

  • Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen

    White,Rhys T., Legione,Alistair R., Taylor-Brown,Alyce, Fernandez,Cristina M., Higgins,Damien P., Timms,Peter and Jelocnik,Martina

    Pathogens 2021;10;12;1543

    PMC: 8703710; DOI: 10.3390/pathogens10121543; URL: https://www.mdpi.com/2076-0817/10/12/1543

  • Post-mortem lung tissue: the fossil record of the pathophysiology and immunopathology of severe COVID-19.

    Milross L, Majo J, Cooper N, Kaye PM, Bayraktar O, Filby A and Fisher AJ

    The Lancet. Respiratory medicine 2021

    PUBMED: 34871544; DOI: 10.1016/S2213-2600(21)00408-2

  • Daily rhythms in gene expression of the human parasite Schistosoma mansoni.

    Rawlinson KA, Reid AJ, Lu Z, Driguez P, Wawer A, Coghlan A, Sankaranarayanan G, Buddenborg SK, Soria CD, McCarthy C et al.

    BMC biology 2021;19;1;255

    PUBMED: 34852797; DOI: 10.1186/s12915-021-01189-9

  • Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.

    Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R et al.

    Nature genetics 2021;53;12;1698-1711

    PUBMED: 34857954; PMC: 8648563; DOI: 10.1038/s41588-021-00972-2

  • RCandy: an R package for visualising homologous recombinations in bacterial genomes.

    Chaguza C, Tonkin-Hill G, Lo SW, Hadfield J, Croucher NJ, Harris SR and Bentley SD

    Bioinformatics (Oxford, England) 2021

    PUBMED: 34864895; PMC: 8826011; DOI: 10.1093/bioinformatics/btab814

  • TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves.

    Cardoso MA, Rizzardi LEA, Kume LW, Groeneveld C, Trefflich S, Morais DAA, Dalmolin RJS, Ponder BAJ, Meyer KB and Castro MAA

    Bioinformatics (Oxford, England) 2021

    PUBMED: 34864914; DOI: 10.1093/bioinformatics/btab819

  • The evolutionary history of Shigella flexneri serotype 6 in Asia.

    Mai ST, Bodhidatta L, Turner P, Wangchuk S, Ha Thanh T, Voong Vinh P, Pham DT, Rabaa MA, Thwaites GE, Thomson NR et al.

    Microbial genomics 2021;7;12

    PUBMED: 34904947; DOI: 10.1099/mgen.0.000736

  • Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria.

    Afolayan AO, Oaikhena AO, Aboderin AO, Olabisi OF, Amupitan AA, Abiri OV, Ogunleye VO, Odih EE, Adeyemo AT, Adeyemo AT et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S308-S315

    PUBMED: 34850837; DOI: 10.1093/cid/ciab769

  • Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs.

    Saavedra SY, Bernal JF, Montilla-Escudero E, Arévalo SA, Prada DA, Valencia MF, Moreno J, Hidalgo AM, García-Vega ÁS, Abrudan M et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S290-S299

    PUBMED: 34850835; DOI: 10.1093/cid/ciab777

  • Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines.

    Carlos CC, Masim MAL, Lagrada ML, Gayeta JM, Macaranas PKV, Sia SB, Facun MAM, Palarca JFC, Olorosa AM, Cueno GAC et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S316-S324

    PUBMED: 34850834; DOI: 10.1093/cid/ciab776

  • High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study.

    Nagaraj G, Shamanna V, Govindan V, Rose S, Sravani D, Akshata KP, Shincy MR, Venkatesha VT, Abrudan M, Argimón S et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S300-S307

    PUBMED: 34850832; DOI: 10.1093/cid/ciab767

  • Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae.

    Aanensen DM, Carlos CC, Donado-Godoy P, Okeke IN, Ravikumar KL and NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S255-S257

    PUBMED: 34850830; DOI: 10.1093/cid/ciab795

  • Integrating Scalable Genome Sequencing Into Microbiology Laboratories for Routine Antimicrobial Resistance Surveillance.

    Kekre M, Arevalo SA, Valencia MF, Lagrada ML, Macaranas PKV, Nagaraj G, Oaikhena AO, Olorosa AM, Aanensen DM and NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Suppl_4;S258-S266

    PUBMED: 34850836; PMC: 8634525; DOI: 10.1093/cid/ciab796

  • Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

    Afolayan AO, Bernal JF, Gayeta JM, Masim ML, Shamanna V, Abrudan M, Abudahab K, Argimón S, Carlos CC, Sia S et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S267-S274

    PUBMED: 34850839; DOI: 10.1093/cid/ciab785

  • Phenotypic and genotypic analysis of benzimidazole resistance in reciprocal genetic crosses of Haemonchus contortus.

    Morrison AA, Chaudhry U, Andrews L, Melville L, Doyle SR, Sargison ND and Bartley DJ

    International journal for parasitology. Drugs and drug resistance 2021;18;1-11

    PUBMED: 34896787; DOI: 10.1016/j.ijpddr.2021.11.001

  • Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.

    Argimón S, David S, Underwood A, Abrudan M, Wheeler NE, Kekre M, Abudahab K, Yeats CA, Goater R, Taylor B et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Supplement_4;S325-S335

    PUBMED: 34850838; DOI: 10.1093/cid/ciab784

  • Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of Antimicrobial Resistance (AMR).

    Abrudan M, Matimba A, Nikolic D, Hughes D, Argimón S, Kekre M, Underwood A, Aanensen DM and NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021;73;Suppl_4;S283-S289

    PUBMED: 34850831; PMC: 8634536; DOI: 10.1093/cid/ciab770

  • Epigenetic Regulation during Primordial Germ Cell Development and Differentiation.

    Ramakrishna NB, Murison K, Miska EA and Leitch HG

    Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation 2021;1-21

    PUBMED: 34847550; DOI: 10.1159/000520412

  • Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers.

    Roberto TN, de Carvalho JA, Beale MA, Hagen F, Fisher MC, Hahn RC, de Camargo ZP and Rodrigues AM

    Studies in mycology 2021;100;100131

    PUBMED: 34934463; PMC: 8645518; DOI: 10.1016/j.simyco.2021.100131

  • What makes a megaplasmid?

    Hall JPJ, Botelho J, Cazares A and Baltrus DA

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2021;377;1842;20200472

    PUBMED: 34839707; DOI: 10.1098/rstb.2020.0472

  • Complexity of immune responses in COVID-19.

    Mather MW, Jardine L, Talks B, Gardner L and Haniffa M

    Seminars in immunology 2021;55;101545

    PUBMED: 34865933; PMC: 8626289; DOI: 10.1016/j.smim.2021.101545

  • Efficient iterative Hi-C scaffolder based on N-best neighbors.

    Guan D, McCarthy SA, Ning Z, Wang G, Wang Y and Durbin R

    BMC bioinformatics 2021;22;1;569

    PUBMED: 34837944; DOI: 10.1186/s12859-021-04453-5

  • The genome sequence of the painted lady, Vanessa cardui Linnaeus 1758.

    Lohse K, Wright C, Talavera G, García-Berro A, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;324

    PUBMED: 37008186; PMC: 10061037; DOI: 10.12688/wellcomeopenres.17358.1

  • The genome sequence of the sycamore, Acronicta aceris (Linnaeus, 1758).

    Boyes D, Crowley L, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;326

    PUBMED: 35028427; PMC: 8729028; DOI: 10.12688/wellcomeopenres.17354.1

  • Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS).

    Bossé JT, Li Y, Leanse LG, Zhou L, Chaudhuri RR, Peters SE, Wang J, Maglennon GA, Holden MTG, Maskell DJ et al.

    Animal diseases 2021;1;1;29

    PUBMED: 34870287; PMC: 8616859; DOI: 10.1186/s44149-021-00026-4

  • Ulcerated Melanoma: Systems Biology Evidence of Inflammatory Imbalance Toward Pro-tumorigenicity.

    Davies J, Muralidhar S, Randerson-Moor J, Harland M, O'Shea S, Diaz J, Walker C, Nsengimana J, Laye J, Mell T et al.

    Pigment cell & melanoma research 2021

    PUBMED: 34826184; DOI: 10.1111/pcmr.13023

  • Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes.

    Ansari-Pour N, Zheng Y, Yoshimatsu TF, Sanni A, Ajani M, Reynier JB, Tapinos A, Pitt JJ, Dentro S, Woodard A et al.

    Nature communications 2021;12;1;6946

    PUBMED: 34836952; DOI: 10.1038/s41467-021-27079-w

  • Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture.

    Álvarez EG, Demeulemeester J, Otero P, Jolly C, García-Souto D, Pequeño-Valtierra A, Zamora J, Tojo M, Temes J, Baez-Ortega A et al.

    Nature communications 2021;12;1;6910

    PUBMED: 34824211; PMC: 8617174; DOI: 10.1038/s41467-021-26805-8

  • Analysis of pir gene expression across the Plasmodium life cycle.

    Little TS, Cunningham DA, Vandomme A, Lopez CT, Amis S, Alder C, Addy JWG, McLaughlin S, Hosking C, Christophides G et al.

    Malaria journal 2021;20;1;445

    PUBMED: 34823519; DOI: 10.1186/s12936-021-03979-6

  • As cancer grows old.

    Baez-Ortega A

    Science (New York, N.Y.) 2021;374;6571;1066

    PUBMED: 34822272; DOI: 10.1126/science.abm8137

  • Aldehyde-driven transcriptional stress triggers an anorexic DNA damage response.

    Mulderrig L, Garaycoechea JI, Tuong ZK, Millington CL, Dingler FA, Ferdinand JR, Gaul L, Tadross JA, Arends MJ, O'Rahilly S et al.

    Nature 2021

    PUBMED: 34819667; DOI: 10.1038/s41586-021-04133-7

  • Epigenetics and tissue immunity-Translating environmental cues into functional adaptations.

    Tuong ZK, Stewart BJ, Guo SA and Clatworthy MR

    Immunological reviews 2021

    PUBMED: 34821397; DOI: 10.1111/imr.13036

  • Expression Atlas update: gene and protein expression in multiple species.

    Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N et al.

    Nucleic acids research 2021

    PUBMED: 34850121; DOI: 10.1093/nar/gkab1030

  • Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.

    Beale MA, Marks M, Cole MJ, Lee MK, Pitt R, Ruis C, Balla E, Crucitti T, Ewens M, Fernández-Naval C et al.

    Nature microbiology 2021;6;12;1549-1560

    PUBMED: 34819643; PMC: 8612932; DOI: 10.1038/s41564-021-01000-z

  • Over-celling fetal microbial exposure.

    Kennedy KM, Bellissimo CJ, Breznik JA, Barrett J, Braun T, Bushman FD, De Goffau M, Elovitz MA, Heimesaat MM, Konnikova L et al.

    Cell 2021;184;24;5839-5841

    PUBMED: 34822779; DOI: 10.1016/j.cell.2021.10.026

  • A Comparative View on Molecular Alterations and Potential Therapeutic Strategies for Canine Oral Melanoma.

    Hardwick L

    Veterinary sciences 2021;8;11

    PUBMED: 34822659; DOI: 10.3390/vetsci8110286

  • Regulatory T-Cell Response to Low-Dose Interleukin-2 in Ischemic Heart Disease.

    Zhao TX, Sriranjan RS, Tuong ZK, Lu Y, Sage AP, Nus M, Hubsch A, Kaloyirou F, Vamvaka E, Helmy J et al.

    NEJM evidence 2021;1;1;EVIDoa2100009

    PUBMED: 38319239; DOI: 10.1056/EVIDoa2100009

  • Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet.

    Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, Kaser A, Kiely CJ, Neville BA, Powell N et al.

    Gut 2021

    PUBMED: 34810234; DOI: 10.1136/gutjnl-2021-325177

  • Salicylic Acid and Risk of Colorectal Cancer: A Two-Sample Mendelian Randomization Study.

    Nounu A, Richmond RC, Stewart ID, Surendran P, Wareham NJ, Butterworth A, Weinstein SJ, Albanes D, Baron JA, Hopper JL et al.

    Nutrients 2021;13;11

    PUBMED: 34836419; PMC: 8620763; DOI: 10.3390/nu13114164

  • Dietary Fatty Acids, Macronutrient Substitutions, Food Sources and Incidence of Coronary Heart Disease: Findings From the EPIC-CVD Case-Cohort Study Across Nine European Countries.

    Steur M, Johnson L, Sharp SJ, Imamura F, Sluijs I, Key TJ, Wood A, Chowdhury R, Guevara M, Jakobsen MU et al.

    Journal of the American Heart Association 2021;e019814

    PUBMED: 34796724; DOI: 10.1161/JAHA.120.019814

  • The WIRE study a phase II, multi-arm, multi-centre, non-randomised window-of-opportunity clinical trial platform using a Bayesian adaptive design for proof-of-mechanism of novel treatment strategies in operable renal cell cancer - a study protocol.

    Ursprung S, Mossop H, Gallagher FA, Sala E, Skells R, Sipple JAN, Mitchell TJ, Chhabra A, Fife K, Matakidou A et al.

    BMC cancer 2021;21;1;1238

    PUBMED: 34794412; PMC: 8600815; DOI: 10.1186/s12885-021-08965-4

  • Artefacts in Volume Data Generated with High Resolution Episcopic Microscopy (HREM)

    Reissig,Lukas F., Geyer,Stefan H., Rose,Julia, Prin,Fabrice, Wilson,Robert, Szumska,Dorota, Galli,Antonella, Tudor,Catherine, White,Jacqueline K., Mohun,Tim J. and Weninger,Wolfgang J.

    Biomedicines 2021;9;11;1711

    DOI: 10.3390/biomedicines9111711

  • Genetic and genomic analysis of acute lymphoblastic leukaemia in older adults reveals a distinct profile of abnormalities: analysis of 210 patients from the UKALL14 and UKALL60+ clinical trials.

    Creasey T, Barretta E, Ryan SL, Butler E, Kirkwood AA, Leongamornlert D, Papaemmanuil E, Patrick P, Clifton-Hadley L, Patel B et al.

    Haematologica 2021

    PUBMED: 34788984; DOI: 10.3324/haematol.2021.279177

  • CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.

    Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ and Iorio F

    BMC genomics 2021;22;1;828

    PUBMED: 34789150; DOI: 10.1186/s12864-021-08129-5

  • Decision-making, attitudes, and understanding among patients and relatives invited to undergo genome sequencing in the 100,000 Genomes Project: A multisite survey study.

    Sanderson SC, Lewis C, Hill M, Peter M, McEntagart M, Gale D, Morris H, Moosajee M, Searle B, Hunter A et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2021

    PUBMED: 34906473; DOI: 10.1016/j.gim.2021.08.010

  • An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis.

    O'Neill CE, Skilton RJ, Forster J, Cleary DW, Pearson SA, Lampe DJ, Thomson NR and Clarke IN

    Wellcome open research 2021;6;312

    PUBMED: 35087955; PMC: 8767425; DOI: 10.12688/wellcomeopenres.16068.1

  • Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments.

    Barbon L, Offord V, Radford EJ, Butler AP, Gerety SS, Adams DJ, Tan HK and Waters AJ

    Bioinformatics (Oxford, England) 2021

    PUBMED: 34791067; PMC: 8796380; DOI: 10.1093/bioinformatics/btab776

  • Locus-specific expression of transposable elements in single cells with CELLO-seq.

    Berrens RV, Yang A, Laumer CE, Lun ATL, Bieberich F, Law CT, Lan G, Imaz M, Bowness JS, Brockdorff N et al.

    Nature biotechnology 2021

    PUBMED: 34782740; DOI: 10.1038/s41587-021-01093-1

  • The genome sequence of the grey wolf, Canis lupus Linnaeus 1758.

    Sinding MS, Gopalakrishnan S, Raundrup K, Dalén L, Threlfall J, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium and Gilbert T

    Wellcome open research 2021;6;310

    PUBMED: 34926833; PMC: 8649967; DOI: 10.12688/wellcomeopenres.17332.1

  • An integrated taxonomy for monogenic inflammatory bowel disease.

    Bolton C, Smillie CS, Pandey S, Elmentaite R, Wei G, Argmann C, Aschenbrenner D, James KR, McGovern DPB, Macchi M et al.

    Gastroenterology 2021

    PUBMED: 34780721; DOI: 10.1053/j.gastro.2021.11.014

  • The reactome pathway knowledgebase 2022.

    Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C et al.

    Nucleic acids research 2021

    PUBMED: 34788843; DOI: 10.1093/nar/gkab1028

  • Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis.

    Dallaire A, Manley BF, Wilkens M, Bista I, Quan C, Evangelisti E, Bradshaw CR, Ramakrishna NB, Schornack S, Butter F et al.

    Genome research 2021

    PUBMED: 34772700; DOI: 10.1101/gr.275752.121

  • 100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care - Preliminary Report.

    100,000 Genomes Project Pilot Investigators, Smedley D, Smith KR, Martin A, Thomas EA, McDonagh EM, Cipriani V, Ellingford JM, Arno G, Tucci A et al.

    The New England journal of medicine 2021;385;20;1868-1880

    PUBMED: 34758253; DOI: 10.1056/NEJMoa2035790

  • Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions.

    Baptista RP, Li Y, Sateriale A, Brooks KL, Tracey A, Sanders MJ, Ansell BRE, Jex AR, Cooper GW, Smith ED et al.

    Genome research 2021

    PUBMED: 34764149; DOI: 10.1101/gr.275325.121

  • The Data Use Ontology to streamline responsible access to human biomedical datasets.

    Lawson J, Cabili MN, Kerry G, Boughtwood T, Thorogood A, Alper P, Bowers SR, Boyles RR, Brookes AJ, Brush M et al.

    Cell genomics 2021;1;2;None

    PUBMED: 34820659; PMC: 8591903; DOI: 10.1016/j.xgen.2021.100028

  • The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775).

    Hayward A, Vila R, Laetsch DR, Lohse K, Baril T, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;304

    PUBMED: 35136843; PMC: 8796007; DOI: 10.12688/wellcomeopenres.17280.1

  • GA4GH: International policies and standards for data sharing across genomic research and healthcare.

    Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T et al.

    Cell genomics 2021;1;2

    PUBMED: 35072136; PMC: 8774288; DOI: 10.1016/j.xgen.2021.100029

  • GA4GH Passport standard for digital identity and access permissions.

    Voisin C, Linden M, Dyke SOM, Bowers SR, Alper P, Barkley MP, Bernick D, Chao J, Courtot M, Jeanson F et al.

    Cell genomics 2021;1;2;None

    PUBMED: 34820660; PMC: 8591913; DOI: 10.1016/j.xgen.2021.100030

  • Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon.

    Sanderson T and Barrett JC

    Wellcome open research 2021;6;305

    PUBMED: 35634532; PMC: 9117943; DOI: 10.12688/wellcomeopenres.17295.1

  • An Expanded Genome-Wide Association Study of Fructosamine Levels Identifies RCN3 as a Replicating Locus and Implicates FCGRT as the Effector Transcript.

    Riveros-Mckay F, Roberts D, Angelantonio ED, Yu B, Soranzo N, Danesh J, Selvin E, Butterworth AS and Barroso I

    Diabetes 2021

    PUBMED: 34753797; DOI: 10.2337/db21-0320

  • Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.

    Blackwell GA, Hunt M, Malone KM, Lima L, Horesh G, Alako BTF, Thomson NR and Iqbal Z

    PLoS biology 2021;19;11;e3001421

    PUBMED: 34752446; DOI: 10.1371/journal.pbio.3001421

  • The genome sequence of the black clock beetle, Pterostichus madidus (Fabricius, 1775).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;301

    PUBMED: 35934999; PMC: 9315234; DOI: 10.12688/wellcomeopenres.17347.1

  • The genome sequence of the long-spined sea scorpion, Taurulus bubalis (Euphrasén, 1786).

    Potter S, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;299

    PUBMED: 36312458; PMC: 9587380; DOI: 10.12688/wellcomeopenres.17356.1

  • Anatomical structures, cell types and biomarkers of the Human Reference Atlas.

    Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa M et al.

    Nature cell biology 2021;23;11;1117-1128

    PUBMED: 34750582; DOI: 10.1038/s41556-021-00788-6

  • Cell type ontologies of the Human Cell Atlas.

    Osumi-Sutherland D, Xu C, Keays M, Levine AP, Kharchenko PV, Regev A, Lein E and Teichmann SA

    Nature cell biology 2021;23;11;1129-1135

    PUBMED: 34750578; DOI: 10.1038/s41556-021-00787-7

  • Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases.

    Ritchie SC, Lambert SA, Arnold M, Teo SM, Lim S, Scepanovic P, Marten J, Zahid S, Chaffin M, Liu Y et al.

    Nature metabolism 2021

    PUBMED: 34750571; DOI: 10.1038/s42255-021-00478-5

  • Return of individual research results from genomic research: A systematic review of stakeholder perspectives.

    Vears DF, Minion JT, Roberts SJ, Cummings J, Machirori M, Blell M, Budin-Ljøsne I, Cowley L, Dyke SOM, Gaff C et al.

    PloS one 2021;16;11;e0258646

    PUBMED: 34748551; DOI: 10.1371/journal.pone.0258646

  • The genome sequence of the spiny starfish, Marthasterias glacialis (Linnaeus, 1758).

    Lawniczak MKN, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;295

    PUBMED: 36936045; PMC: 10015122; DOI: 10.12688/wellcomeopenres.17344.1

  • An Overview of Strategies for Detecting Genotype-Phenotype Associations Across Ancestrally Diverse Populations.

    Simonin-Wilmer I, Orozco-Del-Pino P, Bishop DT, Iles MM and Robles-Espinoza CD

    Frontiers in genetics 2021;12;703901

    PUBMED: 34804113; PMC: 8602802; DOI: 10.3389/fgene.2021.703901

  • Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.

    Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S, 23andMe Research Team et al.

    Nature genetics 2021;53;11;1543-1552

    PUBMED: 34741163; DOI: 10.1038/s41588-021-00950-8

  • Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data.

    Tanner G, Westhead DR, Droop A and Stead LF

    Nature communications 2021;12;1;6396

    PUBMED: 34737285; PMC: 8569188; DOI: 10.1038/s41467-021-26698-7

  • The genome sequence of the devil's coach horse, Ocypus olens (Müller, 1764).

    Crowley L, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;293

    PUBMED: 35572471; PMC: 9069170; DOI: 10.12688/wellcomeopenres.17342.1

  • MC3R links nutritional state to childhood growth and the timing of puberty.

    Lam BYH, Williamson A, Finer S, Day FR, Tadross JA, Gonçalves Soares A, Wade K, Sweeney P, Bedenbaugh MN, Porter DT et al.

    Nature 2021;599;7885;436-441

    PUBMED: 34732894; PMC: 8819628; DOI: 10.1038/s41586-021-04088-9

  • Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.

    Elliott P, Haw D, Wang H, Eales O, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ et al.

    Science (New York, N.Y.) 2021;eabl9551

    PUBMED: 34726481; DOI: 10.1126/science.abl9551

  • Bacterial genomic epidemiology with mixed samples.

    Mäklin T, Kallonen T, Alanko J, Samuelsen Ø, Hegstad K, Mäkinen V, Corander J, Heinz E and Honkela A

    Microbial genomics 2021;7;11

    PUBMED: 34779765; DOI: 10.1099/mgen.0.000691

  • Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation.

    Bossé JT, Li Y, Cohen LM, Stegger M, Angen Ø, Lacouture S, Gottschalk M, Lei L, Koene M, Kuhnert P et al.

    Microbial genomics 2021;7;11

    PUBMED: 34818145; DOI: 10.1099/mgen.0.000687

  • Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa.

    Cornick J, Musicha P, Peno C, Seager E, Iroh Tam PY, Bilima S, Bennett A, Kennedy N, Feasey N, Heinz E and Cain AK

    Microbial genomics 2021;7;11

    PUBMED: 34793293; PMC: 8743538; DOI: 10.1099/mgen.0.000703

  • CDKN2A deletion is a frequent event associated with poor outcome in patients with peripheral T-cell lymphoma not otherwise specified (PTCL-NOS).

    Maura F, Dodero A, Carniti C, Bolli N, Magni M, Monti V, Cabras A, Leongamornlert D, Abascal F, Diamond B et al.

    Haematologica 2021;106;11;2918-2926

    PUBMED: 33054126; PMC: 8561277; DOI: 10.3324/haematol.2020.262659

  • Successful Treatment of Cutaneous Squamous Cell Carcinoma in a Captive Green Iguana (Iguana Iguana).

    van der Weyden L, O'Dell N, Avenant A, Pazzi P and Koeppel KN

    Topics in companion animal medicine 2021;46;100610

    PUBMED: 34715376; DOI: 10.1016/j.tcam.2021.100610

  • An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci.

    Mountjoy E, Schmidt EM, Carmona M, Schwartzentruber J, Peat G, Miranda A, Fumis L, Hayhurst J, Buniello A, Karim MA et al.

    Nature genetics 2021

    PUBMED: 34711957; DOI: 10.1038/s41588-021-00945-5

  • Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study.

    Allen H, Vusirikala A, Flannagan J, Twohig KA, Zaidi A, Chudasama D, Lamagni T and COVID-19 Genomics UK (COG-UK Consortium)

    The Lancet regional health. Europe 2021;100252

    PUBMED: 34729548; PMC: 8552812; DOI: 10.1016/j.lanepe.2021.100252

  • The Emergence of Sars-CoV-2 Variant Lambda (C.37) in South America.

    Romero PE, Dávila-Barclay A, Salvatierra G, González L, Cuicapuza D, Solís L, Marcos-Carbajal P, Huancachoque J, Maturrano L and Tsukayama P

    Microbiology spectrum 2021;9;2;e0078921

    PUBMED: 34704780; PMC: 8549758; DOI: 10.1128/Spectrum.00789-21

  • Estimating dose-response relationships for vitamin D with coronary heart disease, stroke, and all-cause mortality: observational and Mendelian randomisation analyses.

    Emerging Risk Factors Collaboration/EPIC-CVD/Vitamin D Studies Collaboration

    The lancet. Diabetes & endocrinology 2021

    PUBMED: 34717822; DOI: 10.1016/S2213-8587(21)00263-1

  • Genomic surveillance of Acinetobacter baumannii in the Philippines, 2013-2014.

    Chilam J, Argimón S, Limas MT, Masim ML, Gayeta JM, Lagrada ML, Olorosa AM, Cohen V, Hernandez LT, Jeffrey B et al.

    Western Pacific surveillance and response journal : WPSAR 2021;12;4;1-15

    PUBMED: 35251744; PMC: 8873916; DOI: 10.5365/wpsar.2021.12.4.863

  • Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull).

    Moltke I, Korneliussen TS, Seguin-Orlando A, Moreno-Mayar JV, LaPointe E, Billeck W and Willerslev E

    Science advances 2021;7;44;eabh2013

    PUBMED: 34705496; PMC: 8550246; DOI: 10.1126/sciadv.abh2013

  • The genome sequences of the male and female green-veined white, Pieris napi (Linnaeus, 1758).

    Lohse K, Hayward A, Ebdon S, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;288

    PUBMED: 35846179; PMC: 9257262; DOI: 10.12688/wellcomeopenres.17277.1

  • Chiquihuite Cave and America’s Hidden Limestone Industries: A Reply to Chatters et al.

    Ardelean,C.F., Pedersen,M.W., Schwenninger,J-L., Arroyo-Cabrales,J., Gandy,D.A., Sikora,M., Macías-Quintero,J.I., Huerta-Arellano,V., De La Rosa-Díaz,J.J., Ocampo-Díaz,Y.Z.E. et al.

    PaleoAmerica 2021

    DOI: 10.1080/20555563.2021.1985063

  • The genome sequence of the clouded yellow, Colias crocea (Geoffroy, 1785).

    Ebdon S, Mackintosh A, Hayward A, Wotton K, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;284

    PUBMED: 36157970; PMC: 9490288; DOI: 10.12688/wellcomeopenres.17292.1

  • The genome sequence of the common frog, Rana temporaria Linnaeus 1758.

    Streicher JW, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;286

    PUBMED: 35118201; PMC: 8790709; DOI: 10.12688/wellcomeopenres.17296.1

  • The genome sequence of the St Mark's fly, Bibio marci (Linnaeus, 1758).

    Sivell O, Sivell D, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;285

    PUBMED: 35572470; PMC: 9073268; DOI: 10.12688/wellcomeopenres.17265.1

  • A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia.

    Tuong ZK, Lukowski SW, Nguyen QH, Chandra J, Zhou C, Gillinder K, Bashaw AA, Ferdinand JR, Stewart BJ, Teoh SM et al.

    iScience 2021;24;11;103326

    PUBMED: 34805788; PMC: 8586807; DOI: 10.1016/j.isci.2021.103326

  • Transcriptomic effects of rs4845604, an IBD and allergy-associated RORC variant, in stimulated ex vivo CD4+ T cells.

    Wilson PA, Santos Franco S, He L, Galwey NW, Meakin J, McIntyre R, McHugh SM, Nolan MA, Spain SL, Carlson T et al.

    PloS one 2021;16;10;e0258316

    PUBMED: 34673799; PMC: 8530322; DOI: 10.1371/journal.pone.0258316

  • The genome sequence of the common toad, Bufo bufo (Linnaeus, 1758).

    Streicher JW, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;281

    PUBMED: 35028424; PMC: 8729185; DOI: 10.12688/wellcomeopenres.17298.1

  • Late Quaternary dynamics of Arctic biota from ancient environmental genomics.

    Wang Y, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MKF, Fernandez-Guerra A et al.

    Nature 2021

    PUBMED: 34671161; DOI: 10.1038/s41586-021-04016-x

  • Same gene, opposite sexes: Sex-specific divergent expression of a gene required for vertebrate fertilization.

    Bianchi E

    Proceedings of the National Academy of Sciences of the United States of America 2021;118;42

    PUBMED: 34642252; PMC: 8545453; DOI: 10.1073/pnas.2116001118

  • A Global Crowdsourcing Open Call to Improve Research Mentorship in Low- and Middle-Income Countries: A Mixed Methods Analysis.

    Oppong E, Bao H, Tang W, Echavarria Mejia MI, Glozah F, Asanga N, Boinett CJ, Aguilar AM, Valido E, Lestari T and Tucker JD

    The American journal of tropical medicine and hygiene 2021

    PUBMED: 34662869; DOI: 10.4269/ajtmh.21-0607

  • Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence.

    Moody S, Senkin S, Islam SMA, Wang J, Nasrollahzadeh D, Cortez Cardoso Penha R, Fitzgerald S, Bergstrom EN, Atkins J, He Y et al.

    Nature genetics 2021;53;11;1553-1563

    PUBMED: 34663923; DOI: 10.1038/s41588-021-00928-6

  • Prognostic impact of chromosomal abnormalities and copy number alterations in adult B-cell precursor acute lymphoblastic leukaemia: a UKALL14 study.

    Moorman AV, Barretta E, Butler ER, Ward EJ, Twentyman K, Kirkwood AA, Enshaei A, Schwab C, Creasey T, Leongamornlert D et al.

    Leukemia 2021

    PUBMED: 34657128; DOI: 10.1038/s41375-021-01448-2

  • Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma.

    Peri A, Greenstein E, Alon M, Pai JA, Dingjan T, Reich-Zeliger S, Barnea E, Barbolin C, Levy R, Arnedo-Pac C et al.

    The Journal of clinical investigation 2021;131;20

    PUBMED: 34651586; DOI: 10.1172/JCI129466

  • The genome sequence of the bootlace worm, Lineus longissimus (Gunnerus, 1770).

    Kwiatkowski D, Blaxter M, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;272

    PUBMED: 34796280; PMC: 8593623; DOI: 10.12688/wellcomeopenres.17193.1

  • The genome sequence of the garden bumblebee, Bombus hortorum (Linnaeus, 1761).

    Crowley L, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;270

    PUBMED: 34778570; PMC: 8543170; DOI: 10.12688/wellcomeopenres.17187.1

  • The genome sequence of the white ermine, Spilosoma lubricipeda Linnaeus 1758.

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;271

    PUBMED: 34805552; PMC: 8567691; DOI: 10.12688/wellcomeopenres.17190.1

  • Genetic diversity of Salmonella Paratyphi A isolated from enteric fever patients in Bangladesh from 2008 to 2018.

    Rahman SIA, Nguyen TNT, Khanam F, Thomson NR, Dyson ZA, Taylor-Brown A, Chowdhury EK, Dougan G, Baker S and Qadri F

    PLoS neglected tropical diseases 2021;15;10;e0009748

    PUBMED: 34648506; DOI: 10.1371/journal.pntd.0009748

  • Genomic reconstruction of the SARS-CoV-2 epidemic in England.

    Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV et al.

    Nature 2021;600;7889;506-511

    PUBMED: 34649268; PMC: 8674138; DOI: 10.1038/s41586-021-04069-y

  • Non-canonical glutamine transamination sustains efferocytosis by coupling redox buffering to oxidative phosphorylation.

    Merlin J, Ivanov S, Dumont A, Sergushichev A, Gall J, Stunault M, Ayrault M, Vaillant N, Castiglione A, Swain A et al.

    Nature metabolism 2021

    PUBMED: 34650273; DOI: 10.1038/s42255-021-00471-y

  • Wilms tumour.

    Spreafico F, Fernandez CV, Brok J, Nakata K, Vujanic G, Geller JI, Gessler M, Maschietto M, Behjati S, Polanco A et al.

    Nature reviews. Disease primers 2021;7;1;75

    PUBMED: 34650095; DOI: 10.1038/s41572-021-00308-8

  • The genome sequence of the Glanville fritillary, Melitaea cinxia (Linnaeus, 1758).

    Vila R, Hayward A, Lohse K, Wright C, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;266

    PUBMED: 36873711; PMC: 9975429; DOI: 10.12688/wellcomeopenres.17283.1

  • The genome sequence of the peach blossom moth, Thyatira batis (Linnaeus, 1758).

    Boyes D, Holland PWH, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;267

    PUBMED: 35252591; PMC: 8874031; DOI: 10.12688/wellcomeopenres.17268.1

  • Convergent somatic mutations in metabolism genes in chronic liver disease.

    Ng SWK, Rouhani FJ, Brunner SF, Brzozowska N, Aitken SJ, Yang M, Abascal F, Moore L, Nikitopoulou E, Chappell L et al.

    Nature 2021;598;7881;473-478

    PUBMED: 34646017; DOI: 10.1038/s41586-021-03974-6

  • Mutant clones in normal epithelium outcompete and eliminate emerging tumours.

    Colom B, Herms A, Hall MWJ, Dentro SC, King C, Sood RK, Alcolea MP, Piedrafita G, Fernandez-Antoran D, Ong SH et al.

    Nature 2021;598;7881;510-514

    PUBMED: 34646013; PMC: 7612642; DOI: 10.1038/s41586-021-03965-7

  • Simulations reveal that different responses to cell crowding determine the expansion of p53 and Notch mutant clones in squamous epithelia.

    Kostiou V, Hall MWJ, Jones PH and Hall BA

    Journal of the Royal Society, Interface 2021;18;183;20210607

    PUBMED: 34637643; PMC: 8510697; DOI: 10.1098/rsif.2021.0607

  • The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11.

    Lafage-Pochitaloff M, Gerby B, Baccini V, Largeaud L, Fregona V, Prade N, Juvin PY, Jamrog LA, Bories P, Hébrard S et al.

    Blood advances 2021

    PUBMED: 34638130; DOI: 10.1182/bloodadvances.2021005311

  • The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758).

    Lohse K, Mackintosh A, Vila R, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;258

    PUBMED: 36072556; PMC: 9372638; DOI: 10.12688/wellcomeopenres.17204.1

  • The genome sequence of the large white, Pieris brassicae (Linnaeus, 1758).

    Lohse K, Mackintosh A, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;262

    PUBMED: 36312456; PMC: 9608253; DOI: 10.12688/wellcomeopenres.17274.1

  • Navigating COVID-19: Starting a lab during the pandemic.

    Ordovás-Montañés J, Gerlach C, Moraes-Vieira P, Vento-Tormo R, Zhang C and Jurado KA

    Immunity 2021;54;10;2169-2171

    PUBMED: 34644549; PMC: 8506976; DOI: 10.1016/j.immuni.2021.09.020

  • Societal and equity challenges for Brain Health Services. A user manual for Brain Health Services-part 6 of 6.

    Milne R, Altomare D, Ribaldi F, Molinuevo JL, Frisoni GB, Brayne C and European Task Force for Brain Health Services

    Alzheimer's research & therapy 2021;13;1;173

    PUBMED: 34635173; DOI: 10.1186/s13195-021-00885-6

  • Spatial gene expression maps of the intestinal lymphoid follicle and associated epithelium identify zonated expression programs.

    Cohen N, Massalha H, Ben-Moshe S, Egozi A, Rozenberg M, Bahar Halpern K and Itzkovitz S

    PLoS biology 2021;19;10;e3001214

    PUBMED: 34634036; DOI: 10.1371/journal.pbio.3001214

  • Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association.

    Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E et al.

    Environmental research 2021;112183

    PUBMED: 34637759; DOI: 10.1016/j.envres.2021.112183

  • Circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, India.

    Argimón S, Nagaraj G, Shamanna V, Darmavaram S, Vasanth AK, Prasanna A, Poojary A, Bari AK, Underwood A, Kekre M et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021

    PUBMED: 34626469; DOI: 10.1093/cid/ciab897

  • Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders.

    Gardner EJ, Sifrim A, Lindsay SJ, Prigmore E, Rajan D, Danecek P, Gallone G, Eberhardt RY, Martin HC, Wright CF et al.

    American journal of human genetics 2021;108;11;2186-2194

    PUBMED: 34626536; PMC: 8595893; DOI: 10.1016/j.ajhg.2021.09.010

  • High-resolution sweep metagenomics using fast probabilistic inference.

    Mäklin T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J et al.

    Wellcome open research 2021;5;14

    PUBMED: 34746439; PMC: 8543175; DOI: 10.12688/wellcomeopenres.15639.2

  • Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs.

    Burton NO, Willis A, Fisher K, Braukmann F, Price J, Stevens L, Baugh LR, Reinke A and Miska EA

    eLife 2021;10

    PUBMED: 34622777; PMC: 8570697; DOI: 10.7554/eLife.73425

  • Caught in the antiviral crossfire: Ganciclovir-associated mutagenesis in HSC transplant recipients.

    Spencer Chapman M and Nangalia J

    Cell stem cell 2021;28;10;1683-1685

    PUBMED: 34624229; DOI: 10.1016/j.stem.2021.09.011

  • Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes.

    Vernaz G, Malinsky M, Svardal H, Du M, Tyers AM, Santos ME, Durbin R, Genner MJ, Turner GF and Miska EA

    Nature communications 2021;12;1;5870

    PUBMED: 34620871; DOI: 10.1038/s41467-021-26166-2

  • C. elegans genome-wide analysis reveals DNA repair pathways that act cooperatively to preserve genome integrity upon ionizing radiation.

    Meier B, Volkova NV, Wang B, González-Huici V, Bertolini S, Campbell PJ, Gerstung M and Gartner A

    PloS one 2021;16;10;e0258269

    PUBMED: 34614038; PMC: 8494335; DOI: 10.1371/journal.pone.0258269

  • Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen.

    Mullineaux-Sanders C, Carson D, Hopkins EGD, Glegola-Madejska I, Escobar-Zepeda A, Browne HP, Lawley TD and Frankel G

    mBio 2021;12;5;e0241021

    PUBMED: 34609899; PMC: 8510533; DOI: 10.1128/mBio.02410-21

  • Polygenic basis and biomedical consequences of telomere length variation.

    Codd V, Wang Q, Allara E, Musicha C, Kaptoge S, Stoma S, Jiang T, Hamby SE, Braund PS, Bountziouka V et al.

    Nature genetics 2021;53;10;1425-1433

    PUBMED: 34611362; DOI: 10.1038/s41588-021-00944-6

  • Visualizing formation of the active site in the mitochondrial ribosome.

    Chandrasekaran V, Desai N, Burton NO, Yang H, Price J, Miska EA and Ramakrishnan V

    eLife 2021;10

    PUBMED: 34609277; DOI: 10.7554/eLife.68806

  • Genome-Wide Association Study of Peripheral Artery Disease.

    van Zuydam NR, Stiby A, Abdalla M, Austin E, Dahlström EH, McLachlan S, Vlachopoulou E, Ahlqvist E, Di Liao C, Sandholm N et al.

    Circulation. Genomic and precision medicine 2021;CIRCGEN119002862

    PUBMED: 34601942; DOI: 10.1161/CIRCGEN.119.002862

  • Single cell biology-a Keystone Symposia report.

    Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J et al.

    Annals of the New York Academy of Sciences 2021

    PUBMED: 34605044; DOI: 10.1111/nyas.14692

  • Lumefantrine attenuates Plasmodium falciparum artemisinin resistance during the early ring stage.

    Kümpornsin K, Loesbanluechai D, de Cozar C, Kotanan N, Chotivanich K, White NJ, Wilairat P, Gomez-Lorenzo MG, Gamo FJ, Sanz LM et al.

    International journal for parasitology. Drugs and drug resistance 2021;17;186-190

    PUBMED: 34673330; PMC: 8528645; DOI: 10.1016/j.ijpddr.2021.09.005

  • An uneven race: genome editing for parasitic worms.

    Sankaranarayanan G, Berriman M and Rinaldi G

    Nature reviews. Microbiology 2021;19;10;621

    PUBMED: 34404952; DOI: 10.1038/s41579-021-00625-5

  • Enhancer-associated H3K4 methylation safeguards in vitro germline competence.

    Bleckwehl T, Crispatzu G, Schaaf K, Respuela P, Bartusel M, Benson L, Clark SJ, Dorighi KM, Barral A, Laugsch M et al.

    Nature communications 2021;12;1;5771

    PUBMED: 34599190; DOI: 10.1038/s41467-021-26065-6

  • Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil.

    Almeida SCG, Lo SW, Hawkins PA, Gladstone RA, Cassiolato AP, Klugman KP, Breiman RF, Bentley SD, McGee L and Brandileone MC

    Microbial genomics 2021;7;10

    PUBMED: 34609274; PMC: 8627213; DOI: 10.1099/mgen.0.000635

  • Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi.

    Betts M, Jarvis S, Jeffries A, Gori A, Chaguza C, Msefula J, Weight CM, Kwambana-Adams B, French N, Swarthout TD et al.

    Microbiology resource announcements 2021;10;39;e0071521

    PUBMED: 34591678; DOI: 10.1128/MRA.00715-21

  • Differential abundance testing on single-cell data using k-nearest neighbor graphs.

    Dann E, Henderson NC, Teichmann SA, Morgan MD and Marioni JC

    Nature biotechnology 2021

    PUBMED: 34594043; DOI: 10.1038/s41587-021-01033-z

  • Increased somatic mutation burdens in normal human cells due to defective DNA polymerases.

    Robinson PS, Coorens THH, Palles C, Mitchell E, Abascal F, Olafsson S, Lee BCH, Lawson ARJ, Lee-Six H, Moore L et al.

    Nature genetics 2021;53;10;1434-1442

    PUBMED: 34594041; PMC: 8492474; DOI: 10.1038/s41588-021-00930-y

  • MTH1 inhibitor TH1579 induces oxidative DNA damage and mitotic arrest in acute myeloid leukemia.

    Sanjiv K, Calderón-Montaño JM, Pham TM, Erkers T, Tsuber V, Almlöf I, Höglund A, Heshmati Y, Seashore-Ludlow B, Nagesh Danda A et al.

    Cancer research 2021

    PUBMED: 34593524; DOI: 10.1158/0008-5472.CAN-21-0061

  • Preclinical development of a bispecific TNFα/IL-23 neutralising domain antibody as a novel oral treatment for inflammatory bowel disease.

    Roberts KJ, Cubitt MF, Carlton TM, Rodrigues-Duarte L, Maggiore L, Chai R, Clare S, Harcourt K, MacDonald TT, Ray KP et al.

    Scientific reports 2021;11;1;19422

    PUBMED: 34593832; PMC: 8484351; DOI: 10.1038/s41598-021-97236-0

  • The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.

    Aggarwal D, Myers R, Hamilton WL, Bharucha T, Tumelty NM, Brown CS, Meader EJ, Connor T, Smith DL, Bradley DT et al.

    The Lancet. Microbe 2021

    PUBMED: 34608459; PMC: 8480962; DOI: 10.1016/S2666-5247(21)00208-1

  • Blood and immune development in human fetal bone marrow and Down syndrome.

    Jardine L, Webb S, Goh I, Quiroga Londoño M, Reynolds G, Mather M, Olabi B, Stephenson E, Botting RA, Horsfall D et al.

    Nature 2021

    PUBMED: 34588693; DOI: 10.1038/s41586-021-03929-x

  • Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB).

    Mantas MJQ, Nunn PB, Ke Z, Codd GA and Barker D

    Phytochemistry 2021;192;112953

    PUBMED: 34598041; DOI: 10.1016/j.phytochem.2021.112953

  • Protocol for post-processing of bacterial pangenome data using Pagoo pipeline.

    Ferrés I and Iraola G

    STAR protocols 2021;2;4;100802

    PUBMED: 34632414; PMC: 8487088; DOI: 10.1016/j.xpro.2021.100802

  • Seeing the bigger picture.

    Zellmer C, Tran TA and Sridhar S

    Nature reviews. Microbiology 2021;19;12;745

    PUBMED: 34588659; DOI: 10.1038/s41579-021-00640-6

  • Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal.

    Feuerborn TR, Carmagnini A, Losey RJ, Nomokonova T, Askeyev A, Askeyev I, Askeyev O, Antipina EE, Appelt M, Bachura OP et al.

    Proceedings of the National Academy of Sciences of the United States of America 2021;118;39

    PUBMED: 34544854; DOI: 10.1073/pnas.2100338118

  • Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.

    Calland JK, Pascoe B, Bayliss SC, Mourkas E, Berthenet E, Thorpe HA, Hitchings MD, Feil EJ, Corander J, Blaser MJ et al.

    PLoS genetics 2021;17;9;e1009829

    PUBMED: 34582435; DOI: 10.1371/journal.pgen.1009829

  • An object-oriented framework for evolutionary pangenome analysis.

    Ferrés I and Iraola G

    Cell reports methods 2021;1;5;100085

    PUBMED: 35474671; PMC: 9017228; DOI: 10.1016/j.crmeth.2021.100085

  • Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin.

    Hilsdorf AWS, Uliano-Silva M, Coutinho LL, Montenegro H, Almeida-Val VMF and Pinhal D

    GigaByte (Hong Kong, China) 2021;2021;gigabyte29

    PUBMED: 36824330; PMC: 9650303; DOI: 10.46471/gigabyte.29

  • Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ.

    Eckersley A, Ozols M, Chen P, Tam V, Hoyland JA, Trafford A, Chan D and Sherratt MJ

    International journal of molecular sciences 2021;22;19

    PUBMED: 34638745; DOI: 10.3390/ijms221910408

  • Surveillance of strangles in UK horses between 2015 and 2019 based on laboratory detection of Streptococcus equi.

    McGlennon A, Waller A, Verheyen K, Slater J, Grewar J, Aanensen D and Newton R

    The Veterinary record 2021;e948

    PUBMED: 34570896; DOI: 10.1002/vetr.948

  • A gene expression panel for estimating age in males and females of the sleeping sickness vector Glossina morsitans.

    Lucas ER, Darby AC, Torr SJ and Donnelly MJ

    PLoS neglected tropical diseases 2021;15;9;e0009797

    PUBMED: 34555037; DOI: 10.1371/journal.pntd.0009797

  • Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression.

    Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S et al.

    Nature genetics 2021

    PUBMED: 34556857; DOI: 10.1038/s41588-021-00925-9

  • The genome sequence of the common red soldier beetle, Rhagonycha fulva (Scopoli, 1763).

    Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;243

    PUBMED: 36003953; PMC: 9363978; DOI: 10.12688/wellcomeopenres.17198.1

  • Genomic characterization of hepatoid tumors: context matters.

    Lawlor RT, Mafficini A, Sciammarella C, Cantù C, Rusev BC, Piredda ML, Antonello D, Grimaldi S, Bonizzato G, Sperandio N et al.

    Human pathology 2021

    PUBMED: 34562502; DOI: 10.1016/j.humpath.2021.09.006

  • Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α 3.7I form of α-thalassaemia using genome-wide microarray data.

    Ndila CM, Nyirongo V, Macharia AW, Jeffreys AE, Rowlands K, Hubbart C, Busby GBJ, Band G, Harding RM, Rockett KA et al.

    Wellcome open research 2021;5;287

    PUBMED: 34632085; PMC: 8474104; DOI: 10.12688/wellcomeopenres.16320.2

  • Strategies for sample labelling and library preparation in DNA metabarcoding studies.

    Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ and Creer S

    Molecular ecology resources 2021

    PUBMED: 34551203; DOI: 10.1111/1755-0998.13512

  • Variation on a theme: mapping microglial heterogeneity.

    Washer SJ, Bassett AR and Cowley SA

    Trends in genetics : TIG 2021;37;12;1050-1052

    PUBMED: 34563398; DOI: 10.1016/j.tig.2021.09.004

  • The blood metabolome of incident kidney cancer: A case-control study nested within the MetKid consortium.

    Guida F, Tan VY, Corbin LJ, Smith-Byrne K, Alcala K, Langenberg C, Stewart ID, Butterworth AS, Surendran P, Achaintre D et al.

    PLoS medicine 2021;18;9;e1003786

    PUBMED: 34543281; DOI: 10.1371/journal.pmed.1003786

  • Ethanol-induced formation of colorectal tumours and precursors in a mouse model of Lynch Syndrome.

    Cerretelli G, Zhou Y, Müller MF, Adams DJ and Arends MJ

    The Journal of pathology 2021

    PUBMED: 34543445; DOI: 10.1002/path.5796

  • Inferred Ancestral Origin of Cancer Cell Lines Associates with Differential Drug Response.

    Nguyen PBH, Ohnmacht AJ, Sharifli S, Garnett MJ and Menden MP

    International journal of molecular sciences 2021;22;18

    PUBMED: 34576298; DOI: 10.3390/ijms221810135

  • RAPD PCR detects co-colonisation of multiple group B streptococcus genotypes: A practical molecular technique for screening multiple colonies.

    To KN, Powell O, Jamrozy D, Kopunova R, Anastasiadou K, Faal A, Secka O, Chalker V, Le Doare K and Jauneikaite E

    Journal of microbiological methods 2021;190;106322

    PUBMED: 34506810; PMC: 9395992; DOI: 10.1016/j.mimet.2021.106322

  • Ten simple rules to make your computing more environmentally sustainable.

    Lannelongue L, Grealey J, Bateman A and Inouye M

    PLoS computational biology 2021;17;9;e1009324

    PUBMED: 34543272; PMC: 8452068; DOI: 10.1371/journal.pcbi.1009324

  • Importing genetically altered animals: ensuring quality.

    Birling MC, Fray MD, Kasparek P, Kopkanova J, Massimi M, Matteoni R, Montoliu L, Nutter LMJ, Raspa M, Rozman J et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2021

    PUBMED: 34536110; DOI: 10.1007/s00335-021-09908-x

  • High-dimensional structure learning of sparse vector autoregressive models using fractional marginal pseudo-likelihood

    Suotsalo,Kimmo, Xu,Yingying, Corander,Jukka and Pensar,Johan

    Statistics and Computing 2021;31;73

    DOI: 10.1007/s11222-021-10049-z

  • Incipient diploidization of the medicinal plant Perilla within 10,000 years.

    Zhang Y, Shen Q, Leng L, Zhang D, Chen S, Shi Y, Ning Z and Chen S

    Nature communications 2021;12;1;5508

    PUBMED: 34535649; DOI: 10.1038/s41467-021-25681-6

  • The genome sequence of the large tortoiseshell, Nymphalis polychloros (Linnaeus, 1758).

    Lohse K, Laetsch D, Vila R, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium

    Wellcome open research 2021;6;238

    PUBMED: 35528734; PMC: 9039367; DOI: 10.12688/wellcomeopenres.17196.1

  • Hatching of parasitic nematode eggs: a crucial step determining infection.

    Mkandawire TT, Grencis RK, Berriman M and Duque-Correa MA

    Trends in parasitology 2021;38;2;174-187

    PUBMED: 34538735; DOI: 10.1016/j.pt.2021.08.008

  • ISA API: An open platform for interoperable life science experimental metadata.

    Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN et al.

    GigaScience 2021;10;9

    PUBMED: 34528664; PMC: 8444265; DOI: 10.1093/gigascience/giab060

  • SREBP1-induced fatty acid synthesis depletes macrophages antioxidant defences to promote their alternative activation.

    Bidault G, Virtue S, Petkevicius K, Jolin HE, Dugourd A, Guénantin AC, Leggat J, Mahler-Araujo B, Lam BYH, Ma MK et al.

    Nature metabolism 2021

    PUBMED: 34531575; DOI: 10.1038/s42255-021-00440-5

  • Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines.

    De Kegel B, Quinn N, Thompson NA, Adams DJ and Ryan CJ

    Cell systems 2021;12;12;1144-1159.e6

    PUBMED: 34529928; DOI: 10.1016/j.cels.2021.08.006

  • Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population.

    Chung The H, Nguyen Ngoc Minh C, Tran Thi Hong C, Nguyen Thi Nguyen T, Pike LJ, Zellmer C, Pham Duc T, Tran TA, Ha Thanh T, Van MP et al.

    Microbiology spectrum 2021;e0052621

    PUBMED: 34523984; DOI: 10.1128/Spectrum.00526-21

  • Functional Impact of Genomic Complexity on the Transcriptome of Multiple Myeloma.

    Ziccheddu B, Da Vià MC, Lionetti M, Maeda A, Morlupi S, Dugo M, Todoerti K, Oliva S, D'Agostino M, Corradini P et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2021

    PUBMED: 34526359; DOI: 10.1158/1078-0432.CCR-20-4366

  • Prioritization of Molecular Targets for Antimalarial Drug Discovery.

    Forte B, Ottilie S, Plater A, Campo B, Dechering KJ, Gamo FJ, Goldberg DE, Istvan ES, Lee M, Lukens AK et al.

    ACS infectious diseases 2021;7;10;2764-2776

    PUBMED: 34523908; PMC: 8608365; DOI: 10.1021/acsinfecdis.1c00322

  • IKZF1 alterations are not associated with outcome in 498 adults with B-precursor ALL enrolled in the UKALL14 trial.

    Mitchell RJ, Kirkwood AA, Barretta E, Clifton-Hadley L, Lawrie E, Lee S, Leongamornlert D, Marks DI, McMillan AK, Menne TF et al.

    Blood advances 2021;5;17;3322-3332

    PUBMED: 34477813; DOI: 10.1182/bloodadvances.2021004430

  • Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation.

    Campbell NR, Rao A, Hunter MV, Sznurkowska MK, Briker L, Zhang M, Baron M, Heilmann S, Deforet M, Kenny C et al.

    Developmental cell 2021

    PUBMED: 34529939; DOI: 10.1016/j.devcel.2021.08.018

  • Evolution of multidrug resistance in Plasmodium falciparum: a longitudinal study of genetic resistance markers in the Greater Mekong Subregion.

    Imwong M, Suwannasin K, Srisutham S, Vongpromek R, Promnarate C, Saejeng A, Phyo AP, Proux S, Pongvongsa T, Nguon C et al.

    Antimicrobial agents and chemotherapy 2021;AAC0112121

    PUBMED: 34516247; DOI: 10.1128/AAC.01121-21

  • Individual-level variations in malaria susceptibility and acquisition of clinical protection.

    Valletta JJ, Addy JWG, Reid AJ, Ndungu FM, Bediako Y, Mwacharo J, Mohammed KS, Musyoki J, Ngoi JM, Wambua J et al.

    Wellcome open research 2021;6;22

    PUBMED: 35310901; PMC: 8914138; DOI: 10.12688/wellcomeopenres.16524.2

  • Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.

    Kariuki S, Dyson ZA, Mbae C, Ngetich R, Kavai SM, Wairimu C, Anyona S, Gitau N, Onsare RS, Ongandi B et al.

    eLife 2021;10

    PUBMED: 34515028; PMC: 8494480; DOI: 10.7554/eLife.67852

  • The RAD51 recombinase protects mitotic chromatin in human cells.

    Wassing IE, Graham E, Saayman X, Rampazzo L, Ralf C, Bassett A and Esashi F

    Nature communications 2021;12;1;5380

    PUBMED: 34508092; PMC: 8433380; DOI: 10.1038/s41467-021-25643-y

  • Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay.

    Rego N, Salazar C, Paz M, Costábile A, Fajardo A, Ferrés I, Perbolianachis P, Fernández-Calero T, Noya V, Machado MR et al.

    Viruses 2021;13;9

    PUBMED: 34578382; DOI: 10.3390/v13091801

  • Genome-wide analysis of blood lipid metabolites in over 5000 South Asians reveals biological insights at cardiometabolic disease loci.

    Harshfield EL, Fauman EB, Stacey D, Paul DS, Ziemek D, Ong RMY, Danesh J, Butterworth AS, Rasheed A, Sattar T et al.

    BMC medicine 2021;19;1;232

    PUBMED: 34503513; PMC: 8431908; DOI: 10.1186/s12916-021-02087-1

  • Optogenetic modeling of human neuromuscular circuits in Duchenne muscular dystrophy with CRISPR and pharmacological corrections.

    Paredes-Redondo A, Harley P, Maniati E, Ryan D, Louzada S, Meng J, Kowala A, Fu B, Yang F, Liu P et al.

    Science advances 2021;7;37;eabi8787

    PUBMED: 34516770; DOI: 10.1126/sciadv.abi8787

  • A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus).

    Lo Cascio Sætre C, Eroukhmanoff F, Rönkä K, Kluen E, Thorogood R, Torrance J, Tracey A, Chow W, Pelan S, Howe K et al.

    Genome biology and evolution 2021

    PUBMED: 34499122; DOI: 10.1093/gbe/evab212

  • A Combined Phenotypic-Genotypic Predictive Algorithm for In Vitro Detection of Bicarbonate: β-Lactam Sensitization among Methicillin-Resistant Staphylococcus aureus (MRSA).

    Ersoy SC, Rose WE, Patel R, Proctor RA, Chambers HF, Harrison EM, Pak Y and Bayer AS

    Antibiotics (Basel, Switzerland) 2021;10;9

    PUBMED: 34572671; PMC: 8469475; DOI: 10.3390/antibiotics10091089

  • The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens.

    Aunin E, Böhme U, Blake D, Dove A, Smith M, Corton C, Oliver K, Betteridge E, Quail MA, McCarthy SA et al.

    Wellcome open research 2021;6;225

    PUBMED: 34703904; PMC: 8515493; DOI: 10.12688/wellcomeopenres.17100.1

  • A roadmap for the Human Developmental Cell Atlas.

    Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A et al.

    Nature 2021;597;7875;196-205

    PUBMED: 34497388; DOI: 10.1038/s41586-021-03620-1

  • Cells of the human intestinal tract mapped across space and time.

    Elmentaite R, Kumasaka N, Roberts K, Fleming A, Dann E, King HW, Kleshchevnikov V, Dabrowska M, Pritchard S, Bolt L et al.

    Nature 2021;597;7875;250-255

    PUBMED: 34497389; PMC: 8426186; DOI: 10.1038/s41586-021-03852-1

  • Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh.

    Cowley LA, Afrad MH, Rahman SIA, Mamun MMA, Chin T, Mahmud A, Rahman MZ, Billah MM, Khan MH, Sultana S et al.

    Nature microbiology 2021

    PUBMED: 34497354; DOI: 10.1038/s41564-021-00955-3

  • Population genomics of the critically endangered kākāpō.

    Dussex N, van der Valk T, Morales HE, Wheat CW, Díez-Del-Molino D, von Seth J, Foster Y, Kutschera VE, Guschanski K, Rhie A et al.

    Cell genomics 2021;1;1;100002

    PUBMED: 36777713; PMC: 9903828; DOI: 10.1016/j.xgen.2021.100002

  • A compendium of uniformly processed human gene expression and splicing quantitative trait loci.

    Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ et al.

    Nature genetics 2021;53;9;1290-1299

    PUBMED: 34493866; DOI: 10.1038/s41588-021-00924-w

  • Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis.

    Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CL, Tyser RCV, Argelaguet R et al.

    Nature biotechnology 2021;40;1;74-85

    PUBMED: 34489600; PMC: 8763645; DOI: 10.1038/s41587-021-01006-2

  • Whole genome sequence analysis of platelet traits in the NHLBI trans-omics for precision medicine initiative.

    Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, McHugh C, Surendran P, Blackwell TW et al.

    Human molecular genetics 2021

    PUBMED: 34553764; DOI: 10.1093/hmg/ddab252

  • Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.

    Krämer B, Knoll R, Bonaguro L, ToVinh M, Raabe J, Astaburuaga-García R, Schulte-Schrepping J, Kaiser KM, Rieke GJ, Bischoff J et al.

    Immunity 2021

    PUBMED: 34592166; DOI: 10.1016/j.immuni.2021.09.002

  • Patterns of genomic change in residual disease after neoadjuvant chemotherapy for estrogen receptor-positive and HER2-negative breast cancer.

    Chatzipli A, Bonnefoi H, MacGrogan G, Sentis J, Cameron D, Poncet C, EORTC 10994/BIG 1-00 Consortium and Iggo R

    British journal of cancer 2021

    PUBMED: 34480095; DOI: 10.1038/s41416-021-01526-3

  • A NOVEL AIR-DRIED MULTIPLEX HIGH RESOLUTION MELT ASSAY FOR THE DETECTION OF EXTENDED SPECTRUM BETA-LACTAMASE AND CARBAPENEMASE GENES.

    Cubas-Atienzar AI, Williams CT, Karkey A, Dongol S, Sulochana M, Rajendra S, Hobbs G, Evans K, Musicha P, Feasey N et al.

    Journal of global antimicrobial resistance 2021

    PUBMED: 34482019; DOI: 10.1016/j.jgar.2021.08.006

  • Cell reprogramming shapes the mitochondrial DNA landscape.

    Wei W, Gaffney DJ and Chinnery PF

    Nature communications 2021;12;1;5241

    PUBMED: 34475388; DOI: 10.1038/s41467-021-25482-x

  • Genome Assemblies across the Diverse Evolutionary Spectrum of Leishmania Protozoan Parasites.

    Warren WC, Akopyants NS, Dobson DE, Hertz-Fowler C, Lye LF, Myler PJ, Ramasamy G, Shanmugasundram A, Silva-Franco F, Steinbiss S et al.

    Microbiology resource announcements 2021;10;35;e0054521

    PUBMED: 34472979; DOI: 10.1128/MRA.00545-21

  • Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.

    Võsa U, Claringbould A, Westra HJ, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Yazar S et al.

    Nature genetics 2021;53;9;1300-1310

    PUBMED: 34475573; PMC: 8432599; DOI: 10.1038/s41588-021-00913-z

  • Addendum: The mutational constraint spectrum quantified from variation in 141,456 humans.

    Gudmundsson S, Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A et al.

    Nature 2021;597;7874;E3-E4

    PUBMED: 34373650; DOI: 10.1038/s41586-021-03758-y

  • Allostatic hypermetabolic response in PGC1α/β heterozygote mouse despite mitochondrial defects.

    Rodriguez-Cuenca S, Lelliot CJ, Campbell M, Peddinti G, Martinez-Uña M, Ingvorsen C, Dias AR, Relat J, Mora S, Hyötyläinen T et al.

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021;35;9;e21752

    PUBMED: 34369602; DOI: 10.1096/fj.202100262RR

  • Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study.

    Ludden C, Coll F, Gouliouris T, Restif O, Blane B, Blackwell GA, Kumar N, Naydenova P, Crawley C, Brown NM et al.

    The Lancet. Microbe 2021;2;9;e472-e480

    PUBMED: 34485958; PMC: 8410606; DOI: 10.1016/S2666-5247(21)00117-8

  • Different evolutionary trends form the twilight zone of the bacterial pan-genome.

    Horesh G, Taylor-Brown A, McGimpsey S, Lassalle F, Corander J, Heinz E and Thomson NR

    Microbial genomics 2021;7;9

    PUBMED: 34559043; DOI: 10.1099/mgen.0.000670

  • Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource.

    Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, García Guerreiro MP et al.

    Molecular biology and evolution 2021

    PUBMED: 34469576; DOI: 10.1093/molbev/msab259

  • Genome-wide analysis provides a deeper understanding of the population structure of the Salmonella enterica serotype Paratyphi B complex in Bangladesh.

    Rahman SIA, Taylor-Brown A, Khanam F, Khan AI, Horesh G, Dyson ZA, Begum YA, Chowdhury EK, Qadri F, Dougan G and Thomson NR

    Microbial genomics 2021;7;9

    PUBMED: 34550065; DOI: 10.1099/mgen.0.000617

  • Getting ahead of the competition.

    Kane L and Dorman MJ

    Nature reviews. Microbiology 2021;19;9;551

    PUBMED: 34211159; DOI: 10.1038/s41579-021-00599-4

  • Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach.

    Nagaraj G, Govindan V, Ganaie F, Venkatesha VT, Hawkins PA, Gladstone RA, McGee L, Breiman RF, Bentley SD, Klugman KP et al.

    Microbial genomics 2021;7;9

    PUBMED: 34494953; PMC: 8715438; DOI: 10.1099/mgen.0.000645

  • Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis.

    Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD and Heyderman RS

    Microbial genomics 2021;7;9

    PUBMED: 34550067; DOI: 10.1099/mgen.0.000622

  • Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina.

    Gagetti P, Lo SW, Hawkins PA, Gladstone RA, Regueira M, Faccone D, Sireva-Argentina Group, Klugman KP, Breiman RF, McGee L et al.

    Microbial genomics 2021;7;9

    PUBMED: 34586054; PMC: 8715423; DOI: 10.1099/mgen.0.000636

  • Unmet clinical needs in the management of CALR-mutated essential thrombocythaemia: a consensus-based proposal from the European LeukemiaNet.

    Alvarez-Larrán A, Sant'Antonio E, Harrison C, Kiladjian JJ, Griesshammer M, Mesa R, Ianotto JC, Palandri F, Hernández-Boluda JC, Birgegård G et al.

    The Lancet. Haematology 2021;8;9;e658-e665

    PUBMED: 34450103; DOI: 10.1016/S2352-3026(21)00204-0

  • A positively-selected MAGEE2 LoF allele is associated with sexual dimorphism in human brain size, and shows similar phenotypes in Magee2 null mice.

    Szpak M, Collins SC, Li Y, Liu X, Ayub Q, Fischer MC, Vancollie VE, Lelliott CJ, Xue Y, Yalcin B et al.

    Molecular biology and evolution 2021

    PUBMED: 34464968; DOI: 10.1093/molbev/msab243

  • Spatial and genomic data to characterize endemic typhoid transmission.

    Gauld JS, Olgemoeller F, Heinz E, Nkhata R, Bilima S, Wailan AM, Kennedy N, Mallewa J, Gordon MA, Read JM et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021

    PUBMED: 34463736; DOI: 10.1093/cid/ciab745

  • TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells.

    Osnato A, Brown S, Krueger C, Andrews S, Collier AJ, Nakanoh S, Quiroga Londoño M, Wesley BT, Muraro D, Brumm AS et al.

    eLife 2021;10

    PUBMED: 34463252; PMC: 8410071; DOI: 10.7554/eLife.67259

  • Blood leukocyte transcriptomes in gram-positive and gram-negative community-acquired pneumonia.

    Pereverzeva L, Uhel F, Sengers HP, Butler J, van Vught LA, Burnham KL, Davenport EE, Knight JC, Cremer OL, Schultz MJ et al.

    The European respiratory journal 2021

    PUBMED: 34446464; DOI: 10.1183/13993003.01856-2021

  • Expanding the phenotype of ASXL3-related syndrome: A comprehensive description of 45 unpublished individuals with inherited and de novo pathogenic variants in ASXL3.

    Schirwani S, Albaba S, Carere DA, Guillen Sacoto MJ, Milan Zamora F, Si Y, Rabin R, Pappas J, Renaud DL, Hauser N et al.

    American journal of medical genetics. Part A 2021

    PUBMED: 34436830; DOI: 10.1002/ajmg.a.62465

  • Modeling HNF1B-associated monogenic diabetes using human iPSCs reveals an early stage impairment of the pancreatic developmental program.

    El-Khairi R, Olszanowski E, Muraro D, Madrigal P, Tilgner K, Chhatriwala M, Vyas S, Chia CY, Vallier L and Rodríguez-Seguí SA

    Stem cell reports 2021;16;9;2289-2304

    PUBMED: 34450036; PMC: 8452540; DOI: 10.1016/j.stemcr.2021.07.018

  • The mutational landscape of human somatic and germline cells.

    Moore L, Cagan A, Coorens THH, Neville MDC, Sanghvi R, Sanders MA, Oliver TRW, Leongamornlert D, Ellis P, Noorani A et al.

    Nature 2021;597;7876;381-386

    PUBMED: 34433962; DOI: 10.1038/s41586-021-03822-7

  • The role of organ - and daylength - specific gene expression in bulb development and resource management in onion (ALLIUM CEPA L.)

    Cheng, Wei, Rashid, Harun Ar, Stark, Richard and Thomas, Brian

    Scientia Horticulturae 2021;286;110223

    DOI: 10.1016/j.scienta.2021.110223

  • The venous system of E14.5 mouse embryos-reference data and examples for diagnosing malformations in embryos with gene deletions.

    Geyer SH, Maurer-Gesek B, Reissig LF, Rose J, Prin F, Wilson R, Galli A, Tudor C, White JK, Mohun TJ and Weninger WJ

    Journal of anatomy 2021

    PUBMED: 34435363; DOI: 10.1111/joa.13536

  • Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution.

    Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Hemberg M and Ahituv N

    Genome biology 2021;22;1;245

    PUBMED: 34433494; PMC: 8386077; DOI: 10.1186/s13059-021-02459-z

  • Extensive phylogenies of human development inferred from somatic mutations.

    Coorens THH, Moore L, Robinson PS, Sanghvi R, Christopher J, Hewinson J, Przybilla MJ, Lawson ARJ, Spencer Chapman M, Cagan A et al.

    Nature 2021;597;7876;387-392

    PUBMED: 34433963; DOI: 10.1038/s41586-021-03790-y

  • Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.

    Gong C, Krupka JA, Gao J, Grigoropoulos NF, Giotopoulos G, Asby R, Screen M, Usheva Z, Cucco F, Barrans S et al.

    Molecular cell 2021;81;19;4059-4075.e11

    PUBMED: 34437837; DOI: 10.1016/j.molcel.2021.07.041

  • Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage.

    Rillo-Bohn R, Adilardi R, Mitros T, Avşaroğlu B, Stevens L, Köhler S, Bayes J, Wang C, Lin S, Baskevitch KA et al.

    eLife 2021;10

    PUBMED: 34427184; PMC: 8455136; DOI: 10.7554/eLife.70990

  • Machine Learning Prediction of Resistance to Subinhibitory Antimicrobial Concentrations from Escherichia coli Genomes.

    Benkwitz-Bedford S, Palm M, Demirtas TY, Mustonen V, Farewell A, Warringer J, Parts L and Moradigaravand D

    mSystems 2021;e0034621

    PUBMED: 34427505; DOI: 10.1128/mSystems.00346-21

  • Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections.

    Illingworth CJ, Hamilton WL, Warne B, Routledge M, Popay A, Jackson C, Fieldman T, Meredith LW, Houldcroft CJ, Hosmillo M et al.

    eLife 2021;10

    PUBMED: 34425938; DOI: 10.7554/eLife.67308

  • Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases.

    Cai N, Gomez-Duran A, Yonova-Doing E, Kundu K, Burgess AI, Golder ZJ, Calabrese C, Bonder MJ, Camacho M, Lawson RA et al.

    Nature medicine 2021;27;9;1564-1575

    PUBMED: 34426706; DOI: 10.1038/s41591-021-01441-3

  • Who watches the watchmen? RNAi pathway-derived ribosomal small RNAs burgeon in absence of piRNAs.

    Ramakrishna NB and Miska EA

    Developmental cell 2021;56;16;2269-2270

    PUBMED: 34428395; DOI: 10.1016/j.devcel.2021.08.002

  • Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes.

    Velthuijs N, Meldal B, Geessinck Q, Porras P, Medvedeva Y, Zubritskiy A, Orchard S and Logie C

    Biochimica et biophysica acta. Gene regulatory mechanisms 2021;194749

    PUBMED: 34425241; DOI: 10.1016/j.bbagrm.2021.194749

  • Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria.

    Hendry JA, Kwiatkowski D and McVean G

    PLoS computational biology 2021;17;8;e1009287

    PUBMED: 34411093; DOI: 10.1371/journal.pcbi.1009287

  • Fetal exome sequencing for isolated increased nuchal translucency: Should we be doing it?

    Mellis R, Eberhardt RY, Hamilton SJ, PAGE Consortium, McMullan DJ, Kilby MD, Maher ER, Hurles ME, Giordano JL, Aggarwal V et al.

    BJOG : an international journal of obstetrics and gynaecology 2021

    PUBMED: 34411415; DOI: 10.1111/1471-0528.16869

  • Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells.

    Nolan LM, Cain AK, Clamens T, Furniss RCD, Manoli E, Sainz-Polo MA, Dougan G, Albesa-Jové D, Parkhill J, Mavridou DAI and Filloux A

    Nature microbiology 2021;6;9;1199-1210

    PUBMED: 34413503; DOI: 10.1038/s41564-021-00950-8

  • Neutrophils in secondary lymphoid organs.

    Lok LSC and Clatworthy MR

    Immunology 2021

    PUBMED: 34411302; DOI: 10.1111/imm.13406

  • The Transcriptome of Schistosoma mansoni Developing Eggs Reveals Key Mediators in Pathogenesis and Life Cycle Propagation.

    Lu Z, Sankaranarayanan G, Rawlinson KA, Offord V, Brindley PJ, Berriman M and Rinaldi G

    Frontiers in tropical diseases 2021;2;713123

    PUBMED: 36389622; PMC: 7613829; DOI: 10.3389/fitd.2021.713123

  • A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata).

    Nürnberger B, Baird SJE, Čížková D, Bryjová A, Mudd AB, Blaxter ML and Szymura JM

    G3 (Bethesda, Md.) 2021

    PUBMED: 34849761; DOI: 10.1093/g3journal/jkab286

  • An in vitro stem cell model of human epiblast and yolk sac interaction.

    Mackinlay KM, Weatherbee BA, Souza Rosa V, Handford CE, Hudson G, Coorens T, Pereira LV, Behjati S, Vallier L, Shahbazi MN and Zernicka-Goetz M

    eLife 2021;10

    PUBMED: 34403333; DOI: 10.7554/eLife.63930

  • A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance.

    Anisul M, Shilts J, Schwartzentruber J, Hayhurst J, Buniello A, Shaikho E, Zheng J, Holmes M, Ochoa D, Carmona M et al.

    eLife 2021;10

    PUBMED: 34402426; DOI: 10.7554/eLife.69719

  • Group 2 Innate Lymphoid Cells Exhibit Tissue-Specific Dynamic Behaviour During Type 2 Immune Responses.

    Lok LSC, Walker JA, Jolin HE, Scanlon ST, Ishii M, Fallon PG, McKenzie ANJ and Clatworthy MR

    Frontiers in immunology 2021;12;711907

    PUBMED: 34484215; PMC: 8415880; DOI: 10.3389/fimmu.2021.711907

  • Prenatal Diagnosis of Small Supernumerary Marker Chromosome 10 by Array-Based Comparative Genomic Hybridization and Microdissected Chromosome Sequencing.

    Lebedev IN, Karamysheva TV, Elisaphenko EA, Makunin AI, Zhigalina DI, Lopatkina ME, Drozdov GV, Cheremnykh AD, Torkhova NB, Seitova GN et al.

    Biomedicines 2021;9;8

    PUBMED: 34440234; PMC: 8391546; DOI: 10.3390/biomedicines9081030

  • Risk Prediction Using Polygenic Risk Scores for Prevention of Stroke and Other Cardiovascular Diseases.

    Abraham G, Rutten-Jacobs L and Inouye M

    Stroke 2021;STROKEAHA120032619

    PUBMED: 34399584; DOI: 10.1161/STROKEAHA.120.032619

  • RNA sequencing and functional studies of patient-derived cells reveal that neurexin-1 and regulators of this pathway are associated with poor outcomes in Ewing sarcoma.

    Roundhill EA, Chicon-Bosch M, Jeys L, Parry M, Rankin KS, Droop A and Burchill SA

    Cellular oncology (Dordrecht) 2021

    PUBMED: 34403115; DOI: 10.1007/s13402-021-00619-8

  • Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition.

    Nowicki-Osuch K, Zhuang L, Jammula S, Bleaney CW, Mahbubani KT, Devonshire G, Katz-Summercorn A, Eling N, Wilbrey-Clark A, Madissoon E et al.

    Science (New York, N.Y.) 2021;373;6556;760-767

    PUBMED: 34385390; DOI: 10.1126/science.abd1449

  • Patterns of within-host genetic diversity in SARS-CoV-2.

    Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA et al.

    eLife 2021;10

    PUBMED: 34387545; PMC: 8363274; DOI: 10.7554/eLife.66857

  • Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection – Authors’ reply

    Gladstone,R.A., McNally,A., Johnsen,P.J., Samuelsen,O. and Corander,J.

    The Lancet Microbe 2021

    DOI: 10.1016/S2666-5247(21)00176-2

  • The gut microbiome of healthy Vietnamese adults and children is a major reservoir for resistance genes against critical antimicrobials.

    Pereira-Dias J, Nguyen Ngoc Minh C, Tran Thi Hong C, Nguyen Thi Nguyen T, Ha Thanh T, Zellmer C, Chung The H, Pike L, Higginson EE and Baker S

    The Journal of infectious diseases 2021

    PUBMED: 34374428; DOI: 10.1093/infdis/jiab398

  • Cancer Biomarkers in the era of precision oncology: Addressing the needs of patients and health systems.

    Normanno N, Apostolidis K, de Lorenzo F, Beer PA, Henderson R, Sullivan R, Biankin AV, Horgan D and Lawler M

    Seminars in cancer biology 2021;84;293-301

    PUBMED: 34389490; DOI: 10.1016/j.semcancer.2021.08.002

  • Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

    Jacob CG, Thuy-Nhien N, Mayxay M, Maude RJ, Quang HH, Hongvanthong B, Vanisaveth V, Ngo Duc T, Rekol H, van der Pluijm R et al.

    eLife 2021;10

    PUBMED: 34372970; PMC: 8354633; DOI: 10.7554/eLife.62997

  • B-cells are abnormal in psychosocial stress and regulate meningeal myeloid cell activation.

    Lynall ME, Kigar SL, Lehmann ML, DePuyt AE, Tuong ZK, Listwak SJ, Elkahloun AG, Bullmore ET, Herkenham M and Clatworthy MR

    Brain, behavior, and immunity 2021;97;226-238

    PUBMED: 34371135; PMC: 8453122; DOI: 10.1016/j.bbi.2021.08.002

  • Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration.

    Berger DJ, Crellen T, Lamberton PHL, Allan F, Tracey A, Noonan JD, Kabatereine NB, Tukahebwa EM, Adriko M, Holroyd N et al.

    Nature communications 2021;12;1;4776

    PUBMED: 34362894; PMC: 8346512; DOI: 10.1038/s41467-021-24958-0

  • Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle.

    Browne HP, Almeida A, Kumar N, Vervier K, Adoum AT, Viciani E, Dawson NJR, Forster SC, Cormie C, Goulding D and Lawley TD

    Genome biology 2021;22;1;204

    PUBMED: 34348764; PMC: 8340488; DOI: 10.1186/s13059-021-02428-6

  • Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies.

    Alenquer M, Ferreira F, Lousa D, Valério M, Medina-Lopes M, Bergman ML, Gonçalves J, Demengeot J, Leite RB, Lilue J et al.

    PLoS pathogens 2021;17;8;e1009772

    PUBMED: 34352039; PMC: 8341613; DOI: 10.1371/journal.ppat.1009772

  • The genomic history of the Middle East.

    Almarri MA, Haber M, Lootah RA, Hallast P, Al Turki S, Martin HC, Xue Y and Tyler-Smith C

    Cell 2021;184;18;4612-4625.e14

    PUBMED: 34352227; PMC: 8445022; DOI: 10.1016/j.cell.2021.07.013

  • Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages.

    Segawa T, Yonezawa T, Mori H, Akiyoshi A, Allentoft ME, Kohno A, Tokanai F, Willerslev E, Kohno N and Nishihara H

    Royal Society open science 2021;8;8;210518

    PUBMED: 34386259; PMC: 8334828; DOI: 10.1098/rsos.210518

  • Single-cell analysis reveals innate lymphoid cell lineage infidelity in atopic dermatitis.

    Alkon N, Bauer W, Krausgruber T, Goh I, Griss J, Nguyen V, Reininger B, Bangert C, Staud C, Brunner PM et al.

    The Journal of allergy and clinical immunology 2021

    PUBMED: 34363841; DOI: 10.1016/j.jaci.2021.07.025

  • Ancestral physical stress and later immune gene family expansions shaped bivalve mollusc evolution.

    Regan T, Stevens L, Peñaloza C, Houston RD, Robledo D and Bean TP

    Genome biology and evolution 2021

    PUBMED: 34343278; DOI: 10.1093/gbe/evab177

  • Chemogenomics identifies acetyl-coenzyme A synthetase as a target for malaria treatment and prevention.

    Summers RL, Pasaje CFA, Pisco JP, Striepen J, Luth MR, Kumpornsin K, Carpenter EF, Munro JT, Lin D, Plater A et al.

    Cell chemical biology 2021;29;2;191-201.e8

    PUBMED: 34348113; PMC: 8878317; DOI: 10.1016/j.chembiol.2021.07.010

  • Using de novo assembly to identify structural variation of eight complex immune system gene regions.

    Zhang JY, Roberts H, Flores DSC, Cutler AJ, Brown AC, Whalley JP, Mielczarek O, Buck D, Lockstone H, Xella B et al.

    PLoS computational biology 2021;17;8;e1009254

    PUBMED: 34343164; PMC: 8363018; DOI: 10.1371/journal.pcbi.1009254

  • Genomic insights into the diversity, virulence and resistance of Klebsiella pneumoniae extensively drug resistant clinical isolates.

    Lee AHY, Porto WF, de Faria C, Dias SC, Alencar SA, Pickard DJ, Hancock REW and Franco OL

    Microbial genomics 2021;7;8

    PUBMED: 34424159; DOI: 10.1099/mgen.0.000613

  • Metastatic Cutaneous Melanoma in a White African Lioness (Panthera leo).

    van der Weyden L, Caldwell P, van Rooyen L, Mitchell EP and O'Dell N

    Veterinary sciences 2021;8;8

    PUBMED: 34437476; DOI: 10.3390/vetsci8080154

  • ZTTK syndrome: Clinical and molecular findings of 15 cases and a review of the literature.

    Kushary ST, Revah-Politi A, Barua S, Ganapathi M, Accogli A, Aggarwal V, Brunetti-Pierri N, Cappuccio G, Capra V, Fagerberg CR et al.

    American journal of medical genetics. Part A 2021;185;12;3740-3753

    PUBMED: 34331327; PMC: 8595531; DOI: 10.1002/ajmg.a.62445

  • Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.

    O'Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B et al.

    Virus evolution 2021;7;2;veab064

    PUBMED: 34527285; PMC: 8344591; DOI: 10.1093/ve/veab064

  • Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology.

    Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M and Ashford B

    Briefings in bioinformatics 2021

    PUBMED: 34329375; DOI: 10.1093/bib/bbab259

  • Draft Genome Sequence of a blaKPC-2-Carrying Citrobacter braakii Isolate from Pediatric Hospital Wastewater in Peru.

    Salvatierra G, Dávila-Barclay A, Ayzanoa B, Cuicapuza D, Santillán-Salas C and Tsukayama P

    Microbiology resource announcements 2021;10;30;e0056921

    PUBMED: 34323602; DOI: 10.1128/MRA.00569-21

  • Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

    Audain E, Wilsdon A, Breckpot J, Izarzugaza JM, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H et al.

    PLoS genetics 2021;17;7;e1009679

    PUBMED: 34324492; DOI: 10.1371/journal.pgen.1009679

  • METTL1-mediated m7G modification of Arg-TCT tRNA drives oncogenic transformation.

    Orellana EA, Liu Q, Yankova E, Pirouz M, De Braekeleer E, Zhang W, Lim J, Aspris D, Sendinc E, Garyfallos DA et al.

    Molecular cell 2021

    PUBMED: 34352207; DOI: 10.1016/j.molcel.2021.06.031

  • The Cancer Therapy-Related Clonal Hematopoiesis Driver Gene Ppm1d Promotes Inflammation and Non-Ischemic Heart Failure in Mice.

    Yura Y, Miura-Yura E, Katanasaka Y, Min KD, Chavkin NW, Polizio AH, Ogawa H, Horitani K, Doviak H, Evans MA et al.

    Circulation research 2021

    PUBMED: 34315245; DOI: 10.1161/CIRCRESAHA.121.319314

  • Dynamic cell contacts between periportal mesenchyme and ductal epithelium act as a rheostat for liver cell proliferation.

    Cordero-Espinoza L, Dowbaj AM, Kohler TN, Strauss B, Sarlidou O, Belenguer G, Pacini C, Martins NP, Dobie R, Wilson-Kanamori JR et al.

    Cell stem cell 2021

    PUBMED: 34343491; DOI: 10.1016/j.stem.2021.07.002

  • Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data.

    Paganini JA, Plantinga NL, Arredondo-Alonso S, Willems RJL and Schürch AC

    Microorganisms 2021;9;8

    PUBMED: 34442692; PMC: 8400445; DOI: 10.3390/microorganisms9081613

  • The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite.

    Zhang M, Wang C, Oberstaller J, Thomas P, Otto TD, Casandra D, Boyapalle S, Adapa SR, Xu S, Button-Simons K et al.

    Nature communications 2021;12;1;4563

    PUBMED: 34315897; DOI: 10.1038/s41467-021-24814-1

  • The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758.

    Dunn JC, Hamer KC, Morris AJ, Grice PV, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J et al.

    Wellcome open research 2021;6;191

    PUBMED: 39021440; PMC: 11252641; DOI: 10.12688/wellcomeopenres.17060.1

  • Dissecting indirect genetic effects from peers in laboratory mice.

    Baud A, Casale FP, Barkley-Levenson AM, Farhadi N, Montillot C, Yalcin B, Nicod J, Palmer AA and Stegle O

    Genome biology 2021;22;1;216

    PUBMED: 34311762; DOI: 10.1186/s13059-021-02415-x

  • Editorial: Brown Adipose Tissue: From Heat Production in Rodents to Metabolic Health in Humans.

    Chondronikola M, Bartelt A, Vidal-Puig A and Virtanen KA

    Frontiers in endocrinology 2021;12;739065

    PUBMED: 34381425; PMC: 8350568; DOI: 10.3389/fendo.2021.739065

  • Linked surveillance and genetic data uncovers programmatically relevant geographic scale of Guinea worm transmission in Chad.

    Ribado JV, Li N, Thiele E, Lyons H, Cotton JA, Weiss A, Tchindebet Ouakou P, Moundai T, Zirimwabagabo H, Guagliardo SAJ et al.

    PLoS neglected tropical diseases 2021;15;7;e0009609

    PUBMED: 34310598; DOI: 10.1371/journal.pntd.0009609

  • The clinical importance of tandem exon duplication-derived substitutions.

    Martinez Gomez L, Pozo F, Walsh TA, Abascal F and Tress ML

    Nucleic acids research 2021

    PUBMED: 34302486; DOI: 10.1093/nar/gkab623

  • Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

    Stark Z, Foulger RE, Williams E, Thompson BA, Patel C, Lunke S, Snow C, Leong IUS, Puzriakova A, Daugherty LC et al.

    American journal of human genetics 2021

    PUBMED: 34329581; DOI: 10.1016/j.ajhg.2021.06.020

  • Making Research Flourish through ESPGHAN: A Position Paper from the ESPGHAN Special Interest Group for Basic and Translational Research.

    Gasparetto M, Strisciuglio C, Assa A, Gerasimidis K, Giachero F, Novak J, Robinson P, Tél B, Zilbauer M and Jenke A

    Journal of pediatric gastroenterology and nutrition 2021

    PUBMED: 34310437; DOI: 10.1097/MPG.0000000000003250

  • miR-200 deficiency promotes lung cancer metastasis by activating Notch signaling in cancer-associated fibroblasts.

    Xue B, Chuang CH, Prosser HM, Fuziwara CS, Chan C, Sahasrabudhe N, Kühn M, Wu Y, Chen J, Biton A et al.

    Genes & development 2021

    PUBMED: 34301766; DOI: 10.1101/gad.347344.120

  • Shorter leukocyte telomere length is associated with adverse COVID-19 outcomes: A cohort study in UK Biobank.

    Wang Q, Codd V, Raisi-Estabragh Z, Musicha C, Bountziouka V, Kaptoge S, Allara E, Angelantonio ED, Butterworth AS, Wood AM et al.

    EBioMedicine 2021;70;103485

    PUBMED: 34304048; PMC: 8299112; DOI: 10.1016/j.ebiom.2021.103485

  • Signatures of TSPAN8 variants associated with human metabolic regulation and diseases.

    De T, Goncalves A, Speed D, Froguel P, NFBC consortium, Gaffney DJ, Johnson MR, Jarvelin MR and Coin LJ

    iScience 2021;24;8;102893

    PUBMED: 34401672; PMC: 8355918; DOI: 10.1016/j.isci.2021.102893

  • Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence.

    Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B et al.

    Science (New York, N.Y.) 2021

    PUBMED: 34301854; DOI: 10.1126/science.abj0113

  • Evidence generation and reproducibility in cell and gene therapy research: A call to action.

    Abou-El-Enein M, Angelis A, Appelbaum FR, Andrews NC, Bates SE, Bierman AS, Brenner MK, Cavazzana M, Caligiuri MA, Clevers H et al.

    Molecular therapy. Methods & clinical development 2021;22;11-14

    PUBMED: 34377737; PMC: 8322039; DOI: 10.1016/j.omtm.2021.06.012

  • Using genomics to examine the persistence of Streptococcus pneumoniae serotype 19A in Ireland and the emergence of a sub-clade associated with vaccine failures.

    Corcoran M, Mereckiene J, Cotter S, Murchan S, Lo SW, McGee L, Breiman RF, Cunney R, Humphreys H, Bentley SD and Gladstone RA

    Vaccine 2021;39;35;5064-5073

    PUBMED: 34301430; DOI: 10.1016/j.vaccine.2021.06.017

  • Weight shapes the intestinal microbiome in preterm infants: results of a prospective observational study.

    Heida FH, Kooi EMW, Wagner J, Nguyen TY, Hulscher JBF, van Zoonen AGJF, Bos AF, Harmsen HJM and de Goffau MC

    BMC microbiology 2021;21;1;219

    PUBMED: 34289818; DOI: 10.1186/s12866-021-02279-y

  • The PROTACtable genome.

    Schneider M, Radoux CJ, Hercules A, Ochoa D, Dunham I, Zalmas LP, Hessler G, Ruf S, Shanmugasundaram V, Hann MM et al.

    Nature reviews. Drug discovery 2021

    PUBMED: 34285415; DOI: 10.1038/s41573-021-00245-x

  • Modelling PNPLA3-Associated Non-Alcoholic Fatty Liver Disease Using Human Induced Pluripotent Stem Cells.

    Tilson SG, Morell CM, Lenaerts AS, Park SB, Hu Z, Jenkins B, Koulman A, Liang TJ and Vallier L

    Hepatology (Baltimore, Md.) 2021

    PUBMED: 34288010; DOI: 10.1002/hep.32063

  • Genetic screens identify a context-specific PI3K/p27Kip1 node driving extrahepatic biliary cancer.

    Falcomata C, Barthel S, Ulrich A, Diersch S, Veltkamp C, Rad L, Boniolo F, Solar M, Steiger K, Seidler B et al.

    Cancer discovery 2021

    PUBMED: 34282029; DOI: 10.1158/2159-8290.CD-21-0209

  • Genomic insights into myasthenia gravis identify distinct immunological mechanisms in early and late onset disease.

    Handunnetthi L, Knezevic B, Kasela S, Burnham KL, Milani L, Irani SR, Fang H and Knight JC

    Annals of neurology 2021

    PUBMED: 34279044; DOI: 10.1002/ana.26169

  • New Data on Organization and Spatial Localization of B-Chromosomes in Cell Nuclei of the Yellow-Necked Mouse Apodemus flavicollis.

    Karamysheva T, Romanenko S, Makunin A, Rajičić M, Bogdanov A, Trifonov V, Blagojević J, Vujošević M, Orishchenko K and Rubtsov N

    Cells 2021;10;7

    PUBMED: 34359988; PMC: 8305704; DOI: 10.3390/cells10071819

  • Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance.

    Gapp K, Parada GE, Gross F, Corcoba A, Kaur J, Grau E, Hemberg M, Bohacek J and Miska EA

    iScience 2021;24;8;102870

    PUBMED: 34386731; PMC: 8346661; DOI: 10.1016/j.isci.2021.102870

  • Genome Sequences of 15 SARS-CoV-2 Sublineage B.1.617.2 Strains in Bangladesh.

    Afrad MH, Khan MH, Rahman SIA, Bin Manjur OH, Hossain M, Alam AN, Khan FI, Afreen N, Haque FT, Thomson NR et al.

    Microbiology resource announcements 2021;10;28;e0056021

    PUBMED: 34264100; DOI: 10.1128/MRA.00560-21

  • The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci.

    D'Aeth JC, van der Linden MP, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS et al.

    eLife 2021;10

    PUBMED: 34259624; PMC: 8321556; DOI: 10.7554/eLife.67113

  • Germline ATM variants predispose to melanoma: a joint analysis across the GenoMEL and MelaNostrum consortia.

    Dalmasso B, Pastorino L, Nathan V, Shah NN, Palmer JM, Howlie M, Johansson PA, Freedman ND, Carter BD, Beane-Freeman L et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2021

    PUBMED: 34262154; DOI: 10.1038/s41436-021-01240-8

  • Increased Virulence of Outer Membrane Porin Mutants of Mycobacterium abscessus.

    de Moura VCN, Verma D, Everall I, Brown KP, Belardinelli JM, Shanley C, Stapleton M, Parkhill J, Floto RA, Ordway DJ and Jackson M

    Frontiers in microbiology 2021;12;706207

    PUBMED: 34335541; PMC: 8317493; DOI: 10.3389/fmicb.2021.706207

  • An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.

    MalariaGEN, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC et al.

    Wellcome open research 2021;6;42

    PUBMED: 33824913; PMC: 8008441; DOI: 10.12688/wellcomeopenres.16168.2

  • Italian public's views on sharing genetic information and medical information: findings from the 'Your DNA, Your Say' study.

    Romano V, Milne R and Mascalzoni D

    Wellcome open research 2021;6;180

    PUBMED: 35233468; PMC: 8855014; DOI: 10.12688/wellcomeopenres.16909.1

  • Activation of the hypothalamic-pituitary-adrenal axis by exogenous and endogenous GDF15.

    Cimino I, Kim H, Tung YCL, Pedersen K, Rimmington D, Tadross JA, Kohnke SN, Neves-Costa A, Barros A, Joaquim S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2021;118;27

    PUBMED: 34187898; DOI: 10.1073/pnas.2106868118

  • FANCD2-associated nuclease 1 partially compensates for the lack of Exonuclease 1 in mismatch repair.

    Kratz K, Artola-Borán M, Kobayashi-Era S, Koh G, Oliveira G, Kobayashi S, Oliveira A, Zou X, Richter J, Tsuda M et al.

    Molecular and cellular biology 2021;MCB0030321

    PUBMED: 34228493; DOI: 10.1128/MCB.00303-21

  • Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision.

    Watson JA, Ndila CM, Uyoga S, Macharia A, Nyutu G, Mohammed S, Ngetsa C, Mturi N, Peshu N, Tsofa B et al.

    eLife 2021;10

    PUBMED: 34225842; PMC: 8315799; DOI: 10.7554/eLife.69698

  • Predictive immune checkpoint blockade classifiers identify tumors responding to inhibition of PD-1 and/or CTLA-4.

    Krijgsman O, Kemper K, Boshuizen J, Vredevoogd DW, Rozeman EA, Ibanez Molero S, de Bruijn B, Cornelissen-Steijger P, Shahrabi A, Del Castillo Velasco-Herrera M et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2021

    PUBMED: 34230026; DOI: 10.1158/1078-0432.CCR-20-4218

  • Biological basis for novel mesothelioma therapies.

    Obacz J, Yung H, Shamseddin M, Linnane E, Liu X, Azad AA, Rassl DM, Fairen-Jimenez D, Rintoul RC, Nikolić MZ and Marciniak SJ

    British journal of cancer 2021

    PUBMED: 34226685; DOI: 10.1038/s41416-021-01462-2

  • Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation.

    Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C and Göttgens B

    Genome biology 2021;22;1;197

    PUBMED: 34225769; DOI: 10.1186/s13059-021-02414-y

  • Effects of adiposity on the human plasma proteome: observational and Mendelian randomisation estimates.

    Goudswaard LJ, Bell JA, Hughes DA, Corbin LJ, Walter K, Davey Smith G, Soranzo N, Danesh J, Di Angelantonio E, Ouwehand WH et al.

    International journal of obesity (2005) 2021

    PUBMED: 34226637; DOI: 10.1038/s41366-021-00896-1

  • Somatic mutations provide important and unique insights into the biology of complex diseases.

    Olafsson S and Anderson CA

    Trends in genetics : TIG 2021;37;10;872-881

    PUBMED: 34226062; DOI: 10.1016/j.tig.2021.06.012

  • FUT6 deficiency compromises basophil function by selectively abrogating their sialyl-Lewis x expression.

    Puan KJ, San Luis B, Yusof N, Kumar D, Andiappan AK, Lee W, Cajic S, Vuckovic D, Chan J, Döllner T et al.

    Communications biology 2021;4;1;832

    PUBMED: 34215830; DOI: 10.1038/s42003-021-02295-8

  • More than just acral melanoma: the controversies of defining the disease.

    Bernardes SS, Ferreira I, Elder DE, Nobre AB, Martínez-Said H, Adams DJ, Robles-Espinoza CD and Possik PA

    The journal of pathology. Clinical research 2021

    PUBMED: 34213090; DOI: 10.1002/cjp2.233

  • CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

    Nicholls SM, Poplawski R, Bull MJ, Underwood A, Chapman M, Abu-Dahab K, Taylor B, Colquhoun RM, Rowe WPM, Jackson B et al.

    Genome biology 2021;22;1;196

    PUBMED: 34210356; PMC: 8247108; DOI: 10.1186/s13059-021-02395-y

  • Going home: the challenges and rewards of genetics research in Mexico.

    Robles-Espinoza CD

    Nature genetics 2021;53;7;937-939

    PUBMED: 34099929; DOI: 10.1038/s41588-021-00876-1

  • GTTs and ITTs in mice: simple tests, complex answers.

    Virtue S and Vidal-Puig A

    Nature metabolism 2021;3;7;883-886

    PUBMED: 34117483; DOI: 10.1038/s42255-021-00414-7

  • Homologous Recombination Deficiency in Pancreatic Cancer: A Systematic Review and Prevalence Meta-Analysis.

    Casolino R, Paiella S, Azzolina D, Beer PA, Corbo V, Lorenzoni G, Gregori D, Golan T, Braconi C, Froeling FEM et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2021;JCO2003238

    PUBMED: 34197182; DOI: 10.1200/JCO.20.03238

  • Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv.

    Sanoussi CN, Coscolla M, Ofori-Anyinam B, Otchere ID, Antonio M, Niemann S, Parkhill J, Harris S, Yeboah-Manu D, Gagneux S et al.

    Microbial genomics 2021;7;7

    PUBMED: 34241588; DOI: 10.1099/mgen.0.000437

  • Molecular pathology of skin adnexal tumors.

    Plotzke JM, Adams DJ and Harms PW

    Histopathology 2021

    PUBMED: 34197659; DOI: 10.1111/his.14441

  • Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome.

    Cousin MA, Creighton BA, Breau KA, Spillmann RC, Torti E, Dontu S, Tripathi S, Ajit D, Edwards RJ, Afriyie S et al.

    Nature genetics 2021

    PUBMED: 34211179; DOI: 10.1038/s41588-021-00886-z

  • Public trust and genomic medicine in Canada and the UK.

    Savić-Kallesøe S, Middleton A and Milne R

    Wellcome open research 2021;6;124

    PUBMED: 34235273; PMC: 8215560; DOI: 10.12688/wellcomeopenres.16831.2

  • Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates.

    Ndegwa DN, Kundu P, Hostetler JB, Marin-Menendez A, Sanderson T, Mwikali K, Verzier LH, Coyle R, Adjalley S and Rayner JC

    PLoS pathogens 2021;17;7;e1008864

    PUBMED: 34197567; DOI: 10.1371/journal.ppat.1008864

  • A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels.

    Urbonaite G, Lee JTH, Liu P, Parada GE, Hemberg M and Acar M

    Communications biology 2021;4;1;822

    PUBMED: 34193958; DOI: 10.1038/s42003-021-02320-w

  • The potential effects of microplastics on human health: What is known and what is unknown.

    Blackburn K and Green D

    Ambio 2021

    PUBMED: 34185251; DOI: 10.1007/s13280-021-01589-9

  • Diversity and Within-Host Evolution of Leishmania donovani from Visceral Leishmaniasis Patients with and without HIV Coinfection in Northern Ethiopia.

    Franssen SU, Takele Y, Adem E, Sanders MJ, Müller I, Kropf P and Cotton JA

    mBio 2021;e0097121

    PUBMED: 34182785; DOI: 10.1128/mBio.00971-21

  • Genomic and transcriptomic analyses of breast cancer primaries and matched metastases in AURORA, the Breast International Group (BIG) molecular screening initiative.

    Aftimos P, Oliveira M, Irrthum A, Fumagalli D, Sotiriou C, Nili Gal-Yam E, Robson ME, Ndozeng J, Di Leo A, Ciruelos EM et al.

    Cancer discovery 2021

    PUBMED: 34183353; DOI: 10.1158/2159-8290.CD-20-1647

  • Loss of miR-183/96 alters synaptic strength via pre- and postsynaptic mechanisms at a central synapse.

    Krohs C, Körber C, Ebbers L, Altaf F, Hollje G, Hoppe S, Dörflinger Y, Prosser HM and Nothwang HG

    The Journal of neuroscience : the official journal of the Society for Neuroscience 2021

    PUBMED: 34193555; DOI: 10.1523/JNEUROSCI.0139-20.2021

  • Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution.

    Peart CR, Williams C, Pophaly SD, Neely BA, Gulland FMD, Adams DJ, Ng BL, Cheng W, Goebel ME, Fedrigo O et al.

    Molecular ecology resources 2021;21;7;2455-2470

    PUBMED: 34097816; DOI: 10.1111/1755-0998.13443

  • Evaluating Very Deep Convolutional Neural Networks for Nucleus Segmentation from Brightfield Cell Microscopy Images.

    Ali MAS, Misko O, Salumaa SO, Papkov M, Palo K, Fishman D and Parts L

    SLAS discovery : advancing life sciences R & D 2021;24725552211023214

    PUBMED: 34167359; DOI: 10.1177/24725552211023214

  • Optimizing expression quantitative trait locus mapping workflows for single-cell studies.

    Cuomo ASE, Alvari G, Azodi CB, single-cell eQTLGen consortium, McCarthy DJ and Bonder MJ

    Genome biology 2021;22;1;188

    PUBMED: 34167583; PMC: 8223300; DOI: 10.1186/s13059-021-02407-x

  • Successful treatment of early cutaneous squamous cell carcinoma with hypofractionated radiation therapy in an African lion (Panthera leo).

    Van der Weyden L, O'Dell N, Avenant A, Pazzi P and Koeppel KN

    Journal of the South African Veterinary Association 2021;92;0;e1-e6

    PUBMED: 34212735; PMC: 8252176; DOI: 10.4102/jsava.v92i0.2134

  • Cross-species comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma.

    Wong K, Ludwig L, Krijgsman O, Adams DJ, Wood GA and van der Weyden L

    Disease models & mechanisms 2021

    PUBMED: 34160004; DOI: 10.1242/dmm.049044

  • Single cell derived mRNA signals across human kidney tumors.

    Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR et al.

    Nature communications 2021;12;1;3896

    PUBMED: 34162837; PMC: 8222373; DOI: 10.1038/s41467-021-23949-5

  • Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila.

    Machado HE, Bergland A, Taylor RW, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL et al.

    eLife 2021;10

    PUBMED: 34155971; DOI: 10.7554/eLife.67577

  • Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium.

    Sridhar S, Forrest S, Pickard D, Cormie C, Lees EA, Thomson NR, Dougan G and Baker S

    mBio 2021;e0109321

    PUBMED: 34154399; DOI: 10.1128/mBio.01093-21

  • No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study.

    Roach M, Cantu A, Vieri MK, Cotten M, Kellam P, Phan M, Hoek LV, Mandro M, Tepage F, Mambandu G et al.

    Pathogens (Basel, Switzerland) 2021;10;7

    PUBMED: 34206564; DOI: 10.3390/pathogens10070787

  • The clinicopathologic spectrum and genomic landscape of de-/trans-differentiated melanoma.

    Ferreira I, Droop A, Edwards O, Wong K, Harle V, Habeeb O, Gharpuray-Pandit D, Houghton J, Wiedemeyer K, Mentzel T et al.

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2021

    PUBMED: 34155350; DOI: 10.1038/s41379-021-00857-z

  • Genome-enabled discovery of evolutionary divergence in brains and behavior.

    Patil C, Sylvester JB, Abdilleh K, Norsworthy MW, Pottin K, Malinsky M, Bloomquist RF, Johnson ZV, McGrath PT and Streelman JT

    Scientific reports 2021;11;1;13016

    PUBMED: 34155279; DOI: 10.1038/s41598-021-92385-8

  • Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi.

    Tamazian G, Dobrynin P, Zhuk A, Zhernakova DV, Perelman PL, Serdyukova NA, Graphodatsky AS, Komissarov A, Kliver S, Cherkasov N et al.

    The Journal of heredity 2021

    PUBMED: 34146095; DOI: 10.1093/jhered/esab036

  • Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides.

    Blundell-Hunter G, Enright MC, Negus D, Dorman MJ, Beecham GE, Pickard DJ, Wintachai P, Voravuthikunchai SP, Thomson NR and Taylor PW

    Frontiers in cellular and infection microbiology 2021;11;686090

    PUBMED: 34222050; PMC: 8253255; DOI: 10.3389/fcimb.2021.686090

  • Gut-microbiota-derived extracellular vesicles: Overlooked mediators in host-helminth interactions?

    Cortés A, Sotillo J, Rinaldi G and Cantacessi C

    Trends in parasitology 2021;37;8;690-693

    PUBMED: 34154932; DOI: 10.1016/j.pt.2021.05.009

  • RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset.

    Guillermo R, Elena V, Martin K and Chris W

    Bioinformatics (Oxford, England) 2021

    PUBMED: 34145897; DOI: 10.1093/bioinformatics/btab456

  • A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

    Molè MA, Coorens THH, Shahbazi MN, Weberling A, Weatherbee BAT, Gantner CW, Sancho-Serra C, Richardson L, Drinkwater A, Syed N et al.

    Nature communications 2021;12;1;3679

    PUBMED: 34140473; DOI: 10.1038/s41467-021-23758-w

  • Discovery and features of an alkylating signature in colorectal cancer.

    Gurjao C, Zhong R, Haruki K, Li YY, Spurr LF, Lee-Six H, Reardon B, Ugai T, Zhang X, Cherniack AD et al.

    Cancer discovery 2021

    PUBMED: 34140290; DOI: 10.1158/2159-8290.CD-20-1656

  • Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element.

    Baxter JS, Johnson N, Tomczyk K, Gillespie A, Maguire S, Brough R, Fachal L, Michailidou K, Bolla MK, Wang Q et al.

    American journal of human genetics 2021

    PUBMED: 34146516; DOI: 10.1016/j.ajhg.2021.05.013

  • Peopling of the Americas as inferred from ancient genomics.

    Willerslev E and Meltzer DJ

    Nature 2021;594;7863;356-364

    PUBMED: 34135521; DOI: 10.1038/s41586-021-03499-y

  • Plasma Proteomics of Renal Function: A Trans-ethnic Meta-analysis and Mendelian Randomization Study.

    Matías-García P, Wilson R, Guo Q, Zaghlool S, Eales J, Xu X, Charchar F, Dormer J, Maalmi H, Schlosser P et al.

    Journal of the American Society of Nephrology : JASN 2021

    PUBMED: 34135082; PMC: 8425654; DOI: 10.1681/ASN.2020071070

  • Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity.

    Williams DW, Greenwell-Wild T, Brenchley L, Dutzan N, Overmiller A, Sawaya AP, Webb S, Martin D, NIDCD/NIDCR Genomics and Computational Biology Core, Hajishengallis G et al.

    Cell 2021;184;15;4090-4104.e15

    PUBMED: 34129837; PMC: 8359928; DOI: 10.1016/j.cell.2021.05.013

  • Prognostic implications of troponin T variations in inherited cardiomyopathies using systems biology.

    Shakur R, Ochoa JP, Robinson AJ, Niroula A, Chandran A, Rahman T, Vihinen M and Monserrat L

    NPJ genomic medicine 2021;6;1;47

    PUBMED: 34127679; DOI: 10.1038/s41525-021-00204-w

  • Obtaining purified human intestinal epithelia for single-cell analysis and organoid culture.

    Ross ADB, Perrone F, Elmentaite R, Teichmann SA and Zilbauer M

    STAR protocols 2021;2;2;100597

    PUBMED: 34169291; PMC: 8209738; DOI: 10.1016/j.xpro.2021.100597

  • Rare variants in KDR, encoding VEGF Receptor 2, are associated with tetralogy of Fallot.

    Škorić-Milosavljević D, Lahrouchi N, Bosada FM, Dombrowsky G, Williams SG, Lesurf R, Tjong FVY, Walsh R, El Bouchikhi I, Breckpot J et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2021

    PUBMED: 34113005; DOI: 10.1038/s41436-021-01212-y

  • Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis.

    Yarra T, Ramesh K, Blaxter M, Hüning A, Melzner F and Clark MS

    BMC genomics 2021;22;1;437

    PUBMED: 34112105; PMC: 8194122; DOI: 10.1186/s12864-021-07751-7

  • The effect of recombination on the evolution of a population of Neisseria meningitidis.

    MacAlasdair N, Pesonen M, Brynildsrud O, Eldholm V, Kristiansen PA, Corander J, Caugant DA and Bentley SD

    Genome research 2021

    PUBMED: 34108268; DOI: 10.1101/gr.264465.120

  • Genetic and morphological estimates of androgen exposure predict social deficits in multiple neurodevelopmental disorder cohorts.

    McKenna BG, Huang Y, Vervier K, Hofammann D, Cafferata M, Al-Momani S, Lowenthal F, Zhang A, Koh JY, Thenuwara S et al.

    Molecular autism 2021;12;1;43

    PUBMED: 34108004; DOI: 10.1186/s13229-021-00450-w

  • The gut microbiota as a therapeutic target for obesity: a scoping review.

    Santos-Paulo S, Costello S, Forster S, Travis S and Bryant R

    Nutrition research reviews 2021;1-33

    PUBMED: 34100344; DOI: 10.1017/S0954422421000160

  • Analysis of single-cell RNA sequencing data based on autoencoders.

    Tangherloni A, Ricciuti F, Besozzi D, Liò P and Cvejic A

    BMC bioinformatics 2021;22;1;309

    PUBMED: 34103004; PMC: 8186186; DOI: 10.1186/s12859-021-04150-3

  • Extensive remodeling of the extracellular matrix during aging contributes to age-dependent impairments of muscle stem cell functionality.

    Schüler SC, Kirkpatrick JM, Schmidt M, Santinha D, Koch P, Di Sanzo S, Cirri E, Hemberg M, Ori A and von Maltzahn J

    Cell reports 2021;35;10;109223

    PUBMED: 34107247; DOI: 10.1016/j.celrep.2021.109223

  • Arterolane-piperaquine-mefloquine versus arterolane-piperaquine and artemether-lumefantrine in the treatment of uncomplicated Plasmodium falciparum malaria in Kenyan children: a single-centre, open-label, randomised, non-inferiority trial.

    Hamaluba M, van der Pluijm RW, Weya J, Njuguna P, Ngama M, Kalume P, Mwambingu G, Ngetsa C, Wambua J, Boga M et al.

    The Lancet. Infectious diseases 2021

    PUBMED: 34111412; DOI: 10.1016/S1473-3099(20)30929-4

  • Endosymbiont Capture, a Repeated Process of Endosymbiont Transfer with Replacement in Trypanosomatids Angomonas spp.

    Skalický T, Alves JMP, Morais AC, Režnarová J, Butenko A, Lukeš J, Serrano MG, Buck GA, Teixeira MMG, Camargo EP et al.

    Pathogens (Basel, Switzerland) 2021;10;6

    PUBMED: 34200026; PMC: 8229890; DOI: 10.3390/pathogens10060702

  • A map of transcriptional heterogeneity and regulatory variation in human microglia.

    Young AMH, Kumasaka N, Calvert F, Hammond TR, Knights A, Panousis N, Park JS, Schwartzentruber J, Liu J, Kundu K et al.

    Nature genetics 2021

    PUBMED: 34083789; DOI: 10.1038/s41588-021-00875-2

  • Practical segmentation of nuclei in brightfield cell images with neural networks trained on fluorescently labelled samples.

    Fishman D, Salumaa SO, Majoral D, Laasfeld T, Peel S, Wildenhain J, Schreiner A, Palo K and Parts L

    Journal of microscopy 2021

    PUBMED: 34081320; DOI: 10.1111/jmi.13038

  • Scientists on a RAMPAGE to find apicomplexan transcription start sites.

    Hoshizaki J and Lee MCS

    Nature reviews. Microbiology 2021;19;8;483

    PUBMED: 34083794; DOI: 10.1038/s41579-021-00587-8

  • Clinical Exome Sequencing Enables Congenital Sialidosis Type II Diagnosis in Two Siblings Presenting with Unreported Clinical Features from a Rare Homozygous Sequence Variant p.(Tyr370Cys) in NEU1

    Flores-Contreras,E., García-Ortiz,J.E., Robles-Espinoza,C.D., Zomosa-Signoret,V., Becerra-Solano,L., Vidaltamayo,R., Castaneda-García,C., Esparza-García,E., Molina-Aguilar,C., Hernández-Orozco,A.A. and Córdova-Fletes,C.;

    Molecular Syndromology 2021

    PMC: 8339489; DOI: 10.1159/000515081; URL: https://doi.org/10.1159/000515081

  • Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization.

    Abd El Ghany M, Barquist L, Clare S, Brandt C, Mayho M, Joffre E, Sjöling Å, Turner AK, Klena JD, Kingsley RA et al.

    Microbial genomics 2021;7;6

    PUBMED: 34110281; DOI: 10.1099/mgen.0.000554

  • Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection.

    Dorman MJ, Thomson NR and Campos J

    Microbial genomics 2021;7;6

    PUBMED: 34128784; PMC: 8461468; DOI: 10.1099/mgen.0.000580

  • Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.

    Page AJ, Mather AE, Le-Viet T, Meader EJ, Alikhan NF, Kay GL, de Oliveira Martins L, Aydin A, Baker DJ, Trotter AJ et al.

    Microbial genomics 2021;7;6

    PUBMED: 34184982; DOI: 10.1099/mgen.0.000589

  • gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae.

    Fennell TG, Blackwell GA, Thomson NR and Dorman MJ

    Microbial genomics 2021;7;6

    PUBMED: 34100695; DOI: 10.1099/mgen.0.000594

  • Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains.

    Seth-Smith HMB, Bénard A, Bruisten SM, Versteeg B, Herrmann B, Kok J, Carter I, Peuchant O, Bébéar C, Lewis DA et al.

    Microbial genomics 2021;7;6

    PUBMED: 34184981; DOI: 10.1099/mgen.0.000599

  • SARS-CoV-2 variants, spike mutations and immune escape.

    Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A, COVID-19 Genomics UK (COG-UK) Consortium et al.

    Nature reviews. Microbiology 2021;19;7;409-424

    PUBMED: 34075212; PMC: 8167834; DOI: 10.1038/s41579-021-00573-0

  • Through the gut, down the drain.

    Beresford-Jones BS and Shao Y

    Nature reviews. Microbiology 2021;19;6;345

    PUBMED: 33846599; PMC: 8040002; DOI: 10.1038/s41579-021-00558-z

  • The trans-ancestral genomic architecture of glycemic traits.

    Chen J, Spracklen CN, Marenne G, Varshney A, Corbin LJ, Luan J, Willems SM, Wu Y, Zhang X, Horikoshi M et al.

    Nature genetics 2021

    PUBMED: 34059833; DOI: 10.1038/s41588-021-00852-9

  • A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus.

    Makunin A, Korlević P, Park N, Goodwin S, Waterhouse RM, von Wyschetzki K, Jacob CG, Davies R, Kwiatkowski D, St Laurent B et al.

    Molecular ecology resources 2021

    PUBMED: 34053186; DOI: 10.1111/1755-0998.13436

  • Developmental bifurcation of human T follicular regulatory cells.

    Kumar S, Fonseca VR, Ribeiro F, Basto AP, Água-Doce A, Monteiro M, Elessa D, Miragaia RJ, Gomes T, Piaggio E et al.

    Science immunology 2021;6;59

    PUBMED: 34049865; DOI: 10.1126/sciimmunol.abd8411

  • Mayfly taxonomy (Arthropoda: Hexapoda: Ephemeroptera) during the first two decades of the twenty-first century and the concentration of taxonomic publishing

    Jacobus,L.M., Salles,F.F., Price,B., Pereira-Da-Conceicoa,l., Suter,P.J., Molineri,C., Tiunova,T.M. and Sartori,M.

    Zootaxa 2021;4979;1;25-30

    DOI: 10.11646/zootaxa.4979.1.6

  • A single-cell atlas of Plasmodium falciparum transmission through the mosquito.

    Real E, Howick VM, Dahalan FA, Witmer K, Cudini J, Andradi-Brown C, Blight J, Davidson MS, Dogga SK, Reid AJ et al.

    Nature communications 2021;12;1;3196

    PUBMED: 34045457; PMC: 8159942; DOI: 10.1038/s41467-021-23434-z

  • Clonal hematopoiesis and therapy-related myeloid neoplasms following neuroblastoma treatment.

    Coorens THH, Collord G, Lu W, Mitchell E, Ijaz J, Roberts T, Oliver TRW, Burke GAA, Gattens M, Dickens E et al.

    Blood 2021;137;21;2992-2997

    PUBMED: 33598691; PMC: 8160503; DOI: 10.1182/blood.2020010150

  • Lost and Found: Piwi and Argonaute Pathways in Flatworms.

    Fontenla S, Rinaldi G and Tort JF

    Frontiers in cellular and infection microbiology 2021;11;653695

    PUBMED: 34123869; PMC: 8191739; DOI: 10.3389/fcimb.2021.653695

  • Retinoic acid signaling is critical during the totipotency window in early mammalian development.

    Iturbide A, Ruiz Tejada Segura ML, Noll C, Schorpp K, Rothenaigner I, Ruiz-Morales ER, Lubatti G, Agami A, Hadian K, Scialdone A and Torres-Padilla ME

    Nature structural & molecular biology 2021;28;6;521-532

    PUBMED: 34045724; PMC: 8195742; DOI: 10.1038/s41594-021-00590-w

  • An invariant Trypanosoma vivax vaccine antigen induces protective immunity.

    Autheman D, Crosnier C, Clare S, Goulding DA, Brandt C, Harcourt K, Tolley C, Galaway F, Khushu M, Ong H et al.

    Nature 2021;595;7865;96-100

    PUBMED: 34040257; DOI: 10.1038/s41586-021-03597-x

  • Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries.

    Milne R, Morley KI, Almarri MA, Anwer S, Atutornu J, Baranova EE, Bevan P, Cerezo M, Cong Y, Costa A et al.

    Genome medicine 2021;13;1;92

    PUBMED: 34034801; PMC: 8147072; DOI: 10.1186/s13073-021-00903-0

  • Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii.

    Wagah MG, Korlević P, Clarkson C, Miles A, Anopheles gambiae 1000 Genomes Consortium, Lawniczak MKN and Makunin A

    Malaria journal 2021;20;1;234

    PUBMED: 34034756; PMC: 8146665; DOI: 10.1186/s12936-021-03757-4

  • Identifying nootropic drug targets via large-scale cognitive GWAS and transcriptomics.

    Lam M, Chen CY, Ge T, Xia Y, Hill DW, Trampush JW, Yu J, Knowles E, Davies G, Stahl EA et al.

    Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2021

    PUBMED: 34035472; DOI: 10.1038/s41386-021-01023-4

  • Integrated Single Cell Atlas of Endothelial Cells of the Human Lung.

    Schupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP et al.

    Circulation 2021

    PUBMED: 34030460; DOI: 10.1161/CIRCULATIONAHA.120.052318

  • HIV infection and anaemia do not affect HbA1c for the detection of diabetes in black South Africans - evidence from the Durban Diabetes Study.

    Hird TR, Partap U, Moodley P, Pirie FJ, Esterhuizen TM, O'Leary B, McCarthy MI, Young EH, Sandhu MS and Motala AA

    Diabetic medicine : a journal of the British Diabetic Association 2021;e14605

    PUBMED: 34028093; DOI: 10.1111/dme.14605

  • A global metagenomic map of urban microbiomes and antimicrobial resistance.

    Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K et al.

    Cell 2021

    PUBMED: 34043940; DOI: 10.1016/j.cell.2021.05.002

  • Assessing the functional relevance of splice isoforms.

    Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J and Tress ML

    NAR genomics and bioinformatics 2021;3;2;lqab044

    PUBMED: 34046593; PMC: 8140736; DOI: 10.1093/nargab/lqab044

  • Genome-wide CRISPR/Cas9 deletion screen defines mitochondrial gene essentiality and identifies routes for tumour cell viability in hypoxia.

    Thomas LW, Esposito C, Morgan RE, Price S, Young J, Williams SP, Maddalena LA, McDermott U and Ashcroft M

    Communications biology 2021;4;1;615

    PUBMED: 34021238; DOI: 10.1038/s42003-021-02098-x

  • Launching the Tree of Life Gateway.

    Threlfall J and Blaxter M

    Wellcome open research 2021;6;125

    PUBMED: 34095514; PMC: 8142598; DOI: 10.12688/wellcomeopenres.16913.1

  • Leveraging eQTLs to identify individual-level tissue of interest for a complex trait.

    Majumdar A, Giambartolomei C, Cai N, Haldar T, Schwarz T, Gandal M, Flint J and Pasaniuc B

    PLoS computational biology 2021;17;5;e1008915

    PUBMED: 34019542; DOI: 10.1371/journal.pcbi.1008915

  • Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms.

    Wright CF, Quaife NM, Ramos-Hernández L, Danecek P, Ferla MP, Samocha KE, Kaplanis J, Gardner EJ, Eberhardt RY, Chao KR et al.

    American journal of human genetics 2021;108;6;1083-1094

    PUBMED: 34022131; PMC: 8206381; DOI: 10.1016/j.ajhg.2021.04.025

  • REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.

    Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T et al.

    Nature methods 2021

    PUBMED: 34021280; DOI: 10.1038/s41592-021-01166-8

  • A bivalve biomineralization toolbox.

    Yarra T, Blaxter M and Clark MS

    Molecular biology and evolution 2021

    PUBMED: 34014311; DOI: 10.1093/molbev/msab153

  • Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria.

    Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD and Clavel T

    ISME communications 2021;1;1;16

    PUBMED: 36732617; PMC: 9723785; DOI: 10.1038/s43705-021-00017-z

  • Prevalence and predictors of vitamin D deficiency in young African children.

    Mogire RM, Morovat A, Muriuki JM, Mentzer AJ, Webb EL, Kimita W, Ndungu FM, Macharia AW, Cutland CL, Sirima SB et al.

    BMC medicine 2021;19;1;115

    PUBMED: 34011341; DOI: 10.1186/s12916-021-01985-8

  • A 39-Amino-Acid C-Terminal Truncation of GDV1 Disrupts Sexual Commitment in Plasmodium falciparum.

    Tibúrcio M, Hitz E, Niederwieser I, Kelly G, Davies H, Doerig C, Billker O, Voss TS and Treeck M

    mSphere 2021;6;3

    PUBMED: 34011691; DOI: 10.1128/mSphere.01093-20

  • An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

    O'Sullivan DM, Doyle RM, Temisak S, Redshaw N, Whale AS, Logan G, Huang J, Fischer N, Amos GCA, Preston MD et al.

    Scientific reports 2021;11;1;10590

    PUBMED: 34012005; PMC: 8134577; DOI: 10.1038/s41598-021-89881-2

  • Pain management strategies among cervical cancer patients in Zimbabwe.

    Kuguyo O, Misi FD, Chibonda S, Matimba A, Nhachi C and Tsikai N

    Pain management 2021

    PUBMED: 34008417; DOI: 10.2217/pmt-2020-0108

  • The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769.

    Howe K, Dwinell M, Shimoyama M, Corton C, Betteridge E, Dove A, Quail MA, Smith M, Saba L, Williams RW et al.

    Wellcome open research 2021;6;118

    PUBMED: 34660910; PMC: 8495504; DOI: 10.12688/wellcomeopenres.16854.1

  • High-Content Imaging to Phenotype Antimicrobial Effects on Individual Bacteria at Scale.

    Sridhar S, Forrest S, Warne B, Maes M, Baker S, Dougan G and Bartholdson Scott J

    mSystems 2021;6;3

    PUBMED: 34006623; DOI: 10.1128/mSystems.00028-21

  • Mapping Rora expression in resting and activated CD4+ T cells.

    Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L et al.

    PloS one 2021;16;5;e0251233

    PUBMED: 34003838; DOI: 10.1371/journal.pone.0251233

  • A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch.

    Argimón S, Yeats CA, Goater RJ, Abudahab K, Taylor B, Underwood A, Sánchez-Busó L, Wong VK, Dyson ZA, Nair S et al.

    Nature communications 2021;12;1;2879

    PUBMED: 34001879; DOI: 10.1038/s41467-021-23091-2

  • Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics.

    Bentley SD and Lo SW

    Genome medicine 2021;13;1;84

    PUBMED: 34001237; PMC: 8130287; DOI: 10.1186/s13073-021-00901-2

  • The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758.

    Mead D, Ogden R, Meredith A, Peniche G, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J et al.

    Wellcome open research 2021;6;112

    PUBMED: 34671705; PMC: 8499043; DOI: 10.12688/wellcomeopenres.16631.1

  • High-throughput full-length single-cell RNA-seq automation.

    Mamanova L, Miao Z, Jinat A, Ellis P, Shirley L and Teichmann SA

    Nature protocols 2021

    PUBMED: 33990801; DOI: 10.1038/s41596-021-00523-3

  • Self-replicating digital data storage with synthetic chromosomes

    Lu, Xinyu and Ellis, Tom

    National Science Review 2021;8;7;nwab086

    DOI: 10.1093/nsr/nwab086

  • The genome sequence of the brown trout, Salmo trutta Linnaeus 1758.

    Hansen T, Fjelldal PG, Lien S, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Fedrigo O et al.

    Wellcome open research 2021;6;108

    PUBMED: 34632087; PMC: 8488904; DOI: 10.12688/wellcomeopenres.16838.1

  • Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs.

    Aztekin C, Hiscock TW, Gurdon J, Jullien J, Marioni J and Simons BD

    Development (Cambridge, England) 2021

    PUBMED: 33983390; DOI: 10.1242/dev.199158

  • Lineage tracing of human development through somatic mutations.

    Spencer Chapman M, Ranzoni AM, Myers B, Williams N, Coorens THH, Mitchell E, Butler T, Dawson KJ, Hooks Y, Moore L et al.

    Nature 2021;595;7865;85-90

    PUBMED: 33981037; DOI: 10.1038/s41586-021-03548-6

  • Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.

    Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M et al.

    Nature communications 2021;12;1;2684

    PUBMED: 33976138; DOI: 10.1038/s41467-021-22700-4

  • Methylation of histone H3 at lysine 37 by Set1 and Set2 prevents spurious DNA replication.

    Santos-Rosa H, Millán-Zambrano G, Han N, Leonardi T, Klimontova M, Nasiscionyte S, Pandolfini L, Tzelepis K, Bartke T and Kouzarides T

    Molecular cell 2021;81;13;2793-2807.e8

    PUBMED: 33979575; PMC: 7612968; DOI: 10.1016/j.molcel.2021.04.021

  • SETBP1 overexpression acts in the place of class-defining mutations to drive FLT3-ITD-mutant AML.

    Pacharne S, Dovey OM, Cooper JL, Gu M, Friedrich MJ, Rajan SS, Barenboim M, Collord G, Vijayabaskar MS, Ponstingl H et al.

    Blood advances 2021;5;9;2412-2425

    PUBMED: 33956058; PMC: 8114559; DOI: 10.1182/bloodadvances.2020003443

  • Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study.

    Gladstone RA, McNally A, Pöntinen AK, Tonkin-Hill G, Lees JA, Skytén K, Cléon F, Christensen MOK, Haldorsen BC, Bye KK et al.

    The Lancet. Microbe 2021;2;7;e331-e341

    PUBMED: 35544167; PMC: 7614948; DOI: 10.1016/S2666-5247(21)00031-8

  • MYC amplifications are common events in childhood osteosarcoma.

    De Noon S, Ijaz J, Coorens TH, Amary F, Ye H, Strobl A, Lyskjaer I, Flanagan AM and Behjati S

    The journal of pathology. Clinical research 2021

    PUBMED: 33969640; DOI: 10.1002/cjp2.219

  • PPP3CA truncating variants clustered in the regulatory domain cause early-onset refractory epilepsy.

    Panneerselvam S, Wang J, Zhu W, Dai H, Pappas JG, Rabin R, Low KJ, Rosenfeld JA, Emrick L, Xiao R et al.

    Clinical genetics 2021

    PUBMED: 33963760; DOI: 10.1111/cge.13979

  • A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop.

    Ma X, Vaistij FE, Li Y, Jansen van Rensburg WS, Harvey S, Bairu MW, Venter SL, Mavengahama S, Ning Z, Graham IA et al.

    The Plant journal : for cell and molecular biology 2021

    PUBMED: 33960539; DOI: 10.1111/tpj.15298

  • A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.).

    Generalovic TN, McCarthy SA, Warren IA, Wood JMD, Torrance J, Sims Y, Quail M, Howe K, Pipan M, Durbin R and Jiggins CD

    G3 (Bethesda, Md.) 2021;11;5

    PUBMED: 33734373; PMC: 8104945; DOI: 10.1093/g3journal/jkab085

  • Membrane protein regulators of melanoma pulmonary colonisation identified using a CRISPRa screen and spontaneous metastasis assay in mice.

    van der Weyden L, Offord V, Turner G, Swiatkowska A, Speak AO and Adams DJ

    G3 (Bethesda, Md.) 2021

    PUBMED: 33963380; PMC: 8495943; DOI: 10.1093/g3journal/jkab157

  • Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney.

    Eales JM, Jiang X, Xu X, Saluja S, Akbarov A, Cano-Gamez E, McNulty MT, Finan C, Guo H, Wystrychowski W et al.

    Nature genetics 2021;53;5;630-637

    PUBMED: 33958779; DOI: 10.1038/s41588-021-00835-w

  • Contemporary Ne estimation using temporally-spaced data with linked loci.

    Hui TJ, Brenas JH and Burt A

    Molecular ecology resources 2021

    PUBMED: 33950582; DOI: 10.1111/1755-0998.13412

  • Mechanisms of breast cancer metastasis.

    Nathanson SD, Detmar M, Padera TP, Yates LR, Welch DR, Beadnell TC, Scheid AD, Wrenn ED and Cheung K

    Clinical & experimental metastasis 2021

    PUBMED: 33950409; DOI: 10.1007/s10585-021-10090-2

  • Methods for analysing lineage tracing datasets

    Kostiou, Vasiliki, Zhang, Huairen, Hall, Michael W.J., Jones, Philip H. and Hall, Benjamin A.;

    Royal Society Open Science 2021;8;202231

    DOI: 10.1098/rsos.202231

  • Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease.

    Youlten SE, Kemp JP, Logan JG, Ghirardello EJ, Sergio CM, Dack MRG, Guilfoyle SE, Leitch VD, Butterfield NC, Komla-Ebri D et al.

    Nature communications 2021;12;1;2444

    PUBMED: 33953184; DOI: 10.1038/s41467-021-22517-1

  • Induction of APOBEC3 exacerbates DNA replication stress and chromosomal instability in early breast and lung cancer evolution.

    Venkatesan S, Angelova M, Puttick C, Zhai H, Caswell DR, Lu WT, Dietzen M, Galanos P, Evangelou K, Bellelli R et al.

    Cancer discovery 2021

    PUBMED: 33947663; DOI: 10.1158/2159-8290.CD-20-0725

  • Computational principles and challenges in single-cell data integration.

    Argelaguet R, Cuomo ASE, Stegle O and Marioni JC

    Nature biotechnology 2021

    PUBMED: 33941931; DOI: 10.1038/s41587-021-00895-7

  • Efficient computation of positional population counts using SIMD instructions

    Klarqvist,M.D.R., Mula,W. and Lemire,D.

    Concurrency and Computation: Practice and Experience 2021

    DOI: 10.1002/cpe.6304

  • Environmental DNA provides higher resolution assessment of riverine biodiversity and ecosystem function via spatio-temporal nestedness and turnover partitioning.

    Seymour M, Edwards FK, Cosby BJ, Bista I, Scarlett PM, Brailsford FL, Glanville HC, de Bruyn M, Carvalho GR and Creer S

    Communications biology 2021;4;1;512

    PUBMED: 33941836; DOI: 10.1038/s42003-021-02031-2

  • Green Algorithms: Quantifying the Carbon Footprint of Computation

    Lannelongue, Loïc, Grealey, Jason and Inouye, Michael

    Advanced Science 2021;8;12;2100707

    PMC: 8224424; DOI: 10.1002/advs.202100707

  • Identification of a homozygous recessive variant in PTGS1 resulting in a congenital aspirin-like defect in platelet function.

    Chan MV, Hayman MA, Sivapalaratnam S, Crescente M, Allan HE, Edin ML, Zeldin DC, Milne GL, Stephens J, Greene D et al.

    Haematologica 2021;106;5;1423-1432

    PUBMED: 32299908; PMC: 8094108; DOI: 10.3324/haematol.2019.235895

  • Metagenomics for surveillance of respiratory pathogens.

    Carr VR and Chaguza C

    Nature reviews. Microbiology 2021;19;5;285

    PUBMED: 33707741; PMC: 7950416; DOI: 10.1038/s41579-021-00541-8

  • Natural variants suppress mutations in hundreds of essential genes.

    Parts L, Batté A, Lopes M, Yuen MW, Laver M, San Luis BJ, Yue JX, Pons C, Eray E, Aloy P et al.

    Molecular systems biology 2021;17;5;e10138

    PUBMED: 34042294; DOI: 10.15252/msb.202010138

  • Reduced hippocampal ten-eleven translocation 3 (Tet3) protein expression in Tet3 conditional knockout mice.

    Antunes C, Da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Loureiro-Campos E, Branco MR, Sousa N, Reik W, Pinto L and Marques CJ

    Molecular psychiatry 2021;26;5;1425

    PUBMED: 34045681; DOI: 10.1038/s41380-021-01067-4

  • Cut-like homeobox 1 (CUX1) tumor suppressor gene haploinsufficiency induces apoptosis evasion to sustain myeloid leukemia.

    Supper E, Rudat S, Iyer V, Droop A, Wong K, Spinella JF, Thomas P, Sauvageau G, Adams DJ and Wong CC

    Nature communications 2021;12;1;2482

    PUBMED: 33931647; DOI: 10.1038/s41467-021-22750-8

  • Stepwise pathogenic evolution of Mycobacterium abscessus.

    Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, Grogono DM, Peterson CM, Verma D, Evans IE et al.

    Science (New York, N.Y.) 2021;372;6541

    PUBMED: 33926925; DOI: 10.1126/science.abb8699

  • Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.

    Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R et al.

    Genome biology 2021;22;1;120

    PUBMED: 33910595; DOI: 10.1186/s13059-021-02336-9

  • Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time.

    von Mentzer A, Blackwell GA, Pickard D, Boinett CJ, Joffré E, Page AJ, Svennerholm AM, Dougan G and Sjöling Å

    Scientific reports 2021;11;1;9256

    PUBMED: 33927221; DOI: 10.1038/s41598-021-88316-2

  • CLICK-enabled analogues reveal pregnenolone interactomes in cancer and immune cells.

    Roy S, Sipthorp J, Mahata B, Pramanik J, Hennrich ML, Gavin AC, Ley SV and Teichmann SA

    iScience 2021;24;5;102485

    PUBMED: 34036248; PMC: 8138728; DOI: 10.1016/j.isci.2021.102485

  • Common virulence gene expression in adult first-time infected malaria patients and severe cases.

    Wichers JS, Tonkin-Hill G, Thye T, Krumkamp R, Kreuels B, Strauss J, von Thien H, Scholz JAM, Smedegaard Hansson H, Weisel Jensen R et al.

    eLife 2021;10

    PUBMED: 33908865; DOI: 10.7554/eLife.69040

  • Evolutionary and biomedical insights from a marmoset diploid genome assembly.

    Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C et al.

    Nature 2021;594;7862;227-233

    PUBMED: 33910227; DOI: 10.1038/s41586-021-03535-x

  • Genomic surveillance of Pseudomonas aeruginosa in the Philippines, 2013-2014.

    Chilam J, Argimón S, Limas MT, Masim ML, Gayeta JM, Lagrada ML, Olorosa AM, Cohen V, Hernandez LT, Jeffrey B et al.

    Western Pacific surveillance and response journal : WPSAR 2021;12;2;4-18

    PUBMED: 34540307; PMC: 8421739; DOI: 10.5365/wpsar.2020.11.1.006

  • Obesity and pregnancy, the perfect metabolic storm.

    Corrales P, Vidal-Puig A and Medina-Gómez G

    European journal of clinical nutrition 2021

    PUBMED: 33911209; DOI: 10.1038/s41430-021-00914-5

  • Somatic mutation landscapes at single-molecule resolution.

    Abascal F, Harvey LMR, Mitchell E, Lawson ARJ, Lensing SV, Ellis P, Russell AJC, Alcantara RE, Baez-Ortega A, Wang Y et al.

    Nature 2021;593;7859;405-410

    PUBMED: 33911282; DOI: 10.1038/s41586-021-03477-4

  • Towards complete and error-free genome assemblies of all vertebrate species.

    Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J et al.

    Nature 2021;592;7856;737-746

    PUBMED: 33911273; PMC: 8081667; DOI: 10.1038/s41586-021-03451-0

  • Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation.

    Meier B, Volkova NV, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell PJ, Gerstung M and Gartner A

    PloS one 2021;16;4;e0250291

    PUBMED: 33905417; PMC: 8078821; DOI: 10.1371/journal.pone.0250291

  • A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage.

    Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, Agu CA, Badja C, Momen S, Young J et al.

    Nature cancer 2021;2;6;643-657

    PUBMED: 34164627; PMC: 7611045; DOI: 10.1038/s43018-021-00200-0

  • Linking chondrocyte and synovial transcriptional profile to clinical phenotype in osteoarthritis.

    Steinberg J, Southam L, Fontalis A, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Brooks RA, McCaskie AW, Wilkinson JM and Zeggini E

    Annals of the rheumatic diseases 2021

    PUBMED: 33903094; DOI: 10.1136/annrheumdis-2020-219760

  • Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia.

    Yankova E, Blackaby W, Albertella M, Rak J, De Braekeleer E, Tsagkogeorga G, Pilka ES, Aspris D, Leggate D, Hendrick AG et al.

    Nature 2021;593;7860;597-601

    PUBMED: 33902106; DOI: 10.1038/s41586-021-03536-w

  • “Ready for What?”: Timing and Speculation in Alzheimer’s Disease Drug Development

    Brenman,Natassia F. and Milne, Richard

    Science, Technology, & Human Values 2021

    DOI: 10.1177/01622439211007196

  • A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.

    Sánchez-Busó L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, Argimón S, Ma KC, Mortimer TD, Golparian D et al.

    Genome medicine 2021;13;1;61

    PUBMED: 33875000; PMC: 8054416; DOI: 10.1186/s13073-021-00858-2

  • A novel technique capable of taking 'protected' biopsies for reliable assessment of the distribution of microbiota along the colonic mucosa.

    Strobbe F, Bénard MV, Rossen NG, de Vos WM, Kumar N, Lawley TD, Zoetendal EG, Hugenholtz F and Ponsioen CY

    Journal of microbiological methods 2021;185;106204

    PUBMED: 33872639; DOI: 10.1016/j.mimet.2021.106204

  • Towards a Human Cell Atlas: Taking Notes from the Past.

    Lindeboom RGH, Regev A and Teichmann SA

    Trends in genetics : TIG 2021;37;7;625-630

    PUBMED: 33879355; DOI: 10.1016/j.tig.2021.03.007

  • Canine brucellosis in Costa Rica reveals widespread Brucella canis infection and the recent introduction of foreign strains.

    Suárez-Esquivel M, Ruiz-Villalobos N, Hidalgo-Jara W, Chacón-Díaz C, Zúñiga-Pereira AM, Masís-Mora M, Fernández-Fernández E, Hernández-Mora G, Barquero-Calvo E, Chaves-Olarte E et al.

    Veterinary microbiology 2021;257;109072

    PUBMED: 33965789; DOI: 10.1016/j.vetmic.2021.109072

  • Environmental genomics of Late Pleistocene black bears and giant short-faced bears.

    Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z et al.

    Current biology : CB 2021

    PUBMED: 33878301; DOI: 10.1016/j.cub.2021.04.027

  • Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease.

    Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen L, Sims Y, Ecker S, Burden F, Farrow S et al.

    Nature communications 2021;12;1;2298

    PUBMED: 33863903; DOI: 10.1038/s41467-021-22548-8

  • Janus-faced EPHB4-associated disorders: novel pathogenic variants and unreported intrafamilial overlapping phenotypes.

    Martin-Almedina S, Ogmen K, Sackey E, Grigoriadis D, Karapouliou C, Nadarajah N, Ebbing C, Lord J, Mellis R, Kortuem F et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2021

    PUBMED: 33864021; DOI: 10.1038/s41436-021-01136-7

  • Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data.

    Saheb Kashaf S, Almeida A, Segre JA and Finn RD

    Nature protocols 2021

    PUBMED: 33864056; DOI: 10.1038/s41596-021-00508-2

  • Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program.

    Hu Y, Stilp AM, McHugh CP, Rao S, Jai D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH et al.

    American journal of human genetics 2021

    PUBMED: 33887194; DOI: 10.1016/j.ajhg.2021.04.003

  • Psoriasis characteristics for the early detection of psoriatic arthritis.

    Belman S, Walsh JA, Carroll C, Milliken M, Haaland B, Callis Duffin K, Krueger GG and Feng BJ

    The Journal of rheumatology 2021

    PUBMED: 33858978; DOI: 10.3899/jrheum.201123

  • Fetal hydrops and the Incremental yield of Next generation sequencing over standard prenatal Diagnostic testing (FIND) study: prospective cohort study and meta-analysis.

    Mone F, Eberhardt RY, Hurles ME, McMullan DJ, Maher ER, Lord J, Chitty LS, Dempsey E, Homfray T, Giordano JL et al.

    Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology 2021

    PUBMED: 33847422; DOI: 10.1002/uog.23652

  • Molecular epidemiology of Staphylococcus aureus in African children from rural and urban communities with atopic dermatitis.

    Ndhlovu GON, Abotsi RE, Shittu AO, Abdulgader SM, Jamrozy D, Dupont CL, Mankahla A, Nicol MP, Hlela C, Levin ME et al.

    BMC infectious diseases 2021;21;1;348

    PUBMED: 33849482; PMC: 8045247; DOI: 10.1186/s12879-021-06044-4

  • Progress towards an inducible, replication-proficient transposon delivery vector for Chlamydia trachomatis.

    Skilton RJ, O'Neill C, Thomson NR, Lampe DJ and Clarke IN

    Wellcome open research 2021;6;82

    PUBMED: 33997299; PMC: 8097735; DOI: 10.12688/wellcomeopenres.16665.1

  • Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2.

    Suryamohan K, Diwanji D, Stawiski EW, Gupta R, Miersch S, Liu J, Chen C, Jiang YP, Fellouse FA, Sathirapongsasuti JF et al.

    Communications biology 2021;4;1;475

    PUBMED: 33846513; DOI: 10.1038/s42003-021-02030-3

  • Human anogenital monocyte-derived dendritic cells and langerin+cDC2 are major HIV target cells.

    Rhodes JW, Botting RA, Bertram KM, Vine EE, Rana H, Baharlou H, Vegh P, O'Neil TR, Ashhurst AS, Fletcher J et al.

    Nature communications 2021;12;1;2147

    PUBMED: 33846309; DOI: 10.1038/s41467-021-22375-x

  • Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments.

    Delgado-Blas JF, Ovejero CM, David S, Montero N, Calero-Caceres W, Garcillan-Barcia MP, de la Cruz F, Muniesa M, Aanensen DM and Gonzalez-Zorn B

    Communications biology 2021;4;1;457

    PUBMED: 33846529; DOI: 10.1038/s42003-021-01949-x

  • Regulation of B Lymphocyte Development by Histone H2A Deubiquitinase BAP1.

    Lin YH, Liang Y, Wang H, Tung LT, Förster M, Subramani PG, Di Noia JM, Clare S, Langlais D and Nijnik A

    Frontiers in immunology 2021;12;626418

    PUBMED: 33912157; PMC: 8072452; DOI: 10.3389/fimmu.2021.626418

  • Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19.

    Gaziano L, Giambartolomei C, Pereira AC, Gaulton A, Posner DC, Swanson SA, Ho YL, Iyengar SK, Kosik NM, Vujkovic M et al.

    Nature medicine 2021

    PUBMED: 33837377; DOI: 10.1038/s41591-021-01310-z

  • Pooled CRISPR-activation screening coupled with single-cell RNA-seq in mouse embryonic stem cells.

    Alda-Catalinas C, Eckersley-Maslin MA and Reik W

    STAR protocols 2021;2;2;100426

    PUBMED: 33899013; PMC: 8055612; DOI: 10.1016/j.xpro.2021.100426

  • Werner Helicase Is a Synthetic-Lethal Vulnerability in Mismatch Repair-Deficient Colorectal Cancer Refractory to Targeted Therapies, Chemotherapy, and Immunotherapy.

    Picco G, Cattaneo CM, van Vliet EJ, Crisafulli G, Rospo G, Consonni S, Vieira SF, Rodríguez IS, Cancelliere C, Banerjee R et al.

    Cancer discovery 2021;11;8;1923-1937

    PUBMED: 33837064; DOI: 10.1158/2159-8290.CD-20-1508

  • Autocrine IGF2 programmes β-cell plasticity under conditions of increased metabolic demand.

    Sandovici I, Hammerle CM, Virtue S, Vivas-Garcia Y, Izquierdo-Lahuerta A, Ozanne SE, Vidal-Puig A, Medina-Gómez G and Constância M

    Scientific reports 2021;11;1;7717

    PUBMED: 33833312; PMC: 8032793; DOI: 10.1038/s41598-021-87292-x

  • Development of a method for generating SNP interaction-aware polygenic risk scores for radiotherapy toxicity.

    Franco NR, Massi MC, Ieva F, Manzoni A, Paganoni AM, Zunino P, Veldeman L, Ost P, Fonteyne V, Talbot CJ et al.

    Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 2021;159;241-248

    PUBMED: 33838170; PMC: 8754257; DOI: 10.1016/j.radonc.2021.03.024

  • Prenatal Development and Function of Human Mononuclear Phagocytes.

    Miah M, Goh I and Haniffa M

    Frontiers in cell and developmental biology 2021;9;649937

    PUBMED: 33898444; PMC: 8060508; DOI: 10.3389/fcell.2021.649937

  • Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes.

    Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J et al.

    Cell 2021;184;8;2239-2254.e39

    PUBMED: 33831375; PMC: 8054914; DOI: 10.1016/j.cell.2021.03.009

  • Linked electronic health records for research on a nationwide cohort of more than 54 million people in England: data resource.

    Wood A, Denholm R, Hollings S, Cooper J, Ip S, Walker V, Denaxas S, Akbari A, Banerjee A, Whiteley W et al.

    BMJ (Clinical research ed.) 2021;373;n826

    PUBMED: 33827854; DOI: 10.1136/bmj.n826

  • MolluscDB: a genome and transcriptome database for molluscs.

    Caurcel C, Laetsch DR, Challis R, Kumar S, Gharbi K and Blaxter M

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2021;376;1825;20200157

    PUBMED: 33813885; DOI: 10.1098/rstb.2020.0157

  • A resource of targeted mutant mouse lines for 5,061 genes.

    Birling MC, Yoshiki A, Adams DJ, Ayabe S, Beaudet AL, Bottomley J, Bradley A, Brown SDM, Bürger A, Bushell W et al.

    Nature genetics 2021;53;4;416-419

    PUBMED: 33833456; PMC: 8397259; DOI: 10.1038/s41588-021-00825-y

  • Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study.

    Kantele A, Kuenzli E, Dunn SJ, Dance DAB, Newton PN, Davong V, Mero S, Pakkanen SH, Neumayr A, Hatz C et al.

    The Lancet. Microbe 2021;2;4;e151-e158

    PUBMED: 33821248; PMC: 8009952; DOI: 10.1016/S2666-5247(20)30224-X

  • Epidemiologic and Genomic Reidentification of Yaws, Liberia.

    Timothy JWS, Beale MA, Rogers E, Zaizay Z, Halliday KE, Mulbah T, Giddings RK, Walker SL, Thomson NR, Kollie KK et al.

    Emerging infectious diseases 2021;27;4;1123-1132

    PUBMED: 33754988; PMC: 8007311; DOI: 10.3201/eid2704.204442

  • User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.

    Moreno P, Huang N, Manning JR, Mohammed S, Solovyev A, Polanski K, Bacon W, Chazarra R, Talavera-López C, Doyle MA et al.

    Nature methods 2021;18;4;327-328

    PUBMED: 33782609; DOI: 10.1038/s41592-021-01102-w

  • Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data.

    Hills M, Falconer E, O'Neill K, Sanders AD, Howe K, Guryev V and Lansdorp PM

    International journal of molecular sciences 2021;22;7

    PUBMED: 33807210; PMC: 8037727; DOI: 10.3390/ijms22073617

  • A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans.

    Hallast P, Kibena L, Punab M, Arciero E, Rootsi S, Grigorova M, Flores R, Jobling MA, Poolamets O, Pomm K et al.

    eLife 2021;10

    PUBMED: 33781384; PMC: 8009663; DOI: 10.7554/eLife.65420

  • The global dissemination of hospital clones of Enterococcus faecium.

    van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, Hegstad K, Westh HT, Howden BP, Malhotra-Kumar S et al.

    Genome medicine 2021;13;1;52

    PUBMED: 33785076; PMC: 8008517; DOI: 10.1186/s13073-021-00868-0

  • Advances in understanding the pathogenesis of hereditary macrothrombocytopenia.

    Collins J, Astle WJ, Megy K, Mumford AD and Vuckovic D

    British journal of haematology 2021

    PUBMED: 33783834; DOI: 10.1111/bjh.17409

  • Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial.

    Emary KRW, Golubchik T, Aley PK, Ariani CV, Angus B, Bibi S, Blane B, Bonsall D, Cicconi P, Charlton S et al.

    Lancet (London, England) 2021

    PUBMED: 33798499; PMC: 8009612; DOI: 10.1016/S0140-6736(21)00628-0

  • Gain-of-function factor H-related 5 protein impairs glomerular complement regulation resulting in kidney damage.

    Malik TH, Gitterman DP, Lavin DP, Lomax-Browne HJ, Hiemeyer EC, Moran LB, Boroviak K, Cook HT, Gilmore AC, Mandwie M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2021;118;13

    PUBMED: 33753502; DOI: 10.1073/pnas.2022722118

  • KDM5 inhibition offers a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas.

    Heward JA, Koniali L, D'Avola A, Close K, Yeomans A, Philpott M, Dunford JE, Rahim T, Al Seraihi AF, Wang J et al.

    Blood 2021

    PUBMED: 33786580; DOI: 10.1182/blood.2020008743

  • Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.

    Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, O'Toole Á et al.

    Nature 2021;593;7858;266-269

    PUBMED: 33767447; DOI: 10.1038/s41586-021-03470-x

  • Mutagenic mechanisms of cancer-associated DNA polymerase ϵ alleles.

    Herzog M, Alonso-Perez E, Salguero I, Warringer J, Adams DJ, Jackson SP and Puddu F

    Nucleic acids research 2021

    PUBMED: 33764464; DOI: 10.1093/nar/gkab160

  • Whole-genome sequencing reveals progressive versus stable myeloma precursor conditions as two distinct entities.

    Oben B, Froyen G, Maclachlan KH, Leongamornlert D, Abascal F, Zheng-Lin B, Yellapantula V, Derkach A, Geerdens E, Diamond BT et al.

    Nature communications 2021;12;1;1861

    PUBMED: 33767199; PMC: 7994386; DOI: 10.1038/s41467-021-22140-0

  • Control Strategies for Carcinogenic-Associated Helminthiases: An Integrated Overview.

    da Costa JMC, Gouveia MJ, Rinaldi G, Brindley PJ, Santos J and Santos LL

    Frontiers in cellular and infection microbiology 2021;11;626672

    PUBMED: 33842386; PMC: 8025785; DOI: 10.3389/fcimb.2021.626672

  • Macrophage beta2-adrenergic receptor is dispensable for the adipose tissue inflammation and function.

    Petkevicius K, Bidault G, Virtue S, Newland SA, Dale M, Dugourd A, Saez-Rodriguez J, Mallat Z and Vidal-Puig A

    Molecular metabolism 2021;101220

    PUBMED: 33774223; DOI: 10.1016/j.molmet.2021.101220

  • Maternal vitamin B12 in mice positively regulates bone, but not muscle mass and strength in post-weaning and mature offspring.

    Singh P, Telnova S, Zhou B, Mohamed AD, De Mello V, Wackerhage H, Guo XE, Panda AK and Yadav VK

    American journal of physiology. Regulatory, integrative and comparative physiology 2021

    PUBMED: 33759575; DOI: 10.1152/ajpregu.00355.2020

  • Nanopore sequencing indicates that tandem amplification of chromosome 20q11.21 in human pluripotent stem cells is driven by break induced replication.

    Halliwell J, Baker D, Judge K, Quail MA, Oliver K, Betteridge E, Skelton J, Andrews PW and Barbaric I

    Stem cells and development 2021

    PUBMED: 33757297; DOI: 10.1089/scd.2021.0013

  • Unraveling the cartography of the cancer ecosystem.

    Rabbie R, Lau D, White RM and Adams DJ

    Genome biology 2021;22;1;87

    PUBMED: 33761966; PMC: 7988951; DOI: 10.1186/s13059-021-02310-5

  • CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation.

    van der Weyden L, Harle V, Turner G, Offord V, Iyer V, Droop A, Swiatkowska A, Rabbie R, Campbell AD, Sansom OJ et al.

    Communications biology 2021;4;1;395

    PUBMED: 33758365; PMC: 7987976; DOI: 10.1038/s42003-021-01912-w

  • Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro.

    Macchiaroli N, Preza M, Pérez MG, Kamenetzky L, Cucher M, Koziol U, Castillo E, Berriman M, Brehm K and Rosenzvit MC

    PLoS neglected tropical diseases 2021;15;3;e0009297

    PUBMED: 33750964; DOI: 10.1371/journal.pntd.0009297

  • Metabolic profiling of angiopoietin-like protein 3 and 4 inhibition: a drug-target Mendelian randomization analysis.

    Wang Q, Oliver-Williams C, Raitakari OT, Viikari J, Lehtimäki T, Kähönen M, Järvelin MR, Salomaa V, Perola M, Danesh J et al.

    European heart journal 2021;42;12;1160-1169

    PUBMED: 33351885; PMC: 7982288; DOI: 10.1093/eurheartj/ehaa972

  • Potential metabolic resistance mechanisms to ivermectin in Anopheles gambiae: a synergist bioassay study.

    Nicolas P, Kiuru C, Wagah MG, Muturi M, Duthaler U, Hammann F, Maia M and Chaccour C

    Parasites & vectors 2021;14;1;172

    PUBMED: 33743783; PMC: 7981804; DOI: 10.1186/s13071-021-04675-9

  • Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia.

    Chung The H, Bodhidatta L, Pham DT, Mason CJ, Ha Thanh T, Voong Vinh P, Turner P, Hem S, Dance DAB, Newton PN et al.

    Communications biology 2021;4;1;353

    PUBMED: 33742111; DOI: 10.1038/s42003-021-01905-9

  • The landscape of autosomal-recessive pathogenic variants in European populations reveals phenotype-specific effects.

    Fridman H, Yntema HG, Mägi R, Andreson R, Metspalu A, Mezzavila M, Tyler-Smith C, Xue Y, Carmi S, Levy-Lahad E et al.

    American journal of human genetics 2021;108;4;608-619

    PUBMED: 33740458; PMC: 8059335; DOI: 10.1016/j.ajhg.2021.03.004

  • Identification of bacteria-derived HLA-bound peptides in melanoma.

    Kalaora S, Nagler A, Nejman D, Alon M, Barbolin C, Barnea E, Ketelaars SLC, Cheng K, Vervier K, Shental N et al.

    Nature 2021;592;7852;138-143

    PUBMED: 33731925; DOI: 10.1038/s41586-021-03368-8

  • Phylogeographic patterns of the Australian grass trees (Xanthorrhoea Asphodelaceae) shown using targeted amplicon sequencing

    McLay, Todd G.B., Ladiges, Pauline Y., Doyle, Stephen R. and Bayly, Michael J.

    Australian Systematic Botany 2021;34;2;206-225

    DOI: 10.1071/SB20013

  • Temporal evolution of sulfadoxine-pyrimethamine resistance genotypes and genetic diversity in response to a decade of increased interventions against Plasmodium falciparum in northern Ghana.

    Amenga-Etego LN, Asoala V, Agongo G, Jacob C, Goncalves S, Awandare GA, Rockett KA and Kwiatkowski D

    Malaria journal 2021;20;1;152

    PUBMED: 33731134; DOI: 10.1186/s12936-021-03693-3

  • PfMFR3: A Multidrug-Resistant Modulator in Plasmodium falciparum.

    Rocamora F, Gupta P, Istvan ES, Luth MR, Carpenter EF, Kümpornsin K, Sasaki E, Calla J, Mittal N, Carolino K et al.

    ACS infectious diseases 2021;7;4;811-825

    PUBMED: 33715347; PMC: 8042660; DOI: 10.1021/acsinfecdis.0c00676

  • Integrated cross-study datasets of genetic dependencies in cancer.

    Pacini C, Dempster JM, Boyle I, Gonçalves E, Najgebauer H, Karakoc E, van der Meer D, Barthorpe A, Lightfoot H, Jaaks P et al.

    Nature communications 2021;12;1;1661

    PUBMED: 33712601; DOI: 10.1038/s41467-021-21898-7

  • Suppression of insulin-induced gene 1 (INSIG1) function promotes hepatic lipid remodelling and restrains NASH progression.

    Azzu V, Vacca M, Kamzolas I, Hall Z, Leslie J, Carobbio S, Virtue S, Davies SE, Lukasik A, Dale M et al.

    Molecular metabolism 2021;101210

    PUBMED: 33722690; DOI: 10.1016/j.molmet.2021.101210

  • Plasma metabolites to profile pathways in noncommunicable disease multimorbidity.

    Pietzner M, Stewart ID, Raffler J, Khaw KT, Michelotti GA, Kastenmüller G, Wareham NJ and Langenberg C

    Nature medicine 2021;27;3;471-479

    PUBMED: 33707775; DOI: 10.1038/s41591-021-01266-0

  • The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.

    Lambert SA, Gil L, Jupp S, Ritchie SC, Xu Y, Buniello A, McMahon A, Abraham G, Chapman M, Parkinson H et al.

    Nature genetics 2021

    PUBMED: 33692568; DOI: 10.1038/s41588-021-00783-5

  • Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features.

    Di Gregorio S, Haim MS, Vielma Vallenilla J, Cohen V, Rago L, Gulone L, Aanensen DM, Argimón S and Mollerach M

    mSphere 2021;6;2

    PUBMED: 33692199; DOI: 10.1128/mSphere.01297-20

  • Improving reporting standards for polygenic scores in risk prediction studies.

    Wand H, Lambert SA, Tamburro C, Iacocca MA, O'Sullivan JW, Sillari C, Kullo IJ, Rowley R, Dron JS, Brockman D et al.

    Nature 2021;591;7849;211-219

    PUBMED: 33692554; DOI: 10.1038/s41586-021-03243-6

  • Inherent mosaicism and extensive mutation of human placentas.

    Coorens THH, Oliver TRW, Sanghvi R, Sovio U, Cook E, Vento-Tormo R, Haniffa M, Young MD, Rahbari R, Sebire N et al.

    Nature 2021;592;7852;80-85

    PUBMED: 33692543; PMC: 7611644; DOI: 10.1038/s41586-021-03345-1

  • Use of preclinical models for malignant pleural mesothelioma.

    Shamseddin M, Obacz J, Garnett MJ, Rintoul RC, Francies HE and Marciniak SJ

    Thorax 2021

    PUBMED: 33692175; DOI: 10.1136/thoraxjnl-2020-216602

  • Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.

    Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H et al.

    Nature communications 2021;12;1;1523

    PUBMED: 33750782; PMC: 7943827; DOI: 10.1038/s41467-021-21749-5

  • Time-resolved single-cell analysis of Brca1 associated mammary tumourigenesis reveals aberrant differentiation of luminal progenitors.

    Bach K, Pensa S, Zarocsinceva M, Kania K, Stockis J, Pinaud S, Lazarus KA, Shehata M, Simões BM, Greenhalgh AR et al.

    Nature communications 2021;12;1;1502

    PUBMED: 33686070; DOI: 10.1038/s41467-021-21783-3

  • The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii.

    Clarkson CS, Miles A, Harding NJ, O'Reilly AO, Weetman D, Kwiatkowski D, Donnelly MJ and Anopheles gambiae 1000 Genomes Consortium

    Molecular ecology 2021;30;21;5303-5317

    PUBMED: 33590926; PMC: 9019111; DOI: 10.1111/mec.15845

  • Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses.

    Mitchell C, Steward KF, Charbonneau ARL, Walsh S, Wilson H, Timoney JF, Wernery U, Joseph M, Craig D, van Maanen K et al.

    Microbial genomics 2021;7;3

    PUBMED: 33684029; PMC: 8190609; DOI: 10.1099/mgen.0.000528

  • Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR): Holistic Approach to Unravel Antibacterial Resistance in East Africa (HATUA).

    Asiimwe BB, Kiiru J, Mshana SE, Neema S, Keenan K, Kesby M, Mwanga JR, Sloan DJ, Mmbaga BT, Smith VA et al.

    BMJ open 2021;11;3;e041418

    PUBMED: 34006022; PMC: 7942251; DOI: 10.1136/bmjopen-2020-041418

  • Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.

    Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B et al.

    Nature genetics 2021;53;3;313-321

    PUBMED: 33664507; DOI: 10.1038/s41588-021-00800-7

  • Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.

    Jerber J, Seaton DD, Cuomo ASE, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder MJ et al.

    Nature genetics 2021;53;3;304-312

    PUBMED: 33664506; DOI: 10.1038/s41588-021-00801-6

  • Quantifying genetic heterogeneity between continental populations for human height and body mass index.

    Guo J, Bakshi A, Wang Y, Jiang L, Yengo L, Goddard ME, Visscher PM and Yang J

    Scientific reports 2021;11;1;5240

    PUBMED: 33664403; DOI: 10.1038/s41598-021-84739-z

  • Epitope Mapping of Exposed Tegument and Alimentary Tract Proteins Identifies Putative Antigenic Targets of the Attenuated Schistosome Vaccine.

    Farias LP, Vance GM, Coulson PS, Vitoriano-Souza J, Neto APDS, Wangwiwatsin A, Neves LX, Castro-Borges W, McNicholas S, Wilson KS et al.

    Frontiers in immunology 2021;11;624613

    PUBMED: 33763055; PMC: 7982949; DOI: 10.3389/fimmu.2020.624613

  • Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi.

    Talavera-López C, Messenger LA, Lewis MD, Yeo M, Reis-Cunha JL, Matos GM, Bartholomeu DC, Calzada JE, Saldaña A, Ramírez JD et al.

    Frontiers in cellular and infection microbiology 2021;11;614665

    PUBMED: 33747978; PMC: 7966520; DOI: 10.3389/fcimb.2021.614665

  • Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours.

    Custers L, Khabirova E, Coorens THH, Oliver TRW, Calandrini C, Young MD, Vieira Braga FA, Ellis P, Mamanova L, Segers H et al.

    Nature communications 2021;12;1;1407

    PUBMED: 33658498; PMC: 7930245; DOI: 10.1038/s41467-021-21675-6

  • Analysis of multiple chromosomal rearrangements in the genome of Willisornis vidua using BAC-FISH and chromosome painting on a supposed conserved karyotype.

    Ribas TFA, Pieczarka JC, Griffin DK, Kiazim LG, Nagamachi CY, O Brien PCM, Ferguson-Smith MA, Yang F, Aleixo A and O'Connor RE

    BMC ecology and evolution 2021;21;1;34

    PUBMED: 33653261; DOI: 10.1186/s12862-021-01768-y

  • Development, maturation, and maintenance of human prostate inferred from somatic mutations.

    Grossmann S, Hooks Y, Wilson L, Moore L, O'Neill L, Martincorena I, Voet T, Stratton MR, Heer R and Campbell PJ

    Cell stem cell 2021;28;7;1262-1274.e5

    PUBMED: 33657416; PMC: 8260206; DOI: 10.1016/j.stem.2021.02.005

  • Genomic epidemiology of COVID-19 in care homes in the east of England.

    Hamilton WL, Tonkin-Hill G, Smith ER, Aggarwal D, Houldcroft CJ, Warne B, Meredith LW, Hosmillo M, Jahun AS, Curran MD et al.

    eLife 2021;10

    PUBMED: 33650490; PMC: 7997667; DOI: 10.7554/eLife.64618

  • Iron limitation by transferrin promotes simultaneous cheating of pyoverdine and exoprotease in Pseudomonas aeruginosa.

    Tostado-Islas O, Mendoza-Ortiz A, Ramírez-García G, Cabrera-Takane ID, Loarca D, Pérez-González C, Jasso-Chávez R, Jiménez-Cortés JG, Hoshiko Y, Maeda T et al.

    The ISME journal 2021

    PUBMED: 33654265; DOI: 10.1038/s41396-021-00938-6

  • Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru.

    Murray M, Salvatierra G, Dávila-Barclay A, Ayzanoa B, Castillo-Vilcahuaman C, Huang M, Pajuelo MJ, Lescano AG, Cabrera L, Calderón M et al.

    Frontiers in microbiology 2021;12;635871

    PUBMED: 33737922; PMC: 7961087; DOI: 10.3389/fmicb.2021.635871

  • The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges.

    Tang HHF, Teo SM, Sly PD, Holt PG and Inouye M

    The Journal of allergy and clinical immunology 2021;147;3;781-793

    PUBMED: 33678251; DOI: 10.1016/j.jaci.2020.08.026

  • The PML-RARA fusion is not detectable in historical blood samples of acute promyelocytic leukaemia patients.

    Dunn WG, Gu MS, Fabre MA, Cooper J, Nomdedeu JF, Koumas L, Nicolaou K, Chi J, Costeas P and Vassiliou GS

    Annals of hematology 2021;101;2;443-445

    PUBMED: 33650061; PMC: 8742812; DOI: 10.1007/s00277-021-04472-5

  • Fast searches of large collections of single-cell data using scfind.

    Lee JTH, Patikas N, Kiselev VY and Hemberg M

    Nature methods 2021

    PUBMED: 33649586; DOI: 10.1038/s41592-021-01076-9

  • Hybrid schwannoma-perineurioma frequently harbors VGLL3 rearrangement.

    Dickson BC, Antonescu CR, Demicco EG, Leong DI, Anderson ND, Swanson D, Zhang L, Fletcher CDM and Hornick JL

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2021;34;6;1116-1124

    PUBMED: 33649458; PMC: 8154639; DOI: 10.1038/s41379-021-00783-0

  • Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage.

    Witmer K, Dahalan FA, Metcalf T, Talman AM, Howick VM and Lawniczak MKN

    Frontiers in cellular and infection microbiology 2021;11;604129

    PUBMED: 33732658; PMC: 7958875; DOI: 10.3389/fcimb.2021.604129

  • Comprehensive mapping of transposable elements reveals distinct patterns of element accumulation on chromosomes of wild beetles.

    Amorim IC, Sotero-Caio CG, Costa RGC, Xavier C and de Moura RC

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2021

    PUBMED: 33638119; DOI: 10.1007/s10577-021-09655-4

  • The expectations and realities of nutrigenomic testing in australia: A qualitative study.

    Tutty E, Hickerton C, Terrill B, McClaren B, Tytherleigh R, Stackpoole E, Savard J, Newson A, Middleton A, Nisselle A et al.

    Health expectations : an international journal of public participation in health care and health policy 2021;24;2;670-686

    PUBMED: 33635607; PMC: 8077070; DOI: 10.1111/hex.13216

  • A molecular quantitative trait locus map for osteoarthritis.

    Steinberg J, Southam L, Roumeliotis TI, Clark MJ, Jayasuriya RL, Swift D, Shah KM, Butterfield NC, Brooks RA, McCaskie AW et al.

    Nature communications 2021;12;1;1309

    PUBMED: 33637762; PMC: 7910531; DOI: 10.1038/s41467-021-21593-7

  • Combinatorial CRISPR screen identifies fitness effects of gene paralogues.

    Thompson NA, Ranzani M, van der Weyden L, Iyer V, Offord V, Droop A, Behan F, Gonçalves E, Speak A, Iorio F et al.

    Nature communications 2021;12;1;1302

    PUBMED: 33637726; PMC: 7910459; DOI: 10.1038/s41467-021-21478-9

  • Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013-2014.

    Jamoralin MC, Argimón S, Lagrada ML, Villamin AS, Masim ML, Gayeta JM, Boehme KD, Olorosa AM, Sia SB, Hufano CM et al.

    Western Pacific surveillance and response journal : WPSAR 2021;12;1;17-25

    PUBMED: 34094619; PMC: 8143934; DOI: 10.5365/wpsar.2020.11.1.005

  • Genomic surveillance of methicillin-resistant Staphylococcus aureus in the Philippines, 
2013-2014.

    Masim ML, Argimón S, Espiritu HO, Magbanua MA, Lagrada ML, Olorosa AM, Cohen V, Gayeta JM, Jeffrey B, Abudahab K et al.

    Western Pacific surveillance and response journal : WPSAR 2021;12;1;6-16

    PUBMED: 34094618; PMC: 8143927; DOI: 10.5365/wpsar.2020.11.1.004

  • MalDA, Accelerating Malaria Drug Discovery.

    Yang T, Ottilie S, Istvan ES, Godinez-Macias KP, Lukens AK, Baragaña B, Campo B, Walpole C, Niles JC, Chibale K et al.

    Trends in parasitology 2021;37;6;493-507

    PUBMED: 33648890; PMC: 8261838; DOI: 10.1016/j.pt.2021.01.009

  • Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents.

    Tonkin-Hill G, Ruybal-Pesántez S, Tiedje KE, Rougeron V, Duffy MF, Zakeri S, Pumpaibool T, Harnyuttanakorn P, Branch OH, Ruiz-Mesía L et al.

    PLoS genetics 2021;17;2;e1009269

    PUBMED: 33630855; PMC: 7906310; DOI: 10.1371/journal.pgen.1009269

  • Control of oviductal fluid flow by the G-protein coupled receptor Adgrd1 is essential for murine embryo transit.

    Bianchi E, Sun Y, Almansa-Ordonez A, Woods M, Goulding D, Martinez-Martin N and Wright GJ

    Nature communications 2021;12;1;1251

    PUBMED: 33623007; PMC: 7902839; DOI: 10.1038/s41467-021-21512-w

  • Antigen Nonspecific Induction of Distinct Regulatory T Cell States in Oncogene-Driven Hyperproliferative Skin.

    Zhou C, Tuong ZK, Lukowski SW, Chandra J and Frazer IH

    ImmunoHorizons 2021;5;2;102-116

    PUBMED: 33619159; DOI: 10.4049/immunohorizons.2100006

  • Breaking a species barrier by enabling hybrid recombination.

    Bozdag GO, Ono J, Denton JA, Karakoc E, Hunter N, Leu JY and Greig D

    Current biology : CB 2021;31;4;R180-R181

    PUBMED: 33621502; DOI: 10.1016/j.cub.2020.12.038

  • Genome-wide discovery of genetic loci that uncouple excess adiposity from its comorbidities.

    Huang LO, Rauch A, Mazzaferro E, Preuss M, Carobbio S, Bayrak CS, Chami N, Wang Z, Schick UM, Yang N et al.

    Nature metabolism 2021;3;2;228-243

    PUBMED: 33619380; DOI: 10.1038/s42255-021-00346-2

  • Malaria is a cause of iron deficiency in African children.

    Muriuki JM, Mentzer AJ, Mitchell R, Webb EL, Etyang AO, Kyobutungi C, Morovat A, Kimita W, Ndungu FM, Macharia AW et al.

    Nature medicine 2021

    PUBMED: 33619371; DOI: 10.1038/s41591-021-01238-4

  • Gene Correction Recovers Phagocytosis in Retinal Pigment Epithelium Derived from Retinitis Pigmentosa-Human-Induced Pluripotent Stem Cells.

    Artero-Castro A, Long K, Bassett A, Ávila-Fernandez A, Cortón M, Vidal-Puig A, Jendelova P, Rodriguez-Jimenez FJ, Clemente E, Ayuso C and Erceg S

    International journal of molecular sciences 2021;22;4

    PUBMED: 33672445; PMC: 7923278; DOI: 10.3390/ijms22042092

  • Cholangiocyte organoids can repair bile ducts after transplantation in the human liver.

    Sampaziotis F, Muraro D, Tysoe OC, Sawiak S, Beach TE, Godfrey EM, Upponi SS, Brevini T, Wesley BT, Garcia-Bernardo J et al.

    Science (New York, N.Y.) 2021;371;6531;839-846

    PUBMED: 33602855; PMC: 7610478; DOI: 10.1126/science.aaz6964

  • Common clonal origin of conventional T cells and induced regulatory T cells in breast cancer patients.

    Xydia M, Rahbari R, Ruggiero E, Macaulay I, Tarabichi M, Lohmayer R, Wilkening S, Michels T, Brown D, Vanuytven S et al.

    Nature communications 2021;12;1;1119

    PUBMED: 33602930; PMC: 7893042; DOI: 10.1038/s41467-021-21297-y

  • LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.

    Roller M, Stamper E, Villar D, Izuogu O, Martin F, Redmond AM, Ramachanderan R, Harewood L, Odom DT and Flicek P

    Genome biology 2021;22;1;62

    PUBMED: 33602314; PMC: 7890895; DOI: 10.1186/s13059-021-02260-y

  • Massive expansion of human gut bacteriophage diversity.

    Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD and Lawley TD

    Cell 2021;184;4;1098-1109.e9

    PUBMED: 33606979; PMC: 7895897; DOI: 10.1016/j.cell.2021.01.029

  • Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation.

    Machado L, Geara P, Camps J, Dos Santos M, Teixeira-Clerc F, Van Herck J, Varet H, Legendre R, Pawlotsky JM, Sampaolesi M et al.

    Cell stem cell 2021

    PUBMED: 33609440; DOI: 10.1016/j.stem.2021.01.017

  • Tumour gene expression signature in primary melanoma predicts long-term outcomes.

    Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C et al.

    Nature communications 2021;12;1;1137

    PUBMED: 33602918; DOI: 10.1038/s41467-021-21207-2

  • Unraveling the Developmental Roadmap toward Human Brown Adipose Tissue.

    Carobbio S, Guenantin AC, Bahri M, Rodriguez-Fdez S, Honig F, Kamzolas I, Samuelson I, Long K, Awad S, Lukovic D et al.

    Stem cell reports 2021;16;3;641-655

    PUBMED: 33606988; PMC: 7940445; DOI: 10.1016/j.stemcr.2021.01.013

  • Epitope spreading toward wild-type melanocyte-lineage antigens rescues suboptimal immune checkpoint blockade responses.

    Lo JA, Kawakubo M, Juneja VR, Su MY, Erlich TH, LaFleur MW, Kemeny LV, Rashid M, Malehmir M, Rabi SA et al.

    Science translational medicine 2021;13;581

    PUBMED: 33597266; DOI: 10.1126/scitranslmed.abd8636

  • Antibiotic susceptibility of clinical Burkholderia pseudomallei isolates in northeast Thailand during 2015-2018 and the genomic characterization of β-lactam-resistant isolates.

    Fen SHY, Tandhavanant S, Phunpang R, Ekchariyawat P, Saiprom N, Chewapreecha C, Seng R, Thiansukhon E, Morakot C, Sangsa N et al.

    Antimicrobial agents and chemotherapy 2021

    PUBMED: 33593842; PMC: 8092913; DOI: 10.1128/AAC.02230-20

  • Array-based Dynamic Allele Specific Hybridization (Array-DASH): optimization-free microarray processing for multiple simultaneous genomic assays.

    Gibson SJ, Zahra N, Freeman PJ, Howard C, Lancaster O, Veal C, Fontdevila MC, Paredes R, Noguera-Julian M, Slater A and Brookes AJ

    Analytical biochemistry 2021;114124

    PUBMED: 33607059; DOI: 10.1016/j.ab.2021.114124

  • HTSlib: C library for reading/writing high-throughput sequencing data.

    Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T and Davies RM

    GigaScience 2021;10;2

    PUBMED: 33594436; PMC: 7931820; DOI: 10.1093/gigascience/giab007

  • Twelve years of SAMtools and BCFtools.

    Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM and Li H

    GigaScience 2021;10;2

    PUBMED: 33590861; PMC: 7931819; DOI: 10.1093/gigascience/giab008

  • Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.

    Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K et al.

    Nature genetics 2021;53;3;392-402

    PUBMED: 33589840; PMC: 7610386; DOI: 10.1038/s41588-020-00776-w

  • Maturation Block in Childhood Cancer.

    Behjati S, Gilbertson RJ and Pfister SM

    Cancer discovery 2021;11;3;542-544

    PUBMED: 33589423; DOI: 10.1158/2159-8290.CD-20-0926

  • Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae.

    Caputo B, Pichler V, Bottà G, De Marco C, Hubbart C, Perugini E, Pinto J, Rockett KA, Miles A and Della Torre A

    Molecular ecology resources 2021

    PUBMED: 33590707; DOI: 10.1111/1755-0998.13359

  • Transcriptional characterization of human megakaryocyte polyploidization and lineage commitment.

    Choudry FA, Bagger FO, Macaulay IC, Farrow S, Burden F, Kempster C, McKinney H, Olsen LR, Huang N, Downes K et al.

    Journal of thrombosis and haemostasis : JTH 2021

    PUBMED: 33587817; DOI: 10.1111/jth.15271

  • Attitudes of Costa Rican individuals towards donation of personal genetic data for research.

    Chavarria-Soley G, Francis-Cartin F, Jimenez-Gonzalez F, Ávila-Aguirre A, Castro-Gomez MJ, Robarts L, Middleton A and Raventós H

    Personalized medicine 2021

    PUBMED: 33576268; DOI: 10.2217/pme-2020-0113

  • Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics.

    King HW, Orban N, Riches JC, Clear AJ, Warnes G, Teichmann SA and James LK

    Science immunology 2021;6;56

    PUBMED: 33579751; DOI: 10.1126/sciimmunol.abe6291

  • Climate change and epilepsy: Insights from clinical and basic science studies.

    Gulcebi MI, Bartolini E, Lee O, Lisgaras CP, Onat F, Mifsud J, Striano P, Vezzani A, Hildebrand MS, Jimenez-Jimenez D et al.

    Epilepsy & behavior : E&B 2021;116;107791

    PUBMED: 33578223; PMC: 9386889; DOI: 10.1016/j.yebeh.2021.107791

  • High susceptibility to zoliflodacin and conserved target (GyrB) for zoliflodacin among 1209 consecutive clinical Neisseria gonorrhoeae isolates from 25 European countries, 2018.

    Unemo M, Ahlstrand J, Sánchez-Busó L, Day M, Aanensen D, Golparian D, Jacobsson S, Cole MJ, Torreblanca RA, Ásmundsdóttir LR et al.

    The Journal of antimicrobial chemotherapy 2021

    PUBMED: 33564854; DOI: 10.1093/jac/dkab024

  • Clinical practice guidelines for BRCA1 and BRCA2 genetic testing.

    Pujol P, Barberis M, Beer P, Friedman E, Piulats JM, Capoluongo ED, Garcia Foncillas J, Ray-Coquard I, Penault-Llorca F, Foulkes WD et al.

    European journal of cancer (Oxford, England : 1990) 2021;146;30-47

    PUBMED: 33578357; DOI: 10.1016/j.ejca.2020.12.023

  • Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae.

    Batisti Biffignandi G, Gibbon MJ, Corbella M, Thorpe HA, Merla C, Castelli M, Kallonen T, Pegrum K, Brisse S, Corander J et al.

    G3 (Bethesda, Md.) 2021;11;2

    PUBMED: 33615377; PMC: 8022944; DOI: 10.1093/g3journal/jkab019

  • Human lung macrophages: roll up for the MISTRG tour.

    Jardine L and Haniffa M

    Immunity 2021;54;2;194-196

    PUBMED: 33567257; DOI: 10.1016/j.immuni.2021.01.006

  • In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

    Sun L, Li P, Ju X, Rao J, Huang W, Ren L, Zhang S, Xiong T, Xu K, Zhou X et al.

    Cell 2021

    PUBMED: 33636127; PMC: 7871767; DOI: 10.1016/j.cell.2021.02.008

  • Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts.

    Costa D, Lévesque S, Kumar N, Fresia P, Ferrés I, Lawley TD and Iraola G

    Scientific reports 2021;11;1;3431

    PUBMED: 33564053; DOI: 10.1038/s41598-021-82993-9

  • Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history.

    Coscolla M, Gagneux S, Menardo F, Loiseau C, Ruiz-Rodriguez P, Borrell S, Otchere ID, Asante-Poku A, Asare P, Sánchez-Busó L et al.

    Microbial genomics 2021

    PUBMED: 33555243; DOI: 10.1099/mgen.0.000477

  • Replication of HLA class II locus association with susceptibility to podoconiosis in three Ethiopian ethnic groups.

    Gebresilase T, Finan C, Suveges D, Tessema TS, Aseffa A, Davey G, Hatzikotoulas K, Zeggini E, Newport MJ and Tekola-Ayele F

    Scientific reports 2021;11;1;3285

    PUBMED: 33558538; DOI: 10.1038/s41598-021-81836-x

  • The Diagnostic Yield of Prenatal Genetic Technologies in Congenital Heart Disease: A Prospective Cohort Study.

    Mone F, Stott BK, Hamilton S, Seale AN, Quinlan-Jones E, Allen S, Hurles ME, McMullan DJ, Maher ER and Kilby MD

    Fetal diagnosis and therapy 2021;1-8

    PUBMED: 33550297; DOI: 10.1159/000512488

  • Crypt4GH: a file format standard enabling native access to encrypted data.

    Senf A, Davies R, Haziza F, Marshall J, Troncoso-Pastoriza J, Hofmann O and Keane TM

    Bioinformatics (Oxford, England) 2021

    PUBMED: 33543751; PMC: 8522443; DOI: 10.1093/bioinformatics/btab087

  • Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell.

    Kildisiute G, Kholosy WM, Young MD, Roberts K, Elmentaite R, van Hooff SR, Pacyna CN, Khabirova E, Piapi A, Thevanesan C et al.

    Science advances 2021;7;6

    PUBMED: 33547074; PMC: 7864567; DOI: 10.1126/sciadv.abd3311

  • CC-90009, a novel cereblon E3 ligase modulator, targets acute myeloid leukemia blasts and leukemia stem cells.

    Surka C, Jin L, Mbong N, Lu CC, Jang IS, Rychak E, Mendy D, Clayton T, Tindall E, Hsu C et al.

    Blood 2021;137;5;661-677

    PUBMED: 33197925; PMC: 8215192; DOI: 10.1182/blood.2020008676

  • Melanoma models for the next generation of therapies.

    Patton EE, Mueller KL, Adams DJ, Anandasabapathy N, Aplin AE, Bertolotto C, Bosenberg M, Ceol CJ, Burd CE, Chi P et al.

    Cancer cell 2021;39;5;610-631

    PUBMED: 33545064; PMC: 8378471; DOI: 10.1016/j.ccell.2021.01.011

  • A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis.

    Bell S, Rigas AS, Magnusson MK, Ferkingstad E, Allara E, Bjornsdottir G, Ramond A, Sørensen E, Halldorsson GH, Paul DS et al.

    Communications biology 2021;4;1;156

    PUBMED: 33536631; DOI: 10.1038/s42003-020-01575-z

  • A rare case of paediatric astroblastoma with concomitant MN1-GTSE1 and EWSR1-PATZ1 gene fusions altering management.

    Chadda KR, Holland K, Scoffings D, Dean A, Pickles JC, Behjati S, Jacques TS, Trotman J, Tarpey P, Allinson K et al.

    Neuropathology and applied neurobiology 2021

    PUBMED: 33534137; DOI: 10.1111/nan.12701

  • The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription.

    Berkyurek AC, Furlan G, Lampersberger L, Beltran T, Weick EM, Nischwitz E, Cunha Navarro I, Braukmann F, Akay A, Price J et al.

    The EMBO journal 2021;e105565

    PUBMED: 33533030; DOI: 10.15252/embj.2020105565

  • Genome evolution and the emergence of pathogenicity in avian Escherichia coli.

    Mageiros L, Méric G, Bayliss SC, Pensar J, Pascoe B, Mourkas E, Calland JK, Yahara K, Murray S, Wilkinson TS et al.

    Nature communications 2021;12;1;765

    PUBMED: 33536414; PMC: 7858641; DOI: 10.1038/s41467-021-20988-w

  • A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation.

    Cazares D, Cazares A, Figueroa W, Guarneros G, Edwards RA and Vinuesa P

    mSystems 2021;6;1

    PUBMED: 33531404; DOI: 10.1128/mSystems.00773-20

  • Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts.

    Orgeur M, Frigui W, Pawlik A, Clark S, Williams A, Ates LS, Ma L, Bouchier C, Parkhill J, Brodin P and Brosch R

    Microbial genomics 2021

    PUBMED: 33529148; DOI: 10.1099/mgen.0.000505

  • A comprehensive and high-quality collection of Escherichia coli genomes and their genes.

    Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E and Thomson NR

    Microbial genomics 2021;7;2

    PUBMED: 33417534; PMC: 8208696; DOI: 10.1099/mgen.0.000499

  • Editorial overview: The most difficult of years in cancer research.

    Adams DJ, Imielinski M and Robles-Espinoza CD

    Current opinion in genetics & development 2021;66;iii-iv

    PUBMED: 33722351; DOI: 10.1016/j.gde.2021.02.001

  • Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.

    Chazarra-Gil R, van Dongen S, Kiselev VY and Hemberg M

    Nucleic acids research 2021

    PUBMED: 33524142; DOI: 10.1093/nar/gkab004

  • Generation of Nonmosaic, Two-Pore Channel 2 Biallelic Knockout Pigs in One Generation by CRISPR-Cas9 Microinjection Before Oocyte Insemination.

    Navarro-Serna S, Hachem A, Canha-Gouveia A, Hanbashi A, Garrappa G, Lopes JS, París-Oller E, Sarrías-Gil L, Flores-Flores C, Bassett A et al.

    The CRISPR journal 2021;4;1;132-146

    PUBMED: 33616447; DOI: 10.1089/crispr.2020.0078

  • Norepinephrine promotes triglyceride storage in macrophages via beta2-adrenergic receptor activation.

    Petkevicius K, Bidault G, Virtue S, Jenkins B, van Dierendonck XAMH, Dugourd A, Saez-Rodriguez J, Stienstra R, Koulman A and Vidal-Puig A

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021;35;2;e21266

    PUBMED: 33484195; DOI: 10.1096/fj.202001101R

  • Predisposition to cancer in children and adolescents.

    Kratz CP, Jongmans MC, Cavé H, Wimmer K, Behjati S, Guerrini-Rousseau L, Milde T, Pajtler KW, Golmard L, Gauthier-Villars M et al.

    The Lancet. Child & adolescent health 2021;5;2;142-154

    PUBMED: 33484663; DOI: 10.1016/S2352-4642(20)30275-3

  • Second World Congress on Genetic Counseling: An introduction to the special issue.

    McEwen A, Patch C and Biesecker B

    Journal of genetic counseling 2021;30;1;5-6

    PUBMED: 33580589; DOI: 10.1002/jgc4.1376

  • The Stem Cell Revolution Revealing Protozoan Parasites' Secrets and Paving the Way towards Vaccine Development.

    Pance A

    Vaccines 2021;9;2

    PUBMED: 33572549; DOI: 10.3390/vaccines9020105

  • Genetic Toolkits to Design and Build Mammalian Synthetic Systems.

    Di Blasi R, Zouein A, Ellis T and Ceroni F

    Trends in biotechnology 2021;39;10;1004-1018

    PUBMED: 33526300; DOI: 10.1016/j.tibtech.2020.12.007

  • Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella.

    Bruchmann S, Feltwell T, Parkhill J and Short FL

    Pathogens and disease 2021

    PUBMED: 33512418; DOI: 10.1093/femspd/ftab009

  • Hypoglossal Nerve Abnormalities as Biomarkers for Central Nervous System Defects in Mouse Lines Producing Embryonically Lethal Offspring.

    Reissig LF, Seyedian Moghaddam A, Prin F, Wilson R, Galli A, Tudor C, White JK, Geyer SH, Mohun TJ and Weninger WJ

    Frontiers in neuroanatomy 2021;15;625716

    PUBMED: 33584208; PMC: 7876247; DOI: 10.3389/fnana.2021.625716

  • The contribution of X-linked coding variation to severe developmental disorders.

    Martin HC, Gardner EJ, Samocha KE, Kaplanis J, Akawi N, Sifrim A, Eberhardt RY, Tavares ALT, Neville MDC, Niemi MEK et al.

    Nature communications 2021;12;1;627

    PUBMED: 33504798; PMC: 7840967; DOI: 10.1038/s41467-020-20852-3

  • A long-term conserved satellite DNA that remains unexpanded in several genomes of Characiformes fish is actively transcribed.

    Dos Santos RZ, Calegari RM, Silva DMZA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Foresti FP and Utsunomia R

    Genome biology and evolution 2021

    PUBMED: 33502491; DOI: 10.1093/gbe/evab002

  • Pneumococcal colonisation and virulence factors identified via experimental evolution in infection models.

    Green AE, Howarth D, Chaguza C, Echlin H, Langendonk RF, Munro C, Barton TE, Cd Hinton J, Bentley SD, Rosch JW and Neill DR

    Molecular biology and evolution 2021

    PUBMED: 33502519; DOI: 10.1093/molbev/msab018

  • Systematic Identification of Plasmodium Falciparum Sporozoite Membrane Protein Interactions Reveals an Essential Role for the p24 Complex in Host Infection.

    Knöckel J, Dundas K, Yang ASP, Galaway F, Metcalf T, Gemert GV, Sauerwein RW, Rayner JC, Billker O and Wright GJ

    Molecular & cellular proteomics : MCP 2021;20;100038

    PUBMED: 33515807; PMC: 7950211; DOI: 10.1074/mcp.RA120.002432

  • Elevated levels of tissue factor pathway inhibitor in patients with mild to moderate bleeding tendency.

    Mehic D, Tolios A, Hofer S, Ay C, Haslacher H, Rejtö J, Ouwehand WH, Downes K, Haimel M, Pabinger I and Gebhart J

    Blood advances 2021;5;2;391-398

    PUBMED: 33496735; DOI: 10.1182/bloodadvances.2020003464

  • Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction.

    den Hoed J, de Boer E, Voisin N, Dingemans AJM, Guex N, Wiel L, Nellaker C, Amudhavalli SM, Banka S, Bena FS et al.

    American journal of human genetics 2021

    PUBMED: 33513338; DOI: 10.1016/j.ajhg.2021.01.007

  • Neutrophil specific granule and NETosis defects in gray platelet syndrome.

    Aarts CEM, Downes K, Hoogendijk AJ, Sprenkeler EGG, Gazendam RP, Favier R, Favier M, Tool ATJ, van Hamme JL, Kostadima MA et al.

    Blood advances 2021;5;2;549-564

    PUBMED: 33496751; DOI: 10.1182/bloodadvances.2020002442

  • Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes).

    Pinheiro MLS, Nagamachi CY, Ribas TFA, Diniz CG, O Brien PCM, Ferguson-Smith MA, Yang F and Pieczarka JC

    BMC ecology and evolution 2021;21;1;8

    PUBMED: 33514318; PMC: 7853317; DOI: 10.1186/s12862-020-01737-x

  • MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development.

    Parada GE, Munita R, Georgakopoulos-Soares I, Fernandes HJR, Kedlian VR, Metzakopian E, Andres ME, Miska EA and Hemberg M

    Genome biology 2021;22;1;43

    PUBMED: 33482885; PMC: 7821500; DOI: 10.1186/s13059-020-02246-2

  • Reliable, scalable functional genetics in bloodstream-form Trypanosoma congolense in vitro and in vivo.

    Awuah-Mensah G, McDonald J, Steketee PC, Autheman D, Whipple S, D'Archivio S, Brandt C, Clare S, Harcourt K, Wright GJ et al.

    PLoS pathogens 2021;17;1;e1009224

    PUBMED: 33481935; DOI: 10.1371/journal.ppat.1009224

  • The antimalarial efficacy and mechanism of resistance of the novel chemotype DDD01034957.

    Miguel-Blanco C, Murithi JM, Benavente ED, Angrisano F, Sala KA, van Schalkwyk DA, Vanaerschot M, Schwach F, Fuchter MJ, Billker O et al.

    Scientific reports 2021;11;1;1888

    PUBMED: 33479319; PMC: 7820608; DOI: 10.1038/s41598-021-81343-z

  • A CUDA-powered method for the feature extraction and unsupervised analysis of medical images

    Rundo, L., Tangherloni, A., Cazzaniga, P., Mistri, M., Galimberti, S. et al.

    The journal of supercomputing 2021

    DOI: 10.1007/s11227-020-03565-8

  • An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know?

    Chomkatekaew C, Boonklang P, Sangphukieo A and Chewapreecha C

    Frontiers in microbiology 2021;11;612568

    PUBMED: 33552023; PMC: 7858667; DOI: 10.3389/fmicb.2020.612568

  • Minimal genome-wide human CRISPR-Cas9 library.

    Gonçalves E, Thomas M, Behan FM, Picco G, Pacini C, Allen F, Vinceti A, Sharma M, Jackson DA, Price S et al.

    Genome biology 2021;22;1;40

    PUBMED: 33478580; PMC: 7818936; DOI: 10.1186/s13059-021-02268-4

  • Pancreatic β cells control glucose homeostasis via the secretion of exosomal miR-29 family.

    Li J, Zhang Y, Ye Y, Li D, Liu Y, Lee E, Zhang M, Dai X, Zhang X, Wang S et al.

    Journal of extracellular vesicles 2021;10;3;e12055

    PUBMED: 33520119; PMC: 7820156; DOI: 10.1002/jev2.12055

  • Rapid detection and differentiation of mobile colistin resistance, mcr-1 to mcr-10, genes by real time PCR and melt curve analysis.

    Mentasti M, David S, Sands K, Khan S, Davies L, Turner L and Wootton M

    The Journal of hospital infection 2021

    PUBMED: 33485969; DOI: 10.1016/j.jhin.2021.01.010

  • Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus.

    Grau-Bové X, Lucas E, Pipini D, Rippon E, van 't Hof AE, Constant E, Dadzie S, Egyir-Yawson A, Essandoh J, Chabi J et al.

    PLoS genetics 2021;17;1;e1009253

    PUBMED: 33476334; DOI: 10.1371/journal.pgen.1009253

  • Universal toxin-based selection for precise genome engineering in human cells.

    Li S, Akrap N, Cerboni S, Porritt MJ, Wimberger S, Lundin A, Möller C, Firth M, Gordon E, Lazovic B et al.

    Nature communications 2021;12;1;497

    PUBMED: 33479216; PMC: 7820243; DOI: 10.1038/s41467-020-20810-z

  • Accelerating functional gene discovery in osteoarthritis.

    Butterfield NC, Curry KF, Steinberg J, Dewhurst H, Komla-Ebri D, Mannan NS, Adoum AT, Leitch VD, Logan JG, Waung JA et al.

    Nature communications 2021;12;1;467

    PUBMED: 33473114; DOI: 10.1038/s41467-020-20761-5

  • Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.

    Arredondo-Alonso S, Top J, Corander J, Willems RJL and Schürch AC

    Genome medicine 2021;13;1;9

    PUBMED: 33472670; DOI: 10.1186/s13073-020-00825-3

  • Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq).

    Iannucci A, Makunin AI, Lisachov AP, Ciofi C, Stanyon R, Svartman M and Trifonov VA

    Genes 2021;12;1

    PUBMED: 33478118; PMC: 7835784; DOI: 10.3390/genes12010124

  • Freshwater monitoring by nanopore sequencing.

    Urban L, Holzer A, Baronas JJ, Hall MB, Braeuninger-Weimer P, Scherm MJ, Kunz DJ, Perera SN, Martin-Herranz DE, Tipper ET et al.

    eLife 2021;10

    PUBMED: 33461660; PMC: 7815314; DOI: 10.7554/eLife.61504

  • Tumor Necrosis Factor and Schistosoma mansoni egg antigen omega-1 shape distinct aspects of the early egg-induced granulomatous response.

    Takaki KK, Roca FJ, Schramm G, Wilbers RHP, Ittiprasert W, Brindley PJ, Rinaldi G, Berriman M, Ramakrishnan L and Pagán AJ

    PLoS neglected tropical diseases 2021;15;1;e0008814

    PUBMED: 33465071; PMC: 7845976; DOI: 10.1371/journal.pntd.0008814

  • A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes.

    Gonzalez de la Rosa PM, Thomson M, Trivedi U, Tracey A, Tandonnet S and Blaxter M

    G3 (Bethesda, Md.) 2021;11;1

    PUBMED: 33561231; DOI: 10.1093/g3journal/jkaa020

  • Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles.

    Jones C, Webster G, Mullins AJ, Jenner M, Bull MJ, Dashti Y, Spilker T, Parkhill J, Connor TR, LiPuma JJ et al.

    Microbial genomics 2021

    PUBMED: 33459584; DOI: 10.1099/mgen.0.000515

  • The Rab32/BLOC-3-dependent pathway mediates host defense against different pathogens in human macrophages.

    Baldassarre M, Solano-Collado V, Balci A, Colamarino RA, Dambuza IM, Reid DM, Wilson HM, Brown GD, Mukhopadhyay S, Dougan G and Spanò S

    Science advances 2021;7;3

    PUBMED: 33523895; PMC: 7810368; DOI: 10.1126/sciadv.abb1795

  • Evidence for multi-copy Mega-NUMTs in the human genome.

    Lutz-Bonengel S, Niederstätter H, Naue J, Koziel R, Yang F, Sänger T, Huber G, Berger C, Pflugradt R, Strobl C et al.

    Nucleic acids research 2021

    PUBMED: 33450006; DOI: 10.1093/nar/gkaa1271

  • Protection against oxaliplatin-induced mechanical and thermal hypersensitivity in Sarm1-/- mice.

    Gould SA, White M, Wilbrey AL, Pór E, Coleman MP and Adalbert R

    Experimental neurology 2021;113607

    PUBMED: 33460644; DOI: 10.1016/j.expneurol.2021.113607

  • Analysis of disease model iPSCs derived from patients with a novel Fanconi anemia-like IBMFS ADH5/ALDH2 deficiency.

    Mu A, Hira A, Niwa A, Osawa M, Yoshida K, Mori M, Okamoto Y, Inoue K, Kondo K, Kanemaki MT et al.

    Blood 2021

    PUBMED: 33512438; DOI: 10.1182/blood.2020009111

  • Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.

    Georgakopoulos-Soares I, Mouratidis I, Parada GE, Matharu N, Hemberg M and Ahituv N

    Nucleic acids research 2021;49;1;e4

    PUBMED: 33211865; PMC: 7797064; DOI: 10.1093/nar/gkaa1052

  • No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor.

    Shilts J, Crozier TWM, Greenwood EJD, Lehner PJ and Wright GJ

    Scientific reports 2021;11;1;413

    PUBMED: 33432067; DOI: 10.1038/s41598-020-80464-1

  • Ventilator-associated pneumonia in critically ill patients with COVID-19.

    Maes M, Higginson E, Pereira-Dias J, Curran MD, Parmar S, Khokhar F, Cuchet-Lourenço D, Lux J, Sharma-Hajela S, Ravenhill B et al.

    Critical care (London, England) 2021;25;1;25

    PUBMED: 33430915; DOI: 10.1186/s13054-021-03460-5

  • Significantly improving the quality of genome assemblies through curation.

    Howe K, Chow W, Collins J, Pelan S, Pointon DL, Sims Y, Torrance J, Tracey A and Wood J

    GigaScience 2021;10;1

    PUBMED: 33420778; PMC: 7794651; DOI: 10.1093/gigascience/giaa153

  • The Gene Ontology resource: enriching a GOld mine.

    Gene Ontology Consortium

    Nucleic acids research 2021;49;D1;D325-D334

    PUBMED: 33290552; PMC: 7779012; DOI: 10.1093/nar/gkaa1113

  • A high prevalence of blaOXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England.

    Gibbon MJ, Couto N, David S, Barden R, Standerwick R, Jagadeesan K, Birkwood H, Dulyayangkul P, Avison MB, Kannan A et al.

    Microbial genomics 2021

    PUBMED: 33416467; DOI: 10.1099/mgen.0.000509

  • The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.

    Harland LTG, Simon CS, Senft AD, Costello I, Greder L, Imaz-Rosshandler I, Göttgens B, Marioni JC, Bikoff EK, Porcher C et al.

    Nature cell biology 2021;23;1;61-74

    PUBMED: 33420489; DOI: 10.1038/s41556-020-00611-8

  • Comprehensive characterisation of intronic mis-splicing mutations in human cancers.

    Jung H, Lee KS and Choi JK

    Oncogene 2021

    PUBMED: 33420369; DOI: 10.1038/s41388-020-01614-3

  • Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

    du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR et al.

    Science (New York, N.Y.) 2021

    PUBMED: 33419936; DOI: 10.1126/science.abf2946

  • Genomic Epidemiology of Antimalarial Drug Resistance in Plasmodium falciparum in Southern China.

    Huang F, Jacob CG, Takala-Harrison S, Adams M, Yang HL, Liu H, Xia ZG, Zhou SS, Tang LH and Plowe CV

    Frontiers in cellular and infection microbiology 2021;10;610985

    PUBMED: 33489939; PMC: 7820777; DOI: 10.3389/fcimb.2020.610985

  • Haploinsufficiency of the HIRA gene located in the 22q11 deletion syndrome region is associated with abnormal neurodevelopment and impaired dendritic outgrowth.

    Jeanne M, Vuillaume ML, Ung DC, Vancollie VE, Wagner C, Collins SC, Vonwill S, Haye D, Chelloug N, Pfundt R et al.

    Human genetics 2021

    PUBMED: 33417013; DOI: 10.1007/s00439-020-02252-1

  • Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

    Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt EM, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A et al.

    Nucleic acids research 2021;49;D1;D1311-D1320

    PUBMED: 33045747; PMC: 7778936; DOI: 10.1093/nar/gkaa840

  • Open Targets Platform: supporting systematic drug-target identification and prioritisation.

    Ochoa D, Hercules A, Carmona M, Suveges D, Gonzalez-Uriarte A, Malangone C, Miranda A, Fumis L, Carvalho-Silva D, Spitzer M et al.

    Nucleic acids research 2021;49;D1;D1302-D1310

    PUBMED: 33196847; PMC: 7779013; DOI: 10.1093/nar/gkaa1027

  • Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets.

    Dwane L, Behan FM, Gonçalves E, Lightfoot H, Yang W, van der Meer D, Shepherd R, Pignatelli M, Iorio F and Garnett MJ

    Nucleic acids research 2021;49;D1;D1365-D1372

    PUBMED: 33068406; PMC: 7778984; DOI: 10.1093/nar/gkaa882

  • Urogenital Schistosomiasis-History, Pathogenesis, and Bladder Cancer.

    Santos LL, Santos J, Gouveia MJ, Bernardo C, Lopes C, Rinaldi G, Brindley PJ and Costa JMCD

    Journal of clinical medicine 2021;10;2

    PUBMED: 33429985; DOI: 10.3390/jcm10020205

  • A cross-platform approach identifies genetic regulators of human metabolism and health.

    Lotta LA, Pietzner M, Stewart ID, Wittemans LBL, Li C, Bonelli R, Raffler J, Biggs EK, Oliver-Williams C, Auyeung VPW et al.

    Nature genetics 2021;53;1;54-64

    PUBMED: 33414548; DOI: 10.1038/s41588-020-00751-5

  • Characterization of a common progenitor pool of the epicardium and myocardium.

    Tyser RCV, Ibarra-Soria X, McDole K, A Jayaram S, Godwin J, van den Brand TAH, Miranda AMA, Scialdone A, Keller PJ, Marioni JC and Srinivas S

    Science (New York, N.Y.) 2021

    PUBMED: 33414188; DOI: 10.1126/science.abb2986

  • Computational Stem Cell Biology: Open Questions and Guiding Principles.

    Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A and Wells CA

    Cell stem cell 2021;28;1;20-32

    PUBMED: 33417869; PMC: 7799393; DOI: 10.1016/j.stem.2020.12.012

  • Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco.

    Nzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M et al.

    BMC genomics 2021;22;1;39

    PUBMED: 33413118; PMC: 7792055; DOI: 10.1186/s12864-020-07316-0

  • The Phlebotomus papatasi systemic transcriptional response to trypanosomatid-contaminated blood does not differ from the non-infected blood meal.

    Sloan MA, Sadlova J, Lestinova T, Sanders MJ, Cotton JA, Volf P and Ligoxygakis P

    Parasites & vectors 2021;14;1;15

    PUBMED: 33407867; DOI: 10.1186/s13071-020-04498-0

  • Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico.

    Murphy R, Palm M, Mustonen V, Warringer J, Farewell A, Parts L and Moradigaravand D

    mSphere 2021;6;1

    PUBMED: 33408222; DOI: 10.1128/mSphere.00738-20

  • Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures.

    Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C and Croucher NJ

    The ISME journal 2021

    PUBMED: 33408365; DOI: 10.1038/s41396-020-00867-w

  • Platypus and echidna genomes reveal mammalian biology and evolution.

    Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F et al.

    Nature 2021;592;7856;756-762

    PUBMED: 33408411; PMC: 8081666; DOI: 10.1038/s41586-020-03039-0

  • A practical guide to cancer subclonal reconstruction from DNA sequencing.

    Tarabichi M, Salcedo A, Deshwar AG, Ni Leathlobhair M, Wintersinger J, Wedge DC, Van Loo P, Morris QD and Boutros PC

    Nature methods 2021

    PUBMED: 33398189; DOI: 10.1038/s41592-020-01013-2

  • Rapid parallel adaptation despite gene flow in silent crickets.

    Zhang X, Rayner JG, Blaxter M and Bailey NW

    Nature communications 2021;12;1;50

    PUBMED: 33397914; DOI: 10.1038/s41467-020-20263-4

  • Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction.

    Conti DV, Darst BF, Moss LC, Saunders EJ, Sheng X, Chou A, Schumacher FR, Olama AAA, Benlloch S, Dadaev T et al.

    Nature genetics 2021

    PUBMED: 33398198; DOI: 10.1038/s41588-020-00748-0

  • The Impact of Representation on the Optimization of Marker Panels for Single-cell RNA Data

    Tangherloni, Andrea, Riva, Simone G., Spolaor, Simone, Besozzi, Daniela, Nobile, Marco S. and Cazzaniga et al.

    2021 IEEE Congress on Evolutionary Computation (IEEE CEC) 2021

    DOI: 10.1109/CEC45853.2021.9504808

  • Cancer research needs a better map.

    Boehm JS, Garnett MJ, Adams DJ, Francies HE, Golub TR, Hahn WC, Iorio F, McFarland JM, Parts L and Vazquez F

    Nature 2021;589;7843;514-516

    PUBMED: 33500573; DOI: 10.1038/d41586-021-00182-0

  • Developmental cell programs are co-opted in inflammatory skin disease

    Gary Reynolds, Peter Vegh, James Fletcher, Elizabeth F. M. Poyner, Emily Stephenson, Issac Goh, Rachel A. Botting, Ni Huang, Bayanne Olabi, Anna Dubois et al.

    Science 2021;371;6527

    DOI: 10.1126/science.aba6500; URL: https://science.sciencemag.org/content/371/6527/eaba6500

  • Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome.

    van der Vossen EWJ, Bastos D, Stols-Gonçalves D, de Goffau MC, Davids M, Pereira JPB, Li Yim AYF, Henneman P, Netea MG, de Vos WM et al.

    Gut microbes 2021;13;1;1993513

    PUBMED: 34747338; DOI: 10.1080/19490976.2021.1993513

  • Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining.

    Formenti F, Rinaldi G, Cantacessi C and Cortés A

    Methods in molecular biology (Clifton, N.J.) 2021;2369;263-298

    PUBMED: 34313994; DOI: 10.1007/978-1-0716-1681-9_15

  • Inference of Ligand-Receptor Pairs from Single-Cell Transcriptomics Data.

    Efremova M and Vento-Tormo R

    Methods in molecular biology (Clifton, N.J.) 2021;2346;1-10

    PUBMED: 33625677; DOI: 10.1007/7651_2020_343

  • INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing

    No authors listed

    Science Advances 2021

    DOI: 10.1126/sciadv.abe5054; URL: https://doi.org/10.1126/sciadv.abe5054

  • Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum

    Kathryn Milne, Alasdair Ivens, Adam J Reid, Magda E Lotkowska, Aine O'Toole, Geetha Sankaranarayanan, Diana Munoz Sandoval, Wiebke Nahrendorf, Clement Regnault, Nick J Edwards et al.

    2021

    DOI: 10.7554/eLife.62800; URL: https://doi.org/10.7554/eLife.62800

  • Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome.

    Bergero R, Ellis P, Haerty W, Larcombe L, Macaulay I, Mehta T, Mogensen M, Murray D, Nash W, Neale MJ et al.

    Biological reviews of the Cambridge Philosophical Society 2021

    PUBMED: 33615674; DOI: 10.1111/brv.12680

  • Molecular epidemiology and mortality of group B streptococcal meningitis and infant sepsis in the Netherlands: a 30-year nationwide surveillance study.

    van Kassel MN, de Boer G, Teeri SAF, Jamrozy D, Bentley SD, Brouwer MC, van der Ende A, van de Beek D and Bijlsma MW

    The Lancet. Microbe 2021;2;1;e32-e40

    PUBMED: 35544227; DOI: 10.1016/S2666-5247(20)30192-0

  • Noise2Stack: Improving Image Restoration by Learning from Volumetric Data

    Papkov, Mikhail, Roberts, Kenny, Madissoon, Lee Ann, Shilts, Jarrod, Bayraktar, Omer et al.

    2021;99

    DOI: 10.1007/978-3-030-88552-6_10; URL: https://doi.org/10.1007/978-3-030-88552-6_10

  • Periostin: contributor to abnormal airway epithelial function in asthma?

    Janette K. Burgess, Marnix R. Jonker, Marijn Berg, Nick T.H. ten Hacken, Kerstin B. Meyer, Maarten van den Berge, Martijn C. Nawijn and Irene H. Heijink

    European Respiratory Journal 2021;57;2

    DOI: 10.1183/13993003.01286-2020; URL: https://erj.ersjournals.com/content/57/2/2001286

  • Redefining false discoveries in cancer data analyses.

    Najgebauer H, Perron U and Iorio F

    Nature computational science 2021;1;1;22-23

    PUBMED: 38217149; DOI: 10.1038/s43588-020-00008-5

  • Regional Differences in Human Biliary Tissues and Corresponding In Vitro-Derived Organoids.

    Rimland CA, Tilson SG, Morell CM, Tomaz RA, Lu WY, Adams SE, Georgakopoulos N, Otaizo-Carrasquero F, Myers TG, Ferdinand JR et al.

    Hepatology (Baltimore, Md.) 2021;73;1;247-267

    PUBMED: 32222998; PMC: 8641381; DOI: 10.1002/hep.31252

  • SARS-CoV-2 infection of the oral cavity and saliva

    Huang, Ni, Pérez, Paola, Kato, Takafumi, Mikami, Yu, Okuda, Kenichi et al.

    Nature Medicine 2021;27;5;892

    DOI: 10.1038/s41591-021-01296-8; URL: https://doi.org/10.1038/s41591-021-01296-8

  • Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability

    Vasiliki Lagou, Reedik Mägi, Jouke- Jan Hottenga, Harald Grallert, John R. B. Perry, Nabila Bouatia-Naji, Letizia Marullo, Denis Rybin, Rick Jansen, Josine L. Min et al.

    Nature Communications 2021;12;1;1

    DOI: 10.1038/s41467-020-19366-9; URL: https://doi.org/10.1038/s41467-020-19366-9

  • Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

    Muus, Christoph, Luecken, Malte D., Eraslan, Gökcen, Sikkema, Lisa, Waghray, Avinash et al.

    Nature Medicine 2021;27;3;546

    DOI: 10.1038/s41591-020-01227-z; URL: https://doi.org/10.1038/s41591-020-01227-z

  • Single-cell multi-omics analysis of the immune response in COVID-19

    Stephenson, Emily, Reynolds, Gary, Botting, Rachel A., Calero-Nieto, Fernando J., Morgan, Michael D. et al.

    Nature Medicine 2021;27;5;904

    DOI: 10.1038/s41591-021-01329-2; URL: https://doi.org/10.1038/s41591-021-01329-2

  • Single-Cell Transcriptomic Analysis of Hematopoietic Cells.

    Strzelecka PM, Ranzoni AM and Cvejic A

    Methods in molecular biology (Clifton, N.J.) 2021;2185;135-158

    PUBMED: 33165847; DOI: 10.1007/978-1-0716-0810-4_9

2020

  • Allele-specific expression: applications in cancer and technical considerations.

    Robles-Espinoza CD, Mohammadi P, Bonilla X and Gutierrez-Arcelus M

    Current opinion in genetics & development 2020;66;10-19

    PUBMED: 33383480; DOI: 10.1016/j.gde.2020.10.007

  • Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density.

    Swan AL, Schütt C, Rozman J, Del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P et al.

    PLoS genetics 2020;16;12;e1009190

    PUBMED: 33370286; DOI: 10.1371/journal.pgen.1009190

  • Nasal microbiome research in ANCA-associated vasculitis: Strengths, limitations, and future directions.

    Kronbichler A, Harrison EM and Wagner J

    Computational and structural biotechnology journal 2020;19;415-423

    PUBMED: 33489010; PMC: 7804347; DOI: 10.1016/j.csbj.2020.12.031

  • SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data.

    Young MD and Behjati S

    GigaScience 2020;9;12

    PUBMED: 33367645; PMC: 7763177; DOI: 10.1093/gigascience/giaa151

  • Accurate and fast identification of Campylobacter fetus in bulls by real-time PCR targeting a 16S rRNA gene sequence.

    Delpiazzo R, Barcellos M, Barros S, Betancor L, Fraga M, Gil J, Iraola G, Morsella C, Paolicchi F, Pérez R et al.

    Veterinary and animal science 2020;11;100163

    PUBMED: 33490713; PMC: 7807152; DOI: 10.1016/j.vas.2020.100163

  • Common and Rare Variant Prediction and Penetrance of IBD in a Large, Multi-ethnic, Health System-based Biobank Cohort.

    Gettler K, Levantovsky R, Moscati A, Giri M, Wu Y, Hsu NY, Chuang LS, Sazonovs A, Venkateswaran S, Korie U et al.

    Gastroenterology 2020;160;5;1546-1557

    PUBMED: 33359885; PMC: 8237248; DOI: 10.1053/j.gastro.2020.12.034

  • Chromothripsis drives the evolution of gene amplification in cancer.

    Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ et al.

    Nature 2020;591;7848;137-141

    PUBMED: 33361815; PMC: 7933129; DOI: 10.1038/s41586-020-03064-z

  • Pitfalls of Applying Mouse Markers to Human Adrenal Medullary Cells.

    Kildisiute G, Young MD and Behjati S

    Cancer cell 2020

    PUBMED: 33385328; DOI: 10.1016/j.ccell.2020.12.006

  • Hypertension and renin-angiotensin system blockers are not associated with expression of angiotensin-converting enzyme 2 (ACE2) in the kidney.

    Jiang X, Eales JM, Scannali D, Nazgiewicz A, Prestes P, Maier M, Denniff M, Xu X, Saluja S, Cano-Gamez E et al.

    European heart journal 2020;41;48;4580-4588

    PUBMED: 33206176; PMC: 7665509; DOI: 10.1093/eurheartj/ehaa794

  • The Ncoa7 locus regulates V-ATPase formation and function, neurodevelopment and behaviour.

    Castroflorio E, den Hoed J, Svistunova D, Finelli MJ, Cebrian-Serrano A, Corrochano S, Bassett AR, Davies B and Oliver PL

    Cellular and molecular life sciences : CMLS 2020;78;7;3503-3524

    PUBMED: 33340069; PMC: 8038996; DOI: 10.1007/s00018-020-03721-6

  • Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni.

    Diaz Soria CL, Lee J, Chong T, Coghlan A, Tracey A, Young MD, Andrews T, Hall C, Ng BL, Rawlinson K et al.

    Nature communications 2020;11;1;6411

    PUBMED: 33339816; PMC: 7749135; DOI: 10.1038/s41467-020-20092-5

  • SLFN11 informs on standard of care and novel treatments in a wide range of cancer models.

    Winkler C, Armenia J, Jones GN, Tobalina L, Sale MJ, Petreus T, Baird T, Serra V, Wang AT, Lau A et al.

    British journal of cancer 2020

    PUBMED: 33339894; DOI: 10.1038/s41416-020-01199-4

  • The N6-methyladenosine RNA modification in acute myeloid leukemia.

    Yankova E, Aspris D and Tzelepis K

    Current opinion in hematology 2020;Publish Ahead of Print

    PUBMED: 33337619; DOI: 10.1097/MOH.0000000000000636

  • High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies.

    Amuzu DS, Rockett KA, Leffler EM, Ansah F, Amoako N, Morang'a CM, Hubbart C, Rowlands K, Jeffreys AE, Amenga-Etego LN et al.

    Experimental biology and medicine (Maywood, N.J.) 2020;246;8;916-928

    PUBMED: 33325748; PMC: 8022085; DOI: 10.1177/1535370220968545

  • Multi-locus genotyping reveals established endemicity of a geographically distinct Plasmodium vivax population in Mauritania, West Africa.

    Ba H, Auburn S, Jacob CG, Goncalves S, Duffy CW, Stewart LB, Price RN, Deh YB, Diallo MY, Tandia A et al.

    PLoS neglected tropical diseases 2020;14;12;e0008945

    PUBMED: 33326439; DOI: 10.1371/journal.pntd.0008945

  • Screening for functional transcriptional and splicing regulatory variants with GenIE.

    Cooper SE, Schwartzentruber J, Bello E, Coomber EL and Bassett AR

    Nucleic acids research 2020;48;22;e131

    PUBMED: 33152068; PMC: 7736817; DOI: 10.1093/nar/gkaa960

  • Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea.

    Miotto O, Sekihara M, Tachibana SI, Yamauchi M, Pearson RD, Amato R, Gonçalves S, Mehra S, Noviyanti R, Marfurt J et al.

    PLoS pathogens 2020;16;12;e1009133

    PUBMED: 33320907; PMC: 7771869; DOI: 10.1371/journal.ppat.1009133

  • Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.

    Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB and Cvejic A

    Cell stem cell 2020

    PUBMED: 33352111; DOI: 10.1016/j.stem.2020.11.015

  • Urbanized microbiota in infants, immune constitution and later risk of atopic diseases.

    Lehtimäki J, Thorsen J, Rasmussen MA, Hjelmsø M, Shah S, Mortensen MS, Trivedi U, Vestergaard G, Bønnelykke K, Chawes BL et al.

    The Journal of allergy and clinical immunology 2020

    PUBMED: 33338536; DOI: 10.1016/j.jaci.2020.12.621

  • Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects.

    Lewis MA, Di Domenico F, Ingham NJ, Prosser HM and Steel KP

    Disease models & mechanisms 2020

    PUBMED: 33318051; DOI: 10.1242/dmm.047225

  • Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing.

    Ellis P, Moore L, Sanders MA, Butler TM, Brunner SF, Lee-Six H, Osborne R, Farr B, Coorens THH, Lawson ARJ et al.

    Nature protocols 2020;16;2;841-871

    PUBMED: 33318691; DOI: 10.1038/s41596-020-00437-6

  • Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds.

    Campinoti S, Gjinovci A, Ragazzini R, Zanieri L, Ariza-McNaughton L, Catucci M, Boeing S, Park JE, Hutchinson JC, Muñoz-Ruiz M et al.

    Nature communications 2020;11;1;6372

    PUBMED: 33311516; PMC: 7732825; DOI: 10.1038/s41467-020-20082-7

  • MYC-induced human acute myeloid leukemia requires a continuing IL-3/GM-CSF costimulus.

    Bulaeva E, Pellacani D, Nakamichi N, Hammond CA, Beer PA, Lorzadeh A, Moksa M, Carles A, Bilenky M, Lefort S et al.

    Blood 2020;136;24;2764-2773

    PUBMED: 33301029; DOI: 10.1182/blood.2020006374

  • Whole-genome sequencing analysis of the cardiometabolic proteome.

    Gilly A, Park YC, Png G, Barysenka A, Fischer I, Bjørnland T, Southam L, Suveges D, Neumeyer S, Rayner NW et al.

    Nature communications 2020;11;1;6336

    PUBMED: 33303764; DOI: 10.1038/s41467-020-20079-2

  • Evolutionary divergence of novel open reading frames in cichlids speciation.

    Puntambekar S, Newhouse R, San-Miguel J, Chauhan R, Vernaz G, Willis T, Wayland MT, Umrania Y, Miska EA and Prabakaran S

    Scientific reports 2020;10;1;21570

    PUBMED: 33299045; PMC: 7726158; DOI: 10.1038/s41598-020-78555-0

  • Fundamental differences in physiology of Bordetella pertussis dependent on the two-component system Bvg revealed by gene essentiality studies.

    Belcher T, MacArthur I, King JD, Langridge GC, Mayho M, Parkhill J and Preston A

    Microbial genomics 2020;6;12

    PUBMED: 33295860; PMC: 8116675; DOI: 10.1099/mgen.0.000496

  • Integration of intra-sample contextual error modeling for improved detection of somatic mutations from deep sequencing.

    Abelson S, Zeng AGX, Nofech-Mozes I, Wang TT, Ng SWK, Minden MD, Pugh TJ, Awadalla P, Shlush LI, Murphy T et al.

    Science advances 2020;6;50

    PUBMED: 33298453; PMC: 7725472; DOI: 10.1126/sciadv.abe3722

  • The Key Glycolytic Enzyme Phosphofructokinase Is Involved in Resistance to Antiplasmodial Glycosides.

    Fisher GM, Cobbold SA, Jezewski A, Carpenter EF, Arnold M, Cowell AN, Tjhin ET, Saliba KJ, Skinner-Adams TS, Lee MCS et al.

    mBio 2020;11;6

    PUBMED: 33293381; PMC: 7733947; DOI: 10.1128/mBio.02842-20

  • Functional studies of GWAS variants are gaining momentum.

    Lichou F and Trynka G

    Nature communications 2020;11;1;6283

    PUBMED: 33293539; PMC: 7722852; DOI: 10.1038/s41467-020-20188-y

  • Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.

    Elmentaite R, Ross ADB, Roberts K, James KR, Ortmann D, Gomes T, Nayak K, Tuck L, Pritchard S, Bayraktar OA et al.

    Developmental cell 2020;55;6;771-783.e5

    PUBMED: 33290721; PMC: 7762816; DOI: 10.1016/j.devcel.2020.11.010

  • Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans.

    Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M et al.

    The EMBO journal 2020;40;6;e105496

    PUBMED: 33283887; PMC: 7957426; DOI: 10.15252/embj.2020105496

  • Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.

    Andrews TS, Kiselev VY, McCarthy D and Hemberg M

    Nature protocols 2020

    PUBMED: 33288955; DOI: 10.1038/s41596-020-00409-w

  • Histological Characterization of Feline Bladder Urothelial Carcinoma.

    van der Weyden L, O'Donnell M and Plog S

    Journal of comparative pathology 2020;182;9-14

    PUBMED: 33494910; DOI: 10.1016/j.jcpa.2020.11.001

  • KMT2B-related disorders: expansion of the phenotypic spectrum and long-term efficacy of deep brain stimulation.

    Cif L, Demailly D, Lin JP, Barwick KE, Sa M, Abela L, Malhotra S, Chong WK, Steel D, Sanchis-Juan A et al.

    Brain : a journal of neurology 2020;143;11;3242-3261

    PUBMED: 33150406; PMC: 7719027; DOI: 10.1093/brain/awaa304

  • AZD0364 is a potent and selective ERK1/2 inhibitor which enhances anti-tumour activity in KRAS mutant tumour models when combined with the MEK inhibitor selumetinib.

    Flemington V, Davies EJ, Robinson D, Sandin LC, Delpuech O, Zhang P, Hanson L, Farrington P, Bell S, Falenta K et al.

    Molecular cancer therapeutics 2020

    PUBMED: 33273059; DOI: 10.1158/1535-7163.MCT-20-0002

  • COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: prospective cohort study and systematic review.

    Mone F, Eberhardt RY, Morris RK, Hurles ME, McMullan DJ, Maher ER, Lord J, Chitty LS, Giordano JL, Wapner RJ et al.

    Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology 2020;57;1;43-51

    PUBMED: 32388881; DOI: 10.1002/uog.22072

  • Challenges and opportunities for the adoption of molecular diagnostics for anthelmintic resistance.

    Kotze AC, Gilleard JS, Doyle SR and Prichard RK

    International journal for parasitology. Drugs and drug resistance 2020;14;264-273

    PUBMED: 33307336; PMC: 7726450; DOI: 10.1016/j.ijpddr.2020.11.005

  • NRF2 and the Ambiguous Consequences of Its Activation during Initiation and the Subsequent Stages of Tumourigenesis.

    Robertson H, Dinkova-Kostova AT and Hayes JD

    Cancers 2020;12;12

    PUBMED: 33276631; DOI: 10.3390/cancers12123609

  • To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases.

    Supek F, Lehner B and Lindeboom RGH

    Trends in genetics : TIG 2020;37;7;657-668

    PUBMED: 33277042; DOI: 10.1016/j.tig.2020.11.002

  • Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis.

    Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D, Enoch DA, Brown NM, Parkhill J and Peacock SJ

    The Lancet. Microbe 2020;1;8;e328-e335

    PUBMED: 33313577; PMC: 7721685; DOI: 10.1016/S2666-5247(20)30149-X

  • Diverse Routes toward Early Somites in the Mouse Embryo.

    Guibentif C, Griffiths JA, Imaz-Rosshandler I, Ghazanfar S, Nichols J, Wilson V, Göttgens B and Marioni JC

    Developmental cell 2020

    PUBMED: 33308481; DOI: 10.1016/j.devcel.2020.11.013

  • Extracellular non-coding RNA signatures of the metacestode stage of Echinococcus multilocularis.

    Ancarola ME, Lichtenstein G, Herbig J, Holroyd N, Mariconti M, Brunetti E, Berriman M, Albrecht K, Marcilla A, Rosenzvit MC et al.

    PLoS neglected tropical diseases 2020;14;11;e0008890

    PUBMED: 33253209; PMC: 7728270; DOI: 10.1371/journal.pntd.0008890

  • Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium.

    Top J, Arredondo-Alonso S, Schürch AC, Puranen S, Pesonen M, Pensar J, Willems RJL and Corander J

    Microbial genomics 2020;6;12

    PUBMED: 33253085; PMC: 8116687; DOI: 10.1099/mgen.0.000488

  • Structure of the Plasmodium-interspersed repeat proteins of the malaria parasite.

    Harrison TE, Reid AJ, Cunningham D, Langhorne J and Higgins MK

    Proceedings of the National Academy of Sciences of the United States of America 2020;117;50;32098-32104

    PUBMED: 33257570; PMC: 7749308; DOI: 10.1073/pnas.2016775117

  • Plant foods, dietary fibre and risk of ischaemic heart disease in the European prospective investigation into cancer and nutrition (EPIC) cohort.

    Perez-Cornago A, Crowe FL, Appleby PN, Bradbury KE, Wood AM, Jakobsen MU, Johnson L, Sacerdote C, Steur M, Weiderpass E et al.

    International journal of epidemiology 2020

    PUBMED: 33245137; DOI: 10.1093/ije/dyaa155

  • The stem/progenitor landscape is reshaped in a mouse model of essential thrombocythemia and causes excess megakaryocyte production.

    Prins D, Park HJ, Watcham S, Li J, Vacca M, Bastos HP, Gerbaulet A, Vidal-Puig A, Göttgens B and Green AR

    Science advances 2020;6;48

    PUBMED: 33239297; DOI: 10.1126/sciadv.abd3139

  • Genetic predisposition to hypertension is associated with preeclampsia in European and Central Asian women.

    Steinthorsdottir V, McGinnis R, Williams NO, Stefansdottir L, Thorleifsson G, Shooter S, Fadista J, Sigurdsson JK, Auro KM, Berezina G et al.

    Nature communications 2020;11;1;5976

    PUBMED: 33239696; PMC: 7688949; DOI: 10.1038/s41467-020-19733-6

  • Large genome-wide association study identifies three novel risk variants for restless legs syndrome.

    Didriksen M, Nawaz MS, Dowsett J, Bell S, Erikstrup C, Pedersen OB, Sørensen E, Jennum PJ, Burgdorf KS, Burchell B et al.

    Communications biology 2020;3;1;703

    PUBMED: 33239738; DOI: 10.1038/s42003-020-01430-1

  • Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils.

    Kwon YM, Gori K, Park N, Potts N, Swift K, Wang J, Stammnitz MR, Cannell N, Baez-Ortega A, Comte S et al.

    PLoS biology 2020;18;11;e3000926

    PUBMED: 33232318; PMC: 7685465; DOI: 10.1371/journal.pbio.3000926

  • Mining a GWAS of Severe Covid-19.

    Karim M, Ghoussaini M and Dunham I

    The New England journal of medicine 2020;383;26

    PUBMED: 33289971; DOI: 10.1056/NEJMc2025747

  • Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.

    Surendran P, Feofanova EV, Lahrouchi N, Ntalla I, Karthikeyan S, Cook J, Chen L, Mifsud B, Yao C, Kraja AT et al.

    Nature genetics 2020;52;12;1314-1332

    PUBMED: 33230300; DOI: 10.1038/s41588-020-00713-x

  • Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulation.

    Glinos DA, Soskic B, Williams C, Kennedy A, Jostins L, Sansom DM and Trynka G

    Genes and immunity 2020;21;6-8;390-408

    PUBMED: 33223527; PMC: 7785515; DOI: 10.1038/s41435-020-00118-0

  • Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects.

    Duncan AR, Vitobello A, Collins SC, Vancollie VE, Lelliott CJ, Rodan L, Shi J, Seman AR, Agolini E, Novelli A et al.

    American journal of human genetics 2020;107;6;1170-1177

    PUBMED: 33232677; PMC: 7820620; DOI: 10.1016/j.ajhg.2020.11.001

  • Opportunistic genomic screening. Recommendations of the European Society of Human Genetics.

    de Wert G, Dondorp W, Clarke A, Dequeker EMC, Cordier C, Deans Z, van El CG, Fellmann F, Hastings R, Hentze S et al.

    European journal of human genetics : EJHG 2020

    PUBMED: 33223530; DOI: 10.1038/s41431-020-00758-w

  • Protein antibiotics: mind your language.

    Correia A and Weimann A

    Nature reviews. Microbiology 2020

    PUBMED: 33219332; DOI: 10.1038/s41579-020-00485-5

  • Synergistic targeting of FLT3 mutations in AML via combined menin-MLL and FLT3 inhibition.

    Dzama MM, Steiner M, Rausch J, Sasca D, Schönfeld J, Kunz K, Taubert MC, McGeehan GM, Chen CW, Mupo A et al.

    Blood 2020;136;21;2442-2456

    PUBMED: 32589720; PMC: 8215191; DOI: 10.1182/blood.2020005037

  • ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study.

    Gill D, Arvanitis M, Carter P, Hernández Cordero AI, Jo B, Karhunen V, Larsson SC, Li X, Lockhart SM, Mason A et al.

    Royal Society open science 2020;7;11;200958

    PUBMED: 33391794; PMC: 7735342; DOI: 10.1098/rsos.200958

  • Baseline Gut Microbiota Composition Is Associated With Schistosoma mansoni Infection Burden in Rodent Models.

    Cortés A, Clare S, Costain A, Almeida A, McCarthy C, Harcourt K, Brandt C, Tolley C, Rooney J, Berriman M et al.

    Frontiers in immunology 2020;11;593838

    PUBMED: 33329584; PMC: 7718013; DOI: 10.3389/fimmu.2020.593838

  • Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery.

    Muñoz M, Guerrero-Araya E, Cortés-Tapia C, Plaza-Garrido A, Lawley TD and Paredes-Sabja D

    Microbial genomics 2020;6;12

    PUBMED: 33206037; PMC: 8116674; DOI: 10.1099/mgen.0.000476

  • Plasma Vitamin C and Type 2 Diabetes: Genome-Wide Association Study and Mendelian Randomization Analysis in European Populations.

    Zheng JS, Luan J, Sofianopoulou E, Imamura F, Stewart ID, Day FR, Pietzner M, Wheeler E, Lotta LA, Gundersen TE et al.

    Diabetes care 2020

    PUBMED: 33203707; DOI: 10.2337/dc20-1328

  • Three distinct hematological malignancies from a single germ cell tumor: a case report.

    Spencer Chapman M, May PC, Olavarria E and Nadal Melsio E

    Journal of medical case reports 2020;14;1;222

    PUBMED: 33198808; DOI: 10.1186/s13256-020-02558-8

  • Characterization of nuclear mitochondrial insertions in the whole genomes of primates.

    Dayama G, Zhou W, Prado-Martinez J, Marques-Bonet T and Mills RE

    NAR genomics and bioinformatics 2020;2;4;lqaa089

    PUBMED: 33575633; PMC: 7671390; DOI: 10.1093/nargab/lqaa089

  • The changing epidemiology of carbapenemase-producing Klebsiella pneumoniae in Italy: toward polyclonal evolution with emergence of high-risk lineages.

    Di Pilato V, Errico G, Monaco M, Giani T, Del Grosso M, Antonelli A, David S, Lindh E, Camilli R, Aanensen DM et al.

    The Journal of antimicrobial chemotherapy 2020

    PUBMED: 33188415; DOI: 10.1093/jac/dkaa431

  • Find and fuse: Unsolved mysteries in sperm-egg recognition.

    Bianchi E and Wright GJ

    PLoS biology 2020;18;11;e3000953

    PUBMED: 33186358; DOI: 10.1371/journal.pbio.3000953

  • Guidelines for reporting single-cell RNA-seq experiments.

    Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N et al.

    Nature biotechnology 2020

    PUBMED: 33188371; DOI: 10.1038/s41587-020-00744-z

  • Movement of transposable elements contributes to cichlid diversity.

    Carleton KL, Conte MA, Malinsky M, Nandamuri SP, Sandkam BA, Meier JI, Mwaiko S, Seehausen O and Kocher TD

    Molecular ecology 2020;29;24;4956-4969

    PUBMED: 33049090; DOI: 10.1111/mec.15685

  • Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.

    Watanabe A, Miyake K, Nordlund J, Syvänen AC, van der Weyden L, Honda H, Yamasaki N, Nagamachi A, Inaba T, Ikawa T et al.

    Blood 2020;136;20;2319-2333

    PUBMED: 32573712; PMC: 7702480; DOI: 10.1182/blood.2019004090

  • Eco-Evolutionary Effects of Bacterial Cooperation on Phage Therapy: An Unknown Risk?

    Cazares A, García-Contreras R and Pérez-Velázquez J

    Frontiers in microbiology 2020;11;590294

    PUBMED: 33281786; PMC: 7688660; DOI: 10.3389/fmicb.2020.590294

  • Mutagenicity of 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP) in human TP53 knock-in (Hupki) mouse embryo fibroblasts.

    Hölzl-Armstrong L, Moody S, Kucab JE, Zwart EP, Bellamri M, Luijten M, Turesky RJ, Stratton MR, Arlt VM and Phillips DH

    Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association 2020;111855

    PUBMED: 33189884; DOI: 10.1016/j.fct.2020.111855

  • Asynchrony between virus diversity and antibody selection limits influenza virus evolution.

    Morris DH, Petrova VN, Rossine FW, Parker E, Grenfell BT, Neher RA, Levin SA and Russell CA

    eLife 2020;9

    PUBMED: 33174838; DOI: 10.7554/eLife.62105

  • Genetic Variation in Neisseria meningitidis Does Not Influence Disease Severity in Meningococcal Meningitis.

    Kremer PHC, Lees JA, Ferwerda B, van de Ende A, Brouwer MC, Bentley SD and van de Beek D

    Frontiers in medicine 2020;7;594769

    PUBMED: 33262994; PMC: 7686797; DOI: 10.3389/fmed.2020.594769

  • Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection.

    Olson PD, Tracey A, Baillie A, James K, Doyle SR, Buddenborg SK, Rodgers FH, Holroyd N and Berriman M

    BMC biology 2020;18;1;165

    PUBMED: 33167983; DOI: 10.1186/s12915-020-00899-w

  • Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.

    Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K et al.

    Communications biology 2020;3;1;656

    PUBMED: 33168940; PMC: 7652881; DOI: 10.1038/s42003-020-01377-3

  • Genomic landscape and clonal architecture of mouse oral squamous cell carcinomas dictate tumour ecology.

    Sequeira I, Rashid M, Tomás IM, Williams MJ, Graham TA, Adams DJ, Vigilante A and Watt FM

    Nature communications 2020;11;1;5671

    PUBMED: 33168804; DOI: 10.1038/s41467-020-19401-9

  • Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells.

    Chen L, Yang R, Kwan T, Tang C, Watt S, Zhang Y, Bourque G, Ge B, Downes K, Frontini M et al.

    Scientific data 2020;7;1;376

    PUBMED: 33168820; PMC: 7652884; DOI: 10.1038/s41597-020-00719-4

  • Diversify and Conquer: The Vaccine Escapism of Plasmodium falciparum.

    Pance A

    Microorganisms 2020;8;11

    PUBMED: 33171746; DOI: 10.3390/microorganisms8111748

  • The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2.

    Ziv O, Price J, Shalamova L, Kamenova T, Goodfellow I, Weber F and Miska EA

    Molecular cell 2020

    PUBMED: 33259809; DOI: 10.1016/j.molcel.2020.11.004

  • Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria.

    Köstlbacher S, Collingro A, Halter T, Domman D and Horn M

    Current biology : CB 2020;31;2;346-357.e3

    PUBMED: 33157023; PMC: 7846284; DOI: 10.1016/j.cub.2020.10.030

  • Evaluating variants classified as pathogenic in ClinVar in the DDD Study.

    Wright CF, Eberhardt RY, Constantinou P, Hurles ME, FitzPatrick DR, Firth HV and DDD Study

    Genetics in medicine : official journal of the American College of Medical Genetics 2020;23;3;571-575

    PUBMED: 33149276; PMC: 7935711; DOI: 10.1038/s41436-020-01021-9

  • Genomic Characterization of a Rare, de Novo Unbalanced ins(3;1)(p25.3;q21.3q23.3) in a Female Child with Multiple Congenital Anomalies.

    Ornelas-Arana ML, Pérez-Garcia G, Robles-Espinoza CD, Rangel-Sosa MM, Castaneda-Garcia C, Juárez-Vázquez CI, López-Pérez LG, Pérez-Ornelas C, Hernández-Zaragoza G, Lara-Aguilar RA and Córdova-Fletes C

    Cytogenetic and genome research 2020;1-10

    PUBMED: 33152732; DOI: 10.1159/000511234

  • Lineage-Independent Tumors in Bilateral Neuroblastoma.

    Coorens THH, Farndon SJ, Mitchell TJ, Jain N, Lee S, Hubank M, Sebire N, Anderson J and Behjati S

    The New England journal of medicine 2020;383;19;1860-1865

    PUBMED: 33211929; PMC: 7611571; DOI: 10.1056/NEJMoa2000962

  • Phylogenetic Analysis Indicates a Longer Term Presence of the Globally Distributed H58 Haplotype of Salmonella Typhi in Southern India.

    Pragasam AK, Pickard D, Wong V, Dougan G, Kang G, Thompson A, John J, Balaji V and Mutreja A

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020;71;8;1856-1863

    PUBMED: 32003431; PMC: 7643746; DOI: 10.1093/cid/ciz1112

  • Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

    Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M et al.

    Briefings in bioinformatics 2020

    PUBMED: 33147627; DOI: 10.1093/bib/bbaa232

  • Gut-educated IgA plasma cells defend the meningeal venous sinuses.

    Fitzpatrick Z, Frazer G, Ferro A, Clare S, Bouladoux N, Ferdinand J, Tuong ZK, Negro-Demontel ML, Kumar N, Suchanek O et al.

    Nature 2020;587;7834;472-476

    PUBMED: 33149302; PMC: 7748383; DOI: 10.1038/s41586-020-2886-4

  • Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn's disease.

    Diederen K, Li JV, Donachie GE, de Meij TG, de Waart DR, Hakvoort TBM, Kindermann A, Wagner J, Auyeung V, Te Velde AA et al.

    Scientific reports 2020;10;1;18879

    PUBMED: 33144591; DOI: 10.1038/s41598-020-75306-z

  • Modulation of Triple Artemisinin-Based Combination Therapy Pharmacodynamics by Plasmodium falciparum Genotype.

    Ansbro MR, Itkin Z, Chen L, Zahoranszky-Kohalmi G, Amaratunga C, Miotto O, Peryea T, Hobbs CV, Suon S, Sá JM et al.

    ACS pharmacology & translational science 2020;3;6;1144-1157

    PUBMED: 33344893; PMC: 7737215; DOI: 10.1021/acsptsci.0c00110

  • Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain.

    Lall GM, Larmuseau MHD, Wetton JH, Batini C, Hallast P, Huszar TI, Zadik D, Aase S, Baker T, Balaresque P et al.

    European journal of human genetics : EJHG 2020;29;3;512-523

    PUBMED: 33139852; PMC: 7940619; DOI: 10.1038/s41431-020-00747-z

  • Transmission of artemisinin-resistant malaria parasites to mosquitoes under antimalarial drug pressure.

    Witmer K, Dahalan FA, Delves MJ, Yahiya S, Watson OJ, Straschil U, Chiwcharoen D, Sornboon B, Pukrittayakamee S, Pearson RD et al.

    Antimicrobial agents and chemotherapy 2020

    PUBMED: 33139275; DOI: 10.1128/AAC.00898-20

  • High-throughput multivariable Mendelian randomization analysis prioritizes apolipoprotein B as key lipid risk factor for coronary artery disease.

    Zuber V, Gill D, Ala-Korpela M, Langenberg C, Butterworth A, Bottolo L and Burgess S

    International journal of epidemiology 2020

    PUBMED: 33130851; DOI: 10.1093/ije/dyaa216

  • Using genomics to improve preparedness and response of future epidemics or pandemics in Africa.

    Chaguza C, Nyaga MM, Mwenda JM, Esona MD and Jere KC

    The Lancet. Microbe 2020;1;7;e275-e276

    PUBMED: 33345202; PMC: 7729821; DOI: 10.1016/S2666-5247(20)30169-5

  • Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap.

    NIHR Global Health Research Unit on Genomic Surveillance of AMR

    BMJ global health 2020;5;11

    PUBMED: 33239336; PMC: 7689591; DOI: 10.1136/bmjgh-2019-002244

  • Defining the clinical genomic landscape for real-world precision oncology.

    Beer PA, Cooke SL, Chang DK and Biankin AV

    Genomics 2020

    PUBMED: 33144218; DOI: 10.1016/j.ygeno.2020.10.032

  • meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation.

    Mikutis S, Gu M, Sendinc E, Hazemi ME, Kiely-Collins H, Aspris D, Vassiliou GS, Shi Y, Tzelepis K and Bernardes GJL

    ACS central science 2020;6;12;2196-2208

    PUBMED: 33376781; PMC: 7760485; DOI: 10.1021/acscentsci.0c01094

  • Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites.

    Stewart LB, Diaz-Ingelmo O, Claessens A, Abugri J, Pearson RD, Goncalves S, Drury E, Kwiatkowski DP, Awandare GA and Conway DJ

    Communications biology 2020;3;1;624

    PUBMED: 33116247; PMC: 7595149; DOI: 10.1038/s42003-020-01349-7

  • Schistosoma mansoni Eggs Modulate the Timing of Granuloma Formation to Promote Transmission.

    Takaki KK, Rinaldi G, Berriman M, Pagán AJ and Ramakrishnan L

    Cell host & microbe 2020;29;1;58-67.e5

    PUBMED: 33120115; PMC: 7815046; DOI: 10.1016/j.chom.2020.10.002

  • Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.

    Ramos-Madrigal J, Sinding MS, Carøe C, Mak SST, Niemann J, Samaniego Castruita JA, Fedorov S, Kandyba A, Germonpré M, Bocherens H et al.

    Current biology : CB 2020

    PUBMED: 33125870; DOI: 10.1016/j.cub.2020.10.002

  • Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.

    Gouliouris T, Coll F, Ludden C, Blane B, Raven KE, Naydenova P, Crawley C, Török ME, Enoch DA, Brown NM et al.

    Nature microbiology 2020;6;1;103-111

    PUBMED: 33106672; PMC: 7610418; DOI: 10.1038/s41564-020-00806-7

  • Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae.

    Ma KC, Mortimer TD, Duckett MA, Hicks AL, Wheeler NE, Sánchez-Busó L and Grad YH

    Nature communications 2020;11;1;5374

    PUBMED: 33097713; DOI: 10.1038/s41467-020-19250-6

  • Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.

    Azarian T, Martinez PP, Arnold BJ, Qiu X, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R et al.

    PLoS biology 2020;18;10;e3000878

    PUBMED: 33091022; PMC: 7580979; DOI: 10.1371/journal.pbio.3000878

  • Novel manifestations of immune dysregulation and granule defects in gray platelet syndrome.

    Sims MC, Mayer L, Collins JH, Bariana TK, Megy K, Lavenu-Bombled C, Seyres D, Kollipara L, Burden FS, Greene D et al.

    Blood 2020;136;17;1956-1967

    PUBMED: 32693407; PMC: 7582559; DOI: 10.1182/blood.2019004776

  • Positive selection in admixed populations from Ethiopia.

    Walsh S, Pagani L, Xue Y, Laayouni H, Tyler-Smith C and Bertranpetit J

    BMC genetics 2020;21;Suppl 1;108

    PUBMED: 33092534; PMC: 7580818; DOI: 10.1186/s12863-020-00908-5

  • Reference genome and demographic history of the most endangered marine mammal, the vaquita.

    Morin PA, Archer FI, Avila CD, Balacco JR, Bukhman YV, Chow W, Fedrigo O, Formenti G, Fronczek JA, Fungtammasan A et al.

    Molecular ecology resources 2020

    PUBMED: 33089966; DOI: 10.1111/1755-0998.13284

  • A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities.

    Sridhar S, Forrest S, Kean I, Young J, Bartholdson Scott J, Maes M, Pereira-Dias J, Parmar S, Routledge M, Sparkes D et al.

    Wellcome open research 2020;5;110

    PUBMED: 33134554; PMC: 7590889; DOI: 10.12688/wellcomeopenres.15937.2

  • Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site.

    Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC et al.

    Cancer discovery 2020;11;2;340-361

    PUBMED: 33087317; PMC: 7116717; DOI: 10.1158/2159-8290.CD-20-1092

  • A single-cell RNA-sequencing training and analysis suite using the Galaxy framework.

    Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR et al.

    GigaScience 2020;9;10

    PUBMED: 33079170; PMC: 7574357; DOI: 10.1093/gigascience/giaa102

  • High-throughput genotyping of high-homology mutant mouse strains by next-generation sequencing.

    Gleeson D, Sethi D, Platte R, Burvill J, Barrett D, Akhtar S, Bruntraeger M, Bottomley J, Bussell J and Ryder E

    Methods (San Diego, Calif.) 2020

    PUBMED: 33096238; DOI: 10.1016/j.ymeth.2020.10.011

  • Quorum sensing N-Acyl homoserine lactones are a new class of anti-schistosomal.

    Whiteland H, Crusco A, Bloemberg LW, Tibble-Howlings J, Forde-Thomas J, Coghlan A, Murphy PJ and Hoffmann KF

    PLoS neglected tropical diseases 2020;14;10;e0008630

    PUBMED: 33075069; DOI: 10.1371/journal.pntd.0008630

  • A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence.

    Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R et al.

    microLife 2020;1;1;uqaa002

    PUBMED: 37223003; PMC: 10117436; DOI: 10.1093/femsml/uqaa002

  • The association between circulating 25-hydroxyvitamin D metabolites and type 2 diabetes in European populations: A meta-analysis and Mendelian randomisation analysis.

    Zheng JS, Luan J, Sofianopoulou E, Sharp SJ, Day FR, Imamura F, Gundersen TE, Lotta LA, Sluijs I, Stewart ID et al.

    PLoS medicine 2020;17;10;e1003394

    PUBMED: 33064751; DOI: 10.1371/journal.pmed.1003394

  • Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals.

    Folkersen L, Gustafsson S, Wang Q, Hansen DH, Hedman ÅK, Schork A, Page K, Zhernakova DV, Wu Y, Peters J et al.

    Nature metabolism 2020;2;10;1135-1148

    PUBMED: 33067605; DOI: 10.1038/s42255-020-00287-2

  • A Deep Learning Approach Validates Genetic Risk Factors for Late Toxicity After Prostate Cancer Radiotherapy in a REQUITE Multi-National Cohort.

    Massi MC, Gasperoni F, Ieva F, Paganoni AM, Zunino P, Manzoni A, Franco NR, Veldeman L, Ost P, Fonteyne V et al.

    Frontiers in oncology 2020;10;541281

    PUBMED: 33178576; PMC: 7593843; DOI: 10.3389/fonc.2020.541281

  • Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

    Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J et al.

    Science (New York, N.Y.) 2020

    PUBMED: 33060197; DOI: 10.1126/science.abe9403

  • Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.

    Mullins AJ, Jones C, Bull MJ, Webster G, Parkhill J, Connor TR, Murray JAH, Challis GL and Mahenthiralingam E

    Microbiology resource announcements 2020;9;42

    PUBMED: 33060263; PMC: 7561682; DOI: 10.1128/MRA.00485-20

  • Evidence for 28 genetic disorders discovered by combining healthcare and research data.

    Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF et al.

    Nature 2020;586;7831;757-762

    PUBMED: 33057194; PMC: 7116826; DOI: 10.1038/s41586-020-2832-5

  • Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity.

    Panagiotou S, Chaguza C, Yahya R, Audshasai T, Baltazar M, Ressel L, Khandaker S, Alsahag M, Mitchell TJ, Prudhomme M et al.

    Scientific reports 2020;10;1;17313

    PUBMED: 33057054; PMC: 7560715; DOI: 10.1038/s41598-020-73454-w

  • The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.

    Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B et al.

    F1000Research 2020;9

    PUBMED: 34367618; PMC: 8311797; DOI: 10.12688/f1000research.24887.1

  • Single-Cell Transcriptomics of Parkinson's Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses.

    Fernandes HJR, Patikas N, Foskolou S, Field SF, Park JE, Byrne ML, Bassett AR and Metzakopian E

    Cell reports 2020;33;2;108263

    PUBMED: 33053338; DOI: 10.1016/j.celrep.2020.108263

  • Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits.

    Vogelezang S, Bradfield JP, Ahluwalia TS, Curtin JA, Lakka TA, Grarup N, Scholz M, van der Most PJ, Monnereau C, Stergiakouli E et al.

    PLoS genetics 2020;16;10;e1008718

    PUBMED: 33045005; DOI: 10.1371/journal.pgen.1008718

  • SID-2 negatively regulates development likely independent of nutritional dsRNA uptake.

    Braukmann F, Jordan D, Jenkins B, Koulman A and Miska EA

    RNA biology 2020;18;6;888-899

    PUBMED: 33044912; PMC: 8081039; DOI: 10.1080/15476286.2020.1827619

  • Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory.

    Soon MSF, Lee HJ, Engel JA, Straube J, Thomas BS, Pernold CPS, Clarke LS, Laohamonthonkul P, Haldar RN, Williams CG et al.

    Nature immunology 2020

    PUBMED: 33046889; DOI: 10.1038/s41590-020-0800-8

  • Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes.

    Ford A, Kepple D, Abagero BR, Connors J, Pearson R, Auburn S, Getachew S, Ford C, Gunalan K, Miller LH et al.

    PLoS neglected tropical diseases 2020;14;10;e0008234

    PUBMED: 33044985; DOI: 10.1371/journal.pntd.0008234

  • Involvement of circulating factors in the transmission of paternal experiences through the germline.

    van Steenwyk G, Gapp K, Jawaid A, Germain PL, Manuella F, Tanwar DK, Zamboni N, Gaur N, Efimova A, Thumfart KM et al.

    The EMBO journal 2020;e104579

    PUBMED: 33034389; DOI: 10.15252/embj.2020104579

  • Rotavirus Genotypes in Hospitalized Children with Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997 - 2019.

    Mhango C, Mandolo JJ, Chinyama E, Wachepa R, Kanjerwa O, Malamba-Banda C, Matambo PB, Barnes KG, Chaguza C, Shawa IT et al.

    The Journal of infectious diseases 2020

    PUBMED: 33033832; DOI: 10.1093/infdis/jiaa616

  • Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism.

    Chaguza C, Yang M, Cornick JE, du Plessis M, Gladstone RA, Kwambana-Adams BA, Lo SW, Ebruke C, Tonkin-Hill G, Peno C et al.

    Communications biology 2020;3;1;559

    PUBMED: 33033372; PMC: 7545184; DOI: 10.1038/s42003-020-01290-9

  • Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer.

    Dreyer SB, Upstill-Goddard R, Paulus-Hock V, Paris C, Lampraki EM, Dray E, Serrels B, Caligiuri G, Rebus S, Plenker D et al.

    Gastroenterology 2020

    PUBMED: 33039466; DOI: 10.1053/j.gastro.2020.09.043

  • The mutational landscape of melanoma brain metastases presenting as the first visceral site of recurrence.

    Rabbie R, Ferguson P, Wong K, Couturier DL, Moran U, Turner C, Emanuel P, Haas K, Saunus JM, Davidson MR et al.

    British journal of cancer 2020;124;1;156-160

    PUBMED: 33024263; PMC: 7782512; DOI: 10.1038/s41416-020-01090-2

  • Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions.

    Siegel SV, Chappell L, Hostetler JB, Amaratunga C, Suon S, Böhme U, Berriman M, Fairhurst RM and Rayner JC

    Scientific reports 2020;10;1;16667

    PUBMED: 33028892; PMC: 7541449; DOI: 10.1038/s41598-020-73562-7

  • Framework for quality assessment of whole genome cancer sequences.

    Whalley JP, Buchhalter I, Rheinbay E, Raine KM, Stobbe MD, Kleinheinz K, Werner J, Beltran S, Gut M, Hübschmann D et al.

    Nature communications 2020;11;1;5040

    PUBMED: 33028839; PMC: 7541455; DOI: 10.1038/s41467-020-18688-y

  • Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator.

    Bergstrom EN, Barnes M, Martincorena I and Alexandrov LB

    BMC bioinformatics 2020;21;1;438

    PUBMED: 33028213; PMC: 7539472; DOI: 10.1186/s12859-020-03772-3

  • In-depth clinical and biological exploration of DNA Damage Immune Response (DDIR) as a biomarker for oxaliplatin use in colorectal cancer.

    Malla SB, Fisher D, Domingo E, Blake A, Hassanieh S, Redmond KL, Richman SD, Youdell M, Walker S, Logan GE et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2020

    PUBMED: 33028592; DOI: 10.1158/1078-0432.CCR-20-3237

  • Lipopolysaccharide O structure of adherent and invasive Escherichia coli regulates intestinal inflammation via complement C3.

    Ohno M, Hasegawa M, Hayashi A, Caballero-Flores G, Alteri CJ, Lawley TD, Kamada N, Núñez G and Inohara N

    PLoS pathogens 2020;16;10;e1008928

    PUBMED: 33027280; PMC: 7571687; DOI: 10.1371/journal.ppat.1008928

  • Phylogenetic and Evolutionary Analysis Reveals the Recent Dominance of Ciprofloxacin-Resistant Shigella sonnei and Local Persistence of S. flexneri Clones in India.

    Muthuirulandi Sethuvel DP, Mutreja A, Pragasam AK, Vasudevan K, Murugan D, Anandan S, Michael JS, Walia K and Veeraraghavan B

    mSphere 2020;5;5

    PUBMED: 33028681; PMC: 7568650; DOI: 10.1128/mSphere.00569-20

  • Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation.

    Beale MA, Noguera-Julian M, Godornes C, Casadellà M, González-Beiras C, Parera M, Kapa Jnr A, Houinei W, Wangi J, Corbacho-Monne M et al.

    The Lancet. Microbe 2020;1;6;e263-e271

    PUBMED: 35544222; DOI: 10.1016/S2666-5247(20)30113-0

  • Drivers underpinning the malignant transformation of giant cell tumour of bone.

    Fittall MW, Lyskjaer I, Ellery P, Lombard P, Ijaz J, Strobl AC, Oukrif D, Tarabichi M, Sill M, Koelsche C et al.

    The Journal of pathology 2020;252;4;433-440

    PUBMED: 32866294; PMC: 8432151; DOI: 10.1002/path.5537

  • Extensive fragmentation and re-organization of transcription in Systemic Lupus Erythematosus.

    Ntasis VF, Panousis NI, Tektonidou MG, Dermitzakis ET, Boumpas DT, Bertsias GK and Nikolaou C

    Scientific reports 2020;10;1;16648

    PUBMED: 33024230; DOI: 10.1038/s41598-020-73654-4

  • Novel strategies to target the humoral alloimmune response.

    Suchanek O and Clatworthy MR

    HLA 2020

    PUBMED: 33022883; DOI: 10.1111/tan.14092

  • Prophage exotoxins enhance colonization fitness in epidemic scarlet fever-causing Streptococcus pyogenes.

    Brouwer S, Barnett TC, Ly D, Kasper KJ, De Oliveira DMP, Rivera-Hernandez T, Cork AJ, McIntyre L, Jespersen MG, Richter J et al.

    Nature communications 2020;11;1;5018

    PUBMED: 33024089; DOI: 10.1038/s41467-020-18700-5

  • Archaeogenetics: What Can Ancient Genomes Tell Us about the Origin of Syphilis?

    Beale MA and Lukehart SA

    Current biology : CB 2020;30;19;R1092-R1095

    PUBMED: 33022244; DOI: 10.1016/j.cub.2020.08.022

  • Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure.

    Akdemir KC, Le VT, Kim JM, Killcoyne S, King DA, Lin YP, Tian Y, Inoue A, Amin SB, Robinson FS et al.

    Nature genetics 2020;52;11;1178-1188

    PUBMED: 33020667; PMC: 8350746; DOI: 10.1038/s41588-020-0708-0

  • Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer.

    Wong M, Mayoh C, Lau LMS, Khuong-Quang DA, Pinese M, Kumar A, Barahona P, Wilkie EE, Sullivan P, Bowen-James R et al.

    Nature medicine 2020;26;11;1742-1753

    PUBMED: 33020650; DOI: 10.1038/s41591-020-1072-4

  • Application of the LymphGen classification tool to 928 clinically and genetically-characterised cases of diffuse large B cell lymphoma (DLBCL).

    Runge HFP, Lacy S, Barrans S, Beer PA, Painter D, Smith A, Roman E, Burton C, Crouch S, Tooze R and Hodson DJ

    British journal of haematology 2020

    PUBMED: 33010029; DOI: 10.1111/bjh.17132

  • Underpowered PANTS: a response to the conclusions of "Extended Analysis Identifies Drug-Specific Association of Two Distinct HLA Class II Haplotypes for Development of Immunogenicity to Adalimumab and Infliximab".

    Sazonovs A, Ahmad T and Anderson CA

    Gastroenterology 2020

    PUBMED: 33022279; DOI: 10.1053/j.gastro.2020.05.102

  • Extensive heterogeneity in somatic mutation and selection in the human bladder.

    Lawson ARJ, Abascal F, Coorens THH, Hooks Y, O'Neill L, Latimer C, Raine K, Sanders MA, Warren AY, Mahbubani KTA et al.

    Science (New York, N.Y.) 2020;370;6512;75-82

    PUBMED: 33004514; DOI: 10.1126/science.aba8347

  • A coagulation defect arising from heterozygous premature termination of tissue factor.

    Schulman S, El-Darzi E, Florido MH, Friesen M, Merrill-Skoloff G, Brake MA, Schuster CR, Lin L, Westrick RJ, Cowan CA et al.

    The Journal of clinical investigation 2020;130;10;5302-5312

    PUBMED: 32663190; PMC: 7524505; DOI: 10.1172/JCI133780

  • Comment on: "Tumour-agnostic drugs in paediatric cancers", Chisholm et al., BJC 2020.

    Oliver TRW, Jackson TJ, Ogunbiyi O, Sebire N, Slater O, Jorgensen M and Behjati S

    British journal of cancer 2020

    PUBMED: 32999471; DOI: 10.1038/s41416-020-01103-0

  • Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression.

    Grau-Bové X, Tomlinson S, O'Reilly AO, Harding NJ, Miles A, Kwiatkowski D, Donnelly MJ, Weetman D and Anopheles gambiae 1000 Genomes Consortium

    Molecular biology and evolution 2020;37;10;2900-2917

    PUBMED: 32449755; PMC: 7530614; DOI: 10.1093/molbev/msaa128

  • Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae.

    Dorman MJ, Domman D, Poklepovich T, Tolley C, Zolezzi G, Kane L, Viñas MR, Panagópulo M, Moroni M, Binsztein N et al.

    Nature communications 2020;11;1;4918

    PUBMED: 33004800; PMC: 7530988; DOI: 10.1038/s41467-020-18647-7

  • Organ immune responses - don't forget the structural cells.

    Tuong ZK and Clatworthy MR

    Nature reviews. Nephrology 2020;16;10;570-571

    PUBMED: 32792669; DOI: 10.1038/s41581-020-00334-x

  • Seeds of cancer in normal skin.

    Martincorena I

    Nature 2020;586;7830;504-506

    PUBMED: 33028991; DOI: 10.1038/d41586-020-02749-9

  • Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway.

    Chai AWY, Yee PS, Price S, Yee SM, Lee HM, Tiong VK, Gonçalves E, Behan FM, Bateson J, Gilbert J et al.

    eLife 2020;9

    PUBMED: 32990596; DOI: 10.7554/eLife.57761

  • The mutational signature profile of known and suspected human carcinogens in mice.

    Riva L, Pandiri AR, Li YR, Droop A, Hewinson J, Quail MA, Iyer V, Shepherd R, Herbert RA, Campbell PJ et al.

    Nature genetics 2020;52;11;1189-1197

    PUBMED: 32989322; PMC: 7610456; DOI: 10.1038/s41588-020-0692-4

  • AZD4320, A Dual Inhibitor of Bcl-2 and Bcl-xL, Induces Tumor Regression in Hematologic Cancer Models without Dose-limiting Thrombocytopenia.

    Balachander SB, Criscione SW, Byth KF, Cidado J, Adam A, Lewis P, Macintyre T, Wen S, Lawson D, Burke K et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2020;26;24;6535-6549

    PUBMED: 32988967; DOI: 10.1158/1078-0432.CCR-20-0863

  • ESMO recommendations on predictive biomarker testing for homologous recombination deficiency and PARP inhibitor benefit in ovarian cancer.

    Miller RE, Leary A, Scott CL, Serra V, Lord CJ, Bowtell D, Chang DK, Garsed DW, Jonkers J, Ledermann JA et al.

    Annals of oncology : official journal of the European Society for Medical Oncology 2020

    PUBMED: 33004253; DOI: 10.1016/j.annonc.2020.08.2102

  • Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii.

    Anopheles gambiae 1000 Genomes Consortium

    Genome research 2020;30;10;1533-1546

    PUBMED: 32989001; PMC: 7605271; DOI: 10.1101/gr.262790.120

  • Genome-wide association study identifies 48 common genetic variants associated with handedness.

    Cuellar-Partida G, Tung JY, Eriksson N, Albrecht E, Aliev F, Andreassen OA, Barroso I, Beckmann JS, Boks MP, Boomsma DI et al.

    Nature human behaviour 2020

    PUBMED: 32989287; DOI: 10.1038/s41562-020-00956-y

  • Large-scale RNAi screening uncovers therapeutic targets in the parasite Schistosoma mansoni.

    Wang J, Paz C, Padalino G, Coghlan A, Lu Z, Gradinaru I, Collins JNR, Berriman M, Hoffmann KF and Collins JJ

    Science (New York, N.Y.) 2020;369;6511;1649-1653

    PUBMED: 32973031; PMC: 7877197; DOI: 10.1126/science.abb7699

  • Draft Genome Sequence of a New Delhi Metallo-β-Lactamase (NDM-1)-Producing Providencia stuartii Strain Isolated in Lima, Peru.

    Lezameta L, Cuicapuza D, Dávila-Barclay A, Torres S, Salvatierra G, Tsukayama P and Tamariz J

    Microbiology resource announcements 2020;9;39

    PUBMED: 32972938; PMC: 7516149; DOI: 10.1128/MRA.00788-20

  • Functional signatures of evolutionarily young CTCF binding sites.

    Azazi D, Mudge JM, Odom DT and Flicek P

    BMC biology 2020;18;1;132

    PUBMED: 32988407; DOI: 10.1186/s12915-020-00863-8

  • Gene signatures from scRNA-seq accurately quantify mast cells in biopsies in asthma.

    Jiang J, Faiz A, Berg M, Carpaij OA, Vermeulen CJ, Brouwer S, Hesse L, Teichmann SA, Ten Hacken NHT, Timens W et al.

    Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2020;50;12;1428-1431

    PUBMED: 32935368; PMC: 7756890; DOI: 10.1111/cea.13732

  • Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae.

    David S, Cohen V, Reuter S, Sheppard AE, Giani T, Parkhill J, European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) Working Group, ESCMID Study Group for Epidemiological Markers (ESGEM), Rossolini GM, Feil EJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2020

    PUBMED: 32968015; DOI: 10.1073/pnas.2003407117

  • Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants.

    Manenzhe RI, Dube FS, Wright M, Lennard K, Mounaud S, Lo SW, Zar HJ, Nierman WC, Nicol MP and Moodley C

    Frontiers in public health 2020;8;543898

    PUBMED: 33072693; PMC: 7536305; DOI: 10.3389/fpubh.2020.543898

  • Ecological divergence and hybridization of Neotropical Leishmania parasites.

    Van den Broeck F, Savill NJ, Imamura H, Sanders M, Maes I, Cooper S, Mateus D, Jara M, Adaui V, Arevalo J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2020;117;40;25159-25168

    PUBMED: 32958676; PMC: 7547230; DOI: 10.1073/pnas.1920136117

  • Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis.

    Penkava F, Velasco-Herrera MDC, Young MD, Yager N, Nwosu LN, Pratt AG, Lara AL, Guzzo C, Maroof A, Mamanova L et al.

    Nature communications 2020;11;1;4767

    PUBMED: 32958743; PMC: 7505844; DOI: 10.1038/s41467-020-18513-6

  • Global Public Perceptions of Genomic Data Sharing: What Shapes the Willingness to Donate DNA and Health Data?

    Middleton A, Milne R, Almarri MA, Anwer S, Atutornu J, Baranova EE, Bevan P, Cerezo M, Cong Y, Critchley C et al.

    American journal of human genetics 2020;107;4;743-752

    PUBMED: 32946764; PMC: 7536612; DOI: 10.1016/j.ajhg.2020.08.023

  • Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph.

    Martiniano R, Garrison E, Jones ER, Manica A and Durbin R

    Genome biology 2020;21;1;250

    PUBMED: 32943086; DOI: 10.1186/s13059-020-02160-7

  • Population genomics of the Viking world.

    Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW et al.

    Nature 2020;585;7825;390-396

    PUBMED: 32939067; DOI: 10.1038/s41586-020-2688-8

  • Red blood cell tension protects against severe malaria in the Dantu blood group.

    Kariuki SN, Marin-Menendez A, Introini V, Ravenhill BJ, Lin YC, Macharia A, Makale J, Tendwa M, Nyamu W, Kotar J et al.

    Nature 2020;585;7826;579-583

    PUBMED: 32939086; PMC: 7116803; DOI: 10.1038/s41586-020-2726-6

  • Revealing the impact of structural variants in multiple myeloma.

    Rustad EH, Yellapantula VD, Glodzik D, Maclachlan KH, Diamond B, Boyle EM, Ashby C, Blaney P, Gundem G, Hultcrantz M et al.

    Blood cancer discovery 2020;1;3;258-273

    PUBMED: 33392515; PMC: 7774871; DOI: 10.1158/2643-3230.BCD-20-0132

  • Studying Brown Adipose Tissue in a Human in vitro Context.

    Samuelson I and Vidal-Puig A

    Frontiers in endocrinology 2020;11;629

    PUBMED: 33042008; PMC: 7523498; DOI: 10.3389/fendo.2020.00629

  • Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level.

    Imamura H, Monsieurs P, Jara M, Sanders M, Maes I, Vanaerschot M, Berriman M, Cotton JA, Dujardin JC and Domagalska MA

    Scientific reports 2020;10;1;15043

    PUBMED: 32929126; PMC: 7490275; DOI: 10.1038/s41598-020-71882-2

  • Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides.

    Chung WSF, Walker AW, Bosscher D, Garcia-Campayo V, Wagner J, Parkhill J, Duncan SH and Flint HJ

    BMC microbiology 2020;20;1;283

    PUBMED: 32928123; PMC: 7490872; DOI: 10.1186/s12866-020-01968-4

  • A bug's life: Delving into the challenges of helminth microbiome studies.

    Formenti F, Cortés A, Brindley PJ, Cantacessi C and Rinaldi G

    PLoS neglected tropical diseases 2020;14;9;e0008446

    PUBMED: 32911483; DOI: 10.1371/journal.pntd.0008446

  • Innate Immune Mechanisms to Protect Against Infection at the Human Decidual-Placental Interface.

    Hoo R, Nakimuli A and Vento-Tormo R

    Frontiers in immunology 2020;11;2070

    PUBMED: 33013876; PMC: 7511589; DOI: 10.3389/fimmu.2020.02070

  • NRASQ61K melanoma tumor formation is reduced by p38-MAPK14 activation in zebrafish models and NRAS-mutated human melanoma cells.

    Banik I, Cheng PF, Dooley CM, Travnickova J, Merteroglu M, Dummer R, Patton EE, Busch-Nentwich EM and Levesque MP

    Pigment cell & melanoma research 2020

    PUBMED: 32910840; DOI: 10.1111/pcmr.12925

  • The Structure of the Cysteine-Rich Domain of Plasmodium falciparum P113 Identifies the Location of the RH5 Binding Site.

    Campeotto I, Galaway F, Mehmood S, Barfod LK, Quinkert D, Kotraiah V, Phares TW, Wright KE, Snijders AP, Draper SJ et al.

    mBio 2020;11;5

    PUBMED: 32900802; PMC: 7482062; DOI: 10.1128/mBio.01566-20

  • Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem.

    Wang SP, Rubio LA, Duncan SH, Donachie GE, Holtrop G, Lo G, Farquharson FM, Wagner J, Parkhill J, Louis P et al.

    mSystems 2020;5;5

    PUBMED: 32900872; PMC: 7483512; DOI: 10.1128/mSystems.00645-20

  • Analysis of CRISPR-Cas9 screens identifies genetic dependencies in melanoma.

    Christodoulou E, Rashid M, Pacini C, Droop A, Robertson H, Groningen TV, Teunisse AFAS, Iorio F, Jochemsen AG, Adams DJ and Doorn RV

    Pigment cell & melanoma research 2020;34;1;122-131

    PUBMED: 32767816; PMC: 7818247; DOI: 10.1111/pcmr.12919

  • LifeTime and improving European healthcare through cell-based interceptive medicine.

    Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S et al.

    Nature 2020;587;7834;377-386

    PUBMED: 32894860; PMC: 7656507; DOI: 10.1038/s41586-020-2715-9

  • Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases.

    Zheng J, Haberland V, Baird D, Walker V, Haycock PC, Hurle MR, Gutteridge A, Erola P, Liu Y, Luo S et al.

    Nature genetics 2020;52;10;1122-1131

    PUBMED: 32895551; PMC: 7610464; DOI: 10.1038/s41588-020-0682-6

  • ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy

    Rundo, Leonardo, Tangherloni, Andrea, Tyson, Darren R., Betta, Riccardo, Militello, Carmelo et al.

    Applied Sciences 2020;10;8;6187

    PMC: 8297459; DOI: 10.3390/app10186187; URL: https://doi.org/10.3390/app10186187

  • Mutagenicity of acrylamide and glycidamide in human TP53 knock-in (Hupki) mouse embryo fibroblasts.

    Hölzl-Armstrong L, Kucab JE, Moody S, Zwart EP, Loutkotová L, Duffy V, Luijten M, Gamboa da Costa G, Stratton MR, Phillips DH and Arlt VM

    Archives of toxicology 2020;94;12;4173-4196

    PUBMED: 32886187; PMC: 7655573; DOI: 10.1007/s00204-020-02878-0

  • The Polygenic and Monogenic Basis of Blood Traits and Diseases.

    Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, Jiang T, Chen MH, Raffield LM, Tardaguila M, Huffman JE et al.

    Cell 2020;182;5;1214-1231.e11

    PUBMED: 32888494; DOI: 10.1016/j.cell.2020.08.008

  • Chronic loss of STAG2 leads to altered chromatin structure contributing to de-regulated transcription in AML.

    Smith JS, Lappin KM, Craig SG, Liberante FG, Crean CM, McDade SS, Thompson A, Mills KI and Savage KI

    Journal of translational medicine 2020;18;1;339

    PUBMED: 32883299; PMC: 7469420; DOI: 10.1186/s12967-020-02500-y

  • Schistosoma mansoni Vector Snails in Antigua and Montserrat, with Snail-Related Considerations Pertinent to a Declaration of Elimination of Human Schistosomiasis.

    Laidemitt MR, Buddenborg SK, Lewis LL, Michael LE, Sanchez MJ, Hewitt R and Loker ES

    The American journal of tropical medicine and hygiene 2020;103;6;2268-2277

    PUBMED: 32901608; PMC: 7695099; DOI: 10.4269/ajtmh.20-0588

  • Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies.

    Lado S, Elbers JP, Rogers MF, Melo-Ferreira J, Yadamsuren A, Corander J, Horin P and Burger PA

    BMC genomics 2020;21;1;606

    PUBMED: 32883205; PMC: 7468183; DOI: 10.1186/s12864-020-06990-4

  • Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations.

    Chen MH, Raffield LM, Mousas A, Sakaue S, Huffman JE, Moscati A, Trivedi B, Jiang T, Akbari P, Vuckovic D et al.

    Cell 2020;182;5;1198-1213.e14

    PUBMED: 32888493; PMC: 7480402; DOI: 10.1016/j.cell.2020.06.045

  • Pervasive chromosomal instability and karyotype order in tumour evolution.

    Watkins TBK, Lim EL, Petkovic M, Elizalde S, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM et al.

    Nature 2020;587;7832;126-132

    PUBMED: 32879494; PMC: 7611706; DOI: 10.1038/s41586-020-2698-6

  • Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity.

    Liang ZS, Cimino I, Yalcin B, Raghupathy N, Vancollie VE, Ibarra-Soria X, Firth HV, Rimmington D, Farooqi IS, Lelliott CJ et al.

    PLoS genetics 2020;16;9;e1008916

    PUBMED: 32877400; PMC: 7467316; DOI: 10.1371/journal.pgen.1008916

  • Genomics and epidemiological surveillance.

    Lo SW and Jamrozy D

    Nature reviews. Microbiology 2020;18;9;478

    PUBMED: 32690878; PMC: 7371787; DOI: 10.1038/s41579-020-0421-0

  • IL2RA promotes aggressiveness and stem cell-related properties of acute myeloid leukemia.

    Nguyen CH, Schlerka A, Grandits AM, Koller E, van der Kouwe E, Vassiliou GS, Staber PB, Heller G and Wieser R

    Cancer research 2020

    PUBMED: 32873636; DOI: 10.1158/0008-5472.CAN-20-0531

  • Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.

    Burrows N, Bashford-Rogers RJM, Bhute VJ, Peñalver A, Ferdinand JR, Stewart BJ, Smith JEG, Deobagkar-Lele M, Giudice G, Connor TM et al.

    Nature immunology 2020

    PUBMED: 32868930; DOI: 10.1038/s41590-020-0772-8

  • Heterozygous ABCG5 Gene Deficiency and Risk of Coronary Artery Disease.

    Nomura A, Emdin CA, Won HH, Peloso GM, Natarajan P, Ardissino D, Danesh J, Schunkert H, Correa A, Bown MJ et al.

    Circulation. Genomic and precision medicine 2020;13;5;417-423

    PUBMED: 32862661; PMC: 7983048; DOI: 10.1161/CIRCGEN.119.002871

  • Mosquito cellular immunity at single-cell resolution.

    Raddi G, Barletta ABF, Efremova M, Ramirez JL, Cantera R, Teichmann SA, Barillas-Mury C and Billker O

    Science (New York, N.Y.) 2020;369;6507;1128-1132

    PUBMED: 32855340; DOI: 10.1126/science.abc0322

  • Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease.

    Izarzugaza JMG, Ellesøe SG, Doganli C, Ehlers NS, Dalgaard MD, Audain E, Dombrowsky G, Banasik K, Sifrim A, Wilsdon A et al.

    Genome medicine 2020;12;1;76

    PUBMED: 32859249; PMC: 7453558; DOI: 10.1186/s13073-020-00772-z

  • Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases.

    Rabbie R, Ansari-Pour N, Cast O, Lau D, Scott F, Welsh SJ, Parkinson C, Khoja L, Moore L, Tullett M et al.

    Nature communications 2020;11;1;4306

    PUBMED: 32855398; PMC: 7453196; DOI: 10.1038/s41467-020-18060-0

  • Single cell transcriptomics comes of age.

    Aldridge S and Teichmann SA

    Nature communications 2020;11;1;4307

    PUBMED: 32855414; DOI: 10.1038/s41467-020-18158-5

  • Heterotypic cell-cell communication regulates glandular stem cell multipotency.

    Centonze A, Lin S, Tika E, Sifrim A, Fioramonti M, Malfait M, Song Y, Wuidart A, Van Herck J, Dannau A et al.

    Nature 2020;584;7822;608-613

    PUBMED: 32848220; PMC: 7116172; DOI: 10.1038/s41586-020-2632-y

  • Ageing compromises mouse thymus function and remodels epithelial cell differentiation.

    Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F et al.

    eLife 2020;9

    PUBMED: 32840480; PMC: 7490013; DOI: 10.7554/eLife.56221

  • Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.

    Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R et al.

    Communications biology 2020;3;1;437

    PUBMED: 32843717; PMC: 7447786; DOI: 10.1038/s42003-020-01162-2

  • DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans.

    Suen KM, Braukmann F, Butler R, Bensaddek D, Akay A, Lin CC, Milonaitytė D, Doshi N, Sapetschnig A, Lamond A et al.

    Nature communications 2020;11;1;4242

    PUBMED: 32843637; DOI: 10.1038/s41467-020-18089-1

  • A p53-Dependent Checkpoint Induced upon DNA Damage Alters Cell Fate during hiPSC Differentiation.

    Eldridge CB, Allen FJ, Crisp A, Grandy RA, Vallier L and Sale JE

    Stem cell reports 2020

    PUBMED: 32888504; DOI: 10.1016/j.stemcr.2020.08.003

  • Germline variants in HEY2 functional domains lead to congenital heart defects and thoracic aortic aneurysms.

    van Walree ES, Dombrowsky G, Jansen IE, Mirkov MU, Zwart R, Ilgun A, Guo D, Clur SB, Amin AS, Savage JE et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2020

    PUBMED: 32820247; DOI: 10.1038/s41436-020-00939-4

  • CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets.

    Noorani I, Bradley A and de la Rosa J

    Genome biology 2020;21;1;204

    PUBMED: 32811551; PMC: 7437018; DOI: 10.1186/s13059-020-02118-9

  • Detection of simple and complex de novo mutations with multiple reference sequences.

    Garimella KV, Iqbal Z, Krause MA, Campino S, Kekre M, Drury E, Kwiatkowski D, Sá JM, Wellems TE and McVean G

    Genome research 2020;30;8;1154-1169

    PUBMED: 32817236; PMC: 7462078; DOI: 10.1101/gr.255505.119

  • Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex during Red Blood Cell Invasion by Plasmodium falciparum Merozoites.

    More KR, Kaur I, Giai Gianetto Q, Invergo BM, Chaze T, Jain R, Huon C, Gutenbrunner P, Weisser H, Matondo M et al.

    mBio 2020;11;4

    PUBMED: 32817103; PMC: 7439480; DOI: 10.1128/mBio.01287-20

  • Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae.

    Ma KC, Mortimer TD, Hicks AL, Wheeler NE, Sánchez-Busó L, Golparian D, Taiaroa G, Rubin DHF, Wang Y, Williamson DA et al.

    Nature communications 2020;11;1;4126

    PUBMED: 32807804; PMC: 7431566; DOI: 10.1038/s41467-020-17980-1

  • Building genomic infrastructure: Sequencing platinum-standard reference-quality genomes of all cetacean species

    Morin,Phillip A., Alexander,Alana, Blaxter,Mark, Caballero,Susana, Fedrigo,Olivier, Fontaine,Michael C., Foote,Andrew D., Kuraku,Shigehiro, Maloney,Brigid, McCarthy,Morgan L. et al.

    Marine Mammal Science 2020

    DOI: 10.1111/mms.12721

  • Disruption and dislocation in post-COVID futures for digital health

    Milne, Richard and Costa, Alessia

    Big Data & Society 2020;7;2;2053951720949567

    DOI: 10.1177/2053951720949567

  • Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction.

    Djeghloul D, Patel B, Kramer H, Dimond A, Whilding C, Brown K, Kohler AC, Feytout A, Veland N, Elliott J et al.

    Nature communications 2020;11;1;4118

    PUBMED: 32807789; PMC: 7431861; DOI: 10.1038/s41467-020-17823-z

  • Editorial: Novel Frontiers in Helminth Genomics.

    Tort JF, Mitreva M, Brehm KR and Rinaldi G

    Frontiers in genetics 2020;11;791

    PUBMED: 32922432; PMC: 7456986; DOI: 10.3389/fgene.2020.00791

  • Genetic Predisposition to Coronary Artery Disease in Type 2 Diabetes Mellitus.

    van Zuydam NR, Ladenvall C, Voight BF, Strawbridge RJ, Fernandez-Tajes J, Rayner NW, Robertson NR, Mahajan A, Vlachopoulou E, Goel A et al.

    Circulation. Genomic and precision medicine 2020;13;6;e002769

    PUBMED: 33321069; DOI: 10.1161/CIRCGEN.119.002769

  • Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation.

    Ortmann D, Brown S, Czechanski A, Aydin S, Muraro D, Huang Y, Tomaz RA, Osnato A, Canu G, Wesley BT et al.

    Cell stem cell 2020;27;3;470-481.e6

    PUBMED: 32795399; PMC: 7487768; DOI: 10.1016/j.stem.2020.07.019

  • The binding mechanism of the virulence factor Streptococcus suis adhesin P subtype to globotetraosylceramide is associated with systemic disease.

    Madar Johansson M, Bélurier E, Papageorgiou AC, Sundin AP, Rahkila J, Kallonen T, Nilsson UJ, Maatsola S, Nyholm TKM, Käpylä J et al.

    The Journal of biological chemistry 2020;295;42;14305-14324

    PUBMED: 32796033; PMC: 7573278; DOI: 10.1074/jbc.RA120.014818

  • High laboratory mouse pre-weaning mortality associated with litter overlap, advanced dam age, small and large litters.

    Morello GM, Hultgren J, Capas-Peneda S, Wiltshire M, Thomas A, Wardle-Jones H, Brajon S, Gilbert C and Olsson IAS

    PloS one 2020;15;8;e0236290

    PUBMED: 32785214; PMC: 7423063; DOI: 10.1371/journal.pone.0236290

  • Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium.

    Teulet A, Gully D, Rouy Z, Camuel A, Koebnik R, Giraud E and Lassalle F

    Microbial genomics 2020;6;9

    PUBMED: 32783800; PMC: 7643967; DOI: 10.1099/mgen.0.000407

  • Analysis of erythrocyte signalling pathways during Plasmodium falciparum infection identifies targets for host-directed antimalarial intervention.

    Adderley JD, John von Freyend S, Jackson SA, Bird MJ, Burns AL, Anar B, Metcalf T, Semblat JP, Billker O, Wilson DW and Doerig C

    Nature communications 2020;11;1;4015

    PUBMED: 32782246; PMC: 7419518; DOI: 10.1038/s41467-020-17829-7

  • Development and validation of a universal blood donor genotyping platform: a multinational prospective study.

    Gleadall NS, Veldhuisen B, Gollub J, Butterworth AS, Ord J, Penkett CJ, Timmer TC, Sauer CM, van der Bolt N, Brown C et al.

    Blood advances 2020;4;15;3495-3506

    PUBMED: 32750130; PMC: 7422129; DOI: 10.1182/bloodadvances.2020001894

  • Validation of a Genome-Wide Polygenic Score for Coronary Artery Disease in South Asians.

    Wang M, Menon R, Mishra S, Patel AP, Chaffin M, Tanneeru D, Deshmukh M, Mathew O, Apte S, Devanboo CS et al.

    Journal of the American College of Cardiology 2020;76;6;703-714

    PUBMED: 32762905; PMC: 7592606; DOI: 10.1016/j.jacc.2020.06.024

  • Considerations in assessing germline variant pathogenicity using cosegregation analysis.

    Belman S, Parsons MT, Spurdle AB, Goldgar DE and Feng BJ

    Genetics in medicine : official journal of the American College of Medical Genetics 2020

    PUBMED: 32773770; DOI: 10.1038/s41436-020-0920-4

  • Diversification in immunogenicity genes caused by selective pressures in invasive meningococci.

    Kremer PHC, Lees JA, Ferwerda B, Bijlsma MW, MacAlasdair N, van der Ende A, Brouwer MC, Bentley SD and van de Beek D

    Microbial genomics 2020;6;9

    PUBMED: 32776867; PMC: 7643973; DOI: 10.1099/mgen.0.000422

  • Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation.

    Cairns J, Jokela R, Becks L, Mustonen V and Hiltunen T

    Nature ecology & evolution 2020

    PUBMED: 32778754; DOI: 10.1038/s41559-020-1272-9

  • Effects of maternal high fat/high sucrose dieton hepatic lipid metabolism in rat offspring.

    Ingvorsen C, Lelliott CJ, Brix S and Hellgren LI

    Clinical and experimental pharmacology & physiology 2020

    PUBMED: 32772427; DOI: 10.1111/1440-1681.13396

  • Evolution and dissemination of L and M plasmid lineages carrying antibiotic resistance genes in diverse Gram-negative bacteria.

    Blackwell GA, Doughty EL and Moran RA

    Plasmid 2020;102528

    PUBMED: 32781088; DOI: 10.1016/j.plasmid.2020.102528

  • Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota.

    Gupta S, Hjelmsø MH, Lehtimäki J, Li X, Mortensen MS, Russel J, Trivedi U, Rasmussen MA, Stokholm J, Bisgaard H and Sørensen SJ

    Microbiome 2020;8;1;115

    PUBMED: 32767985; PMC: 7414761; DOI: 10.1186/s40168-020-00895-w

  • The Application of Single-Cell RNA Sequencing in Vaccinology.

    Noé A, Cargill TN, Nielsen CM, Russell AJC and Barnes E

    Journal of immunology research 2020;2020;8624963

    PUBMED: 32802896; PMC: 7411487; DOI: 10.1155/2020/8624963

  • A point mutation decouples the lipid transfer activities of microsomal triglyceride transfer protein.

    Wilson MH, Rajan S, Danoff A, White RJ, Hensley MR, Quinlivan VH, Recacha R, Thierer JH, Tan FJ, Busch-Nentwich EM et al.

    PLoS genetics 2020;16;8;e1008941

    PUBMED: 32760060; DOI: 10.1371/journal.pgen.1008941

  • Dynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disorders.

    Gerrard DT, Berry AA, Jennings RE, Birket MJ, Zarrineh P, Garstang MG, Withey SL, Short P, Jiménez-Gancedo S, Firbas PN et al.

    Nature communications 2020;11;1;3920

    PUBMED: 32764605; PMC: 7413392; DOI: 10.1038/s41467-020-17305-2

  • Genome-wide methylation patterns predict clinical benefit of immunotherapy in lung cancer.

    Kim JY, Choi JK and Jung H

    Clinical epigenetics 2020;12;1;119

    PUBMED: 32762727; PMC: 7410160; DOI: 10.1186/s13148-020-00907-4

  • KAT7 is a genetic vulnerability of acute myeloid leukemias driven by MLL rearrangements.

    Au YZ, Gu M, De Braekeleer E, Gozdecka M, Aspris D, Tarumoto Y, Cooper J, Yu J, Ong SH, Chen X et al.

    Leukemia 2020;35;4;1012-1022

    PUBMED: 32764680; PMC: 7610570; DOI: 10.1038/s41375-020-1001-z

  • STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.

    Bharucha T, Oeser C, Balloux F, Brown JR, Carbo EC, Charlett A, Chiu CY, Claas ECJ, de Goffau MC, de Vries JJC et al.

    The Lancet. Infectious diseases 2020;20;10;e251-e260

    PUBMED: 32768390; PMC: 7406238; DOI: 10.1016/S1473-3099(20)30199-7

  • An infant with ETV6-NTRK3 fusion-positive congenital infantile fibrosarcoma and delayed response to conventional chemotherapy avoiding the need for TRK inhibition.

    Vedi A, Holland K, Cross J, Muthusamy B, Behjati S, Hook CE and Murray MJ

    Pediatric blood & cancer 2020;e28628

    PUBMED: 32748441; DOI: 10.1002/pbc.28628

  • Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys.

    Aunin E, Böhme U, Sanderson T, Simons ND, Goldberg TL, Ting N, Chapman CA, Newbold CI, Berriman M and Reid AJ

    PLoS pathogens 2020;16;8;e1008717

    PUBMED: 32745123; PMC: 7425995; DOI: 10.1371/journal.ppat.1008717

  • High relatedness of invasive multi-drug resistant non-typhoidal Salmonella genotypes among patients and asymptomatic carriers in endemic informal settlements in Kenya.

    Kariuki S, Mbae C, Van Puyvelde S, Onsare R, Kavai S, Wairimu C, Ngetich R, Clemens J and Dougan G

    PLoS neglected tropical diseases 2020;14;8;e0008440

    PUBMED: 32745137; PMC: 7425985; DOI: 10.1371/journal.pntd.0008440

  • ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung.

    Schuijs MJ, Png S, Richard AC, Tsyben A, Hamm G, Stockis J, Garcia C, Pinaud S, Nicholls A, Ros XR et al.

    Nature immunology 2020

    PUBMED: 32747815; DOI: 10.1038/s41590-020-0745-y

  • A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning.

    Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R and Jiggins CD

    GigaScience 2020;9;8

    PUBMED: 32808665; PMC: 7433188; DOI: 10.1093/gigascience/giaa088

  • Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx.

    Gladstone RA, Bojang E, Hart J, Harding-Esch EM, Mabey D, Sillah A, Bailey RL, Burr SE, Roca A, Bentley SD and Holland MJ

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020

    PUBMED: 32750538; DOI: 10.1016/j.cmi.2020.07.039

  • Rift valley fever: diagnostic challenges and investment needs for vaccine development.

    Petrova V, Kristiansen P, Norheim G and Yimer SA

    BMJ global health 2020;5;8

    PUBMED: 32816810; PMC: 7437696; DOI: 10.1136/bmjgh-2020-002694

  • Three-Dimensional Printed Molds for Image-Guided Surgical Biopsies: An Open Source Computational Platform.

    Crispin-Ortuzar M, Gehrung M, Ursprung S, Gill AB, Warren AY, Beer L, Gallagher FA, Mitchell TJ, Mendichovszky IA, Priest AN et al.

    JCO clinical cancer informatics 2020;4;736-748

    PUBMED: 32804543; PMC: 7469624; DOI: 10.1200/CCI.20.00026

  • B Lymphocyte-Derived CCL7 Augments Neutrophil and Monocyte Recruitment, Exacerbating Acute Kidney Injury.

    Inaba A, Tuong ZK, Riding AM, Mathews RJ, Martin JL, Saeb-Parsy K and Clatworthy MR

    Journal of immunology (Baltimore, Md. : 1950) 2020;205;5;1376-1384

    PUBMED: 32737150; PMC: 7444279; DOI: 10.4049/jimmunol.2000454

  • Distinct genetic architectures and environmental factors associate with host response to the γ2-herpesvirus infections.

    Sallah N, Miley W, Labo N, Carstensen T, Fatumo S, Gurdasani D, Pollard MO, Dilthey AT, Mentzer AJ, Marshall V et al.

    Nature communications 2020;11;1;3849

    PUBMED: 32737300; PMC: 7395761; DOI: 10.1038/s41467-020-17696-2

  • A Way Straight-Forward for Leishmania Genetics.

    Cotton JA and Franssen SU

    Trends in parasitology 2020

    PUBMED: 32741600; DOI: 10.1016/j.pt.2020.07.005

  • PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas.

    Noorani I, de la Rosa J, Choi YH, Strong A, Ponstingl H, Vijayabaskar MS, Lee J, Lee E, Richard-Londt A, Friedrich M et al.

    Genome biology 2020;21;1;181

    PUBMED: 32727536; PMC: 7392733; DOI: 10.1186/s13059-020-02092-2

  • A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics.

    Frentrup M, Zhou Z, Steglich M, Meier-Kolthoff JP, Göker M, Riedel T, Bunk B, Spröer C, Overmann J, Blaschitz M et al.

    Microbial genomics 2020

    PUBMED: 32726198; DOI: 10.1099/mgen.0.000410

  • Comparison of visualization tools for single-cell RNAseq data.

    Cakir B, Prete M, Huang N, van Dongen S, Pir P and Kiselev VY

    NAR genomics and bioinformatics 2020;2;3;lqaa052

    PUBMED: 32766548; PMC: 7391988; DOI: 10.1093/nargab/lqaa052

  • Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration.

    Choi J, Park JE, Tsagkogeorga G, Yanagita M, Koo BK, Han N and Lee JH

    Cell stem cell 2020

    PUBMED: 32750316; DOI: 10.1016/j.stem.2020.06.020

  • Mechanisms of stretch-mediated skin expansion at single-cell resolution.

    Aragona M, Sifrim A, Malfait M, Song Y, Van Herck J, Dekoninck S, Gargouri S, Lapouge G, Swedlund B, Dubois C et al.

    Nature 2020;584;7820;268-273

    PUBMED: 32728211; PMC: 7116042; DOI: 10.1038/s41586-020-2555-7

  • Transcriptional activity and strain-specific history of mouse pseudogenes.

    Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane TM, Hubbard T et al.

    Nature communications 2020;11;1;3695

    PUBMED: 32728065; PMC: 7392758; DOI: 10.1038/s41467-020-17157-w

  • The architecture and stabilisation of flagellotropic tailed bacteriophages.

    Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T and Coulibaly F

    Nature communications 2020;11;1;3748

    PUBMED: 32719311; PMC: 7385642; DOI: 10.1038/s41467-020-17505-w

  • APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis.

    Maciejowski J, Chatzipli A, Dananberg A, Chu K, Toufektchan E, Klimczak LJ, Gordenin DA, Campbell PJ and de Lange T

    Nature genetics 2020;52;9;884-890

    PUBMED: 32719516; PMC: 7484228; DOI: 10.1038/s41588-020-0667-5

  • Comprehensive molecular comparison of BRCA1 hypermethylated and BRCA1 mutated triple negative breast cancers.

    Glodzik D, Bosch A, Hartman J, Aine M, Vallon-Christersson J, Reuterswärd C, Karlsson A, Mitra S, Niméus E, Holm K et al.

    Nature communications 2020;11;1;3747

    PUBMED: 32719340; PMC: 7385112; DOI: 10.1038/s41467-020-17537-2

  • DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance.

    D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J et al.

    Genome biology 2020;21;1;182

    PUBMED: 32718321; DOI: 10.1186/s13059-020-02087-z

  • Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia-Pacific region.

    Noviyanti R, Miotto O, Barry A, Marfurt J, Siegel S, Thuy-Nhien N, Quang HH, Anggraeni ND, Laihad F, Liu Y et al.

    Malaria journal 2020;19;1;271

    PUBMED: 32718342; PMC: 7385952; DOI: 10.1186/s12936-020-03330-5

  • Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis

    Fu,Yu, Jung,Alexander W., Torne,Ramon Viñas, Gonzalez,Santiago, Vöhringer, Harald, Shmatko,Artem, Yates,Lucy R., Jimenez-Linan, Mercedes et al.

    Nature cancer 2020;1;8;800-810

    PMC: 35122049; DOI: 10.1038/s43018-020-0085-8

  • A novel therapeutic antibody screening method using bacterial high-content imaging reveals functional antibody binding phenotypes of Escherichia coli ST131.

    Maes M, Dyson ZA, Smith SE, Goulding DA, Ludden C, Baker S, Kellam P, Reece ST, Dougan G and Bartholdson Scott J

    Scientific reports 2020;10;1;12414

    PUBMED: 32709982; PMC: 7382476; DOI: 10.1038/s41598-020-69300-8

  • Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age.

    Mühlemann B, Vinner L, Margaryan A, Wilhelmson H, de la Fuente Castro C, Allentoft ME, de Barros Damgaard P, Hansen AJ, Holtsmark Nielsen S, Strand LM et al.

    Science (New York, N.Y.) 2020;369;6502

    PUBMED: 32703849; DOI: 10.1126/science.aaw8977

  • Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni.

    Sankaranarayanan G, Coghlan A, Driguez P, Lotkowska ME, Sanders M, Holroyd N, Tracey A, Berriman M and Rinaldi G

    Wellcome open research 2020;5;178

    PUBMED: 32789192; PMC: 7405262; DOI: 10.12688/wellcomeopenres.16031.1

  • Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.

    Lee YR, Khan K, Armfield-Uhas K, Srikanth S, Thompson NA, Pardo M, Yu L, Norris JW, Peng Y, Gripp KW et al.

    Nature communications 2020;11;1;3698

    PUBMED: 32703943; PMC: 7378245; DOI: 10.1038/s41467-020-17452-6

  • Reply to E. Hindié.

    Maurichi A, Miceli R, Eriksson H, Newton-Bishop J, Nsengimana J, Chan M, Hayes AJ, Heelan K, Adams D, Patuzzo R et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2020;JCO2001460

    PUBMED: 32701413; DOI: 10.1200/JCO.20.01460

  • Characterization of putative drug resistant biomarkers in Plasmodium falciparum isolated from Ghanaian blood donors.

    Aninagyei E, Duedu KO, Rufai T, Tetteh CD, Chandi MG, Ampomah P and Acheampong DO

    BMC infectious diseases 2020;20;1;533

    PUBMED: 32698879; PMC: 7376723; DOI: 10.1186/s12879-020-05266-2

  • Evidence of human occupation in Mexico around the Last Glacial Maximum.

    Ardelean CF, Becerra-Valdivia L, Pedersen MW, Schwenninger JL, Oviatt CG, Macías-Quintero JI, Arroyo-Cabrales J, Sikora M, Ocampo-Díaz YZE, Rubio-Cisneros II et al.

    Nature 2020;584;7819;87-92

    PUBMED: 32699412; DOI: 10.1038/s41586-020-2509-0

  • Producing polished prokaryotic pangenomes with the Panaroo pipeline.

    Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA et al.

    Genome biology 2020;21;1;180

    PUBMED: 32698896; PMC: 7376924; DOI: 10.1186/s13059-020-02090-4

  • Somatic Evolution in Non-neoplastic IBD-Affected Colon.

    Olafsson S, McIntyre RE, Coorens T, Butler T, Jung H, Robinson PS, Lee-Six H, Sanders MA, Arestang K, Dawson C et al.

    Cell 2020;182;3;672-684.e11

    PUBMED: 32697969; PMC: 7427325; DOI: 10.1016/j.cell.2020.06.036

  • A unified catalog of 204,938 reference genomes from the human gut microbiome.

    Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P et al.

    Nature biotechnology 2020

    PUBMED: 32690973; DOI: 10.1038/s41587-020-0603-3

  • Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using deep learning.

    Sirinukunwattana K, Domingo E, Richman SD, Redmond KL, Blake A, Verrill C, Leedham SJ, Chatzipli A, Hardy C, Whalley CM et al.

    Gut 2020

    PUBMED: 32690604; DOI: 10.1136/gutjnl-2019-319866

  • Tumors induce de novo steroid biosynthesis in T cells to evade immunity.

    Mahata B, Pramanik J, van der Weyden L, Polanski K, Kar G, Riedel A, Chen X, Fonseca NA, Kundu K, Campos LS et al.

    Nature communications 2020;11;1;3588

    PUBMED: 32680985; PMC: 7368057; DOI: 10.1038/s41467-020-17339-6

  • Inhibition of indole production increases the activity of quinolone antibiotics against E. coli persisters.

    Zarkan A, Matuszewska M, Trigg SB, Zhang M, Belgami D, Croft C, Liu J, El-Ouisi S, Greenhalgh J, Duboff JS et al.

    Scientific reports 2020;10;1;11742

    PUBMED: 32678197; PMC: 7366635; DOI: 10.1038/s41598-020-68693-w

  • Tissue-Biased Expansion of DNMT3A-Mutant Clones in a Mosaic Individual Is Associated with Conserved Epigenetic Erosion.

    Tovy A, Reyes JM, Gundry MC, Brunetti L, Lee-Six H, Petljak M, Park HJ, Guzman AG, Rosas C, Jeffries AR et al.

    Cell stem cell 2020;27;2;326-335.e4

    PUBMED: 32673568; PMC: 7494054; DOI: 10.1016/j.stem.2020.06.018

  • Viability PCR shows that non-ocular surfaces could contribute to transmission of Chlamydia trachomatis infection in trachoma.

    Versteeg B, Vasileva H, Houghton J, Last A, Shafi Abdurahman O, Sarah V, Macleod D, Solomon AW, Holland MJ, Thomson N and Burton MJ

    PLoS neglected tropical diseases 2020;14;7;e0008449

    PUBMED: 32667914; DOI: 10.1371/journal.pntd.0008449

  • A Southeast Asian origin for present-day non-African human Y chromosomes.

    Hallast P, Agdzhoyan A, Balanovsky O, Xue Y and Tyler-Smith C

    Human genetics 2020;140;2;299-307

    PUBMED: 32666166; PMC: 7864842; DOI: 10.1007/s00439-020-02204-9

  • Molecular epidemiology of resistance to antimalarial drugs in the Greater Mekong subregion: an observational study.

    Imwong M, Dhorda M, Myo Tun K, Thu AM, Phyo AP, Proux S, Suwannasin K, Kunasol C, Srisutham S, Duanguppama J et al.

    The Lancet. Infectious diseases 2020

    PUBMED: 32679084; DOI: 10.1016/S1473-3099(20)30228-0

  • Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.

    Meredith LW, Hamilton WL, Warne B, Houldcroft CJ, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL et al.

    The Lancet. Infectious diseases 2020

    PUBMED: 32679081; DOI: 10.1016/S1473-3099(20)30562-4

  • Telomere-to-telomere assembly of a complete human X chromosome.

    Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA et al.

    Nature 2020;585;7823;79-84

    PUBMED: 32663838; PMC: 7484160; DOI: 10.1038/s41586-020-2547-7

  • Investigating higher-order interactions in single-cell data with scHOT.

    Ghazanfar S, Lin Y, Su X, Lin DM, Patrick E, Han ZG, Marioni JC and Yang JYH

    Nature methods 2020

    PUBMED: 32661426; DOI: 10.1038/s41592-020-0885-x

  • Pathogen genomic surveillance of typhoidal Salmonella infection in adults and children reveals no association between clinical outcomes and infecting genotypes.

    Britto CD, Mathias S, Bosco A, Dyson ZA, Dougan G, Raveendran S, Abin VL, Jose S, Nagaraj S, Holt KE and Pollard AJ

    Tropical medicine and health 2020;48;58

    PUBMED: 32684794; PMC: 7359007; DOI: 10.1186/s41182-020-00247-2

  • Development of caecaloids to study host-pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum.

    Duque-Correa MA, Schreiber F, Rodgers FH, Goulding D, Forrest S, White R, Buck A, Grencis RK and Berriman M

    International journal for parasitology 2020;50;9;707-718

    PUBMED: 32659277; PMC: 7435689; DOI: 10.1016/j.ijpara.2020.06.001

  • Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host.

    White R, Kumar S, Chow FW, Robertson E, Hayes KS, Grencis RK, Duque-Correa MA and Buck AH

    International journal for parasitology 2020;50;9;719-729

    PUBMED: 32659276; PMC: 7435682; DOI: 10.1016/j.ijpara.2020.06.002

  • Spontaneously occurring melanoma in animals and their relevance to human melanoma.

    van der Weyden L, Brenn T, Patton EE, Wood GA and Adams DJ

    The Journal of pathology 2020

    PUBMED: 32652526; DOI: 10.1002/path.5505

  • Structural basis for RIFIN-mediated activation of LILRB1 in malaria.

    Harrison TE, Mørch AM, Felce JH, Sakoguchi A, Reid AJ, Arase H, Dustin ML and Higgins MK

    Nature 2020;587;7833;309-312

    PUBMED: 32650338; PMC: 7116854; DOI: 10.1038/s41586-020-2530-3

  • Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.

    Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F et al.

    Nature communications 2020;11;1;3442

    PUBMED: 32651390; PMC: 7351774; DOI: 10.1038/s41467-020-17327-w

  • Genetic diversity and neutral selection in Plasmodium vivax erythrocyte binding protein correlates with patient antigenicity.

    Han JH, Cho JS, Ong JJY, Park JH, Nyunt MH, Sutanto E, Trimarsanto H, Petros B, Aseffa A, Getachew S et al.

    PLoS neglected tropical diseases 2020;14;7;e0008202

    PUBMED: 32645098; DOI: 10.1371/journal.pntd.0008202

  • SF3B1-mutant MDS as a distinct disease subtype: a proposal from the International Working Group for the Prognosis of MDS.

    Malcovati L, Stevenson K, Papaemmanuil E, Neuberg D, Bejar R, Boultwood J, Bowen DT, Campbell PJ, Ebert BL, Fenaux P et al.

    Blood 2020;136;2;157-170

    PUBMED: 32347921; PMC: 7362582; DOI: 10.1182/blood.2020004850

  • Single-cell transcriptomics of alloreactive CD4+ T cells over time reveals divergent fates during gut graft-versus-host disease.

    Engel JA, Lee HJ, Williams CG, Kuns R, Olver S, Lansink LI, Soon MS, Andersen SB, Powell JE, Svensson V et al.

    JCI insight 2020;5;13

    PUBMED: 32484791; PMC: 7406307; DOI: 10.1172/jci.insight.137990

  • Association of plasma biomarkers of fruit and vegetable intake with incident type 2 diabetes: EPIC-InterAct case-cohort study in eight European countries.

    Zheng JS, Sharp SJ, Imamura F, Chowdhury R, Gundersen TE, Steur M, Sluijs I, van der Schouw YT, Agudo A, Aune D et al.

    BMJ (Clinical research ed.) 2020;370;m2194

    PUBMED: 32641421; DOI: 10.1136/bmj.m2194

  • PRL3-DDX21 Transcriptional Control of Endolysosomal Genes Restricts Melanocyte Stem Cell Differentiation.

    Johansson JA, Marie KL, Lu Y, Brombin A, Santoriello C, Zeng Z, Zich J, Gautier P, von Kriegsheim A, Brunsdon H et al.

    Developmental cell 2020

    PUBMED: 32652076; DOI: 10.1016/j.devcel.2020.06.013

  • GM-CSF Calibrates Macrophage Defense and Wound Healing Programs during Intestinal Infection and Inflammation.

    Castro-Dopico T, Fleming A, Dennison TW, Ferdinand JR, Harcourt K, Stewart BJ, Cader Z, Tuong ZK, Jing C, Lok LSC et al.

    Cell reports 2020;32;1;107857

    PUBMED: 32640223; PMC: 7351110; DOI: 10.1016/j.celrep.2020.107857

  • IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms.

    Nadeu F, Mas-de-Les-Valls R, Navarro A, Royo R, Martín S, Villamor N, Suárez-Cisneros H, Mares R, Lu J, Enjuanes A et al.

    Nature communications 2020;11;1;3390

    PUBMED: 32636395; PMC: 7341758; DOI: 10.1038/s41467-020-17095-7

  • Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions.

    Lees JA, Mai TT, Galardini M, Wheeler NE, Horsfield ST, Parkhill J and Corander J

    mBio 2020;11;4

    PUBMED: 32636251; PMC: 7343994; DOI: 10.1128/mBio.01344-20

  • Insights Into Aboriginal Australian Mortuary Practices: Perspectives From Ancient DNA

    Wasef, Sally, Wright, Joanne L., Adams, Shaun, Westaway, Michael C., Flinders, Clarence et al.

    Frontiers in Ecology and Evolution 2020;8;217

    DOI: 10.3389/fevo.2020.00217; URL: https://doi.org/10.3389/fevo.2020.00217

  • Investigation of sequential outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum β-lactamase producing Klebsiella species in a West African tertiary hospital neonatal unit: a retrospective genomic analysis.

    Okomo U, Senghore M, Darboe S, Bojang E, Zaman SMA, Hossain MJ, Nwakanma D, Le Doare K, Holt KE, Hos NJ et al.

    The Lancet. Microbe 2020;1;3;e119-e129

    PUBMED: 35544262; DOI: 10.1016/S2666-5247(20)30061-6

  • Cell Surface Remodeling of Mycobacterium abscessus under Cystic Fibrosis Airway Growth Conditions.

    Wiersma CJ, Belardinelli JM, Avanzi C, Angala SK, Everall I, Angala B, Kendall E, de Moura VCN, Verma D, Benoit J et al.

    ACS infectious diseases 2020

    PUBMED: 32551551; DOI: 10.1021/acsinfecdis.0c00214

  • Defining multiplicity of vector uptake in transfected Plasmodium parasites.

    Carrasquilla M, Adjalley S, Sanderson T, Marin-Menendez A, Coyle R, Montandon R, Rayner JC, Pance A and Lee MCS

    Scientific reports 2020;10;1;10894

    PUBMED: 32616799; PMC: 7331667; DOI: 10.1038/s41598-020-67791-z

  • High genetic similarity between non-typhoidal Salmonella isolated from paired blood and stool samples of children in the Democratic Republic of the Congo.

    Phoba MF, Barbé B, Ley B, Van Puyvelde S, Post A, Mattheus W, Deborggraeve S, Lunguya O and Jacobs J

    PLoS neglected tropical diseases 2020;14;7;e0008377

    PUBMED: 32614856; DOI: 10.1371/journal.pntd.0008377

  • Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens.

    Ayestaran I, Galhoz A, Spiegel E, Sidders B, Dry JR, Dondelinger F, Bender A, McDermott U, Iorio F and Menden MP

    Patterns (New York, N.Y.) 2020;1;5;100065

    PUBMED: 33205120; PMC: 7660407; DOI: 10.1016/j.patter.2020.100065

  • An antiviral response beyond immune cells.

    Gomes T and Teichmann SA

    Nature 2020;583;7815;206-207

    PUBMED: 32623443; DOI: 10.1038/d41586-020-01916-2

  • Analysis of endothelial-to-haematopoietic transition at the single cell level identifies cell cycle regulation as a driver of differentiation.

    Canu G, Athanasiadis E, Grandy RA, Garcia-Bernardo J, Strzelecka PM, Vallier L, Ortmann D and Cvejic A

    Genome biology 2020;21;1;157

    PUBMED: 32611441; PMC: 7329542; DOI: 10.1186/s13059-020-02058-4

  • Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens.

    Gonçalves E, Segura-Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, Coker EA, van der Meer D, Barthorpe A, Lightfoot H et al.

    Molecular systems biology 2020;16;7;e9405

    PUBMED: 32627965; PMC: 7336273; DOI: 10.15252/msb.20199405

  • Interferon-induced Protein-44 and Interferon-induced Protein 44-like restrict replication of Respiratory Syncytial Virus.

    Busse DC, Habgood-Coote D, Clare S, Brandt C, Bassano I, Kaforou M, Herberg J, Levin M, Eleouet JF, Kellam P and Tregoning JS

    Journal of virology 2020

    PUBMED: 32611756; DOI: 10.1128/JVI.00297-20

  • Peripheral T3 signaling is target of pesticides in zebrafish larvae and adult liver.

    Colella M, Nittoli V, Porciello A, Porreca I, Reale C, Russo F, Russo NA, Roberto L, Albano F, De Felice M et al.

    The Journal of endocrinology 2020

    PUBMED: 32738127; DOI: 10.1530/JOE-20-0134

  • The network effect: studying COVID-19 pathology with the Human Cell Atlas.

    Teichmann S and Regev A

    Nature reviews. Molecular cell biology 2020

    PUBMED: 32606379; DOI: 10.1038/s41580-020-0267-3

  • COVID-19 autopsy in people who died in community settings: the first series.

    Youd E and Moore L

    Journal of clinical pathology 2020

    PUBMED: 32605920; DOI: 10.1136/jclinpath-2020-206710

  • The Global Meningitis Genome Partnership.

    Rodgers E, Bentley SD, Borrow R, Bratcher HB, Brisse S, Brueggemann AB, Caugant DA, Findlow J, Fox L, Glennie L et al.

    The Journal of infection 2020

    PUBMED: 32615197; DOI: 10.1016/j.jinf.2020.06.064

  • A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program.

    Alda-Catalinas C, Bredikhin D, Hernando-Herraez I, Santos F, Kubinyecz O, Eckersley-Maslin MA, Stegle O and Reik W

    Cell systems 2020

    PUBMED: 32634384; DOI: 10.1016/j.cels.2020.06.004

  • Fine capsule variation affects bacteriophage susceptibility in Klebsiella pneumoniae ST258.

    Venturini C, Ben Zakour NL, Bowring B, Morales S, Cole R, Kovach Z, Branston S, Kettle E, Thomson N and Iredell JR

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2020

    PUBMED: 32598522; DOI: 10.1096/fj.201902735R

  • Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation.

    Moskowitz JE, Doran AG, Lei Z, Busi SB, Hart ML, Franklin CL, Sumner LW, Keane TM and Amos-Landgraf JM

    BMC cancer 2020;20;1;600

    PUBMED: 32600361; DOI: 10.1186/s12885-020-07007-9

  • Rapid and sensitive large-scale screening of low affinity extracellular receptor protein interactions by using reaction induced inhibition of Gaussia luciferase.

    Galaway F and Wright GJ

    Scientific reports 2020;10;1;10522

    PUBMED: 32601498; PMC: 7324543; DOI: 10.1038/s41598-020-67468-7

  • Structural variation of the malaria-associated human glycophorin A-B-E region.

    Louzada S, Algady W, Weyell E, Zuccherato LW, Brajer P, Almalki F, Scliar MO, Naslavsky MS, Yamamoto GL, Duarte YAO et al.

    BMC genomics 2020;21;1;446

    PUBMED: 32600246; DOI: 10.1186/s12864-020-06849-8

  • A Maturity Matrix for Nurse Leaders to Facilitate and Benchmark Progress in Genomic Healthcare Policy, Infrastructure, Education, and Delivery.

    Tonkin E, Calzone KA, Badzek L, Benjamin C, Middleton A, Patch C and Kirk M

    Journal of nursing scholarship : an official publication of Sigma Theta Tau International Honor Society of Nursing 2020

    PUBMED: 32592453; DOI: 10.1111/jnu.12586

  • Arctic-adapted dogs emerged at the Pleistocene-Holocene transition.

    Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J et al.

    Science (New York, N.Y.) 2020;368;6498;1495-1499

    PUBMED: 32587022; DOI: 10.1126/science.aaz8599

  • Nosocomial outbreak of the Middle East Respiratory Syndrome coronavirus: A phylogenetic, epidemiological, clinical and infection control analysis.

    Barry M, Phan MV, Akkielah L, Al-Majed F, Alhetheel A, Somily A, Alsubaie SS, McNabb SJ, Cotten M, Zumla A and Memish ZA

    Travel medicine and infectious disease 2020;101807

    PUBMED: 32599173; DOI: 10.1016/j.tmaid.2020.101807

  • Investigating Cellular Recognition Using CRISPR/Cas9 Genetic Screening.

    Chong ZS, Wright GJ and Sharma S

    Trends in cell biology 2020

    PUBMED: 32595062; DOI: 10.1016/j.tcb.2020.05.005

  • Persistent and emerging pneumococcal carriage serotypes in a rural Gambian community after ten years of pneumococcal conjugate vaccine pressure.

    Usuf E, Christian B, Gladstone R, Bojang E, Jawneh K, Cox I, Jallow E, Bojang A, Greenwood B, Adegbola RA et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020

    PUBMED: 32584973; DOI: 10.1093/cid/ciaa856

  • An enhanced toolkit for the generation of knockout and marker-free fluorescent Plasmodium chabaudi.

    Marr EJ, Milne RM, Anar B, Girling G, Schwach F, Mooney JP, Nahrendorf W, Spence PJ, Cunningham D, Baker DA et al.

    Wellcome open research 2020;5;71

    PUBMED: 32500098; PMC: 7236590; DOI: 10.12688/wellcomeopenres.15587.2

  • The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861).

    Bista I, McCarthy SA, Wood J, Ning Z, Detrich Iii HW, Desvignes T, Postlethwait J, Chow W, Howe K, Torrance J et al.

    Wellcome open research 2020;5;148

    PUBMED: 33195818; PMC: 7649722; DOI: 10.12688/wellcomeopenres.16012.1

  • Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas.

    Tunjić Cvitanić M, Vojvoda Zeljko T, Pasantes JJ, García-Souto D, Gržan T, Despot-Slade E, Plohl M and Šatović E

    Genes 2020;11;6

    PUBMED: 32599860; PMC: 7348941; DOI: 10.3390/genes11060695

  • Whole-genome sequencing of patients with rare diseases in a national health system.

    Turro E, Astle WJ, Megy K, Gräf S, Greene D, Shamardina O, Allen HL, Sanchis-Juan A, Frontini M, Thys C et al.

    Nature 2020;583;7814;96-102

    PUBMED: 32581362; PMC: 7610553; DOI: 10.1038/s41586-020-2434-2

  • An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria.

    Elliott AG, Huang JX, Neve S, Zuegg J, Edwards IA, Cain AK, Boinett CJ, Barquist L, Lundberg CV, Steen J et al.

    Nature communications 2020;11;1;3184

    PUBMED: 32576824; PMC: 7311426; DOI: 10.1038/s41467-020-16950-x

  • SpeS: A Novel Superantigen and Its Potential as a Vaccine Adjuvant against Strangles.

    Dominguez-Medina CC, Rash NL, Robillard S, Robinson C, Efstratiou A, Broughton K, Parkhill J, Holden MTG, Lopez-Alvarez MR, Paillot R and Waller AS

    International journal of molecular sciences 2020;21;12

    PUBMED: 32586031; DOI: 10.3390/ijms21124467

  • Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment.

    Eckersley-Maslin MA, Parry A, Blotenburg M, Krueger C, Ito Y, Franklin VNR, Narita M, D'Santos CS and Reik W

    Nature structural & molecular biology 2020;27;8;696-705

    PUBMED: 32572255; DOI: 10.1038/s41594-020-0443-3

  • Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19.

    Jones NK, Rivett L, Sparkes D, Forrest S, Sridhar S, Young J, Pereira-Dias J, Cormie C, Gill H, Reynolds N et al.

    eLife 2020;9

    PUBMED: 32558644; PMC: 7326489; DOI: 10.7554/eLife.59391

  • Functional Microbiomics Reveals Alterations of the Gut Microbiome and Host Co-Metabolism in Patients With Alcoholic Hepatitis.

    Gao B, Duan Y, Lang S, Barupal D, Wu TC, Valdiviez L, Roberts B, Choy YY, Shen T, Byram G et al.

    Hepatology communications 2020;4;8;1168-1182

    PUBMED: 32766476; PMC: 7395072; DOI: 10.1002/hep4.1537

  • Genomic signatures of domestication in Old World camels.

    Fitak RR, Mohandesan E, Corander J, Yadamsuren A, Chuluunbat B, Abdelhadi O, Raziq A, Nagy P, Walzer C, Faye B and Burger PA

    Communications biology 2020;3;1;316

    PUBMED: 32561887; DOI: 10.1038/s42003-020-1039-5

  • Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains.

    Masembe C, Phan MVT, Robertson DL and Cotten M

    Virus evolution 2020;6;2;veaa044

    PUBMED: 32913663; PMC: 7474929; DOI: 10.1093/ve/veaa044

  • Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing.

    Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V et al.

    Nature communications 2020;11;1;3126

    PUBMED: 32561710; PMC: 7305308; DOI: 10.1038/s41467-020-16857-7

  • ctDNA monitoring using patient-specific sequencing and integration of variant reads.

    Wan JCM, Heider K, Gale D, Murphy S, Fisher E, Mouliere F, Ruiz-Valdepenas A, Santonja A, Morris J, Chandrananda D et al.

    Science translational medicine 2020;12;548

    PUBMED: 32554709; DOI: 10.1126/scitranslmed.aaz8084

  • Epstein-Barr virus reactivation in sepsis due to community-acquired pneumonia is associated with increased morbidity and an immunosuppressed host transcriptomic endotype.

    Goh C, Burnham KL, Ansari MA, de Cesare M, Golubchik T, Hutton P, Overend LE, Davenport EE, Hinds CJ, Bowden R and Knight JC

    Scientific reports 2020;10;1;9838

    PUBMED: 32555213; PMC: 7299986; DOI: 10.1038/s41598-020-66713-3

  • Factors associated with occurrence of salmonellosis among children living in Mukuru slum, an urban informal settlement in Kenya.

    Mbae C, Mwangi M, Gitau N, Irungu T, Muendo F, Wakio Z, Wambui R, Kavai S, Onsare R, Wairimu C et al.

    BMC infectious diseases 2020;20;1;422

    PUBMED: 32552753; PMC: 7302364; DOI: 10.1186/s12879-020-05134-z

  • Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli.

    Wang Y, Huang JM, Zhou YL, Almeida A, Finn RD, Danchin A and He LS

    BMC genomics 2020;21;1;408

    PUBMED: 32552739; PMC: 7301438; DOI: 10.1186/s12864-020-06807-4

  • Reticular Fibroblasts Expressing the Transcription Factor WT1 Define a Stromal Niche That Maintains and Replenishes Splenic Red Pulp Macrophages.

    Bellomo A, Mondor I, Spinelli L, Lagueyrie M, Stewart BJ, Brouilly N, Malissen B, Clatworthy MR and Bajénoff M

    Immunity 2020

    PUBMED: 32562599; DOI: 10.1016/j.immuni.2020.06.008

  • Unsupervised generative and graph representation learning for modelling cell differentiation.

    Bica I, Andrés-Terré H, Cvejic A and Liò P

    Scientific reports 2020;10;1;9790

    PUBMED: 32555334; DOI: 10.1038/s41598-020-66166-8

  • Association between bacterial homoplastic variants and radiological pathology in tuberculosis.

    Grandjean L, Monteserin J, Gilman R, Pauschardt J, Rokadiya S, Bonilla C, Ritacco V, Vidal JR, Parkhill J, Peacock S et al.

    Thorax 2020

    PUBMED: 32546574; DOI: 10.1136/thoraxjnl-2019-213281

  • Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis.

    Jing C, Castro-Dopico T, Richoz N, Tuong ZK, Ferdinand JR, Lok LSC, Loudon KW, Banham GD, Mathews RJ, Cader Z et al.

    Proceedings of the National Academy of Sciences of the United States of America 2020

    PUBMED: 32541026; DOI: 10.1073/pnas.2000943117

  • Reply to: 'Browning capabilities of human primary adipose-derived stromal cells compared to SGBS cells'.

    Yeo CR, Agrawal M, Hoon S, Shabbir A, Shrivastava MK, Huang S, Khoo CM, Chhay V, Shabeer M, Shyong Tai E et al.

    Scientific reports 2020;10;1;9634

    PUBMED: 32541770; DOI: 10.1038/s41598-020-64706-w

  • Sociodemographic inequities associated with participation in leisure-time physical activity in sub-Saharan Africa: an individual participant data meta-analysis.

    Barr AL, Partap U, Young EH, Agoudavi K, Balde N, Kagaruki GB, Mayige MT, Longo-Mbenza B, Mutungi G, Mwalim O et al.

    BMC public health 2020;20;1;927

    PUBMED: 32539702; PMC: 7296740; DOI: 10.1186/s12889-020-08987-w

  • De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay.

    Vissers LELM, Kalvakuri S, de Boer E, Geuer S, Oud M, van Outersterp I, Kwint M, Witmond M, Kersten S, Polla DL et al.

    American journal of human genetics 2020

    PUBMED: 32553196; DOI: 10.1016/j.ajhg.2020.05.017

  • Increasing incidence of group B streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23.

    Jamrozy D, Bijlsma MW, de Goffau MC, van de Beek D, Kuijpers TW, Parkhill J, van der Ende A and Bentley SD

    Scientific reports 2020;10;1;9539

    PUBMED: 32533007; PMC: 7293262; DOI: 10.1038/s41598-020-66214-3

  • Lentiviral gene therapy rescues p47phox chronic granulomatous disease and the ability to fight Salmonella infection in mice.

    Schejtman A, Aragão-Filho WC, Clare S, Zinicola M, Weisser M, Burns SO, Booth C, Gaspar HB, Thomas DC, Condino-Neto A et al.

    Gene therapy 2020

    PUBMED: 32533104; DOI: 10.1038/s41434-020-0164-6

  • Targeting NLRP3 and staphylococcal pore-forming toxin receptors in human-induced pluripotent stem cell-derived macrophages.

    Chow SH, Deo P, Yeung ATY, Kostoulias XP, Jeon Y, Gao ML, Seidi A, Olivier FAB, Sridhar S, Nethercott C et al.

    Journal of leukocyte biology 2020

    PUBMED: 32531864; DOI: 10.1002/JLB.4MA0420-497R

  • Nearly Complete Genome Sequence of Brugia malayi Strain FR3.

    Tracey A, Foster JM, Paulini M, Grote A, Mattick J, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A et al.

    Microbiology resource announcements 2020;9;24

    PUBMED: 32527783; PMC: 7291094; DOI: 10.1128/MRA.00154-20

  • Population Structure, Stratification, and Introgression of Human Structural Variation.

    Almarri MA, Bergström A, Prado-Martinez J, Yang F, Fu B, Dunham AS, Chen Y, Hurles ME, Tyler-Smith C and Xue Y

    Cell 2020;182;1;189-199.e15

    PUBMED: 32531199; PMC: 7369638; DOI: 10.1016/j.cell.2020.05.024

  • Screening of a library of recombinant Schistosoma mansoni proteins with sera from murine and human controlled infections identifies early serological markers.

    Crosnier C, Hokke CH, Protasio AV, Brandt C, Rinaldi G, Langenberg MCC, Clare S, Janse JJ, Wilson S, Berriman M et al.

    The Journal of infectious diseases 2020

    PUBMED: 32524140; DOI: 10.1093/infdis/jiaa329

  • A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility.

    Turner AK, Eckert SE, Turner DJ, Yasir M, Webber MA, Charles IG, Parkhill J and Wain J

    The Journal of antimicrobial chemotherapy 2020

    PUBMED: 32514543; DOI: 10.1093/jac/dkaa204

  • Bone morphogenetic protein 8B promotes the progression of non-alcoholic steatohepatitis.

    Vacca M, Leslie J, Virtue S, Lam BYH, Govaere O, Tiniakos D, Snow S, Davies S, Petkevicius K, Tong Z et al.

    Nature metabolism 2020;2;6;514-531

    PUBMED: 32694734; DOI: 10.1038/s42255-020-0214-9

  • Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting.

    Huang SSY, Makhlouf M, AbouMoussa EH, Ruiz Tejada Segura ML, Mathew LS, Wang K, Leung MC, Chaussabel D, Logan DW, Scialdone A et al.

    Molecular metabolism 2020;40;101038

    PUBMED: 32526449; PMC: 7339127; DOI: 10.1016/j.molmet.2020.101038

  • Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.

    Bawn M, Alikhan NF, Thilliez G, Kirkwood M, Wheeler NE, Petrovska L, Dallman TJ, Adriaenssens EM, Hall N and Kingsley RA

    PLoS genetics 2020;16;6;e1008850

    PUBMED: 32511244; DOI: 10.1371/journal.pgen.1008850

  • Genomic profiling reveals distinct routes to complement resistance in Klebsiella pneumoniae.

    Short FL, Di Sario G, Reichmann NT, Kleanthous C, Parkhill J and Taylor PW

    Infection and immunity 2020

    PUBMED: 32513855; DOI: 10.1128/IAI.00043-20

  • Professional duties are now considered legal duties of care within genomic medicine.

    Anna M, Christine P, Jonathan R, Richard M, Alessia C, Lauren R and Jerome A

    European journal of human genetics : EJHG 2020

    PUBMED: 32514131; DOI: 10.1038/s41431-020-0663-3

  • Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq.

    Chappell L, Ross P, Orchard L, Russell TJ, Otto TD, Berriman M, Rayner JC and Llinás M

    BMC genomics 2020;21;1;395

    PUBMED: 32513207; DOI: 10.1186/s12864-020-06787-5

  • Societal considerations in host genome testing for COVID-19.

    Milne R

    Genetics in medicine : official journal of the American College of Medical Genetics 2020

    PUBMED: 32514089; DOI: 10.1038/s41436-020-0861-y

  • Translating Basic Cancer Discoveries to the Clinic.

    No authors listed

    Cancer cell 2020;37;6;735-737

    PUBMED: 32516583; DOI: 10.1016/j.ccell.2020.05.017

  • Cell Surface Receptor Identification Using Genome-Scale CRISPR/Cas9 Genetic Screens.

    Sharma S and Wright GJ

    Journal of visualized experiments : JoVE 2020;160

    PUBMED: 32568240; DOI: 10.3791/60803

  • Evolution in interacting species alters predator life-history traits, behaviour and morphology in experimental microbial communities.

    Cairns J, Moerman F, Fronhofer EA, Altermatt F and Hiltunen T

    Proceedings. Biological sciences 2020;287;1928;20200652

    PUBMED: 32486984; PMC: 7341940; DOI: 10.1098/rspb.2020.0652

  • Human BDNF/TrkB variants impair hippocampal synaptogenesis and associate with neurobehavioural abnormalities.

    Sonoyama T, Stadler LKJ, Zhu M, Keogh JM, Henning E, Hisama F, Kirwan P, Jura M, Blaszczyk BK, DeWitt DC et al.

    Scientific reports 2020;10;1;9028

    PUBMED: 32493978; DOI: 10.1038/s41598-020-65531-x

  • Refinement of the clinical and mutational spectrum of UBE2A deficiency syndrome.

    Cordeddu V, Macke EL, Radio FC, Lo Cicero S, Pantaleoni F, Tatti M, Bellacchio E, Ciolfi A, Agolini E, Bruselles A et al.

    Clinical genetics 2020;98;2;172-178

    PUBMED: 32415735; DOI: 10.1111/cge.13775

  • An integrated national scale SARS-CoV-2 genomic surveillance network.

    COVID-19 Genomics UK (COG-UK) consortiumcontact@cogconsortium.uk</span>

    The Lancet. Microbe 2020;1;3;e99-e100

    PUBMED: 32835336; PMC: 7266609; DOI: 10.1016/S2666-5247(20)30054-9

  • Exome Sequencing Identifies Genes and Gene Sets Contributing to Severe Childhood Obesity, Linking PHIP Variants to Repressed POMC Transcription.

    Marenne G, Hendricks AE, Perdikari A, Bounds R, Payne F, Keogh JM, Lelliott CJ, Henning E, Pathan S, Ashford S et al.

    Cell metabolism 2020;31;6;1107-1119.e12

    PUBMED: 32492392; PMC: 7267775; DOI: 10.1016/j.cmet.2020.05.007

  • Interferon-gamma polymorphisms and risk of iron deficiency and anaemia in Gambian children.

    Abuga KM, Rockett KA, Muriuki JM, Koch O, Nairz M, Sirugo G, Bejon P, Kwiatkowski DP, Prentice AM and Atkinson SH

    Wellcome open research 2020;5;40

    PUBMED: 32420456; PMC: 7202087; DOI: 10.12688/wellcomeopenres.15750.2

  • Stratification and prediction of drug synergy based on target functional similarity.

    Yang M, Jaaks P, Dry J, Garnett M, Menden MP and Saez-Rodriguez J

    NPJ systems biology and applications 2020;6;1;16

    PUBMED: 32487991; PMC: 7265486; DOI: 10.1038/s41540-020-0136-x

  • TMEM95 is a sperm membrane protein essential for mammalian fertilization.

    Lamas-Toranzo I, Hamze JG, Bianchi E, Fernández-Fuertes B, Pérez-Cerezales S, Laguna-Barraza R, Fernández-González R, Lonergan P, Gutiérrez-Adán A, Wright GJ et al.

    eLife 2020;9

    PUBMED: 32484434; PMC: 7295574; DOI: 10.7554/eLife.53913

  • Using Reactome to build an autophagy mechanism knowledgebase.

    Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E and Hermjakob H

    Autophagy 2020;1-12

    PUBMED: 32486891; DOI: 10.1080/15548627.2020.1761659

  • An improved pig reference genome sequence to enable pig genetics and genomics research.

    Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P et al.

    GigaScience 2020;9;6

    PUBMED: 32543654; PMC: 7448572; DOI: 10.1093/gigascience/giaa051

  • gplas: a comprehensive tool for plasmid analysis using short-read graphs.

    Arredondo-Alonso S, Bootsma M, Hein Y, Rogers MRC, Corander J, Willems RJL and Schürch AC

    Bioinformatics (Oxford, England) 2020;36;12;3874-3876

    PUBMED: 32271863; PMC: 7320608; DOI: 10.1093/bioinformatics/btaa233

  • halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.

    Krasheninnikova K, Diekhans M, Armstrong J, Dievskii A, Paten B and O'Brien S

    GigaScience 2020;9;6

    PUBMED: 32463100; DOI: 10.1093/gigascience/giaa047

  • Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines.

    Argimón S, Masim MAL, Gayeta JM, Lagrada ML, Macaranas PKV, Cohen V, Limas MT, Espiritu HO, Palarca JC, Chilam J et al.

    Nature communications 2020;11;1;2719

    PUBMED: 32483195; PMC: 7264328; DOI: 10.1038/s41467-020-16322-5

  • Lineage specific evolution and gene flow in Listeria monocytogenes is independent of bacteriophages.

    Zamudio R, Haigh RD, Ralph JD, De Ste Croix M, Tasara T, Zurfluh K, Kwun MJ, Millard AD, Bentley SD, Croucher NJ et al.

    Environmental microbiology 2020

    PUBMED: 32483914; DOI: 10.1111/1462-2920.15111

  • Lipoprotein(a) in Alzheimer, Atherosclerotic, Cerebrovascular, Thrombotic, and Valvular Disease: Mendelian Randomization Investigation.

    Larsson SC, Gill D, Mason AM, Jiang T, Bäck M, Butterworth AS and Burgess S

    Circulation 2020;141;22;1826-1828

    PUBMED: 32479194; DOI: 10.1161/CIRCULATIONAHA.120.045826

  • Multihost Transmission of Schistosoma mansoni in Senegal, 2015-2018.

    Catalano S, Léger E, Fall CB, Borlase A, Diop SD, Berger D, Webster BL, Faye B, Diouf ND, Rollinson D et al.

    Emerging infectious diseases 2020;26;6;1234-1242

    PUBMED: 32441625; PMC: 7258455; DOI: 10.3201/eid2606.200107

  • Novel 2D and 3D Assays to Determine the Activity of Anti-Leishmanial Drugs.

    O'Keeffe A, Hale C, Cotton JA, Yardley V, Gupta K, Ananthanarayanan A, Murdan S and Croft SL

    Microorganisms 2020;8;6

    PUBMED: 32492796; PMC: 7356592; DOI: 10.3390/microorganisms8060831

  • DNAJC6 Mutations Disrupt Dopamine Homeostasis in Juvenile Parkinsonism-Dystonia.

    Ng J, Cortès-Saladelafont E, Abela L, Termsarasab P, Mankad K, Sudhakar S, Gorman KM, Heales SJR, Pope S, Biassoni L et al.

    Movement disorders : official journal of the Movement Disorder Society 2020;35;8;1357-1368

    PUBMED: 32472658; PMC: 8425408; DOI: 10.1002/mds.28063

  • Multiple GYPB gene deletions associated with the U- phenotype in those of African ancestry.

    Lane WJ, Gleadall NS, Aeschlimann J, Vege S, Sanchis-Juan A, Stephens J, Sullivan JC, Mah HH, Aguad M, Smeland-Wagman R et al.

    Transfusion 2020

    PUBMED: 32473076; DOI: 10.1111/trf.15839

  • Identification of a conserved var gene in different Plasmodium falciparum strains.

    Dimonte S, Bruske EI, Enderes C, Otto TD, Turner L, Kremsner P and Frank M

    Malaria journal 2020;19;1;194

    PUBMED: 32471507; PMC: 7260770; DOI: 10.1186/s12936-020-03257-x

  • A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years.

    Haber M, Nassar J, Almarri MA, Saupe T, Saag L, Griffith SJ, Doumet-Serhal C, Chanteau J, Saghieh-Beydoun M, Xue Y et al.

    American journal of human genetics 2020;107;1;149-157

    PUBMED: 32470374; PMC: 7332655; DOI: 10.1016/j.ajhg.2020.05.008

  • High-Throughput Quantitative RT-PCR in Single and Bulk C. elegans Samples Using Nanofluidic Technology.

    Chauve L, Le Pen J, Hodge F, Todtenhaupt P, Biggins L, Miska EA, Andrews S and Casanueva O

    Journal of visualized experiments : JoVE 2020;159

    PUBMED: 32538915; DOI: 10.3791/61132

  • The concerted action of two B3-like prophage genes exclude superinfecting bacteriophages by blocking DNA entry into Pseudomonas aeruginosa.

    Carballo-Ontiveros MA, Cazares A, Vinuesa P, Kameyama L and Guarneros G

    Journal of virology 2020

    PUBMED: 32461312; DOI: 10.1128/JVI.00953-20

  • The mutational constraint spectrum quantified from variation in 141,456 humans.

    Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al.

    Nature 2020;581;7809;434-443

    PUBMED: 32461654; PMC: 7334197; DOI: 10.1038/s41586-020-2308-7

  • Evaluating drug targets through human loss-of-function genetic variation.

    Minikel EV, Karczewski KJ, Martin HC, Cummings BB, Whiffin N, Rhodes D, Alföldi J, Trembath RC, van Heel DA, Daly MJ et al.

    Nature 2020;581;7809;459-464

    PUBMED: 32461653; PMC: 7272226; DOI: 10.1038/s41586-020-2267-z

  • Personalized and graph genomes reveal missing signal in epigenomic data.

    Groza C, Kwan T, Soranzo N, Pastinen T and Bourque G

    Genome biology 2020;21;1;124

    PUBMED: 32450900; PMC: 7249353; DOI: 10.1186/s13059-020-02038-8

  • Evolutionary genomics at the human-environment interface in Africa.

    Svardal H, Rusuwa B, Linderoth T, Kiran A, Charmantier A, Lattorff HMG, Cagan A, Ommeh SC, Kamng'ona A, Katongo C et al.

    Molecular biology and evolution 2020

    PUBMED: 32442309; DOI: 10.1093/molbev/msaa132

  • Genomics-guided pre-clinical development of cancer therapies.

    Francies HE, McDermott U and Garnett MJ

    Nature cancer 2020;1;5;482-492

    PUBMED: 35121986; DOI: 10.1038/s43018-020-0067-x

  • A Novel Chemically Differentiated Mouse Embryonic Stem Cell-Based Model to Study Liver Stages of Plasmodium berghei.

    Tripathi J, Segeritz CP, Griffiths G, Bushell W, Vallier L, Skarnes WC, Mota MM and Billker O

    Stem cell reports 2020;14;6;1123-1134

    PUBMED: 32442532; PMC: 7355138; DOI: 10.1016/j.stemcr.2020.04.010

  • Longitudinal Cytokine Profiling Identifies GRO-α and EGF as Potential Biomarkers of Disease Progression in Essential Thrombocythemia.

    Øbro NF, Grinfeld J, Belmonte M, Irvine M, Shepherd MS, Rao TN, Karow A, Riedel LM, Harris OB, Baxter EJ et al.

    HemaSphere 2020;4;3;e371

    PUBMED: 32647796; PMC: 7306314; DOI: 10.1097/HS9.0000000000000371

  • CELLector: Genomics-Guided Selection of Cancer In Vitro Models.

    Najgebauer H, Yang M, Francies HE, Pacini C, Stronach EA, Garnett MJ, Saez-Rodriguez J and Iorio F

    Cell systems 2020;10;5;424-432.e6

    PUBMED: 32437684; DOI: 10.1016/j.cels.2020.04.007

  • Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae.

    Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C and Mostowy RJ

    Science advances 2020;6;21;eaaz6137

    PUBMED: 32671212; PMC: 7314567; DOI: 10.1126/sciadv.aaz6137

  • A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus.

    Ganaie F, Saad JS, McGee L, van Tonder AJ, Bentley SD, Lo SW, Gladstone RA, Turner P, Keenan JD, Breiman RF and Nahm MH

    mBio 2020;11;3

    PUBMED: 32430472; PMC: 7240158; DOI: 10.1128/mBio.00937-20

  • Genomic heterogeneity in myeloproliferative neoplasms and applications to clinical practice.

    Lee J, Godfrey AL and Nangalia J

    Blood reviews 2020;42;100708

    PUBMED: 32571583; DOI: 10.1016/j.blre.2020.100708

  • Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth.

    Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R, Hagai T, Chen X et al.

    Cell reports 2020;31;7;107628

    PUBMED: 32433953; PMC: 7242909; DOI: 10.1016/j.celrep.2020.107628

  • Genomically Aided Diagnosis of Severe Developmental Disorders.

    FitzPatrick DR and Firth HV

    Annual review of genomics and human genetics 2020

    PUBMED: 32421356; DOI: 10.1146/annurev-genom-120919-082329

  • Putative cell type discovery from single-cell gene expression data.

    Miao Z, Moreno P, Huang N, Papatheodorou I, Brazma A and Teichmann SA

    Nature methods 2020;17;6;621-628

    PUBMED: 32424270; DOI: 10.1038/s41592-020-0825-9

  • Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium.

    Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH et al.

    Nature genetics 2020;52;6;604-614

    PUBMED: 32424351; PMC: 7116672; DOI: 10.1038/s41588-020-0624-3

  • The prevalence and implications of single nucleotide polymorphisms in genes encoding the RNA polymerase of clinical isolates of Staphylococcus aureus.

    Krishna A, Liu B, Peacock SJ and Wigneshweraraj S

    MicrobiologyOpen 2020;9;7;e1058

    PUBMED: 32419302; PMC: 7349150; DOI: 10.1002/mbo3.1058

  • Germs and germlines: how "public" B-cell clones evolve in the gut.

    James KR and King HW

    Immunology and cell biology 2020

    PUBMED: 32418276; DOI: 10.1111/imcb.12340

  • Stimulation strength controls the rate of initiation but not the molecular organization of TCR-induced signalling.

    Ma CY, Marioni JC, Griffiths GM and Richard AC

    eLife 2020;9

    PUBMED: 32412411; DOI: 10.7554/eLife.53948

  • Targeted sequencing in DLBCL, molecular subtypes, and outcomes: a Haematological Malignancy Research Network report.

    Lacy SE, Barrans SL, Beer PA, Painter D, Smith AG, Roman E, Cooke SL, Ruiz C, Glover P, Van Hoppe SJL et al.

    Blood 2020;135;20;1759-1771

    PUBMED: 32187361; PMC: 7259825; DOI: 10.1182/blood.2019003535

  • A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells.

    Nasrallah R, Imianowski CJ, Bossini-Castillo L, Grant FM, Dogan M, Placek L, Kozhaya L, Kuo P, Sadiyah F, Whiteside SK et al.

    Nature 2020;583;7816;447-452

    PUBMED: 32499651; PMC: 7116706; DOI: 10.1038/s41586-020-2296-7

  • Development of copy number assays for detection and surveillance of piperaquine resistance associated plasmepsin 2/3 copy number variation in Plasmodium falciparum.

    Ansbro MR, Jacob CG, Amato R, Kekre M, Amaratunga C, Sreng S, Suon S, Miotto O, Fairhurst RM, Wellems TE and Kwiatkowski DP

    Malaria journal 2020;19;1;181

    PUBMED: 32404110; DOI: 10.1186/s12936-020-03249-x

  • From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases.

    Cano-Gamez E and Trynka G

    Frontiers in genetics 2020;11;424

    PUBMED: 32477401; PMC: 7237642; DOI: 10.3389/fgene.2020.00424

  • MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.

    Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC and Stegle O

    Genome biology 2020;21;1;111

    PUBMED: 32393329; DOI: 10.1186/s13059-020-02015-1

  • Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission.

    Rivett L, Sridhar S, Sparkes D, Routledge M, Jones NK, Forrest S, Young J, Pereira-Dias J, Hamilton WL, Ferris M et al.

    eLife 2020;9

    PUBMED: 32392129; PMC: 7314537; DOI: 10.7554/eLife.58728

  • Prenatal development of human immunity.

    Park JE, Jardine L, Gottgens B, Teichmann SA and Haniffa M

    Science (New York, N.Y.) 2020;368;6491;600-603

    PUBMED: 32381715; DOI: 10.1126/science.aaz9330

  • High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells.

    Beumer J, Puschhof J, Bauzá-Martinez J, Martínez-Silgado A, Elmentaite R, James KR, Ross A, Hendriks D, Artegiani B, Busslinger GA et al.

    Cell 2020

    PUBMED: 32407674; DOI: 10.1016/j.cell.2020.04.036

  • Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population.

    Horesh G, Fino C, Harms A, Dorman MJ, Parts L, Gerdes K, Heinz E and Thomson NR

    Nucleic acids research 2020;48;8;4357-4370

    PUBMED: 32232417; PMC: 7192599; DOI: 10.1093/nar/gkaa198

  • Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.

    Rifkin RF, Vikram S, Ramond JB, Rey-Iglesia A, Brand TB, Porraz G, Val A, Hall G, Woodborne S, Le Bailly M et al.

    Microbiome 2020;8;1;62

    PUBMED: 32375874; DOI: 10.1186/s40168-020-00832-x

  • Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development.

    Wangwiwatsin A, Protasio AV, Wilson S, Owusu C, Holroyd NE, Sanders MJ, Keane J, Doenhoff MJ, Rinaldi G and Berriman M

    PLoS neglected tropical diseases 2020;14;5;e0007743

    PUBMED: 32374726; PMC: 7263636; DOI: 10.1371/journal.pntd.0007743

  • Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

    Thaventhiran JED, Lango Allen H, Burren OS, Rae W, Greene D, Staples E, Zhang Z, Farmery JHR, Simeoni I, Rivers E et al.

    Nature 2020;583;7814;90-95

    PUBMED: 32499645; PMC: 7334047; DOI: 10.1038/s41586-020-2265-1

  • Interstitial Cell Remodeling Promotes Aberrant Adipogenesis in Dystrophic Muscles.

    Camps J, Breuls N, Sifrim A, Giarratana N, Corvelyn M, Danti L, Grosemans H, Vanuytven S, Thiry I, Belicchi M et al.

    Cell reports 2020;31;5;107597

    PUBMED: 32375047; DOI: 10.1016/j.celrep.2020.107597

  • NtrBC Regulates Invasiveness and Virulence of Pseudomonas aeruginosa During High-Density Infection.

    Alford MA, Baghela A, Yeung ATY, Pletzer D and Hancock REW

    Frontiers in microbiology 2020;11;773

    PUBMED: 32431676; PMC: 7214821; DOI: 10.3389/fmicb.2020.00773

  • A microsporidian impairs Plasmodium falciparum transmission in Anopheles arabiensis mosquitoes.

    Herren JK, Mbaisi L, Mararo E, Makhulu EE, Mobegi VA, Butungi H, Mancini MV, Oundo JW, Teal ET, Pinaud S et al.

    Nature communications 2020;11;1;2187

    PUBMED: 32366903; PMC: 7198529; DOI: 10.1038/s41467-020-16121-y

  • Reconstructing human DC, monocyte and macrophage development in utero using single cell technologies.

    Jardine L and Haniffa M

    Molecular immunology 2020;123;1-6

    PUBMED: 32380279; DOI: 10.1016/j.molimm.2020.04.023

  • Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells.

    Pfannschmidt T, Terry MJ, Van Aken O and Quiros PM

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2020;375;1801;20190396

    PUBMED: 32362267; DOI: 10.1098/rstb.2019.0396

  • Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes.

    Heaton H, Talman AM, Knights A, Imaz M, Gaffney DJ, Durbin R, Hemberg M and Lawniczak MKN

    Nature methods 2020;17;6;615-620

    PUBMED: 32366989; DOI: 10.1038/s41592-020-0820-1

  • The gene-rich genome of the scallop Pecten maximus.

    Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD et al.

    GigaScience 2020;9;5

    PUBMED: 32352532; PMC: 7191990; DOI: 10.1093/gigascience/giaa037

  • The open targets post-GWAS analysis pipeline.

    Peat G, Jones W, Nuhn M, Marugán JC, Newell W, Dunham I and Zerbino D

    Bioinformatics (Oxford, England) 2020;36;9;2936-2937

    PUBMED: 31930349; PMC: 7203748; DOI: 10.1093/bioinformatics/btaa020

  • Identifying and removing haplotypic duplication in primary genome assemblies.

    Guan D, McCarthy SA, Wood J, Howe K, Wang Y and Durbin R

    Bioinformatics (Oxford, England) 2020;36;9;2896-2898

    PUBMED: 31971576; PMC: 7203741; DOI: 10.1093/bioinformatics/btaa025

  • Mutational signatures are jointly shaped by DNA damage and repair.

    Volkova NV, Meier B, González-Huici V, Bertolini S, Gonzalez S, Vöhringer H, Abascal F, Martincorena I, Campbell PJ, Gartner A and Gerstung M

    Nature communications 2020;11;1;2169

    PUBMED: 32358516; PMC: 7195458; DOI: 10.1038/s41467-020-15912-7

  • Cell Atlas technologies and insights into tissue architecture.

    Wilbrey-Clark A, Roberts K and Teichmann SA

    The Biochemical journal 2020;477;8;1427-1442

    PUBMED: 32339226; PMC: 7200628; DOI: 10.1042/BCJ20190341

  • Genetic Markers in S. Paratyphi C Reveal Primary Adaptation to Pigs.

    Nair S, Fookes M, Corton C, Thomson NR, Wain J and Langridge GC

    Microorganisms 2020;8;5

    PUBMED: 32365926; PMC: 7285187; DOI: 10.3390/microorganisms8050657

  • Inhibition of Resistance-Refractory P. falciparum Kinase PKG Delivers Prophylactic, Blood Stage, and Transmission-Blocking Antiplasmodial Activity.

    Vanaerschot M, Murithi JM, Pasaje CFA, Ghidelli-Disse S, Dwomoh L, Bird M, Spottiswoode N, Mittal N, Arendse LB, Owen ES et al.

    Cell chemical biology 2020;27;7;806-816.e8

    PUBMED: 32359426; PMC: 7369637; DOI: 10.1016/j.chembiol.2020.04.001

  • Molecular characterization of Brucella ovis in Argentina.

    Alvarez LP, Ruiz-Villalobos N, Suárez-Esquivel M, Thomson NR, Marcellino R, Víquez-Ruiz E, Robles CA and Guzmán-Verri C

    Veterinary microbiology 2020;245;108703

    PUBMED: 32456808; DOI: 10.1016/j.vetmic.2020.108703

  • Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.

    Gladstone RA, Lo SW, Goater R, Yeats C, Taylor B, Hadfield J, Lees JA, Croucher NJ, van Tonder AJ, Bentley LJ et al.

    Microbial genomics 2020;6;5

    PUBMED: 32375991; PMC: 7371119; DOI: 10.1099/mgen.0.000357

  • Acral lentiginous melanoma: Basic facts, biological characteristics and research perspectives of an understudied disease.

    Basurto-Lozada P, Molina-Aguilar C, Castañeda-Garcia C, Vázquez-Cruz ME, Garcia-Salinas OI, Álvarez-Cano A, Martínez-Said H, Roldán-Marín R, Adams DJ, Possik PA and Robles-Espinoza CD

    Pigment cell & melanoma research 2020

    PUBMED: 32330367; DOI: 10.1111/pcmr.12885

  • Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts.

    Georgakopoulos-Soares I, Koh G, Momen SE, Jiricny J, Hemberg M and Nik-Zainal S

    Nature communications 2020;11;1;1980

    PUBMED: 32332764; PMC: 7181645; DOI: 10.1038/s41467-020-15901-w

  • Sex chromosome evolution in parasitic nematodes of humans.

    Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N et al.

    Nature communications 2020;11;1;1964

    PUBMED: 32327641; PMC: 7181701; DOI: 10.1038/s41467-020-15654-6

  • The mutational landscape of normal human endometrial epithelium.

    Moore L, Leongamornlert D, Coorens THH, Sanders MA, Ellis P, Dentro SC, Dawson KJ, Butler T, Rahbari R, Mitchell TJ et al.

    Nature 2020;580;7805;640-646

    PUBMED: 32350471; DOI: 10.1038/s41586-020-2214-z

  • Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros.

    Louis M, Skovrind M, Samaniego Castruita JA, Garilao C, Kaschner K, Gopalakrishnan S, Haile JS, Lydersen C, Kovacs KM, Garde E et al.

    Proceedings. Biological sciences 2020;287;1925;20192964

    PUBMED: 32315590; PMC: 7211449; DOI: 10.1098/rspb.2019.2964

  • Malat1 Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells.

    Hewitson JP, West KA, James KR, Rani GF, Dey N, Romano A, Brown N, Teichmann SA, Kaye PM and Lagos D

    Journal of immunology (Baltimore, Md. : 1950) 2020

    PUBMED: 32321759; DOI: 10.4049/jimmunol.1900940

  • A framework for an evidence-based gene list relevant to autism spectrum disorder.

    Schaaf CP, Betancur C, Yuen RKC, Parr JR, Skuse DH, Gallagher L, Bernier RA, Buchanan JA, Buxbaum JD, Chen CA et al.

    Nature reviews. Genetics 2020

    PUBMED: 32317787; DOI: 10.1038/s41576-020-0231-2

  • Timing the initiation of multiple myeloma.

    Rustad EH, Yellapantula V, Leongamornlert D, Bolli N, Ledergor G, Nadeu F, Angelopoulos N, Dawson KJ, Mitchell TJ, Osborne RJ et al.

    Nature communications 2020;11;1;1917

    PUBMED: 32317634; PMC: 7174344; DOI: 10.1038/s41467-020-15740-9

  • Genomic analysis of natural intra-specific hybrids among Ethiopian isolates of Leishmania donovani.

    Cotton JA, Durrant C, Franssen SU, Gelanew T, Hailu A, Mateus D, Sanders MJ, Berriman M, Volf P, Miles MA and Yeo M

    PLoS neglected tropical diseases 2020;14;4;e0007143

    PUBMED: 32310945; PMC: 7237039; DOI: 10.1371/journal.pntd.0007143

  • Insights into the intracellular localization, protein associations and artemisinin resistance properties of Plasmodium falciparum K13.

    Gnädig NF, Stokes BH, Edwards RL, Kalantarov GF, Heimsch KC, Kuderjavy M, Crane A, Lee MCS, Straimer J, Becker K et al.

    PLoS pathogens 2020;16;4;e1008482

    PUBMED: 32310999; PMC: 7192513; DOI: 10.1371/journal.ppat.1008482

  • Effect of long-lasting insecticidal nets with and without piperonyl butoxide on malaria indicators in Uganda (LLINEUP): a pragmatic, cluster-randomised trial embedded in a national LLIN distribution campaign.

    Staedke SG, Gonahasa S, Dorsey G, Kamya MR, Maiteki-Sebuguzi C, Lynd A, Katureebe A, Kyohere M, Mutungi P, Kigozi SP et al.

    Lancet (London, England) 2020;395;10232;1292-1303

    PUBMED: 32305094; DOI: 10.1016/S0140-6736(20)30214-2

  • A Roadmap for Global Acceleration of Genomics Integration Across Nursing.

    Tonkin E, Calzone KA, Badzek L, Benjamin C, Middleton A, Patch C and Kirk M

    Journal of nursing scholarship : an official publication of Sigma Theta Tau International Honor Society of Nursing 2020;52;3;329-338

    PUBMED: 32301236; PMC: 7202994; DOI: 10.1111/jnu.12552

  • Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.

    Lavaert M, Liang KL, Vandamme N, Park JE, Roels J, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D et al.

    Immunity 2020;52;6;1088-1104.e6

    PUBMED: 32304633; DOI: 10.1016/j.immuni.2020.03.019

  • Mechanisms generating cancer genome complexity from a single cell division error.

    Umbreit NT, Zhang CZ, Lynch LD, Blaine LJ, Cheng AM, Tourdot R, Sun L, Almubarak HF, Judge K, Mitchell TJ et al.

    Science (New York, N.Y.) 2020;368;6488

    PUBMED: 32299917; PMC: 7347108; DOI: 10.1126/science.aba0712

  • IRF5 Promotes Influenza Virus-Induced Inflammatory Responses in Human Induced Pluripotent Stem Cell-Derived Myeloid Cells and Murine Models.

    Forbester JL, Clement M, Wellington D, Yeung A, Dimonte S, Marsden M, Chapman L, Coomber EL, Tolley C, Lees E et al.

    Journal of virology 2020;94;9

    PUBMED: 32075938; PMC: 7163152; DOI: 10.1128/JVI.00121-20

  • A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division.

    Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC et al.

    Nature communications 2020;11;1;1851

    PUBMED: 32296040; PMC: 7160116; DOI: 10.1038/s41467-020-14978-7

  • ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing.

    Karatzas E, Zamora JE, Athanasiadis E, Dellis D, Cournia Z and Spyrou GM

    Bioinformatics (Oxford, England) 2020;36;8;2602-2604

    PUBMED: 31913451; PMC: 7178400; DOI: 10.1093/bioinformatics/btz976

  • Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway.

    LaMonte GM, Rocamora F, Marapana DS, Gnädig NF, Ottilie S, Luth MR, Worgall TS, Goldgof GM, Mohunlal R, Santha Kumar TR et al.

    Nature communications 2020;11;1;1780

    PUBMED: 32286267; PMC: 7156427; DOI: 10.1038/s41467-020-15440-4

  • Persistence of Brucella abortus lineages revealed by genomic characterization and phylodynamic analysis.

    Suárez-Esquivel M, Hernández-Mora G, Ruiz-Villalobos N, Barquero-Calvo E, Chacón-Díaz C, Ladner JT, Oviedo-Sánchez G, Foster JT, Rojas-Campos N, Chaves-Olarte E et al.

    PLoS neglected tropical diseases 2020;14;4;e0008235

    PUBMED: 32287327; PMC: 7182279; DOI: 10.1371/journal.pntd.0008235

  • Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines.

    Cano-Gamez E, Soskic B, Roumeliotis TI, So E, Smyth DJ, Baldrighi M, Willé D, Nakic N, Esparza-Gordillo J, Larminie CGC et al.

    Nature communications 2020;11;1;1801

    PUBMED: 32286271; PMC: 7156481; DOI: 10.1038/s41467-020-15543-y

  • A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease.

    Emdin CA, Haas ME, Khera AV, Aragam K, Chaffin M, Klarin D, Hindy G, Jiang L, Wei WQ, Feng Q et al.

    PLoS genetics 2020;16;4;e1008629

    PUBMED: 32282858; DOI: 10.1371/journal.pgen.1008629

  • Aberrant cell migration contributes to defective airway epithelial repair in childhood wheeze.

    Iosifidis T, Sutanto EN, Buckley AG, Coleman L, Gill EE, Lee AH, Ling KM, Hillas J, Looi K, Garratt LW et al.

    JCI insight 2020;5;7

    PUBMED: 32208383; PMC: 7205257; DOI: 10.1172/jci.insight.133125

  • Cysteine synthases CYSL-1 and CYSL-2 mediate C. elegans heritable adaptation to P. vranovensis infection.

    Burton NO, Riccio C, Dallaire A, Price J, Jenkins B, Koulman A and Miska EA

    Nature communications 2020;11;1;1741

    PUBMED: 32269224; PMC: 7142082; DOI: 10.1038/s41467-020-15555-8

  • Defining the Design Principles of Skin Epidermis Postnatal Growth.

    Dekoninck S, Hannezo E, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, de Neunheuser C, Dubois C, Voet T et al.

    Cell 2020;181;3;604-620.e22

    PUBMED: 32259486; PMC: 7198979; DOI: 10.1016/j.cell.2020.03.015

  • Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand.

    Loraine J, Heinz E, Soontarach R, Blackwell GA, Stabler RA, Voravuthikunchai SP, Srimanote P, Kiratisin P, Thomson NR and Taylor PW

    Frontiers in microbiology 2020;11;548

    PUBMED: 32328045; PMC: 7153491; DOI: 10.3389/fmicb.2020.00548

  • A Genome-Wide Screen in Mice To Identify Cell-Extrinsic Regulators of Pulmonary Metastatic Colonisation.

    van der Weyden L, Swiatkowska A, Iyer V, Speak AO and Adams DJ

    G3 (Bethesda, Md.) 2020

    PUBMED: 32245826; DOI: 10.1534/g3.120.401128

  • Lung function and microbiota diversity in cystic fibrosis.

    Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, Ashare A, Elborn JS, De Soyza A, Carroll MP et al.

    Microbiome 2020;8;1;45

    PUBMED: 32238195; PMC: 7114784; DOI: 10.1186/s40168-020-00810-3

  • Non-typhoidal Salmonella bloodstream infections in Kisantu, DR Congo: Emergence of O5-negative Salmonella Typhimurium and extensive drug resistance.

    Tack B, Phoba MF, Barbé B, Kalonji LM, Hardy L, Van Puyvelde S, Ingelbeen B, Falay D, Ngbonda D, van der Sande MAB et al.

    PLoS neglected tropical diseases 2020;14;4;e0008121

    PUBMED: 32240161; DOI: 10.1371/journal.pntd.0008121

  • An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa.

    Mathieson I, Abascal F, Vinner L, Skoglund P, Pomilla C, Mitchell P, Arthur C, Gurdasani D, Willerslev E, Sandhu MS and Dewar G

    Genome biology and evolution 2020;12;4;407-412

    PUBMED: 32022848; PMC: 7197492; DOI: 10.1093/gbe/evaa019

  • The dental proteome of Homo antecessor.

    Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Rakownikow Jersie-Christensen R, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M et al.

    Nature 2020;580;7802;235-238

    PUBMED: 32269345; PMC: 7582224; DOI: 10.1038/s41586-020-2153-8

  • Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation.

    Svardal H, Quah FX, Malinsky M, Ngatunga BP, Miska EA, Salzburger W, Genner MJ, Turner GF and Durbin R

    Molecular biology and evolution 2020;37;4;1100-1113

    PUBMED: 31821500; PMC: 7086168; DOI: 10.1093/molbev/msz294

  • Expanding the genotype-phenotype correlation of de novo heterozygous missense variants in YWHAG as a cause of developmental and epileptic encephalopathy.

    Kanani F, Titheradge H, Cooper N, Elmslie F, Lees MM, Juusola J, Pisani L, McKenna C, Mignot C, Valence S et al.

    American journal of medical genetics. Part A 2020;182;4;713-720

    PUBMED: 31926053; DOI: 10.1002/ajmg.a.61483

  • Nature via Nurture, the Martin Way.

    Martin HC

    Twin research and human genetics : the official journal of the International Society for Twin Studies 2020;23;2;137-138

    PUBMED: 32482185; DOI: 10.1017/thg.2020.40

  • Outbreak of Dirkmeia churashimaensis Fungemia in a Neonatal Intensive Care Unit, India.

    Chowdhary A, Sharada K, Singh PK, Bhagwani DK, Kumar N, de Groot T and Meis JF

    Emerging infectious diseases 2020;26;4;764-768

    PUBMED: 32186501; PMC: 7101094; DOI: 10.3201/eid2604.190847

  • Willingness to donate genomic and other medical data: results from Germany.

    Voigt TH, Holtz V, Niemiec E, Howard HC, Middleton A and Prainsack B

    European journal of human genetics : EJHG 2020

    PUBMED: 32238912; DOI: 10.1038/s41431-020-0611-2

  • Defining metrics for whole-genome sequence analysis of MRSA in clinical practice.

    Raven KE, Blane B, Kumar N, Leek D, Bragin E, Coll F, Parkhill J and Peacock SJ

    Microbial genomics 2020;6;4

    PUBMED: 32228804; PMC: 7276698; DOI: 10.1099/mgen.0.000354

  • Minimal phenotyping yields genome-wide association signals of low specificity for major depression.

    Cai N, Revez JA, Adams MJ, Andlauer TFM, Breen G, Byrne EM, Clarke TK, Forstner AJ, Grabe HJ, Hamilton SP et al.

    Nature genetics 2020

    PUBMED: 32231276; DOI: 10.1038/s41588-020-0594-5

  • Mosaicism in ASXL3-related syndrome: Description of five patients from three families.

    Schirwani S, Hauser N, Platt A, Punj S, Prescott K, Canham N, Study DDD, Mansour S and Balasubramanian M

    European journal of medical genetics 2020;63;6;103925

    PUBMED: 32240826; DOI: 10.1016/j.ejmg.2020.103925

  • Novel Insights Into the Spread of Enteric Pathogens Using Genomics.

    Domman D, Ruis C, Dorman MJ, Shakya M and Chain PSG

    The Journal of infectious diseases 2020;221;Suppl 3;S319-S330

    PUBMED: 31538189; DOI: 10.1093/infdis/jiz220

  • The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche.

    Ataca D, Aouad P, Constantin C, Laszlo C, Beleut M, Shamseddin M, Rajaram RD, Jeitziner R, Mead TJ, Caikovski M et al.

    Nature communications 2020;11;1;1571

    PUBMED: 32218432; PMC: 7099066; DOI: 10.1038/s41467-020-15357-y

  • Global genome diversity of the Leishmania donovani complex.

    Franssen SU, Durrant C, Stark O, Moser B, Downing T, Imamura H, Dujardin JC, Sanders MJ, Mauricio I, Miles MA et al.

    eLife 2020;9

    PUBMED: 32209228; DOI: 10.7554/eLife.51243

  • Identification of slit3 as a locus affecting nicotine preference in zebrafish and human smoking behaviour.

    García-González J, Brock AJ, Parker MO, Riley RJ, Joliffe D, Sudwarts A, Teh MT, Busch-Nentwich EM, Stemple DL, Martineau AR et al.

    eLife 2020;9

    PUBMED: 32209227; PMC: 7096180; DOI: 10.7554/eLife.51295

  • Leupaxin Expression Is Dispensable for B Cell Immune Responses.

    Bonaud A, Clare S, Bisio V, Sowerby JM, Yao S, Ostergaard H, Balabanian K, Smith KGC and Espéli M

    Frontiers in immunology 2020;11;466

    PUBMED: 32269569; PMC: 7109257; DOI: 10.3389/fimmu.2020.00466

  • Characterising a healthy adult with a rare HAO1 knockout to support a therapeutic strategy for primary hyperoxaluria.

    McGregor TL, Hunt KA, Yee E, Mason D, Nioi P, Ticau S, Pelosi M, Loken PR, Finer S, Lawlor DA et al.

    eLife 2020;9

    PUBMED: 32207686; PMC: 7108859; DOI: 10.7554/eLife.54363

  • Low rates of mutation in clinical grade human pluripotent stem cells under different culture conditions.

    Thompson O, von Meyenn F, Hewitt Z, Alexander J, Wood A, Weightman R, Gregory S, Krueger F, Andrews S, Barbaric I et al.

    Nature communications 2020;11;1;1528

    PUBMED: 32251294; PMC: 7089967; DOI: 10.1038/s41467-020-15271-3

  • Obstacles to detecting isoforms using full-length scRNA-seq data.

    Westoby J, Artemov P, Hemberg M and Ferguson-Smith A

    Genome biology 2020;21;1;74

    PUBMED: 32293520; DOI: 10.1186/s13059-020-01981-w

  • Schistosoma species detection by environmental DNA assays in African freshwaters.

    Alzaylaee H, Collins RA, Rinaldi G, Shechonge A, Ngatunga B, Morgan ER and Genner MJ

    PLoS neglected tropical diseases 2020;14;3;e0008129

    PUBMED: 32203507; DOI: 10.1371/journal.pntd.0008129

  • Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones.

    Ludden C, Decano AG, Jamrozy D, Pickard D, Morris D, Parkhill J, Peacock SJ, Cormican M and Downing T

    Microbial genomics 2020;6;4

    PUBMED: 32213258; PMC: 7276707; DOI: 10.1099/mgen.0.000352

  • Insights into human genetic variation and population history from 929 diverse genomes.

    Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, Chen Y, Felkel S, Hallast P, Kamm J et al.

    Science (New York, N.Y.) 2020;367;6484

    PUBMED: 32193295; PMC: 7115999; DOI: 10.1126/science.aay5012

  • Local and Universal Action: The Paradoxes of Indole Signalling in Bacteria.

    Zarkan A, Liu J, Matuszewska M, Gaimster H and Summers DK

    Trends in microbiology 2020;28;7;566-577

    PUBMED: 32544443; DOI: 10.1016/j.tim.2020.02.007

  • Lean, mean, learning machines.

    Wheeler NE, Sánchez-Busó L, Argimón S and Jeffrey B

    Nature reviews. Microbiology 2020

    PUBMED: 32203299; DOI: 10.1038/s41579-020-0357-4

  • An intestinal zinc sensor regulates food intake and developmental growth.

    Redhai S, Pilgrim C, Gaspar P, Giesen LV, Lopes T, Riabinina O, Grenier T, Milona A, Chanana B, Swadling JB et al.

    Nature 2020;580;7802;263-268

    PUBMED: 32269334; DOI: 10.1038/s41586-020-2111-5

  • A single-progenitor model as the unifying paradigm of epidermal and esophageal epithelial maintenance in mice.

    Piedrafita G, Kostiou V, Wabik A, Colom B, Fernandez-Antoran D, Herms A, Murai K, Hall BA and Jones PH

    Nature communications 2020;11;1;1429

    PUBMED: 32188860; PMC: 7080751; DOI: 10.1038/s41467-020-15258-0

  • Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data.

    Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng'ona A et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020;70;7;1294-1303

    PUBMED: 31094423; PMC: 7768739; DOI: 10.1093/cid/ciz404

  • FGFR1 Oncogenic Activation Reveals an Alternative Cell of Origin of SCLC in Rb1/p53 Mice.

    Ferone G, Song JY, Krijgsman O, van der Vliet J, Cozijnsen M, Semenova EA, Adams DJ, Peeper D and Berns A

    Cell reports 2020;30;11;3837-3850.e3

    PUBMED: 32187553; PMC: 7090386; DOI: 10.1016/j.celrep.2020.02.052

  • Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders.

    Lal D, May P, Perez-Palma E, Samocha KE, Kosmicki JA, Robinson EB, Møller RS, Krause R, Nürnberg P, Weckhuysen S et al.

    Genome medicine 2020;12;1;28

    PUBMED: 32183904; DOI: 10.1186/s13073-020-00725-6

  • Update on the pathology, genetics and somatic landscape of sebaceous tumours.

    Ferreira I, Wiedemeyer K, Demetter P, Adams DJ, Arends MJ and Brenn T

    Histopathology 2020;76;5;640-649

    PUBMED: 31821583; DOI: 10.1111/his.14044

  • Wikidata as a knowledge graph for the life sciences.

    Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K et al.

    eLife 2020;9

    PUBMED: 32180547; PMC: 7077981; DOI: 10.7554/eLife.52614

  • The immunological network in the developing human skin.

    Botting RA and Haniffa M

    Immunology 2020

    PUBMED: 32173857; DOI: 10.1111/imm.13192

  • Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map.

    Bayraktar OA, Bartels T, Holmqvist S, Kleshchevnikov V, Martirosyan A, Polioudakis D, Ben Haim L, Young AMH, Batiuk MY, Prakash K et al.

    Nature neuroscience 2020;23;4;500-509

    PUBMED: 32203496; PMC: 7116562; DOI: 10.1038/s41593-020-0602-1

  • Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

    McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R, HipSci Consortium, Wang W et al.

    Nature methods 2020;17;4;414-421

    PUBMED: 32203388; DOI: 10.1038/s41592-020-0766-3

  • Dissecting the early steps of MLL induced leukaemogenic transformation using a mouse model of AML.

    Basilico S, Wang X, Kennedy A, Tzelepis K, Giotopoulos G, Kinston SJ, Quiros PM, Wong K, Adams DJ, Carnevalli LS et al.

    Nature communications 2020;11;1;1407

    PUBMED: 32179751; PMC: 7075888; DOI: 10.1038/s41467-020-15220-0

  • Establishment, optimisation and quantitation of a bioluminescent murine infection model of visceral leishmaniasis for systematic vaccine screening.

    Ong HB, Clare S, Roberts AJ, Wilson ME and Wright GJ

    Scientific reports 2020;10;1;4689

    PUBMED: 32170135; DOI: 10.1038/s41598-020-61662-3

  • Factors Affecting Sentinel Node Metastasis in Thin (T1) Cutaneous Melanomas: Development and External Validation of a Predictive Nomogram.

    Maurichi A, Miceli R, Eriksson H, Newton-Bishop J, Nsengimana J, Chan M, Hayes AJ, Heelan K, Adams D, Patuzzo R et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2020;JCO1901902

    PUBMED: 32167862; DOI: 10.1200/JCO.19.01902

  • Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.

    Morgan MD, Patin E, Jagla B, Hasan M, Quintana-Murci L and Marioni JC

    PLoS genetics 2020;16;3;e1008686

    PUBMED: 32168362; PMC: 7094872; DOI: 10.1371/journal.pgen.1008686

  • Does Intensive Treatment Select for Praziquantel Resistance in High-Transmission Settings? Parasitological Trends and Treatment Efficacy Within a Cluster-Randomized Trial.

    Tushabe JV, Lubyayi L, Sserubanja J, Kabuubi P, Abayo E, Kiwanuka S, Nassuuna J, Kaweesa J, Corstjens P, van Dam G et al.

    Open forum infectious diseases 2020;7;4;ofaa091

    PUBMED: 32296727; PMC: 7148002; DOI: 10.1093/ofid/ofaa091

  • Triple artemisinin-based combination therapies versus artemisinin-based combination therapies for uncomplicated Plasmodium falciparum malaria: a multicentre, open-label, randomised clinical trial.

    van der Pluijm RW, Tripura R, Hoglund RM, Pyae Phyo A, Lek D, Ul Islam A, Anvikar AR, Satpathi P, Satpathi S, Behera PK et al.

    Lancet (London, England) 2020;395;10233;1345-1360

    PUBMED: 32171078; PMC: 8204272; DOI: 10.1016/S0140-6736(20)30552-3

  • The influence of rare variants in circulating metabolic biomarkers.

    Riveros-Mckay F, Oliver-Williams C, Karthikeyan S, Walter K, Kundu K, Ouwehand WH, Roberts D, Di Angelantonio E, Soranzo N, Danesh J et al.

    PLoS genetics 2020;16;3;e1008605

    PUBMED: 32150548; PMC: 7108731; DOI: 10.1371/journal.pgen.1008605

  • The single-cell eQTLGen consortium.

    van der Wijst MG, de Vries DH, Groot HE, Trynka G, Hon CC, Bonder MJ, Stegle O, Nawijn M, Idaghdour Y, van der Harst P et al.

    eLife 2020;9

    PUBMED: 32149610; DOI: 10.7554/eLife.52155

  • Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein.

    Oyen D, Torres JL, Aoto PC, Flores-Garcia Y, Binter S, Pholcharee T, Carroll S, Reponen S, Wash R, Liang Q et al.

    PLoS pathogens 2020;16;3;e1008373

    PUBMED: 32150583; DOI: 10.1371/journal.ppat.1008373

  • The Nature and Extent of Plasmid Variation in Chlamydia trachomatis.

    Jones CA, Hadfield J, Thomson NR, Cleary DW, Marsh P, Clarke IN and O'Neill CE

    Microorganisms 2020;8;3

    PUBMED: 32155798; PMC: 7143637; DOI: 10.3390/microorganisms8030373

  • Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.

    Li C, Stoma S, Lotta LA, Warner S, Albrecht E, Allione A, Arp PP, Broer L, Buxton JL, Da Silva Couto Alves A et al.

    American journal of human genetics 2020;106;3;389-404

    PUBMED: 32109421; PMC: 7058826; DOI: 10.1016/j.ajhg.2020.02.006

  • Identification of region-specific astrocyte subtypes at single cell resolution.

    Batiuk MY, Martirosyan A, Wahis J, de Vin F, Marneffe C, Kusserow C, Koeppen J, Viana JF, Oliveira JF, Voet T et al.

    Nature communications 2020;11;1;1220

    PUBMED: 32139688; PMC: 7058027; DOI: 10.1038/s41467-019-14198-8

  • Detecting extra-ocular Chlamydia trachomatis in a trachoma-endemic community in Ethiopia: Identifying potential routes of transmission.

    Last A, Versteeg B, Shafi Abdurahman O, Robinson A, Dumessa G, Abraham Aga M, Shumi Bejiga G, Negussu N, Greenland K, Czerniewska A et al.

    PLoS neglected tropical diseases 2020;14;3;e0008120

    PUBMED: 32130213; DOI: 10.1371/journal.pntd.0008120

  • Mapping the travel patterns of people with malaria in Bangladesh.

    Sinha I, Sayeed AA, Uddin D, Wesolowski A, Zaman SI, Faiz MA, Ghose A, Rahman MR, Islam A, Karim MJ et al.

    BMC medicine 2020;18;1;45

    PUBMED: 32127002; PMC: 7055101; DOI: 10.1186/s12916-020-1512-5

  • Applying single-cell technologies to clinical pathology: progress in nephropathology.

    Stewart BJ and Clatworthy MR

    The Journal of pathology 2020

    PUBMED: 32125696; DOI: 10.1002/path.5417

  • Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons.

    Barnes IHA, Ibarra-Soria X, Fitzgerald S, Gonzalez JM, Davidson C, Hardy MP, Manthravadi D, Van Gerven L, Jorissen M, Zeng Z et al.

    BMC genomics 2020;21;1;196

    PUBMED: 32126975; PMC: 7055050; DOI: 10.1186/s12864-020-6583-3

  • Microarray analyses reveal strain-specific antibody responses to Plasmodium falciparum apical membrane antigen 1 variants following natural infection and vaccination.

    Bailey JA, Berry AA, Travassos MA, Ouattara A, Boudova S, Dotsey EY, Pike A, Jacob CG, Adams M, Tan JC et al.

    Scientific reports 2020;10;1;3952

    PUBMED: 32127565; DOI: 10.1038/s41598-020-60551-z

  • Polyclonal Campylobacter fetus Infections Among Unrelated Patients, Montevideo, Uruguay, 2013-2018.

    Costa D, Betancor L, Gadea P, Cabezas L, Caiata L, Palacio R, Seija V, Galiana A, Vieytes M, Cristophersen I et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020;70;6;1236-1239

    PUBMED: 31309972; DOI: 10.1093/cid/ciz657

  • Uptake of Plasmodium falciparum Gametocytes During Mosquito Bloodmeal by Direct and Membrane Feeding.

    Talman AM, Ouologuem DTD, Love K, Howick VM, Mulamba C, Haidara A, Dara N, Sylla D, Sacko A, Coulibaly MM et al.

    Frontiers in microbiology 2020;11;246

    PUBMED: 32194521; PMC: 7062676; DOI: 10.3389/fmicb.2020.00246

  • The global epidemiology of emerging Histoplasma species in recent years.

    Rodrigues AM, Beale MA, Hagen F, Fisher MC, Terra PPD, de Hoog S, Brilhante RSN, de Aguiar Cordeiro R, de Souza Collares Maia Castelo-Branco D, Rocha MFG et al.

    Studies in mycology 2020;97;100095

    PUBMED: 33335607; PMC: 7714791; DOI: 10.1016/j.simyco.2020.02.001

  • Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni.

    Lu L, Loker ES, Zhang SM, Buddenborg SK and Bu L

    BMC genomics 2020;21;1;190

    PUBMED: 32122294; PMC: 7053062; DOI: 10.1186/s12864-020-6534-z

  • The fix is in.

    Bentley S

    Nature microbiology 2020;5;3;393-394

    PUBMED: 32103172; DOI: 10.1038/s41564-020-0677-1

  • The influence of tumour mutational burden on renal cancer immune infiltration and survival.

    Byrne MHV and Mitchell TJ

    Annals of translational medicine 2020;8;6;271

    PUBMED: 32355715; PMC: 7186744; DOI: 10.21037/atm.2020.02.77

  • A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa.

    Lo SW, Gladstone RA, van Tonder AJ, Du Plessis M, Cornick JE, Hawkins PA, Madhi SA, Nzenze SA, Kandasamy R, Ravikumar KL et al.

    The Journal of antimicrobial chemotherapy 2020;75;3;512-520

    PUBMED: 31789384; PMC: 7021099; DOI: 10.1093/jac/dkz477

  • 'Community evolution' - laboratory strains and pedigrees in the age of genomics.

    Dorman MJ and Thomson NR

    Microbiology (Reading, England) 2020;166;3;233-238

    PUBMED: 31958052; PMC: 7376263; DOI: 10.1099/mic.0.000869

  • Evaluation of circulating leukocyte transcriptome and its relationship with immune function and blood markers in dairy cows during the transition period.

    Minuti A, Jahan N, Lopreiato V, Piccioli-Cappelli F, Bomba L, Capomaccio S, Loor JJ, Ajmone-Marsan P and Trevisi E

    Functional & integrative genomics 2020;20;2;293-305

    PUBMED: 31654229; DOI: 10.1007/s10142-019-00720-0

  • Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation.

    Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM and Tress ML

    NAR genomics and bioinformatics 2020;2;1;lqz023

    PUBMED: 31886458; PMC: 6924539; DOI: 10.1093/nargab/lqz023

  • Genomic and Phenotypic Variability in Neisseria gonorrhoeae Antimicrobial Susceptibility, England.

    Town K, Harris S, Sánchez-Busó L, Cole MJ, Pitt R, Fifer H, Mohammed H, Field N and Hughes G

    Emerging infectious diseases 2020;26;3;505-515

    PUBMED: 32091356; PMC: 7045833; DOI: 10.3201/eid2603.190732

  • GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution.

    Strauss ME, Kirk PDW, Reid JE and Wernisch L

    Bioinformatics (Oxford, England) 2020;36;5;1484-1491

    PUBMED: 31608923; PMC: 7703763; DOI: 10.1093/bioinformatics/btz778

  • Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases.

    McDougall S, Clausen L, Ha HJ, Gibson I, Bryan M, Hadjirin N, Lay E, Raisen C, Ba X, Restif O et al.

    Veterinary microbiology 2020;242;108592

    PUBMED: 32122596; DOI: 10.1016/j.vetmic.2020.108592

  • Molecular epidemiology and intercontinental spread of cholera.

    Mutreja A and Dougan G

    Vaccine 2020;38 Suppl 1;A46-A51

    PUBMED: 31345641; DOI: 10.1016/j.vaccine.2019.07.038

  • Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors.

    Smith CG, Moser T, Mouliere F, Field-Rayner J, Eldridge M, Riediger AL, Chandrananda D, Heider K, Wan JCM, Warren AY et al.

    Genome medicine 2020;12;1;23

    PUBMED: 32111235; PMC: 7048087; DOI: 10.1186/s13073-020-00723-8

  • Spatio-temporal dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast.

    Knudson A, González-Casabianca F, Feged-Rivadeneira A, Pedreros MF, Aponte S, Olaya A, Castillo CF, Mancilla E, Piamba-Dorado A, Sanchez-Pedraza R et al.

    Scientific reports 2020;10;1;3756

    PUBMED: 32111872; PMC: 7048816; DOI: 10.1038/s41598-020-60676-1

  • Comparative genomics of Salmonella enterica serovar Enteritidis ST-11 isolated in Uruguay reveals lineages associated with particular epidemiological traits.

    D'Alessandro B, Pérez Escanda V, Balestrazzi L, Grattarola F, Iriarte A, Pickard D, Yim L, Chabalgoity JA and Betancor L

    Scientific reports 2020;10;1;3638

    PUBMED: 32109937; PMC: 7046640; DOI: 10.1038/s41598-020-60502-8

  • Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016.

    Rahman SIA, Dyson ZA, Klemm EJ, Khanam F, Holt KE, Chowdhury EK, Dougan G and Qadri F

    PLoS neglected tropical diseases 2020;14;2;e0008036

    PUBMED: 32106221; PMC: 7064254; DOI: 10.1371/journal.pntd.0008036

  • CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.

    Efremova M, Vento-Tormo M, Teichmann SA and Vento-Tormo R

    Nature protocols 2020;15;4;1484-1506

    PUBMED: 32103204; DOI: 10.1038/s41596-020-0292-x

  • Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids.

    Georgakopoulos N, Prior N, Angres B, Mastrogiovanni G, Cagan A, Harrison D, Hindley CJ, Arnes-Benito R, Liau SS, Curd A et al.

    BMC developmental biology 2020;20;1;4

    PUBMED: 32098630; PMC: 7043048; DOI: 10.1186/s12861-020-0209-5

  • Tet3 ablation in adult brain neurons increases anxiety-like behavior and regulates cognitive function in mice.

    Antunes C, Da Silva JD, Guerra-Gomes S, Alves ND, Ferreira F, Loureiro-Campos E, Branco MR, Sousa N, Reik W, Pinto L and Marques CJ

    Molecular psychiatry 2020

    PUBMED: 32103150; DOI: 10.1038/s41380-020-0695-7

  • Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease.

    Serra EG, Schwerd T, Moutsianas L, Cavounidis A, Fachal L, Pandey S, Kammermeier J, Croft NM, Posovszky C, Rodrigues A et al.

    Nature communications 2020;11;1;995

    PUBMED: 32081864; PMC: 7035382; DOI: 10.1038/s41467-019-14275-y

  • Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses.

    Lassalle F, Beale MA, Bharucha T, Williams CA, Williams RJ, Cudini J, Goldstein R, Haque T, Depledge DP and Breuer J

    Virus evolution 2020;6;1;veaa012

    PUBMED: 32099667; PMC: 7031915; DOI: 10.1093/ve/veaa012

  • The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758.

    Mead D, Hailer F, Chadwick E, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan JD et al.

    Wellcome open research 2020;5;33

    PUBMED: 32258427; PMC: 7097881; DOI: 10.12688/wellcomeopenres.15722.1

  • Immunology in the Era of Single-Cell Technologies.

    Efremova M, Vento-Tormo R, Park JE, Teichmann SA and James KR

    Annual review of immunology 2020

    PUBMED: 32075461; DOI: 10.1146/annurev-immunol-090419-020340

  • Tumor necrosis factor receptor family costimulation increases regulatory T-cell activation and function via NF-κB.

    Lubrano di Ricco M, Ronin E, Collares D, Divoux J, Grégoire S, Wajant H, Gomes T, Grinberg-Bleyer Y, Baud V, Marodon G and Salomon BL

    European journal of immunology 2020;50;7;972-985

    PUBMED: 32012260; PMC: 7383872; DOI: 10.1002/eji.201948393

  • BlobToolKit - Interactive Quality Assessment of Genome Assemblies.

    Challis R, Richards E, Rajan J, Cochrane G and Blaxter M

    G3 (Bethesda, Md.) 2020

    PUBMED: 32071071; DOI: 10.1534/g3.119.400908

  • Mouse Models of Myeloid Malignancies.

    Basheer F and Vassiliou G

    Cold Spring Harbor perspectives in medicine 2020

    PUBMED: 32071146; DOI: 10.1101/cshperspect.a035535

  • Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies.

    Munn-Chernoff MA, Johnson EC, Chou YL, Coleman JRI, Thornton LM, Walters RK, Yilmaz Z, Baker JH, Hübel C, Gordon S et al.

    Addiction biology 2020;e12880

    PUBMED: 32064741; DOI: 10.1111/adb.12880

  • simurg: simulate bacterial pangenomes in R.

    Ferrés I, Fresia P and Iraola G

    Bioinformatics (Oxford, England) 2020;36;4;1273-1274

    PUBMED: 31584605; DOI: 10.1093/bioinformatics/btz735

  • Mutational signatures: experimental design and analytical framework.

    Koh G, Zou X and Nik-Zainal S

    Genome biology 2020;21;1;37

    PUBMED: 32059681; PMC: 7023746; DOI: 10.1186/s13059-020-1951-5

  • The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788.

    Mead D, Fingland K, Cripps R, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J et al.

    Wellcome open research 2020;5;27

    PUBMED: 33215047; PMC: 7653645; DOI: 10.12688/wellcomeopenres.15721.1

  • Adipose Tissue-Liver Cross Talk in the Control of Whole-Body Metabolism: Implications in Nonalcoholic Fatty Liver Disease.

    Azzu V, Vacca M, Virtue S, Allison M and Vidal-Puig A

    Gastroenterology 2020;158;7;1899-1912

    PUBMED: 32061598; DOI: 10.1053/j.gastro.2019.12.054

  • Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.

    Arredondo-Alonso S, Top J, McNally A, Puranen S, Pesonen M, Pensar J, Marttinen P, Braat JC, Rogers MRC, van Schaik W et al.

    mBio 2020;11;1

    PUBMED: 32047136; PMC: 7018651; DOI: 10.1128/mBio.03284-19

  • Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

    Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F et al.

    Nature communications 2020;11;1;810

    PUBMED: 32041960; PMC: 7010688; DOI: 10.1038/s41467-020-14457-z

  • Eleven grand challenges in single-cell data science.

    Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A et al.

    Genome biology 2020;21;1;31

    PUBMED: 32033589; PMC: 7007675; DOI: 10.1186/s13059-020-1926-6

  • The evolutionary history of 2,658 cancers.

    Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K et al.

    Nature 2020;578;7793;122-128

    PUBMED: 32025013; PMC: 7054212; DOI: 10.1038/s41586-019-1907-7

  • Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system.

    Rawji KS, Young AMH, Ghosh T, Michaels NJ, Mirzaei R, Kappen J, Kolehmainen KL, Alaeiilkhchi N, Lozinski B, Mishra MK et al.

    Acta neuropathologica 2020;139;5;893-909

    PUBMED: 32030468; PMC: 7181452; DOI: 10.1007/s00401-020-02129-7

  • A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

    Jiao W, Atwal G, Polak P, Karlic R, Cuppen E, PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP et al.

    Nature communications 2020;11;1;728

    PUBMED: 32024849; PMC: 7002586; DOI: 10.1038/s41467-019-13825-8

  • The repertoire of mutational signatures in human cancer.

    Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN et al.

    Nature 2020;578;7793;94-101

    PUBMED: 32025018; PMC: 7054213; DOI: 10.1038/s41586-020-1943-3

  • Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

    Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z et al.

    Nature 2020;578;7793;102-111

    PUBMED: 32025015; PMC: 7054214; DOI: 10.1038/s41586-020-1965-x

  • Butler enables rapid cloud-based analysis of thousands of human genomes.

    Yakneen S, Waszak SM, PCAWG Technical Working Group, Gertz M, Korbel JO and PCAWG Consortium

    Nature biotechnology 2020;38;3;288-292

    PUBMED: 32024987; PMC: 7062635; DOI: 10.1038/s41587-019-0360-3

  • Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

    Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, PCAWG Drivers and Functional Interpretation Group, Johnson R and PCAWG Consortium

    Communications biology 2020;3;1;56

    PUBMED: 32024996; PMC: 7002399; DOI: 10.1038/s42003-019-0741-7

  • Combined burden and functional impact tests for cancer driver discovery using DriverPower.

    Shuai S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein LD and PCAWG Consortium

    Nature communications 2020;11;1;734

    PUBMED: 32024818; PMC: 7002750; DOI: 10.1038/s41467-019-13929-1

  • Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.

    Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS et al.

    Nature genetics 2020;52;3;331-341

    PUBMED: 32025003; PMC: 7058534; DOI: 10.1038/s41588-019-0576-7

  • Comprehensive molecular characterization of mitochondrial genomes in human cancers.

    Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN et al.

    Nature genetics 2020;52;3;342-352

    PUBMED: 32024997; PMC: 7058535; DOI: 10.1038/s41588-019-0557-x

  • Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.

    Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA et al.

    Nature genetics 2020;52;3;294-305

    PUBMED: 32024999; PMC: 7058537; DOI: 10.1038/s41588-019-0564-y

  • Genomic basis for RNA alterations in cancer.

    PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y et al.

    Nature 2020;578;7793;129-136

    PUBMED: 32025019; PMC: 7054216; DOI: 10.1038/s41586-020-1970-0

  • Genomic footprints of activated telomere maintenance mechanisms in cancer.

    Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R et al.

    Nature communications 2020;11;1;733

    PUBMED: 32024817; PMC: 7002710; DOI: 10.1038/s41467-019-13824-9

  • Integrative pathway enrichment analysis of multivariate omics data.

    Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J and PCAWG Consortium

    Nature communications 2020;11;1;735

    PUBMED: 32024846; PMC: 7002665; DOI: 10.1038/s41467-019-13983-9

  • Pan-cancer analysis of whole genomes.

    ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium

    Nature 2020;578;7793;82-93

    PUBMED: 32025007; PMC: 7025898; DOI: 10.1038/s41586-020-1969-6

  • Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

    Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D et al.

    Nature genetics 2020;52;3;306-319

    PUBMED: 32024998; PMC: 7058536; DOI: 10.1038/s41588-019-0562-0

  • Pathway and network analysis of more than 2500 whole cancer genomes.

    Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P et al.

    Nature communications 2020;11;1;729

    PUBMED: 32024854; PMC: 7002574; DOI: 10.1038/s41467-020-14367-0

  • Patterns of somatic structural variation in human cancer genomes.

    Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE et al.

    Nature 2020;578;7793;112-121

    PUBMED: 32025012; PMC: 7025897; DOI: 10.1038/s41586-019-1913-9

  • Genome-Wide Association Study of Cryptosporidiosis in Infants Implicates PRKCA.

    Wojcik GL, Korpe P, Marie C, Mentzer AJ, Carstensen T, Mychaleckyj J, Kirkpatrick BD, Rich SS, Concannon P, Faruque ASG et al.

    mBio 2020;11;1

    PUBMED: 32019797; PMC: 7002356; DOI: 10.1128/mBio.03343-19

  • Minimal spatial heterogeneity in chronic lymphocytic leukemia at diagnosis.

    Nadeu F, Royo R, Maura F, Dawson KJ, Dueso-Barroso A, Aymerich M, Pinyol M, Beà S, López-Guillermo A, Delgado J et al.

    Leukemia 2020;34;7;1929-1933

    PUBMED: 32020046; DOI: 10.1038/s41375-020-0730-3

  • Type 1 Interferon Responses Underlie Tumor-Selective Replication of Oncolytic Measles Virus.

    Aref S, Castleton AZ, Bailey K, Burt R, Dey A, Leongamornlert D, Mitchell RJ, Okasha D and Fielding AK

    Molecular therapy : the journal of the American Society of Gene Therapy 2020;28;4;1043-1055

    PUBMED: 32087150; PMC: 7132605; DOI: 10.1016/j.ymthe.2020.01.027

  • The Deep Genome Project.

    Lloyd KCK, Adams DJ, Baynam G, Beaudet AL, Bosch F, Boycott KM, Braun RE, Caulfield M, Cohn R, Dickinson ME et al.

    Genome biology 2020;21;1;18

    PUBMED: 32008577; PMC: 6996159; DOI: 10.1186/s13059-020-1931-9

  • The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758.

    Mead D, Fingland K, Cripps R, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J et al.

    Wellcome open research 2020;5;18

    PUBMED: 32587897; PMC: 7309416; DOI: 10.12688/wellcomeopenres.15679.1

  • Designing ecologically optimized pneumococcal vaccines using population genomics.

    Colijn C, Corander J and Croucher NJ

    Nature microbiology 2020;5;3;473-485

    PUBMED: 32015499; PMC: 7614922; DOI: 10.1038/s41564-019-0651-y

  • Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928-2013): antimicrobial use/misuse selects for resistance and drives evolution.

    Golparian D, Harris SR, Sánchez-Busó L, Hoffmann S, Shafer WM, Bentley SD, Jensen JS and Unemo M

    BMC genomics 2020;21;1;116

    PUBMED: 32013864; PMC: 6998845; DOI: 10.1186/s12864-020-6511-6

  • Loss of IL-10 signaling in macrophages limits bacterial killing driven by prostaglandin E2.

    Mukhopadhyay S, Heinz E, Porreca I, Alasoo K, Yeung A, Yang HT, Schwerd T, Forbester JL, Hale C, Agu CA et al.

    The Journal of experimental medicine 2020;217;2

    PUBMED: 31819956; PMC: 7041704; DOI: 10.1084/jem.20180649

  • A practical framework and online tool for mutational signature analyses show inter-tissue variation and driver dependencies.

    Degasperi A, Amarante TD, Czarnecki J, Shooter S, Zou X, Glodzik D, Morganella S, Nanda AS, Badja C, Koh G et al.

    Nature cancer 2020;1;2;249-263

    PUBMED: 32118208; PMC: 7048622; DOI: 10.1038/s43018-020-0027-5

  • A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity.

    Akkaya M, Bansal A, Sheehan PW, Pena M, Molina-Cruz A, Orchard LM, Cimperman CK, Qi CF, Ross P, Yazew T et al.

    Science advances 2020;6;6;eaaw6957

    PUBMED: 32076635; PMC: 7002124; DOI: 10.1126/sciadv.aaw6957

  • Analysis pipelines for cancer genome sequencing in mice.

    Lange S, Engleitner T, Mueller S, Maresch R, Zwiebel M, González-Silva L, Schneider G, Banerjee R, Yang F, Vassiliou GS et al.

    Nature protocols 2020;15;2;266-315

    PUBMED: 31907453; DOI: 10.1038/s41596-019-0234-7

  • ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response.

    Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada JG, Couturier DL, Kumar S, Kishore K et al.

    Nature genetics 2020;52;2;187-197

    PUBMED: 31913353; DOI: 10.1038/s41588-019-0541-5

  • Cell-type-specific visualisation and biochemical isolation of endogenous synaptic proteins in mice.

    Zhu F, Collins MO, Harmse J, Choudhary JS, Grant SGN and Komiyama NH

    The European journal of neuroscience 2020;51;3;793-805

    PUBMED: 31621109; DOI: 10.1111/ejn.14597

  • Cohort Profile: East London Genes & Health (ELGH), a community-based population genomics and health study in British Bangladeshi and British Pakistani people.

    Finer S, Martin HC, Khan A, Hunt KA, MacLaughlin B, Ahmed Z, Ashcroft R, Durham C, MacArthur DG, McCarthy MI et al.

    International journal of epidemiology 2020;49;1;20-21i

    PUBMED: 31504546; PMC: 7124496; DOI: 10.1093/ije/dyz174

  • Companion canines: an under-utilised model to aid in translating anti-metastatics to the clinic.

    van der Weyden L, Starkey M, Abu-Helil B, Mutsaers AJ and Wood GA

    Clinical & experimental metastasis 2020;37;1;7-12

    PUBMED: 31691156; PMC: 7007897; DOI: 10.1007/s10585-019-10002-5

  • Deciphering immunity at high plexity and resolution.

    Domínguez Conde C and Teichmann SA

    Nature reviews. Immunology 2020;20;2;77-78

    PUBMED: 31797907; DOI: 10.1038/s41577-019-0254-0

  • Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.

    Doyle RM, O'Sullivan DM, Aller SD, Bruchmann S, Clark T, Coello Pelegrin A, Cormican M, Diez Benavente E, Ellington MJ, McGrath E et al.

    Microbial genomics 2020;6;2

    PUBMED: 32048983; DOI: 10.1099/mgen.0.000335

  • Muzlifah Haniffa-a new era for collaborative and supportive medical research.

    Haniffa M

    Nature medicine 2020;26;2;155

    PUBMED: 32047323; DOI: 10.1038/s41591-020-0767-x

  • Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China.

    Zhou K, Xiao T, David S, Wang Q, Zhou Y, Guo L, Aanensen D, Holt KE, Thomson NR, Grundmann H et al.

    Emerging infectious diseases 2020;26;2;289-297

    PUBMED: 31961299; PMC: 6986851; DOI: 10.3201/eid2602.190594

  • Organoids - New Models for Host-Helminth Interactions.

    Duque-Correa MA, Maizels RM, Grencis RK and Berriman M

    Trends in parasitology 2020;36;2;170-181

    PUBMED: 31791691; DOI: 10.1016/j.pt.2019.10.013

  • Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.

    Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ and Saez-Rodriguez J

    Molecular systems biology 2020;16;2;e8664

    PUBMED: 32073727; PMC: 7029724; DOI: 10.15252/msb.20188664

  • Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent.

    Britto CD, Dyson ZA, Mathias S, Bosco A, Dougan G, Jose S, Nagaraj S, Holt KE and Pollard AJ

    The Journal of antimicrobial chemotherapy 2020;75;2;337-341

    PUBMED: 31665304; PMC: 7223262; DOI: 10.1093/jac/dkz435

  • Single cell sequencing shines a light on malaria parasite relatedness in complex infections.

    Siegel SV and Rayner JC

    Trends in parasitology 2020;36;2;83-85

    PUBMED: 31883706; DOI: 10.1016/j.pt.2019.12.007

  • Human and mouse essentiality screens as a resource for disease gene discovery.

    Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H et al.

    Nature communications 2020;11;1;655

    PUBMED: 32005800; PMC: 6994715; DOI: 10.1038/s41467-020-14284-2

  • Therapeutic targeting of preleukemia cells in a mouse model of NPM1 mutant acute myeloid leukemia.

    Uckelmann HJ, Kim SM, Wong EM, Hatton C, Giovinazzo H, Gadrey JY, Krivtsov AV, Rücker FG, Döhner K, McGeehan GM et al.

    Science (New York, N.Y.) 2020;367;6477;586-590

    PUBMED: 32001657; PMC: 7754791; DOI: 10.1126/science.aax5863

  • We need to think about data governance for dementia research in a digital era.

    Milne R and Brayne C

    Alzheimer's research & therapy 2020;12;1;17

    PUBMED: 32005135; PMC: 6995068; DOI: 10.1186/s13195-020-0584-y

  • Adult Human Glioblastomas Harbor Radial Glia-like Cells.

    Wang R, Sharma R, Shen X, Laughney AM, Funato K, Clark PJ, Shpokayte M, Morgenstern P, Navare M, Xu Y et al.

    Stem cell reports 2020;14;2;338-350

    PUBMED: 32004492; PMC: 7014025; DOI: 10.1016/j.stemcr.2020.01.007

  • Tracking hematopoietic stem cells and their progeny using whole-genome sequencing.

    Lee-Six H and Kent DG

    Experimental hematology 2020

    PUBMED: 32007478; DOI: 10.1016/j.exphem.2020.01.004

  • Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition.

    Oatley M, Bölükbası ÖV, Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV, Milchevskaya V, Foteva V, Natarajan KN et al.

    Nature communications 2020;11;1;586

    PUBMED: 31996681; PMC: 6989687; DOI: 10.1038/s41467-019-14171-5

  • Tobacco smoking and somatic mutations in human bronchial epithelium.

    Yoshida K, Gowers KHC, Lee-Six H, Chandrasekharan DP, Coorens T, Maughan EF, Beal K, Menzies A, Millar FR, Anderson E et al.

    Nature 2020;578;7794;266-272

    PUBMED: 31996850; PMC: 7021511; DOI: 10.1038/s41586-020-1961-1

  • The Antimalarial Natural Product Salinipostin A Identifies Essential α/β Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites.

    Yoo E, Schulze CJ, Stokes BH, Onguka O, Yeo T, Mok S, Gnädig NF, Zhou Y, Kurita K, Foe IT et al.

    Cell chemical biology 2020;27;2;143-157.e5

    PUBMED: 31978322; PMC: 8027986; DOI: 10.1016/j.chembiol.2020.01.001

  • Concordance for clonal hematopoiesis is limited in elderly twins.

    Fabre MA, McKerrell T, Zwiebel M, Vijayabaskar MS, Park N, Wells PM, Rad R, Deloukas P, Small K, Steves CJ and Vassiliou GS

    Blood 2020;135;4;269-273

    PUBMED: 31697828; PMC: 6978156; DOI: 10.1182/blood.2019001807

  • Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization

    Totis,N., Tagherloni,A., Beccuti,M., Cazzaniga,P., Nobile,M.S., Besozzi,D., Pennisi,M. and Pappalardo,F.

    Lecture Notes in Computer Science 2020;11925;187-202

    DOI: 10.1007/978-3-030-34585-3_17

  • FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle.

    Cader MZ, de Almeida Rodrigues RP, West JA, Sewell GW, Md-Ibrahim MN, Reikine S, Sirago G, Unger LW, Iglesias-Romero AB, Ramshorn K et al.

    Cell 2020;180;2;278-295.e23

    PUBMED: 31978345; PMC: 6978800; DOI: 10.1016/j.cell.2019.12.017

  • Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank.

    Coleman JRI, Peyrot WJ, Purves KL, Davis KAS, Rayner C, Choi SW, Hübel C, Gaspar HA, Kan C, Van der Auwera S et al.

    Molecular psychiatry 2020;25;7;1430-1446

    PUBMED: 31969693; PMC: 7305950; DOI: 10.1038/s41380-019-0546-6

  • Exome Sequencing for Prenatal Detection of Genetic Abnormalities in Fetal Ultrasound Anomalies: An Economic Evaluation.

    Kodabuckus SS, Quinlan-Jones E, McMullan DJ, Maher ER, Hurles ME, Barton PM and Kilby MD

    Fetal diagnosis and therapy 2020;47;7;554-564

    PUBMED: 31962312; PMC: 7446299; DOI: 10.1159/000504976

  • Phylogenomic analysis of Neisseria gonorrhoeae transmission to assess sexual mixing and HIV transmission risk in England: a cross-sectional, observational, whole-genome sequencing study.

    Town K, Field N, Harris SR, Sánchez-Busó L, Cole MJ, Pitt R, Fifer H, Mohammed H and Hughes G

    The Lancet. Infectious diseases 2020;20;4;478-486

    PUBMED: 31978353; PMC: 7099395; DOI: 10.1016/S1473-3099(19)30610-3

  • Vitamin D Receptor Controls Cell Stemness in Acute Myeloid Leukemia and in Normal Bone Marrow.

    Paubelle E, Zylbersztejn F, Maciel TT, Carvalho C, Mupo A, Cheok M, Lieben L, Sujobert P, Decroocq J, Yokoyama A et al.

    Cell reports 2020;30;3;739-754.e4

    PUBMED: 31968250; DOI: 10.1016/j.celrep.2019.12.055

  • Mutational signatures in tumours induced by high and low energy radiation in Trp53 deficient mice.

    Rose Li Y, Halliwill KD, Adams CJ, Iyer V, Riva L, Mamunur R, Jen KY, Del Rosario R, Fredlund E, Hirst G et al.

    Nature communications 2020;11;1;394

    PUBMED: 31959748; PMC: 6971050; DOI: 10.1038/s41467-019-14261-4

  • A panel of recombinant proteins from human-infective Plasmodium species for serological surveillance.

    Müller-Sienerth N, Shilts J, Kadir KA, Yman V, Homann MV, Asghar M, Ngasala B, Singh B, Färnert A and Wright GJ

    Malaria journal 2020;19;1;31

    PUBMED: 31952523; PMC: 6969409; DOI: 10.1186/s12936-020-3111-5

  • A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome.

    Cuvertino S, Hartill V, Colyer A, Garner T, Nair N, Al-Gazali L, Canham N, Faundes V, Flinter F, Hertecant J et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;5;867-877

    PUBMED: 31949313; PMC: 7200597; DOI: 10.1038/s41436-019-0743-3

  • Functional analysis of vasa/PL10-like genes in the ovary of Schistosoma mansoni.

    Skinner DE, Popratiloff A, Alrefaei YN, Mann VH, Rinaldi G and Brindley PJ

    Molecular and biochemical parasitology 2020;236;111259

    PUBMED: 31958469; DOI: 10.1016/j.molbiopara.2020.111259

  • Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia.

    Wyres KL, Nguyen TNT, Lam MMC, Judd LM, van Vinh Chau N, Dance DAB, Ip M, Karkey A, Ling CL, Miliya T et al.

    Genome medicine 2020;12;1;11

    PUBMED: 31948471; PMC: 6966826; DOI: 10.1186/s13073-019-0706-y

  • Haplotype-aware graph indexes.

    Sirén J, Garrison E, Novak AM, Paten B and Durbin R

    Bioinformatics (Oxford, England) 2020;36;2;400-407

    PUBMED: 31406990; PMC: 7223266; DOI: 10.1093/bioinformatics/btz575

  • Nasal DNA methylation profiling of asthma and rhinitis.

    Qi C, Jiang Y, Yang IV, Forno E, Wang T, Vonk JM, Gehring U, Smit HA, Milanzi EB, Carpaij OA et al.

    The Journal of allergy and clinical immunology 2020;145;6;1655-1663

    PUBMED: 31953105; PMC: 7282965; DOI: 10.1016/j.jaci.2019.12.911

  • Reply to Jensen and Kowalik: Consideration of mixed infections is central to understanding HCMV intrahost diversity.

    Houldcroft CJ, Cudini J, Goldstein RA and Breuer J

    Proceedings of the National Academy of Sciences of the United States of America 2020;117;2;818-819

    PUBMED: 31874929; PMC: 6969508; DOI: 10.1073/pnas.1918955117

  • The Evolutionary Genomics of Host Specificity in Staphylococcus aureus.

    Matuszewska M, Murray GGR, Harrison EM, Holmes MA and Weinert LA

    Trends in microbiology 2020;28;6;465-477

    PUBMED: 31948727; DOI: 10.1016/j.tim.2019.12.007

  • High-throughput discovery of genetic determinants of circadian misalignment.

    Zhang T, Xie P, Dong Y, Liu Z, Zhou F, Pan D, Huang Z, Zhai Q, Gu Y, Wu Q et al.

    PLoS genetics 2020;16;1;e1008577

    PUBMED: 31929527; PMC: 6980734; DOI: 10.1371/journal.pgen.1008577

  • In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer.

    Annunziato S, Lutz C, Henneman L, Bhin J, Wong K, Siteur B, van Gerwen B, de Korte-Grimmerink R, Zafra MP, Schatoff EM et al.

    The EMBO journal 2020;39;5;e102169

    PUBMED: 31930530; PMC: 7049816; DOI: 10.15252/embj.2019102169

  • Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.

    Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J et al.

    Nature genetics 2020;52;2;231-240

    PUBMED: 31932696; DOI: 10.1038/s41588-019-0566-9

  • Formin, an opinion.

    Davison A, McDowell GS, Holden JM, Johnson HF, Wade CM, Chiba S, Jackson DJ, Levin M and Blaxter ML

    Development (Cambridge, England) 2020;147;1

    PUBMED: 31919229; DOI: 10.1242/dev.187427

  • A brief history of human disease genetics.

    Claussnitzer M, Cho JH, Collins R, Cox NJ, Dermitzakis ET, Hurles ME, Kathiresan S, Kenny EE, Lindgren CM, MacArthur DG et al.

    Nature 2020;577;7789;179-189

    PUBMED: 31915397; PMC: 7405896; DOI: 10.1038/s41586-019-1879-7

  • Expression Atlas update: from tissues to single cells.

    Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N et al.

    Nucleic acids research 2020;48;D1;D77-D83

    PUBMED: 31665515; PMC: 7145605; DOI: 10.1093/nar/gkz947

  • MGnify: the microbiome analysis resource in 2020.

    Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ et al.

    Nucleic acids research 2020;48;D1;D570-D578

    PUBMED: 31696235; PMC: 7145632; DOI: 10.1093/nar/gkz1035

  • WormBase: a modern Model Organism Information Resource.

    Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Cho J, Davis P, Gao S, Grove CA, Kishore R et al.

    Nucleic acids research 2020;48;D1;D762-D767

    PUBMED: 31642470; PMC: 7145598; DOI: 10.1093/nar/gkz920

  • Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.

    Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M and Flicek P

    Genome biology 2020;21;1;5

    PUBMED: 31910870; PMC: 6945661; DOI: 10.1186/s13059-019-1894-x

  • Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma.

    Noorani A, Li X, Goddard M, Crawte J, Alexandrov LB, Secrier M, Eldridge MD, Bower L, Weaver J, Lao-Sirieix P et al.

    Nature genetics 2020;52;1;74-83

    PUBMED: 31907488; PMC: 7100916; DOI: 10.1038/s41588-019-0551-3

  • Reply.

    Goode EC, Hirschfield GM and Rushbrook SM

    Hepatology (Baltimore, Md.) 2020;71;1;399-400

    PUBMED: 31550385; DOI: 10.1002/hep.30963

  • A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England.

    Ludden C, Moradigaravand D, Jamrozy D, Gouliouris T, Blane B, Naydenova P, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020;70;2;219-226

    PUBMED: 30840764; PMC: 6938978; DOI: 10.1093/cid/ciz174

  • A Robust Method Uncovers Significant Context-Specific Heritability in Diverse Complex Traits.

    Dahl A, Nguyen K, Cai N, Gandal MJ, Flint J and Zaitlen N

    American journal of human genetics 2020;106;1;71-91

    PUBMED: 31901249; PMC: 7042488; DOI: 10.1016/j.ajhg.2019.11.015

  • Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells.

    Dhalla F, Baran-Gale J, Maio S, Chappell L, Holländer GA and Ponting CP

    The EMBO journal 2020;39;1;e101828

    PUBMED: 31657037; PMC: 6939203; DOI: 10.15252/embj.2019101828

  • Draft Genome Sequences of the Type Strains of Actinobacillus indolicus (46K2C) and Actinobacillus porcinus (NM319), Two NAD-Dependent Bacterial Species Found in the Respiratory Tract of Pigs.

    Bossé JT, Li Y, Fernandez Crespo R, Angen Ø, Holden MTG, Weinert LA, Maskell DJ, Tucker AW, Wren BW, Rycroft AN et al.

    Microbiology resource announcements 2020;9;1

    PUBMED: 31896621; PMC: 6940273; DOI: 10.1128/MRA.00716-19

  • Functional analysis of candidate genes from genome-wide association studies of hearing.

    Ingham NJ, Rook V, Di Domenico F, James E, Lewis MA, Girotto G, Buniello A and Steel KP

    Hearing research 2020;387;107879

    PUBMED: 31927188; PMC: 6996162; DOI: 10.1016/j.heares.2019.107879

  • A cell atlas of human thymic development defines T cell repertoire formation

    Jong-Eun Park, Rachel A. Botting, Cecilia Domínguez Conde, Dorin-Mirel Popescu, Marieke Lavaert, Daniel J. Kunz, Issac Goh, Emily Stephenson, Roberta Ragazzini, Elizabeth Tuck et al.

    Science 2020;367;6480

    DOI: 10.1126/science.aay3224; URL: https://science.sciencemag.org/content/367/6480/eaay3224

  • A community effort to create standards for evaluating tumor subclonal reconstruction.

    Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M et al.

    Nature biotechnology 2020;38;1;97-107

    PUBMED: 31919445; PMC: 6956735; DOI: 10.1038/s41587-019-0364-z

  • The Organoid Cell Atlas

    Bock, Christoph, Boutros, Michael, Camp, J. Gray, Clarke, Laura, Clevers, Hans et al.

    Nature Biotechnology 2020;39;1;13

    DOI: 10.1038/s41587-020-00762-x; URL: https://doi.org/10.1038/s41587-020-00762-x

  • The role of haematological traits in risk of ischaemic stroke and its subtypes.

    Harshfield EL, Sims MC, Traylor M, Ouwehand WH and Markus HS

    Brain : a journal of neurology 2020;143;1;210-221

    PUBMED: 31755939; PMC: 6935746; DOI: 10.1093/brain/awz362

  • Atypical, milder presentation in a child with CC2D2A and KIDINS220 variants.

    Lam Z, Albaba S, Study D and Balasubramanian M

    Clinical dysmorphology 2020;29;1;10-16

    PUBMED: 31577543; DOI: 10.1097/MCD.0000000000000298

  • Automation of Multiplexed RNAscope Single-Molecule Fluorescent In Situ Hybridization and Immunohistochemistry for Spatial Tissue Mapping.

    Roberts K and Bayraktar OA

    Methods in molecular biology (Clifton, N.J.) 2020;2148;229-244

    PUBMED: 32394386; DOI: 10.1007/978-1-0716-0623-0_15

  • Bacterial survival: evolve and adapt or perish.

    Chaguza C

    Nature reviews. Microbiology 2020;18;1;5

    PUBMED: 31748737; DOI: 10.1038/s41579-019-0303-5

  • Cells of the adult human heart

    Litviňuková, Monika, Talavera-López, Carlos, Maatz, Henrike, Reichart, Daniel, Worth, Catherine L. et al.

    Nature 2020;588;7838;466

    DOI: 10.1038/s41586-020-2797-4; URL: https://doi.org/10.1038/s41586-020-2797-4

  • CEN-tools: an integrative platform to identify the contexts of essential genes

    Sumana Sharma, Cansu Dincer, Paula Weidem&#xfc;ller, Gavin J Wright and Evangelia Petsalaki

    Molecular Systems Biology 2020;16;10;e9698

    DOI: 10.15252/msb.20209698; URL: https://doi.org/10.15252/msb.20209698

  • Computational Intelligence for Life Sciences

    Besozzi, Daniela, Manzoni, Luca, Nobile, Marco S., Spolaor, Simone, Castelli, Mauro et al.

    Fundamenta Informaticae 2020;171;1-4;57

    DOI: 10.3233/FI-2020-1872; URL: https://doi.org/10.3233/FI-2020-1872

  • Computational methods for single-cell omics across modalities.

    Efremova M and Teichmann SA

    Nature methods 2020;17;1;14-17

    PUBMED: 31907463; DOI: 10.1038/s41592-019-0692-4

  • Cytogenetic Investigations in Emballonuroidea. I. Taphozoinae and Emballonurinae Karyotypes Evolve at Different Rates and Share No Derived Chromosomal Characters

    Marianne Volleth, Stefan Müller, Faisal A. Anwarali Khan, Hoi-Sen Yong, Klaus-Gerhard Heller, Robert J. Baker, David A Ray and Cibele G. Sotero-Caio

    Acta Chiropterologica 2020;21;2;257

    DOI: 10.3161/15081109ACC2019.21.2.002; URL: https://doi.org/10.3161/15081109ACC2019.21.2.002

  • Distinct microbial and immune niches of the human colon

    James, Kylie R., Gomes, Tomas, Elmentaite, Rasa, Kumar, Nitin, Gulliver, Emily L. et al.

    Nature Immunology 2020;21;3;343

    DOI: 10.1038/s41590-020-0602-z; URL: https://doi.org/10.1038/s41590-020-0602-z

  • Gene Silencing in the Liver Fluke Fasciola hepatica: RNA Interference.

    Rinaldi G, Dell'Oca N, Castillo E and Tort JF

    Methods in molecular biology (Clifton, N.J.) 2020;2137;67-92

    PUBMED: 32399922; DOI: 10.1007/978-1-0716-0475-5_6

  • Genome sequence of the root-knot nematode Meloidogyne luci.

    Susič N, Koutsovoulos GD, Riccio C, Danchin EGJ, Blaxter ML, Lunt DH, Strajnar P, Širca S, Urek G and Stare BG

    Journal of nematology 2020;52;1-5

    PUBMED: 32180388; PMC: 7266024; DOI: 10.21307/jofnem-2020-025

  • Loss of ADAMTS19 causes progressive non-syndromic heart valve disease.

    Wünnemann F, Ta-Shma A, Preuss C, Leclerc S, van Vliet PP, Oneglia A, Thibeault M, Nordquist E, Lincoln J, Scharfenberg F et al.

    Nature genetics 2020;52;1;40-47

    PUBMED: 31844321; DOI: 10.1038/s41588-019-0536-2

  • Molecular Evolution of IDH Wild-Type Glioblastomas Treated With Standard of Care Affects Survival and Design of Precision Medicine Trials: A Report From the EORTC 1542 Study.

    Draaisma K, Chatzipli A, Taphoorn M, Kerkhof M, Weyerbrock A, Sanson M, Hoeben A, Lukacova S, Lombardi G, Leenstra S et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2020;38;1;81-99

    PUBMED: 31743054; DOI: 10.1200/JCO.19.00367

  • N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells.

    Abakir A, Giles TC, Cristini A, Foster JM, Dai N, Starczak M, Rubio-Roldan A, Li M, Eleftheriou M, Crutchley J et al.

    Nature genetics 2020;52;1;48-55

    PUBMED: 31844323; PMC: 6974403; DOI: 10.1038/s41588-019-0549-x

  • Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensis

    Caroline Durrant, Elizabeth A. Thiele, Nancy Holroyd, Stephen R. Doyle, Guillaume Sallé, Alan Tracey, Geetha Sankaranarayanan, Magda E. Lotkowska, Hayley M. Bennett, Thomas Huckvale et al.

    PLOS Neglected Tropical Diseases 2020;14;11;e0008623

    DOI: 10.1371/journal.pntd.0008623; URL: https://doi.org/10.1371/journal.pntd.0008623

  • Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation

    Chen, Yi-Ling, Gomes, Tomas, Hardman, Clare S., Vieira Braga, Felipe A., Gutowska-Owsiak, Danuta et al.

    Journal of Experimental Medicine 2020;217;3

    DOI: 10.1084/jem.20190811; URL: https://doi.org/10.1084/jem.20190811

  • VarSite: Disease variants and protein structure.

    Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA and Thornton JM

    Protein science : a publication of the Protein Society 2020;29;1;111-119

    PUBMED: 31606900; PMC: 6933866; DOI: 10.1002/pro.3746

2019

  • scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.

    Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, Harding P, Polanski K, Huang N, Nowicki-Osuch K et al.

    Genome biology 2019;21;1;1

    PUBMED: 31892341; PMC: 6937944; DOI: 10.1186/s13059-019-1906-x

  • Emergence of carbapenemase-producing Enterobacteriaceae in Malawi.

    Lewis JM, Lester R, Mphasa M, Banda R, Edwards T, Thomson NR and Feasey N

    Journal of global antimicrobial resistance 2019;20;225-227

    PUBMED: 31899349; PMC: 7049292; DOI: 10.1016/j.jgar.2019.12.017

  • The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor.

    Coe EA, Tan JY, Shapiro M, Louphrasitthiphol P, Bassett AR, Marques AC, Goding CR and Vance KW

    PLoS genetics 2019;15;12;e1008501

    PUBMED: 31881017; PMC: 6934268; DOI: 10.1371/journal.pgen.1008501

  • Signalling lymphocyte activation molecule family member 9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection.

    Wilson TJ, Clare S, Mikulin J, Johnson CM, Harcourt K, Lyons PA, Dougan G and Smith KGC

    Immunology 2019

    PUBMED: 31880316; DOI: 10.1111/imm.13169

  • Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves.

    Šatović E, Luchetti A, Pasantes JJ, García-Souto D, Cedilak A, Mantovani B and Plohl M

    Scientific reports 2019;9;1;19962

    PUBMED: 31882746; PMC: 6934838; DOI: 10.1038/s41598-019-56502-y

  • Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster.

    Machado HE, Lawrie DS and Petrov DA

    Genetics 2019;214;2;511-528

    PUBMED: 31871131; PMC: 7017021; DOI: 10.1534/genetics.119.302542

  • Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.

    Dempster JM, Pacini C, Pantel S, Behan FM, Green T, Krill-Burger J, Beaver CM, Younger ST, Zhivich V, Najgebauer H et al.

    Nature communications 2019;10;1;5817

    PUBMED: 31862961; PMC: 6925302; DOI: 10.1038/s41467-019-13805-y

  • Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains.

    Shaw CD, Imamura H, Downing T, Blackburn G, Westrop GD, Cotton JA, Berriman M, Sanders M, Rijal S, Coombs GH et al.

    Antimicrobial agents and chemotherapy 2019;64;1

    PUBMED: 31658971; PMC: 7187574; DOI: 10.1128/AAC.00904-19

  • Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke.

    Abraham G, Malik R, Yonova-Doing E, Salim A, Wang T, Danesh J, Butterworth AS, Howson JMM, Inouye M and Dichgans M

    Nature communications 2019;10;1;5819

    PUBMED: 31862893; PMC: 6925280; DOI: 10.1038/s41467-019-13848-1

  • The resistome and genomic reconnaissance in the age of malaria elimination.

    Kümpornsin K, Kochakarn T and Chookajorn T

    Disease models & mechanisms 2019;12;12

    PUBMED: 31874839; PMC: 6955228; DOI: 10.1242/dmm.040717

  • Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.

    Loog L, Thalmann O, Sinding MS, Schuenemann VJ, Perri A, Germonpré M, Bocherens H, Witt KE, Samaniego Castruita JA, Velasco MS et al.

    Molecular ecology 2019

    PUBMED: 31840921; DOI: 10.1111/mec.15329

  • High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation.

    Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak AO, Duque-Correa MA, White JK, Ramirez-Solis R, Saran N et al.

    Nature immunology 2019;21;1;86-100

    PUBMED: 31844327; PMC: 7338221; DOI: 10.1038/s41590-019-0549-0

  • Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania.

    Malaria Genomic Epidemiology Network

    Nature communications 2019;10;1;5732

    PUBMED: 31844061; PMC: 6914791; DOI: 10.1038/s41467-019-13480-z

  • RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons.

    Chagas VS, Groeneveld CS, Oliveira KG, Trefflich S, de Almeida RC, Ponder BAJ, Meyer KB, Jones SJM, Robertson AG and Castro MAA

    Bioinformatics (Oxford, England) 2019;35;24;5357-5358

    PUBMED: 31250887; DOI: 10.1093/bioinformatics/btz534

  • A Dietary Pattern with High Sugar Content Is Associated with Cardiometabolic Risk Factors in the Pomak Population.

    Farmaki AE, Rayner NW, Kafyra M, Matchan A, Ntaoutidou K, Feritoglou P, Athanasiadis A, Gilly A, Mamakou V, Zengini E et al.

    Nutrients 2019;11;12

    PUBMED: 31847144; PMC: 6950453; DOI: 10.3390/nu11123043

  • Investigating the drivers of the spatio-temporal patterns of genetic differences between Plasmodium falciparum malaria infections in Kilifi County, Kenya.

    Malinga J, Mogeni P, Omedo I, Rockett K, Hubbart C, Jeffreys A, Williams T, Kwiatkowski D, Bejon P and Ross A

    Scientific reports 2019;9;1;19018

    PUBMED: 31836742; PMC: 6911066; DOI: 10.1038/s41598-019-54348-y

  • Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies.

    Sasca D, Yun H, Giotopoulos G, Szybinski J, Evan T, Wilson NK, Gerstung M, Gallipoli P, Green AR, Hills R et al.

    Blood 2019;134;24;2195-2208

    PUBMED: 31515253; PMC: 7484777; DOI: 10.1182/blood.2019001553

  • Moving From Cancer Burden to Cancer Genomics for Smoldering Myeloma: A Review.

    Maura F, Bolli N, Rustad EH, Hultcrantz M, Munshi N and Landgren O

    JAMA oncology 2019

    PUBMED: 31830214; DOI: 10.1001/jamaoncol.2019.4659

  • Toward a Common Coordinate Framework for the Human Body.

    Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G et al.

    Cell 2019;179;7;1455-1467

    PUBMED: 31835027; PMC: 6934046; DOI: 10.1016/j.cell.2019.11.019

  • HBO1 is required for the maintenance of leukaemia stem cells.

    MacPherson L, Anokye J, Yeung MM, Lam EYN, Chan YC, Weng CF, Yeh P, Knezevic K, Butler MS, Hoegl A et al.

    Nature 2019;577;7789;266-270

    PUBMED: 31827282; DOI: 10.1038/s41586-019-1835-6

  • Multi-omics profiling of mouse gastrulation at single-cell resolution.

    Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW et al.

    Nature 2019;576;7787;487-491

    PUBMED: 31827285; PMC: 6924995; DOI: 10.1038/s41586-019-1825-8

  • The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression.

    Turner CE, Holden MTG, Blane B, Horner C, Peacock SJ and Sriskandan S

    mBio 2019;10;6

    PUBMED: 31822586; PMC: 6904876; DOI: 10.1128/mBio.02521-19

  • PYLFIRE: Python implementation of likelihood-free inference by ratio estimation.

    Kokko J, Remes U, Thomas O, Pesonen H and Corander J

    Wellcome open research 2019;4;197

    PUBMED: 32133422; PMC: 7041362; DOI: 10.12688/wellcomeopenres.15583.1

  • Pancreatic cancer organoids recapitulate disease and allow personalized drug screening.

    Driehuis E, van Hoeck A, Moore K, Kolders S, Francies HE, Gulersonmez MC, Stigter ECA, Burgering B, Geurts V, Gracanin A et al.

    Proceedings of the National Academy of Sciences of the United States of America 2019

    PUBMED: 31818951; PMC: 6936689; DOI: 10.1073/pnas.1911273116

  • Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution.

    Fan H, Wu Q, Wei F, Yang F, Ng BL and Hu Y

    Genome biology 2019;20;1;267

    PUBMED: 31810476; PMC: 6898958; DOI: 10.1186/s13059-019-1889-7

  • Embryonal precursors of Wilms tumor.

    Coorens THH, Treger TD, Al-Saadi R, Moore L, Tran MGB, Mitchell TJ, Tugnait S, Thevanesan C, Young MD, Oliver TRW et al.

    Science (New York, N.Y.) 2019;366;6470;1247-1251

    PUBMED: 31806814; PMC: 6914378; DOI: 10.1126/science.aax1323

  • Combining Stage Specificity and Metabolomic Profiling to Advance Antimalarial Drug Discovery.

    Murithi JM, Owen ES, Istvan ES, Lee MCS, Ottilie S, Chibale K, Goldberg DE, Winzeler EA, Llinás M, Fidock DA and Vanaerschot M

    Cell chemical biology 2019;27;2;158-171.e3

    PUBMED: 31813848; PMC: 7031696; DOI: 10.1016/j.chembiol.2019.11.009

  • Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders.

    Downes K, Megy K, Duarte D, Vries M, Gebhart J, Hofer S, Shamardina O, Deevi SVV, Stephens J, Mapeta R et al.

    Blood 2019;134;23;2082-2091

    PUBMED: 31064749; PMC: 6993014; DOI: 10.1182/blood.2018891192

  • Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae.

    Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC and Milner JJ

    Plant biotechnology journal 2019;18;5;1296-1306

    PUBMED: 31705720; PMC: 7152609; DOI: 10.1111/pbi.13294

  • A causal role for TRESK loss of function in migraine mechanisms.

    Pettingill P, Weir GA, Wei T, Wu Y, Flower G, Lalic T, Handel A, Duggal G, Chintawar S, Cheung J et al.

    Brain : a journal of neurology 2019;142;12;3852-3867

    PUBMED: 31742594; PMC: 6906598; DOI: 10.1093/brain/awz342

  • Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.

    Wei W, Hennig BP, Wang J, Zhang Y, Piazza I, Pareja Sanchez Y, Chabbert CD, Adjalley SH, Steinmetz LM and Pelechano V

    Genome research 2019;29;12;1974-1984

    PUBMED: 31740578; PMC: 6886497; DOI: 10.1101/gr.243378.118

  • Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum.

    Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Herrera G, Ríos-Chaparro DI, Díaz-Arévalo D, Patarroyo MA, Lawley TD and Ramírez JD

    Virulence 2019;10;1;657-676

    PUBMED: 31304854; PMC: 6629180; DOI: 10.1080/21505594.2019.1637699

  • Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops.

    Czechowska K, Lannigan J, Aghaeepour N, Back JB, Begum J, Behbehani G, Bispo C, Bitoun D, Fernández AB, Boova ST et al.

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2019;95;12;1236-1274

    PUBMED: 31833655; DOI: 10.1002/cyto.a.23941

  • Deciphering the role of miR-71 in Echinococcus multilocularis early development in vitro.

    Pérez MG, Spiliotis M, Rego N, Macchiaroli N, Kamenetzky L, Holroyd N, Cucher MA, Brehm K and Rosenzvit MC

    PLoS neglected tropical diseases 2019;13;12;e0007932

    PUBMED: 31881019; PMC: 6957206; DOI: 10.1371/journal.pntd.0007932

  • Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.

    Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S et al.

    Genome research 2019;29;12;2073-2087

    PUBMED: 31537640; PMC: 6886504; DOI: 10.1101/gr.246462.118

  • Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS.

    Pérez-Vázquez M, Sola Campoy PJ, Ortega A, Bautista V, Monzón S, Ruiz-Carrascoso G, Mingorance J, González-Barberá EM, Gimeno C, Aracil B et al.

    The Journal of antimicrobial chemotherapy 2019;74;12;3489-3496

    PUBMED: 31504589; DOI: 10.1093/jac/dkz366

  • Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent.

    Domagalska MA, Imamura H, Sanders M, Van den Broeck F, Bhattarai NR, Vanaerschot M, Maes I, D'Haenens E, Rai K, Rijal S et al.

    PLoS neglected tropical diseases 2019;13;12;e0007900

    PUBMED: 31830038; PMC: 6932831; DOI: 10.1371/journal.pntd.0007900

  • Imipridone ONC212 activates orphan G protein-coupled receptor GPR132 and integrated stress response in acute myeloid leukemia.

    Nii T, Prabhu VV, Ruvolo V, Madhukar N, Zhao R, Mu H, Heese L, Nishida Y, Kojima K, Garnett MJ et al.

    Leukemia 2019;33;12;2805-2816

    PUBMED: 31127149; PMC: 6874902; DOI: 10.1038/s41375-019-0491-z

  • Lipoprotein signatures of cholesteryl ester transfer protein and HMG-CoA reductase inhibition.

    Kettunen J, Holmes MV, Allara E, Anufrieva O, Ohukainen P, Oliver-Williams C, Wang Q, Tillin T, Hughes AD, Kähönen M et al.

    PLoS biology 2019;17;12;e3000572

    PUBMED: 31860674; PMC: 6944381; DOI: 10.1371/journal.pbio.3000572

  • Mapping and predicting gene-enhancer interactions.

    Gaffney DJ

    Nature genetics 2019;51;12;1662-1663

    PUBMED: 31784730; DOI: 10.1038/s41588-019-0540-6

  • Studying immune to non-immune cell cross-talk using single-cell technologies.

    Elmentaite R, Teichmann SA and Madissoon E

    Current opinion in systems biology 2019;18;87-94

    PUBMED: 32984660; PMC: 7493433; DOI: 10.1016/j.coisb.2019.10.005

  • Transcriptional responses of Biomphalaria pfeifferi and Schistosoma mansoni following exposure to niclosamide, with evidence for a synergistic effect on snails following exposure to both stressors.

    Buddenborg SK, Kamel B, Bu L, Zhang SM, Mkoji GM and Loker ES

    PLoS neglected tropical diseases 2019;13;12;e0006927

    PUBMED: 31841501; PMC: 6936870; DOI: 10.1371/journal.pntd.0006927

  • Vitamin D-VDR Signaling Inhibits Wnt/β-Catenin-Mediated Melanoma Progression and Promotes Antitumor Immunity.

    Muralidhar S, Filia A, Nsengimana J, Poźniak J, O'Shea SJ, Diaz JM, Harland M, Randerson-Moor JA, Reichrath J, Laye JP et al.

    Cancer research 2019;79;23;5986-5998

    PUBMED: 31690667; DOI: 10.1158/0008-5472.CAN-18-3927

  • A bird's-eye view of Italian genomic variation through whole-genome sequencing.

    Cocca M, Barbieri C, Concas MP, Robino A, Brumat M, Gandin I, Trudu M, Sala CF, Vuckovic D, Girotto G et al.

    European journal of human genetics : EJHG 2019;28;4;435-444

    PUBMED: 31784700; PMC: 7080768; DOI: 10.1038/s41431-019-0551-x

  • Members of the public in the USA, UK, Canada and Australia expressing genetic exceptionalism say they are more willing to donate genomic data.

    Middleton A, Milne R, Howard H, Niemiec E, Robarts L, Critchley C, Nicol D, Prainsack B, Atutornu J, Vears DF et al.

    European journal of human genetics : EJHG 2019;28;4;424-434

    PUBMED: 31784701; PMC: 7080803; DOI: 10.1038/s41431-019-0550-y

  • Genome Sequencing during a Patient's Journey through Cancer.

    Nangalia J and Campbell PJ

    The New England journal of medicine 2019;381;22;2145-2156

    PUBMED: 31774959; DOI: 10.1056/NEJMra1910138

  • Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent.

    Steinig EJ, Duchene S, Robinson DA, Monecke S, Yokoyama M, Laabei M, Slickers P, Andersson P, Williamson D, Kearns A et al.

    mBio 2019;10;6

    PUBMED: 31772058; PMC: 6879714; DOI: 10.1128/mBio.01105-19

  • Profiling microRNAs through development of the parasitic nematode Haemonchus identifies nematode-specific miRNAs that suppress larval development.

    Marks ND, Winter AD, Gu HY, Maitland K, Gillan V, Ambroz M, Martinelli A, Laing R, MacLellan R, Towne J et al.

    Scientific reports 2019;9;1;17594

    PUBMED: 31772378; PMC: 6879476; DOI: 10.1038/s41598-019-54154-6

  • Should doctors have a legal duty to warn relatives of their genetic risks?

    Middleton A, Milne R, Robarts L, Roberts J and Patch C

    Lancet (London, England) 2019;394;10215;2133-2135

    PUBMED: 31784025; DOI: 10.1016/S0140-6736(19)32941-1

  • The long non-coding RNA HOXB-AS3 regulates ribosomal RNA transcription in NPM1-mutated acute myeloid leukemia.

    Papaioannou D, Petri A, Dovey OM, Terreri S, Wang E, Collins FA, Woodward LA, Walker AE, Nicolet D, Pepe F et al.

    Nature communications 2019;10;1;5351

    PUBMED: 31767858; PMC: 6877618; DOI: 10.1038/s41467-019-13259-2

  • DNA methylation aging clocks: challenges and recommendations.

    Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S et al.

    Genome biology 2019;20;1;249

    PUBMED: 31767039; PMC: 6876109; DOI: 10.1186/s13059-019-1824-y

  • Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.

    Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D et al.

    Communications biology 2019;2;428

    PUBMED: 31799430; PMC: 6874650; DOI: 10.1038/s42003-019-0678-x

  • The ribosomal P-stalk couples amino acid starvation to GCN2 activation in mammalian cells.

    Harding HP, Ordonez A, Allen F, Parts L, Inglis AJ, Williams RL and Ron D

    eLife 2019;8

    PUBMED: 31749445; PMC: 6919976; DOI: 10.7554/eLife.50149

  • Draft Genome Sequences of 40 Pathogenic Leptospira Strains Isolated from Cattle in Uruguay.

    Nieves C, Ferrés I, Díaz-Viraqué F, Buschiazzo A, Zarantonelli L and Iraola G

    Microbiology resource announcements 2019;8;47

    PUBMED: 31753938; PMC: 6872880; DOI: 10.1128/MRA.00893-19

  • Genetic predisposition to mosaic Y chromosome loss in blood.

    Thompson DJ, Genovese G, Halvardson J, Ulirsch JC, Wright DJ, Terao C, Davidsson OB, Day FR, Sulem P, Jiang Y et al.

    Nature 2019;575;7784;652-657

    PUBMED: 31748747; PMC: 6887549; DOI: 10.1038/s41586-019-1765-3

  • Alzheimer's disease and the development of a post-genomic science

    Milne R and Latimer J

    New Genetics and Society 2019

    DOI: 10.1080/14636778.2019.1683213; URL: https://doi.org/10.1080/14636778.2019.1683213

  • Chemokine receptor trafficking coordinates neutrophil clustering and dispersal at wounds in zebrafish.

    Coombs C, Georgantzoglou A, Walker HA, Patt J, Merten N, Poplimont H, Busch-Nentwich EM, Williams S, Kotsi C, Kostenis E and Sarris M

    Nature communications 2019;10;1;5166

    PUBMED: 31727891; PMC: 6856356; DOI: 10.1038/s41467-019-13107-3

  • Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage.

    Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V et al.

    Cell 2019;179;5;1112-1128.e26

    PUBMED: 31730853; PMC: 6904910; DOI: 10.1016/j.cell.2019.10.030

  • Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease.

    Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M et al.

    Nature 2019;575;7783;505-511

    PUBMED: 31723265; PMC: 6872939; DOI: 10.1038/s41586-019-1742-x

  • Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.

    Wasef S, Subramanian S, O'Rorke R, Huynen L, El-Marghani S, Curtis C, Popinga A, Holland B, Ikram S, Millar C et al.

    PloS one 2019;14;11;e0223964

    PUBMED: 31721774; PMC: 6853290; DOI: 10.1371/journal.pone.0223964

  • Genome-wide association study of eosinophilic granulomatosis with polyangiitis reveals genomic loci stratified by ANCA status.

    Lyons PA, Peters JE, Alberici F, Liley J, Coulson RMR, Astle W, Baldini C, Bonatti F, Cid MC, Elding H et al.

    Nature communications 2019;10;1;5120

    PUBMED: 31719529; PMC: 6851141; DOI: 10.1038/s41467-019-12515-9

  • Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis.

    Dobie R, Wilson-Kanamori JR, Henderson BEP, Smith JR, Matchett KP, Portman JR, Wallenborg K, Picelli S, Zagorska A, Pendem SV et al.

    Cell reports 2019;29;7;1832-1847.e8

    PUBMED: 31722201; PMC: 6856722; DOI: 10.1016/j.celrep.2019.10.024

  • Identification of predictors of drug sensitivity using patient-derived models of esophageal squamous cell carcinoma.

    Su D, Zhang D, Jin J, Ying L, Han M, Chen K, Li B, Wu J, Xie Z, Zhang F et al.

    Nature communications 2019;10;1;5076

    PUBMED: 31700061; PMC: 6838071; DOI: 10.1038/s41467-019-12846-7

  • The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases.

    de Magalhães JP and Wang J

    EMBO reports 2019;20;11;e48054

    PUBMED: 31633864; PMC: 6831998; DOI: 10.15252/embr.201948054

  • In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages.

    Zamani Esteki M, Viltrop T, Tšuiko O, Tiirats A, Koel M, Nõukas M, Žilina O, Teearu K, Marjonen H, Kahila H et al.

    Nature medicine 2019;25;11;1699-1705

    PUBMED: 31686035; DOI: 10.1038/s41591-019-0620-2

  • The impact of antimicrobials on gonococcal evolution.

    Sánchez-Busó L, Golparian D, Corander J, Grad YH, Ohnishi M, Flemming R, Parkhill J, Bentley SD, Unemo M and Harris SR

    Nature microbiology 2019;4;11;1941-1950

    PUBMED: 31358980; PMC: 6817357; DOI: 10.1038/s41564-019-0501-y

  • The male mosquito contribution towards malaria transmission: Mating influences the Anopheles female midgut transcriptome and increases female susceptibility to human malaria parasites.

    Dahalan FA, Churcher TS, Windbichler N and Lawniczak MKN

    PLoS pathogens 2019;15;11;e1008063

    PUBMED: 31697788; PMC: 6837289; DOI: 10.1371/journal.ppat.1008063

  • Detection of Cell Surface Ligands for Human Synovial γδ T Cells.

    Collins C, Lui Y, Santos AM, Ballif BA, Gogerly-Moragoda AM, Brouwer H, Ross R, Balagurunathan K, Sharma S, Wright GJ et al.

    Journal of immunology (Baltimore, Md. : 1950) 2019;203;9;2369-2376

    PUBMED: 31548331; PMC: 6804759; DOI: 10.4049/jimmunol.1900451

  • Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study.

    Lynskey NN, Jauneikaite E, Li HK, Zhi X, Turner CE, Mosavie M, Pearson M, Asai M, Lobkowicz L, Chow JY et al.

    The Lancet. Infectious diseases 2019;19;11;1209-1218

    PUBMED: 31519541; PMC: 6838661; DOI: 10.1016/S1473-3099(19)30446-3

  • Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration.

    Aloia L, McKie MA, Vernaz G, Cordero-Espinoza L, Aleksieva N, van den Ameele J, Antonica F, Font-Cunill B, Raven A, Aiese Cigliano R et al.

    Nature cell biology 2019;21;11;1321-1333

    PUBMED: 31685987; PMC: 6940196; DOI: 10.1038/s41556-019-0402-6

  • Genomic architecture and introgression shape a butterfly radiation.

    Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE et al.

    Science (New York, N.Y.) 2019;366;6465;594-599

    PUBMED: 31672890; PMC: 7197882; DOI: 10.1126/science.aaw2090

  • Immunology Driven by Large-Scale Single-Cell Sequencing.

    Gomes T, Teichmann SA and Talavera-López C

    Trends in immunology 2019;40;11;1011-1021

    PUBMED: 31645299; DOI: 10.1016/j.it.2019.09.004

  • Incomplete genetic reconstitution of B cell pools contributes to prolonged immunosuppression after measles.

    Petrova VN, Sawatsky B, Han AX, Laksono BM, Walz L, Parker E, Pieper K, Anderson CA, de Vries RD, Lanzavecchia A et al.

    Science immunology 2019;4;41

    PUBMED: 31672862; DOI: 10.1126/sciimmunol.aay6125

  • Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia.

    Khubrani YM, Hallast P, Jobling MA and Wetton JH

    Forensic science international. Genetics 2019;43;102164

    PUBMED: 31585345; DOI: 10.1016/j.fsigen.2019.102164

  • Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders.

    Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;11;2413-2421

    PUBMED: 31182824; PMC: 6831729; DOI: 10.1038/s41436-019-0554-6

  • Mouse protein coding diversity: What's left to discover?

    Lilue J, Shivalikanjli A, Adams DJ and Keane TM

    PLoS genetics 2019;15;11;e1008446

    PUBMED: 31725724; PMC: 6855407; DOI: 10.1371/journal.pgen.1008446

  • Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014).

    Blackburn RM, Frampton D, Smith CM, Fragaszy EB, Watson SJ, Ferns RB, Binter Š, Coen PG, Grant P, Shallcross LJ et al.

    Influenza and other respiratory viruses 2019;13;6;556-563

    PUBMED: 31536169; PMC: 6800305; DOI: 10.1111/irv.12679

  • PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.

    Kamat MA, Blackshaw JA, Young R, Surendran P, Burgess S, Danesh J, Butterworth AS and Staley JR

    Bioinformatics (Oxford, England) 2019;35;22;4851-4853

    PUBMED: 31233103; PMC: 6853652; DOI: 10.1093/bioinformatics/btz469

  • Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks.

    Brown NM, Blane B, Raven KE, Kumar N, Leek D, Bragin E, Rhodes PA, Enoch DA, Thaxter R, Parkhill J and Peacock SJ

    Journal of clinical microbiology 2019;57;11

    PUBMED: 31462548; PMC: 6813015; DOI: 10.1128/JCM.00858-19

  • Reasons to be testing: the dawn of complex molecular profiling in routine oncology practice.

    Beer PA, Cooke SL, Chang DK and Biankin AV

    Annals of oncology : official journal of the European Society for Medical Oncology 2019;30;11;1691-1694

    PUBMED: 31665210; DOI: 10.1093/annonc/mdz392

  • RTNsurvival: an R/Bioconductor package for regulatory network survival analysis.

    Groeneveld CS, Chagas VS, Jones SJM, Robertson AG, Ponder BAJ, Meyer KB and Castro MAA

    Bioinformatics (Oxford, England) 2019;35;21;4488-4489

    PUBMED: 30923832; PMC: 6821288; DOI: 10.1093/bioinformatics/btz229

  • SNP barcoding based on decision tree algorithm: A new tool for identification of mosquito species with special reference to Anopheles.

    Swain SN, Makunin A, Dora AS and Barik TK

    Acta tropica 2019;199;105152

    PUBMED: 31445898; DOI: 10.1016/j.actatropica.2019.105152

  • Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania.

    Sloan MA, Brooks K, Otto TD, Sanders MJ, Cotton JA and Ligoxygakis P

    PLoS genetics 2019;15;11;e1008452

    PUBMED: 31710597; PMC: 6872171; DOI: 10.1371/journal.pgen.1008452

  • Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data.

    Mitchell HD, Mikhail AFW, Painset A, Dallman TJ, Jenkins C, Thomson NR, Field N and Hughes G

    Microbial genomics 2019;5;11

    PUBMED: 31682221; PMC: 6927305; DOI: 10.1099/mgen.0.000311

  • VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.

    Stephenson JD, Laskowski RA, Nightingale A, Hurles ME and Thornton JM

    Bioinformatics (Oxford, England) 2019;35;22;4854-4856

    PUBMED: 31192369; PMC: 6853667; DOI: 10.1093/bioinformatics/btz482

  • VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects.

    Ossio R, Garcia-Salinas OI, Anaya-Mancilla DS, Garcia-Sotelo JS, Aguilar LA, Adams DJ and Robles-Espinoza CD

    Bioinformatics (Oxford, England) 2019;35;22;4803-4805

    PUBMED: 31161195; PMC: 6853650; DOI: 10.1093/bioinformatics/btz458

  • GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways.

    López-Isac E, Acosta-Herrera M, Kerick M, Assassi S, Satpathy AT, Granja J, Mumbach MR, Beretta L, Simeón CP, Carreira P et al.

    Nature communications 2019;10;1;4955

    PUBMED: 31672989; PMC: 6823490; DOI: 10.1038/s41467-019-12760-y

  • Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

    Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C et al.

    iScience 2019;21;664-680

    PUBMED: 31733513; PMC: 6889472; DOI: 10.1016/j.isci.2019.10.059

  • Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.

    Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I et al.

    Cell 2019;179;4;984-1002.e36

    PUBMED: 31675503; PMC: 7202134; DOI: 10.1016/j.cell.2019.10.004

  • Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511.

    Turnbull JD, Russell JE, Fazal MA, Grayson NE, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J and Alexander S

    Microbiology resource announcements 2019;8;44

    PUBMED: 31672735; PMC: 6953506; DOI: 10.1128/MRA.00256-19

  • Clinical spectrum of POLR3-related leukodystrophy caused by biallelic POLR1C pathogenic variants.

    Gauquelin L, Cayami FK, Sztriha L, Yoon G, Tran LT, Guerrero K, Hocke F, van Spaendonk RML, Fung EL, D'Arrigo S et al.

    Neurology. Genetics 2019;5;6;e369

    PUBMED: 32042905; PMC: 6927361; DOI: 10.1212/NXG.0000000000000369

  • Nedd8 hydrolysis by UCH proteases in Plasmodium parasites.

    Karpiyevich M, Adjalley S, Mol M, Ascher DB, Mason B, van der Heden van Noort GJ, Laman H, Ovaa H, Lee MCS and Artavanis-Tsakonas K

    PLoS pathogens 2019;15;10;e1008086

    PUBMED: 31658303; PMC: 6837540; DOI: 10.1371/journal.ppat.1008086

  • RNAmut: robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing.

    Gu M, Zwiebel M, Ong SH, Boughton N, Nomdedeu J, Basheer F, Nannya Y, Quiros PM, Ogawa S, Cazzola M et al.

    Haematologica 2019;105;6;e290-e293

    PUBMED: 31649132; PMC: 7271607; DOI: 10.3324/haematol.2019.230821

  • The landscape of somatic mutation in normal colorectal epithelial cells.

    Lee-Six H, Olafsson S, Ellis P, Osborne RJ, Sanders MA, Moore L, Georgakopoulos N, Torrente F, Noorani A, Goddard M et al.

    Nature 2019;574;7779;532-537

    PUBMED: 31645730; DOI: 10.1038/s41586-019-1672-7

  • Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei.

    Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S et al.

    Nature communications 2019;10;1;4828

    PUBMED: 31645551; PMC: 6811581; DOI: 10.1038/s41467-019-12823-0

  • Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity.

    Cheng H, Capponi S, Wakeling E, Marchi E, Li Q, Zhao M, Weng C, Stefan PG, Ahlfors H, Kleyner R et al.

    Human mutation 2019

    PUBMED: 31646703; PMC: 7187541; DOI: 10.1002/humu.23936

  • Somatic mutations and clonal dynamics in healthy and cirrhotic human liver.

    Brunner SF, Roberts ND, Wylie LA, Moore L, Aitken SJ, Davies SE, Sanders MA, Ellis P, Alder C, Hooks Y et al.

    Nature 2019;574;7779;538-542

    PUBMED: 31645727; PMC: 6837891; DOI: 10.1038/s41586-019-1670-9

  • Tet3 regulates cellular identity and DNA methylation in neural progenitor cells.

    Santiago M, Antunes C, Guedes M, Iacovino M, Kyba M, Reik W, Sousa N, Pinto L, Branco MR and Marques CJ

    Cellular and molecular life sciences : CMLS 2019;77;14;2871-2883

    PUBMED: 31646359; PMC: 7326798; DOI: 10.1007/s00018-019-03335-7

  • The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study.

    Wagner J, Harrison EM, Martinez Del Pero M, Blane B, Mayer G, Leierer J, Gopaluni S, Holmes MA, Parkhill J, Peacock SJ et al.

    Microbiome 2019;7;1;137

    PUBMED: 31640771; PMC: 6806544; DOI: 10.1186/s40168-019-0753-z

  • The global diversity of Haemonchus contortus is shaped by human intervention and climate.

    Sallé G, Doyle SR, Cortet J, Cabaret J, Berriman M, Holroyd N and Cotton JA

    Nature communications 2019;10;1;4811

    PUBMED: 31641125; PMC: 6805936; DOI: 10.1038/s41467-019-12695-4

  • Extraocular, rod-like photoreceptors in a flatworm express xenopsin photopigment.

    Rawlinson KA, Lapraz F, Ballister ER, Terasaki M, Rodgers J, McDowell RJ, Girstmair J, Criswell KE, Boldogkoi M, Simpson F et al.

    eLife 2019;8

    PUBMED: 31635694; PMC: 6805122; DOI: 10.7554/eLife.45465

  • Technological challenges and milestones for writing genomes.

    Ostrov N, Beal J, Ellis T, Gordon DB, Karas BJ, Lee HH, Lenaghan SC, Schloss JA, Stracquadanio G, Trefzer A et al.

    Science (New York, N.Y.) 2019;366;6463;310-312

    PUBMED: 31624201; DOI: 10.1126/science.aay0339

  • Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome.

    Davies HR, Hodgson K, Schwalbe E, Coxhead J, Sinclair N, Zou X, Cockell S, Husain A, Nik-Zainal S and Rajan N

    Nature communications 2019;10;1;4717

    PUBMED: 31624251; PMC: 6797807; DOI: 10.1038/s41467-019-12746-w

  • Systematic screening of 96 Schistosoma mansoni cell-surface and secreted antigens does not identify any strongly protective vaccine candidates in a mouse model of infection.

    Crosnier C, Brandt C, Rinaldi G, McCarthy C, Barker C, Clare S, Berriman M and Wright GJ

    Wellcome open research 2019;4;159

    PUBMED: 31728414; PMC: 6833992; DOI: 10.12688/wellcomeopenres.15487.1

  • Cross-disorder analysis of schizophrenia and 19 immune-mediated diseases identifies shared genetic risk.

    Pouget JG, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Han B, Wu Y, Mignot E, Ollila HM, Barker J, Spain S, Dand N, Trembath R et al.

    Human molecular genetics 2019;28;20;3498-3513

    PUBMED: 31211845; PMC: 6891073; DOI: 10.1093/hmg/ddz145

  • Defective tubulin detyrosination causes structural brain abnormalities with cognitive deficiency in humans and mice.

    Pagnamenta AT, Heemeryck P, Martin HC, Bosc C, Peris L, Uszynski I, Gory-Fauré S, Couly S, Deshpande C, Siddiqui A et al.

    Human molecular genetics 2019;28;20;3391-3405

    PUBMED: 31363758; PMC: 6891070; DOI: 10.1093/hmg/ddz186

  • Next-generation sequencing for the diagnosis of MYH9-RD: Predicting pathogenic variants.

    Bury L, Megy K, Stephens JC, Grassi L, Greene D, Gleadall N, Althaus K, Allsup D, Bariana TK, Bonduel M et al.

    Human mutation 2019;41;1;277-290

    PUBMED: 31562665; PMC: 6972977; DOI: 10.1002/humu.23927

  • Resurrection of the ancestral RH5 invasion ligand provides a molecular explanation for the origin of P. falciparum malaria in humans.

    Galaway F, Yu R, Constantinou A, Prugnolle F and Wright GJ

    PLoS biology 2019;17;10;e3000490

    PUBMED: 31613878; PMC: 6793842; DOI: 10.1371/journal.pbio.3000490

  • Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome.

    Shi W, Massaia A, Louzada S, Handsaker J, Chow W, McCarthy S, Collins J, Hallast P, Howe K, Church DM et al.

    Genome biology 2019;20;1;207

    PUBMED: 31610793; PMC: 6790999; DOI: 10.1186/s13059-019-1816-y

  • GeneDB and Wikidata.

    Manske M, Böhme U, Püthe C and Berriman M

    Wellcome open research 2019;4;114

    PUBMED: 31723674; PMC: 6823904; DOI: 10.12688/wellcomeopenres.15355.2

  • Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion.

    Houldcroft CJ

    Pathogens (Basel, Switzerland) 2019;8;4

    PUBMED: 31614759; PMC: 6963362; DOI: 10.3390/pathogens8040186

  • Contribution of retrotransposition to developmental disorders.

    Gardner EJ, Prigmore E, Gallone G, Danecek P, Samocha KE, Handsaker J, Gerety SS, Ironfield H, Short PJ, Sifrim A et al.

    Nature communications 2019;10;1;4630

    PUBMED: 31604926; PMC: 6789007; DOI: 10.1038/s41467-019-12520-y

  • Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae.

    Sánchez-Busó L, Golparian D, Parkhill J, Unemo M and Harris SR

    Scientific reports 2019;9;1;14685

    PUBMED: 31605008; PMC: 6789123; DOI: 10.1038/s41598-019-51102-2

  • Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK.

    Cain AK, Nolan LM, Sullivan GJ, Whitchurch CB, Filloux A and Parkhill J

    Microbiology resource announcements 2019;8;41

    PUBMED: 31601664; PMC: 6787321; DOI: 10.1128/MRA.00865-19

  • Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

    Aitken S, Firth HV, McRae J, Halachev M, Kini U, Parker MJ, Lees MM, Lachlan K, Sarkar A, Joss S et al.

    American journal of human genetics 2019;105;5;933-946

    PUBMED: 31607427; PMC: 6848993; DOI: 10.1016/j.ajhg.2019.09.015

  • Genome-wide epistasis and co-selection study using mutual information.

    Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L et al.

    Nucleic acids research 2019;47;18;e112

    PUBMED: 31361894; PMC: 6765119; DOI: 10.1093/nar/gkz656

  • The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre.

    Dunstan RA, Pickard D, Dougan S, Goulding D, Cormie C, Hardy J, Li F, Grinter R, Harcourt K, Yu L et al.

    Molecular microbiology 2019;112;6;1831-1846

    PUBMED: 31556164; DOI: 10.1111/mmi.14396

  • The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

    HuBMAP Consortium

    Nature 2019;574;7777;187-192

    PUBMED: 31597973; PMC: 6800388; DOI: 10.1038/s41586-019-1629-x

  • Decoding human fetal liver haematopoiesis.

    Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M et al.

    Nature 2019;574;7778;365-371

    PUBMED: 31597962; PMC: 6861135; DOI: 10.1038/s41586-019-1652-y

  • A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Salmonella Infection.

    Yeung ATY, Choi YH, Lee AHY, Hale C, Ponstingl H, Pickard D, Goulding D, Thomas M, Gill E, Kim JK et al.

    mBio 2019;10;5

    PUBMED: 31594818; PMC: 6786873; DOI: 10.1128/mBio.02169-19

  • HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease.

    Sazonovs A, Kennedy NA, Moutsianas L, Heap GA, Rice DL, Reppell M, Bewshea CM, Chanchlani N, Walker GJ, Perry MH et al.

    Gastroenterology 2019;158;1;189-199

    PUBMED: 31600487; DOI: 10.1053/j.gastro.2019.09.041

  • Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease.

    Ricaño-Ponce I, Gutierrez-Achury J, Costa AF, Deelen P, Kurilshikov A, Zorro MM, Platteel M, van der Graaf A, Consortium for the study of genetic associations of celiac disease in Latin-America, Sanna S et al.

    European journal of human genetics : EJHG 2019;28;3;313-323

    PUBMED: 31591516; PMC: 7028987; DOI: 10.1038/s41431-019-0520-4

  • The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis.

    Capalbo L, Bassi ZI, Geymonat M, Todesca S, Copoiu L, Enright AJ, Callaini G, Riparbelli MG, Yu L, Choudhary JS et al.

    Nature communications 2019;10;1;4513

    PUBMED: 31586073; PMC: 6778137; DOI: 10.1038/s41467-019-12507-9

  • Adaptation of Plasmodium falciparum to humans involved the loss of an ape-specific erythrocyte invasion ligand.

    Proto WR, Siegel SV, Dankwa S, Liu W, Kemp A, Marsden S, Zenonos ZA, Unwin S, Sharp PM, Wright GJ et al.

    Nature communications 2019;10;1;4512

    PUBMED: 31586047; PMC: 6778099; DOI: 10.1038/s41467-019-12294-3

  • Genetic modification of primary human B cells to model high-grade lymphoma.

    Caeser R, Di Re M, Krupka JA, Gao J, Lara-Chica M, Dias JML, Cooke SL, Fenner R, Usheva Z, Runge HFP et al.

    Nature communications 2019;10;1;4543

    PUBMED: 31586074; PMC: 6778131; DOI: 10.1038/s41467-019-12494-x

  • High-Content Imaging for Large-Scale Detection of Low-Affinity Extracellular Protein Interactions.

    Wood L and Wright GJ

    SLAS discovery : advancing life sciences R & D 2019;24;10;987-999

    PUBMED: 31578119; PMC: 6873222; DOI: 10.1177/2472555219879053

  • Widening of the genetic and clinical spectrum of Lamb-Shaffer syndrome, a neurodevelopmental disorder due to SOX5 haploinsufficiency.

    Zawerton A, Mignot C, Sigafoos A, Blackburn PR, Haseeb A, McWalter K, Ichikawa S, Nava C, Keren B, Charles P et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2019;22;3;524-537

    PUBMED: 31578471; PMC: 9063678; DOI: 10.1038/s41436-019-0657-0

  • Zebrafish MITF-Low Melanoma Subtype Models Reveal Transcriptional Subclusters and MITF-Independent Residual Disease.

    Travnickova J, Wojciechowska S, Khamseh A, Gautier P, Brown DV, Lefevre T, Brombin A, Ewing A, Capper A, Spitzer M et al.

    Cancer research 2019;79;22;5769-5784

    PUBMED: 31582381; PMC: 7116150; DOI: 10.1158/0008-5472.CAN-19-0037

  • A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis.

    Masschelein J, Sydor PK, Hobson C, Howe R, Jones C, Roberts DM, Ling Yap Z, Parkhill J, Mahenthiralingam E and Challis GL

    Nature chemistry 2019;11;10;906-912

    PUBMED: 31548673; DOI: 10.1038/s41557-019-0309-7

  • A genome-wide association and replication study of blood pressure in Ugandan early adolescents.

    Lule SA, Mentzer AJ, Namara B, Muwenzi AG, Nassanga B, Kizito D, Akurut H, Lubyayi L, Tumusiime J, Zziwa C et al.

    Molecular genetics & genomic medicine 2019;7;10;e00950

    PUBMED: 31469255; PMC: 6785527; DOI: 10.1002/mgg3.950

  • Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases.

    Blohmke CJ, Muller J, Gibani MM, Dobinson H, Shrestha S, Perinparajah S, Jin C, Hughes H, Blackwell L, Dongol S et al.

    EMBO molecular medicine 2019;11;10;e10431

    PUBMED: 31468702; PMC: 6783646; DOI: 10.15252/emmm.201910431

  • Mendelian Randomization Analysis Reveals a Causal Influence of Circulating Sclerostin Levels on Bone Mineral Density and Fractures.

    Zheng J, Maerz W, Gergei I, Kleber M, Drechsler C, Wanner C, Brandenburg V, Reppe S, Gautvik KM, Medina-Gomez C et al.

    Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2019;34;10;1824-1836

    PUBMED: 31170332; PMC: 6899787; DOI: 10.1002/jbmr.3803

  • Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host.

    Furi L, Crawford LA, Rangel-Pineros G, Manso AS, De Ste Croix M, Haigh RD, Kwun MJ, Engelsen Fjelland K, Gilfillan GD, Bentley SD et al.

    Journal of bacteriology 2019;201;19

    PUBMED: 31285240; PMC: 6755750; DOI: 10.1128/JB.00370-19

  • Oral Anti-Tumour Necrosis Factor Domain Antibody V565 Provides High Intestinal Concentrations, and Reduces Markers of Inflammation in Ulcerative Colitis Patients.

    Nurbhai S, Roberts KJ, Carlton TM, Maggiore L, Cubitt MF, Ray KP, Reckless J, Mohammed H, Irving P, MacDonald TT et al.

    Scientific reports 2019;9;1;14042

    PUBMED: 31575982; PMC: 6773840; DOI: 10.1038/s41598-019-50545-x

  • RRAD mutation causes electrical and cytoskeletal defects in cardiomyocytes derived from a familial case of Brugada syndrome.

    Belbachir N, Portero V, Al Sayed ZR, Gourraud JB, Dilasser F, Jesel L, Guo H, Wu H, Gaborit N, Guilluy C et al.

    European heart journal 2019;40;37;3081-3094

    PUBMED: 31114854; PMC: 6769825; DOI: 10.1093/eurheartj/ehz308

  • Supervised clustering for single-cell analysis.

    Lee JTH and Hemberg M

    Nature methods 2019;16;10;965-966

    PUBMED: 31501544; DOI: 10.1038/s41592-019-0534-4

  • Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso.

    Post AS, Diallo SN, Guiraud I, Lompo P, Tahita MC, Maltha J, Van Puyvelde S, Mattheus W, Ley B, Thriemer K et al.

    PLoS neglected tropical diseases 2019;13;10;e0007782

    PUBMED: 31609964; PMC: 6812844; DOI: 10.1371/journal.pntd.0007782

  • Type III secretion system confers enhanced virulence in clinical non-O1/non-O139 Vibrio cholerae.

    Zeb S, Shah MA, Yasir M, Awan HM, Prommeenate P, Klanchui A, Wren BW, Thomson N and Bokhari H

    Microbial pathogenesis 2019;135;103645

    PUBMED: 31356927; DOI: 10.1016/j.micpath.2019.103645

  • Voices in methods development.

    Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW et al.

    Nature methods 2019;16;10;945-951

    PUBMED: 31562479; PMC: 7075469; DOI: 10.1038/s41592-019-0585-6

  • The in vivo transcriptome of Schistosoma mansoni in the prominent vector species Biomphalaria pfeifferi with supporting observations from Biomphalaria glabrata.

    Buddenborg SK, Kamel B, Hanelt B, Bu L, Zhang SM, Mkoji GM and Loker ES

    PLoS neglected tropical diseases 2019;13;9;e0007013

    PUBMED: 31568484; PMC: 6797213; DOI: 10.1371/journal.pntd.0007013

  • A new patient-derived iPSC model for dystroglycanopathies validates a compound that increases glycosylation of α-dystroglycan.

    Kim J, Lana B, Torelli S, Ryan D, Catapano F, Ala P, Luft C, Stevens E, Konstantinidis E, Louzada S et al.

    EMBO reports 2019;20;11;e47967

    PUBMED: 31566294; PMC: 6832011; DOI: 10.15252/embr.201947967

  • Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study.

    Staaf J, Glodzik D, Bosch A, Vallon-Christersson J, Reuterswärd C, Häkkinen J, Degasperi A, Amarante TD, Saal LH, Hegardt C et al.

    Nature medicine 2019;25;10;1526-1533

    PUBMED: 31570822; PMC: 6859071; DOI: 10.1038/s41591-019-0582-4

  • Studying the effects of diet on DNA methylation: challenges, pitfalls and a way forward.

    Meeks KAC, Nicolaou M, Young E and Adeyemo A

    The British journal of nutrition 2019;122;6;717-718

    PUBMED: 31167669; PMC: 6895408; DOI: 10.1017/S000711451900093X

  • Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility.

    International Multiple Sclerosis Genetics Consortium

    Science (New York, N.Y.) 2019;365;6460

    PUBMED: 31604244; DOI: 10.1126/science.aav7188

  • Spatiotemporal immune zonation of the human kidney.

    Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Vieira Braga FA et al.

    Science (New York, N.Y.) 2019;365;6460;1461-1466

    PUBMED: 31604275; PMC: 7343525; DOI: 10.1126/science.aat5031

  • The transferability of lipid loci across African, Asian and European cohorts.

    Kuchenbaecker K, Telkar N, Reiker T, Walters RG, Lin K, Eriksson A, Gurdasani D, Gilly A, Southam L, Tsafantakis E et al.

    Nature communications 2019;10;1;4330

    PUBMED: 31551420; PMC: 6760173; DOI: 10.1038/s41467-019-12026-7

  • Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium.

    Lee MCS, Lindner SE, Lopez-Rubio JJ and Llinás M

    Briefings in functional genomics 2019;18;5;281-289

    PUBMED: 31365053; PMC: 6859820; DOI: 10.1093/bfgp/elz012

  • Genomic characterization of novel Neisseria species.

    Diallo K, MacLennan J, Harrison OB, Msefula C, Sow SO, Daugla DM, Johnson E, Trotter C, MacLennan CA, Parkhill J et al.

    Scientific reports 2019;9;1;13742

    PUBMED: 31551478; PMC: 6760525; DOI: 10.1038/s41598-019-50203-2

  • A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.

    Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, Miyahara R, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B et al.

    Scientific reports 2019;9;1;13718

    PUBMED: 31548561; PMC: 6757101; DOI: 10.1038/s41598-019-50078-3

  • Bayesian localization of CNV candidates in WGS data within minutes.

    Wiedenhoeft J, Cagan A, Kozhemyakina R, Gulevich R and Schliep A

    Algorithms for molecular biology : AMB 2019;14;20

    PUBMED: 31572486; PMC: 6757390; DOI: 10.1186/s13015-019-0154-7

  • Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases.

    Soskic B, Cano-Gamez E, Smyth DJ, Rowan WC, Nakic N, Esparza-Gordillo J, Bossini-Castillo L, Tough DF, Larminie CGC, Bronson PG et al.

    Nature genetics 2019;51;10;1486-1493

    PUBMED: 31548716; PMC: 6872452; DOI: 10.1038/s41588-019-0493-9

  • Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook.

    Ghansah A, Kamau E, Amambua-Ngwa A, Ishengoma DS, Maiga-Ascofare O, Amenga-Etego L, Deme A, Yavo W, Randrianarivelojosia M, Plasmodium Diversity Network Africa et al.

    Malaria journal 2019;18;1;324

    PUBMED: 31547818; PMC: 6757370; DOI: 10.1186/s12936-019-2944-2

  • Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing.

    Doyle SR, Sankaranarayanan G, Allan F, Berger D, Jimenez Castro PD, Collins JB, Crellen T, Duque-Correa MA, Ellis P, Jaleta TG et al.

    Frontiers in genetics 2019;10;826

    PUBMED: 31616465; PMC: 6764475; DOI: 10.3389/fgene.2019.00826

  • An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation.

    Van Puyvelde S, Pickard D, Vandelannoote K, Heinz E, Barbé B, de Block T, Clare S, Coomber EL, Harcourt K, Sridhar S et al.

    Nature communications 2019;10;1;4280

    PUBMED: 31537784; PMC: 6753159; DOI: 10.1038/s41467-019-11844-z

  • Activation of Skeletal Stem and Progenitor Cells for Bone Regeneration Is Driven by PDGFRβ Signaling.

    Böhm AM, Dirckx N, Tower RJ, Peredo N, Vanuytven S, Theunis K, Nefyodova E, Cardoen R, Lindner V, Voet T et al.

    Developmental cell 2019;51;2;236-254.e12

    PUBMED: 31543445; DOI: 10.1016/j.devcel.2019.08.013

  • Pathogenomics of Emerging Campylobacter Species.

    Costa D and Iraola G

    Clinical microbiology reviews 2019;32;4

    PUBMED: 31270126; PMC: 6750134; DOI: 10.1128/CMR.00072-18

  • Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth.

    Shao Y, Forster SC, Tsaliki E, Vervier K, Strang A, Simpson N, Kumar N, Stares MD, Rodger A, Brocklehurst P et al.

    Nature 2019;574;7776;117-121

    PUBMED: 31534227; PMC: 6894937; DOI: 10.1038/s41586-019-1560-1

  • Trust in genomic data sharing among members of the general public in the UK, USA, Canada and Australia.

    Milne R, Morley KI, Howard H, Niemiec E, Nicol D, Critchley C, Prainsack B, Vears D, Smith J, Steed C et al.

    Human genetics 2019;138;11-12;1237-1246

    PUBMED: 31531740; PMC: 6874520; DOI: 10.1007/s00439-019-02062-0

  • A high throughput multi-locus insecticide resistance marker panel for tracking resistance emergence and spread in Anopheles gambiae.

    Lucas ER, Rockett KA, Lynd A, Essandoh J, Grisales N, Kemei B, Njoroge H, Hubbart C, Rippon EJ, Morgan J et al.

    Scientific reports 2019;9;1;13335

    PUBMED: 31527637; PMC: 6746726; DOI: 10.1038/s41598-019-49892-6

  • Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis.

    Jackstadt R, van Hooff SR, Leach JD, Cortes-Lavaud X, Lohuis JO, Ridgway RA, Wouters VM, Roper J, Kendall TJ, Roxburgh CS et al.

    Cancer cell 2019;36;3;319-336.e7

    PUBMED: 31526760; PMC: 6853173; DOI: 10.1016/j.ccell.2019.08.003

  • Population-wide copy number variation calling using variant call format files from 6,898 individuals.

    Png G, Suveges D, Park YC, Walter K, Kundu K, Ntalla I, Tsafantakis E, Karaleftheri M, Dedoussis G, Zeggini E and Gilly A

    Genetic epidemiology 2019;44;1;79-89

    PUBMED: 31520489; DOI: 10.1002/gepi.22260

  • The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus.

    Rezansoff AM, Laing R, Martinelli A, Stasiuk S, Redman E, Bartley D, Holroyd N, Devaney E, Sargison ND, Doyle S et al.

    International journal for parasitology 2019

    PUBMED: 31525371; DOI: 10.1016/j.ijpara.2019.05.012

  • A real-time PCR for specific detection of the Legionella pneumophila serogroup 1 ST1 complex.

    Ginevra C, Chastang J, David S, Mentasti M, Yakunin E, Chalker VJ, Chalifa-Caspi V, Valinsky L, Jarraud S, Moran-Gilad J and ESCMID Study Group for Legionella Infections (ESGLI)

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019

    PUBMED: 31525518; DOI: 10.1016/j.cmi.2019.09.002

  • The recent emergence of a highly related virulent Clostridium difficile clade with unique characteristics.

    Shaw HA, Preston MD, Vendrik KEW, Cairns MD, Browne HP, Stabler RA, Crobach MJT, Corver J, Pituch H, Ingebretsen A et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019;26;4;492-498

    PUBMED: 31525517; PMC: 7167513; DOI: 10.1016/j.cmi.2019.09.004

  • Detection of Epidemic Scarlet Fever Group A Streptococcus in Australia.

    Walker MJ, Brouwer S, Forde BM, Worthing KA, McIntyre L, Sundac L, Maloney S, Roberts LW, Barnett TC, Richter J et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019;69;7;1232-1234

    PUBMED: 30721938; DOI: 10.1093/cid/ciz099

  • Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae.

    Kwun MJ, Oggioni MR, Bentley SD, Fraser C and Croucher NJ

    Genes 2019;10;9

    PUBMED: 31540216; PMC: 6771155; DOI: 10.3390/genes10090707

  • Cell cycle regulators control mesoderm specification in human pluripotent stem cells.

    Yiangou L, Grandy RA, Osnato A, Ortmann D, Sinha S and Vallier L

    The Journal of biological chemistry 2019;294;47;17903-17914

    PUBMED: 31515269; PMC: 6879335; DOI: 10.1074/jbc.RA119.008251

  • Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

    Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M et al.

    Nature 2019;574;7776;103-107

    PUBMED: 31511700; PMC: 6894936; DOI: 10.1038/s41586-019-1555-y

  • Genome architecture and stability in the Saccharomyces cerevisiae knockout collection.

    Puddu F, Herzog M, Selivanova A, Wang S, Zhu J, Klein-Lavi S, Gordon M, Meirman R, Millan-Zambrano G, Ayestaran I et al.

    Nature 2019;573;7774;416-420

    PUBMED: 31511699; PMC: 6774800; DOI: 10.1038/s41586-019-1549-9

  • Similarities and differences in patterns of germline mutation between mice and humans.

    Lindsay SJ, Rahbari R, Kaplanis J, Keane T and Hurles ME

    Nature communications 2019;10;1;4053

    PUBMED: 31492841; PMC: 6731245; DOI: 10.1038/s41467-019-12023-w

  • Distinct Molecular Trajectories Converge to Induce Naive Pluripotency.

    Stuart HT, Stirparo GG, Lohoff T, Bates LE, Kinoshita M, Lim CY, Sousa EJ, Maskalenka K, Radzisheuskaya A, Malcolm AA et al.

    Cell stem cell 2019;25;3;388-406.e8

    PUBMED: 31422912; PMC: 6731995; DOI: 10.1016/j.stem.2019.07.009

  • Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex.

    Chiner-Oms Á, Berney M, Boinett C, González-Candelas F, Young DB, Gagneux S, Jacobs WR, Parkhill J, Cortes T and Comas I

    Nature communications 2019;10;1;3994

    PUBMED: 31488832; PMC: 6728331; DOI: 10.1038/s41467-019-11948-6

  • Unconventional forms of inheritance.

    Gapp K

    Seminars in cell & developmental biology 2019;97;84-85

    PUBMED: 31495666; DOI: 10.1016/j.semcdb.2019.08.003

  • Clonality of circulating tumor cells in breast cancer brain metastasis patients.

    Riebensahm C, Joosse SA, Mohme M, Hanssen A, Matschke J, Goy Y, Witzel I, Lamszus K, Kropidlowski J, Petersen C et al.

    Breast cancer research : BCR 2019;21;1;101

    PUBMED: 31481116; PMC: 6720990; DOI: 10.1186/s13058-019-1184-2

  • Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.

    Hicks AL, Wheeler N, Sánchez-Busó L, Rakeman JL, Harris SR and Grad YH

    PLoS computational biology 2019;15;9;e1007349

    PUBMED: 31479500; PMC: 6743791; DOI: 10.1371/journal.pcbi.1007349

  • Mucosal IgG in inflammatory bowel disease - a question of (sub)class?

    Castro-Dopico T and Clatworthy MR

    Gut microbes 2019;1-9

    PUBMED: 31480888; DOI: 10.1080/19490976.2019.1651596

  • A stromal cell niche sustains ILC2-mediated type-2 conditioning in adipose tissue.

    Rana BMJ, Jou E, Barlow JL, Rodriguez-Rodriguez N, Walker JA, Knox C, Jolin HE, Hardman CS, Sivasubramaniam M, Szeto A et al.

    The Journal of experimental medicine 2019;216;9;1999-2009

    PUBMED: 31248899; PMC: 6719433; DOI: 10.1084/jem.20190689

  • Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center.

    Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M, Cain AK, Henson SP, Gleadall N, Boinett CJ, Dougan G et al.

    Genome biology 2019;20;1;184

    PUBMED: 31477167; PMC: 6717969; DOI: 10.1186/s13059-019-1785-1

  • The ferroportin Q248H mutation protects from anemia, but not malaria or bacteremia.

    Muriuki JM, Mentzer AJ, Band G, Gilchrist JJ, Carstensen T, Lule SA, Goheen MM, Joof F, Kimita W, Mogire R et al.

    Science advances 2019;5;9;eaaw0109

    PUBMED: 31517041; PMC: 6726445; DOI: 10.1126/sciadv.aaw0109

  • A Report from a Workshop of the International Stem Cell Banking Initiative, Held in Collaboration of Global Alliance for iPSC Therapies and the Harvard Stem Cell Institute, Boston, 2017.

    Kim JH, Alderton A, Crook JM, Benvenisty N, Brandsten C, Firpo M, Harrison PW, Kawamata S, Kawase E, Kurtz A et al.

    Stem cells (Dayton, Ohio) 2019;37;9;1130-1135

    PUBMED: 31021472; DOI: 10.1002/stem.3003

  • Bacterial Population Genomics

    Corander, J., Croucher, N.J., Harris, S.R., Lees, J.A. and Tonkin‐Hill, G.

    In: Handbook of Statistical Genomics, 4th edition. Balding, D., Moltke, I. and Marioni, J. (eds.), Wiley, Hoboken, NJ, USA 2019;997-1020

    DOI: 10.1002/9781119487845.ch36

  • Challenges in measuring and understanding biological noise.

    Eling N, Morgan MD and Marioni JC

    Nature reviews. Genetics 2019;20;9;536-548

    PUBMED: 31114032; DOI: 10.1038/s41576-019-0130-6

  • Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study.

    van der Pluijm RW, Imwong M, Chau NH, Hoa NT, Thuy-Nhien NT, Thanh NV, Jittamala P, Hanboonkunupakarn B, Chutasmit K, Saelow C et al.

    The Lancet. Infectious diseases 2019;19;9;952-961

    PUBMED: 31345710; PMC: 6715822; DOI: 10.1016/S1473-3099(19)30391-3

  • Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study.

    Hamilton WL, Amato R, van der Pluijm RW, Jacob CG, Quang HH, Thuy-Nhien NT, Hien TT, Hongvanthong B, Chindavongsa K, Mayxay M et al.

    The Lancet. Infectious diseases 2019;19;9;943-951

    PUBMED: 31345709; PMC: 6715858; DOI: 10.1016/S1473-3099(19)30392-5

  • Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance.

    Lo E, Hostetler JB, Yewhalaw D, Pearson RD, Hamid MMA, Gunalan K, Kepple D, Ford A, Janies DA, Rayner JC et al.

    PLoS neglected tropical diseases 2019;13;9;e0007222

    PUBMED: 31509523; PMC: 6756552; DOI: 10.1371/journal.pntd.0007222

  • Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.

    McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL et al.

    Genome biology and evolution 2019;11;9;2678-2690

    PUBMED: 31400206; PMC: 6764479; DOI: 10.1093/gbe/evz163

  • Genomics of disease risk in globally diverse populations.

    Gurdasani D, Barroso I, Zeggini E and Sandhu MS

    Nature reviews. Genetics 2019;20;9;520-535

    PUBMED: 31235872; DOI: 10.1038/s41576-019-0144-0

  • Low RUNX3 expression alters dendritic cell function in patients with systemic sclerosis and contributes to enhanced fibrosis.

    Affandi AJ, Carvalheiro T, Ottria A, Broen JC, Bossini-Castillo L, Tieland RG, Bon LV, Chouri E, Rossato M, Mertens JS et al.

    Annals of the rheumatic diseases 2019;78;9;1249-1259

    PUBMED: 31126957; DOI: 10.1136/annrheumdis-2018-214991

  • Multi-Compartment Profiling of Bacterial and Host Metabolites Identifies Intestinal Dysbiosis and Its Functional Consequences in the Critically Ill Child.

    Wijeyesekera A, Wagner J, De Goffau M, Thurston S, Rodrigues Sabino A, Zaher S, White D, Ridout J, Peters MJ, Ramnarayan P et al.

    Critical care medicine 2019;47;9;e727-e734

    PUBMED: 31169619; PMC: 6699985; DOI: 10.1097/CCM.0000000000003841

  • Statistical Methods for Single‐Cell RNA‐Sequencing

    Andrews, T.S., Kiselev, V.Y. and Hemberg, M.

    In: Handbook of Statistical Genomics, 4th edition. Balding, D., Moltke, I. and Marioni, J. (eds.), Wiley, Hoboken, NJ, USA 2019;735-720

    DOI: 10.1002/9781119487845.ch26

  • We are falling behind on TB elimination targets: can whole-genome sequencing guide our efforts?

    Wheeler N

    Thorax 2019;74;9;833-834

    PUBMED: 31331948; PMC: 6824606; DOI: 10.1136/thoraxjnl-2019-213098

  • Porcine antiviral activity is increased by CRISPRa-SAM system.

    Jiang J, Sun Y, Xiao R, Wai K, Ahmad MJ, Khan FA, Zhou H, Li Z, Zhang Y, Zhou A and Zhang S

    Bioscience reports 2019;39;8

    PUBMED: 31371630; PMC: 6702355; DOI: 10.1042/BSR20191496

  • Resolving outbreak dynamics using approximate Bayesian computation for stochastic birth-death models.

    Lintusaari J, Blomstedt P, Rose B, Sivula T, Gutmann MU, Kaski S and Corander J

    Wellcome open research 2019;4;14

    PUBMED: 37744419; PMC: 10514576; DOI: 10.12688/wellcomeopenres.15048.2

  • SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events.

    Bergstrom EN, Huang MN, Mahto U, Barnes M, Stratton MR, Rozen SG and Alexandrov LB

    BMC genomics 2019;20;1;685

    PUBMED: 31470794; PMC: 6717374; DOI: 10.1186/s12864-019-6041-2

  • Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets.

    Ilardo M, Bose R, Meringer M, Rasulev B, Grefenstette N, Stephenson J, Freeland S, Gillams RJ, Butch CJ and Cleaves HJ

    Scientific reports 2019;9;1;12468

    PUBMED: 31462646; PMC: 6713743; DOI: 10.1038/s41598-019-47574-x

  • Screening the Saccharomyces cerevisiae non-essential gene deletion library reveals diverse mechanisms of action for antifungal plant defensins.

    Parisi K, Doyle SR, Lee E, Lowe RG, van der Weerden NL, Anderson MA and Bleackley MR

    Antimicrobial agents and chemotherapy 2019

    PUBMED: 31451498; DOI: 10.1128/AAC.01097-19

  • The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.

    Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC et al.

    Science (New York, N.Y.) 2019;365;6455

    PUBMED: 31439762; PMC: 7056351; DOI: 10.1126/science.aaw2619

  • Genomic landscape and chronological reconstruction of driver events in multiple myeloma.

    Maura F, Bolli N, Angelopoulos N, Dawson KJ, Leongamornlert D, Martincorena I, Mitchell TJ, Fullam A, Gonzalez S, Szalat R et al.

    Nature communications 2019;10;1;3835

    PUBMED: 31444325; PMC: 6707220; DOI: 10.1038/s41467-019-11680-1

  • Major subpopulations of Plasmodium falciparum in sub-Saharan Africa.

    Amambua-Ngwa A, Amenga-Etego L, Kamau E, Amato R, Ghansah A, Golassa L, Randrianarivelojosia M, Ishengoma D, Apinjoh T, Maïga-Ascofaré O et al.

    Science (New York, N.Y.) 2019;365;6455;813-816

    PUBMED: 31439796; DOI: 10.1126/science.aav5427

  • The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

    Webster G, Mullins AJ, Bettridge AS, Jones C, Cunningham-Oakes E, Connor TR, Parkhill J and Mahenthiralingam E

    Microbiology resource announcements 2019;8;34

    PUBMED: 31439701; PMC: 6706693; DOI: 10.1128/MRA.00778-19

  • FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.

    Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, Caldera S, McGeever A, Dimitrov B, King R et al.

    Nucleic acids research 2019;47;14;e83

    PUBMED: 31114866; PMC: 6698650; DOI: 10.1093/nar/gkz418

  • Heparan sulfates are critical regulators of the inhibitory megakaryocyte-platelet receptor G6b-B.

    Vögtle T, Sharma S, Mori J, Nagy Z, Semeniak D, Scandola C, Geer MJ, Smith CW, Lane J, Pollack S et al.

    eLife 2019;8

    PUBMED: 31436532; PMC: 6742478; DOI: 10.7554/eLife.46840

  • Visualization and analysis of RNA-Seq assembly graphs.

    Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M et al.

    Nucleic acids research 2019;47;14;7262-7275

    PUBMED: 31305886; PMC: 6698738; DOI: 10.1093/nar/gkz599

  • Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity.

    Petkevicius K, Virtue S, Bidault G, Jenkins B, Çubuk C, Morgantini C, Aouadi M, Dopazo J, Serlie MJ, Koulman A and Vidal-Puig A

    eLife 2019;8

    PUBMED: 31418690; PMC: 6748830; DOI: 10.7554/eLife.47990

  • Conservation of the Threatened Species, Pulsatilla vulgaris Mill. (Pasqueflower), is Aided by Reproductive System and Polyploidy.

    Gargiulo R, Worswick G, Arnold C, Pike LJ, Cowan RS, Hardwick KA, Chapman T and Fay MF

    The Journal of heredity 2019;110;5;618-628

    PUBMED: 31102445; DOI: 10.1093/jhered/esz035

  • Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome.

    Shi W, Louzada S, Grigorova M, Massaia A, Arciero E, Kibena L, Ge XJ, Chen Y, Ayub Q, Poolamets O et al.

    Human molecular genetics 2019;28;16;2785-2798

    PUBMED: 31108506; PMC: 6687947; DOI: 10.1093/hmg/ddz101

  • M3Drop: dropout-based feature selection for scRNASeq.

    Andrews TS and Hemberg M

    Bioinformatics (Oxford, England) 2019;35;16;2865-2867

    PUBMED: 30590489; PMC: 6691329; DOI: 10.1093/bioinformatics/bty1044

  • The Microbiome in Paediatric Crohn's Disease-A Longitudinal, Prospective, 
Single-Centre Study.

    Kansal S, Catto-Smith AG, Boniface K, Thomas S, Cameron DJ, Oliver M, Alex G, Kirkwood CD and Wagner J

    Journal of Crohn's & colitis 2019;13;8;1044-1054

    PUBMED: 30927743; DOI: 10.1093/ecco-jcc/jjz016

  • Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

    Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W and Thornton JM

    Genome biology 2019;20;1;146

    PUBMED: 31409373; PMC: 6693144; DOI: 10.1186/s13059-019-1753-9

  • Adaptation of host transmission cycle during Clostridium difficile speciation.

    Kumar N, Browne HP, Viciani E, Forster SC, Clare S, Harcourt K, Stares MD, Dougan G, Fairley DJ, Roberts P et al.

    Nature genetics 2019;51;9;1315-1320

    PUBMED: 31406348; DOI: 10.1038/s41588-019-0478-8

  • BBKNN: Fast Batch Alignment of Single Cell Transcriptomes.

    Polański K, Park JE, Young MD, Miao Z, Meyer KB and Teichmann SA

    Bioinformatics (Oxford, England) 2019

    PUBMED: 31400197; DOI: 10.1093/bioinformatics/btz625

  • Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.

    Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O and Beltrao P

    Molecular & cellular proteomics : MCP 2019;18;8 suppl 1;S114-S125

    PUBMED: 31239291; PMC: 6692786; DOI: 10.1074/mcp.RA118.001280

  • Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.

    Chen W, Morabito SJ, Kessenbrock K, Enver T, Meyer KB and Teschendorff AE

    Communications biology 2019;2;306

    PUBMED: 31428694; PMC: 6689007; DOI: 10.1038/s42003-019-0554-8

  • Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality.

    Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O and Choudhary JS

    Cell reports 2019;28;6;1635-1647.e5

    PUBMED: 31390575; PMC: 6693557; DOI: 10.1016/j.celrep.2019.07.019

  • STXBP1-associated neurodevelopmental disorder: a comparative study of behavioural characteristics.

    O'Brien S, Ng-Cordell E, DDD Study, Astle DE, Scerif G and Baker K

    Journal of neurodevelopmental disorders 2019;11;1;17

    PUBMED: 31387522; PMC: 6683428; DOI: 10.1186/s11689-019-9278-9

  • Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus.

    Silva Martins WF, Wilding CS, Isaacs AT, Rippon EJ, Megy K and Donnelly MJ

    Scientific reports 2019;9;1;11406

    PUBMED: 31388075; PMC: 6684662; DOI: 10.1038/s41598-019-47850-w

  • Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia.

    Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Camargo M, Díaz-Arévalo D, Roa-Molina NS, Tellez MA, Herrera G, Ríos-Chaparro DI et al.

    Scientific reports 2019;9;1;11293

    PUBMED: 31383872; PMC: 6683185; DOI: 10.1038/s41598-019-47688-2

  • Disruption of chromatin organisation causes MEF2C gene overexpression in intellectual disability: a case report.

    Yauy K, Schneider A, Ng BL, Gaillard JB, Sati S, Coubes C, Wells C, Tournaire M, Guignard T, Bouret P et al.

    BMC medical genomics 2019;12;1;116

    PUBMED: 31375103; PMC: 6679470; DOI: 10.1186/s12920-019-0558-8

  • Patient-derived xenografts and matched cell lines identify pharmacogenomic vulnerabilities in colorectal cancer.

    Lazzari L, Corti G, Picco G, Isella C, Montone M, Arcella P, Durinikova E, Zanella ER, Novara L, Barbosa F et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2019

    PUBMED: 31375513; DOI: 10.1158/1078-0432.CCR-18-3440

  • Somatic evolution and global expansion of an ancient transmissible cancer lineage.

    Baez-Ortega A, Gori K, Strakova A, Allen JL, Allum KM, Bansse-Issa L, Bhutia TN, Bisson JL, Briceño C, Castillo Domracheva A et al.

    Science (New York, N.Y.) 2019;365;6452

    PUBMED: 31371581; PMC: 7116271; DOI: 10.1126/science.aau9923

  • The impact of donor and recipient common clinical and genetic variation on estimated glomerular filtration rate in a European renal transplant population.

    Stapleton CP, Heinzel A, Guan W, van der Most PJ, van Setten J, Lord GM, Keating BJ, Israni AK, de Borst MH, Bakker SJL et al.

    American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2019;19;8;2262-2273

    PUBMED: 30920136; PMC: 6989089; DOI: 10.1111/ajt.15326

  • The Col4a2em1(IMPC)Wtsi mouse line: lessons from the Deciphering the Mechanisms of Developmental Disorders program.

    Reissig LF, Herdina AN, Rose J, Maurer-Gesek B, Lane JL, Prin F, Wilson R, Hardman E, Galli A, Tudor C et al.

    Biology open 2019;8;8

    PUBMED: 31331924; PMC: 6737985; DOI: 10.1242/bio.042895

  • The speciation and hybridization history of the genus Salmonella.

    Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D and Brisse S

    Microbial genomics 2019;5;8

    PUBMED: 31347998; PMC: 6755497; DOI: 10.1099/mgen.0.000284

  • AbRSA: A robust tool for antibody numbering.

    Li L, Chen S, Miao Z, Liu Y, Liu X, Xiao ZX and Cao Y

    Protein science : a publication of the Protein Society 2019;28;8;1524-1531

    PUBMED: 31020723; PMC: 6635766; DOI: 10.1002/pro.3633

  • De Novo Variants Disturbing the Transactivation Capacity of POU3F3 Cause a Characteristic Neurodevelopmental Disorder.

    Snijders Blok L, Kleefstra T, Venselaar H, Maas S, Kroes HY, Lachmeijer AMA, van Gassen KLI, Firth HV, Tomkins S, Bodek S et al.

    American journal of human genetics 2019;105;2;403-412

    PUBMED: 31303265; PMC: 6698880; DOI: 10.1016/j.ajhg.2019.06.007

  • Expanded potential stem cell media as a tool to study human developmental hematopoiesis in vitro.

    Wilkinson AC, Ryan DJ, Kucinski I, Wang W, Yang J, Nestorowa S, Diamanti E, Tsang JC, Wang J, Campos LS et al.

    Experimental hematology 2019;76;1-12.e5

    PUBMED: 31326613; DOI: 10.1016/j.exphem.2019.07.003

  • Genetically modulated educational attainment and coronary disease risk.

    Zeng L, Ntalla I, Kessler T, Kastrati A, Erdmann J, UK Biobank CardioMetabolic Consortium CHD Working Group, Danesh J, Watkins H, Samani NJ, Deloukas P and Schunkert H

    European heart journal 2019;40;29;2413-2420

    PUBMED: 31170283; PMC: 6669407; DOI: 10.1093/eurheartj/ehz328

  • Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa.

    Watson HJ, Yilmaz Z, Thornton LM, Hübel C, Coleman JRI, Gaspar HA, Bryois J, Hinney A, Leppä VM, Mattheisen M et al.

    Nature genetics 2019;51;8;1207-1214

    PUBMED: 31308545; PMC: 6779477; DOI: 10.1038/s41588-019-0439-2

  • Genome-wide screening of mouse knockouts reveals novel genes required for normal integumentary and oculocutaneous structure and function.

    Moore BA, Flenniken AM, Clary D, Moshiri AS, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M et al.

    Scientific reports 2019;9;1;11211

    PUBMED: 31371754; PMC: 6672016; DOI: 10.1038/s41598-019-47286-2

  • Large-scale neuroanatomical study uncovers 198 gene associations in mouse brain morphogenesis.

    Collins SC, Mikhaleva A, Vrcelj K, Vancollie VE, Wagner C, Demeure N, Whitley H, Kannan M, Balz R, Anthony LFE et al.

    Nature communications 2019;10;1;3465

    PUBMED: 31371714; PMC: 6671969; DOI: 10.1038/s41467-019-11431-2

  • Multilocus Analysis Resolves the European Finch Epidemic Strain of Trichomonas gallinae and Suggests Introgression from Divergent Trichomonads.

    Alrefaei AF, Low R, Hall N, Jardim R, Dávila A, Gerhold R, John S, Steinbiss S, Cunningham AA, Lawson B et al.

    Genome biology and evolution 2019;11;8;2391-2402

    PUBMED: 31364699; PMC: 6735722; DOI: 10.1093/gbe/evz164

  • Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways.

    Lam M, Hill WD, Trampush JW, Yu J, Knowles E, Davies G, Stahl E, Huckins L, Liewald DC, Djurovic S et al.

    American journal of human genetics 2019;105;2;334-350

    PUBMED: 31374203; PMC: 6699140; DOI: 10.1016/j.ajhg.2019.06.012

  • Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.

    Blane B, Raven KE, Leek D, Brown N, Parkhill J and Peacock SJ

    The Journal of antimicrobial chemotherapy 2019;74;8;2153-2156

    PUBMED: 31039248; PMC: 6640301; DOI: 10.1093/jac/dkz170

  • Recombination of the Phase-Variable spnIII Locus Is Independent of All Known Pneumococcal Site-Specific Recombinases.

    De Ste Croix M, Chen KY, Vacca I, Manso AS, Johnston C, Polard P, Kwun MJ, Bentley SD, Croucher NJ, Bayliss CD et al.

    Journal of bacteriology 2019;201;15

    PUBMED: 31085693; PMC: 6620402; DOI: 10.1128/JB.00233-19

  • Refugia and anthelmintic resistance: Concepts and challenges.

    Hodgkinson JE, Kaplan RM, Kenyon F, Morgan ER, Park AW, Paterson S, Babayan SA, Beesley NJ, Britton C, Chaudhry U et al.

    International journal for parasitology. Drugs and drug resistance 2019;10;51-57

    PUBMED: 31125837; PMC: 6531808; DOI: 10.1016/j.ijpddr.2019.05.001

  • Sequencing cell-type-specific transcriptomes with SLAM-ITseq.

    Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL and Miska EA

    Nature protocols 2019;14;8;2261-2278

    PUBMED: 31243395; PMC: 6997029; DOI: 10.1038/s41596-019-0179-x

  • Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis.

    MacFadyen AC, Leroy S, Harrison EM, Parkhill J, Holmes MA and Paterson GK

    International journal of systematic and evolutionary microbiology 2019;69;8;2208-2213

    PUBMED: 31225789; DOI: 10.1099/ijsem.0.003416

  • Very low-depth whole-genome sequencing in complex trait association studies.

    Gilly A, Southam L, Suveges D, Kuchenbaecker K, Moore R, Melloni GEM, Hatzikotoulas K, Farmaki AE, Ritchie G, Schwartzentruber J et al.

    Bioinformatics (Oxford, England) 2019;35;15;2555-2561

    PUBMED: 30576415; PMC: 6662288; DOI: 10.1093/bioinformatics/bty1032

  • Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes.

    Lucas ER, Miles A, Harding NJ, Clarkson CS, Lawniczak MKN, Kwiatkowski DP, Weetman D, Donnelly MJ and Anopheles gambiae 1000 Genomes Consortium

    Genome research 2019;29;8;1250-1261

    PUBMED: 31345938; PMC: 6673711; DOI: 10.1101/gr.245795.118

  • Human placenta has no microbiome but can contain potential pathogens.

    de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS and Smith GCS

    Nature 2019;572;7769;329-334

    PUBMED: 31367035; PMC: 6697540; DOI: 10.1038/s41586-019-1451-5

  • Relating evolutionary selection and mutant clonal dynamics in normal epithelia.

    Hall MWJ, Jones PH and Hall BA

    Journal of the Royal Society, Interface 2019;16;156;20190230

    PUBMED: 31362624; PMC: 6685019; DOI: 10.1098/rsif.2019.0230

  • Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.

    David S, Reuter S, Harris SR, Glasner C, Feltwell T, Argimon S, Abudahab K, Goater R, Giani T, Errico G et al.

    Nature microbiology 2019;4;11;1919-1929

    PUBMED: 31358985; DOI: 10.1038/s41564-019-0492-8

  • Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors.

    Segal JM, Kent D, Wesche DJ, Ng SS, Serra M, Oulès B, Kar G, Emerton G, Blackford SJI, Darmanis S et al.

    Nature communications 2019;10;1;3350

    PUBMED: 31350390; PMC: 6659636; DOI: 10.1038/s41467-019-11266-x

  • NPM1c alters FLT3-D835Y localization and signaling in acute myeloid leukemia.

    Rudorf A, Müller TA, Klingeberg C, Kreutmair S, Poggio T, Gorantla SP, Rückert T, Schmitt-Graeff A, Gengenbacher A, Paschka P et al.

    Blood 2019;134;4;383-388

    PUBMED: 31186273; PMC: 6659255; DOI: 10.1182/blood.2018883140

  • USE-Net: Incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets

    Rundo L, Han C, Nagano Y, Zhang J, Hataya R, Militello C, Tangherloni A and Nobile MS

    Neurocomputing 2019;365;31-43

    DOI: 10.1016/j.neucom.2019.07.006

  • Efficiently inferring the demographic history of many populations with allele count data.

    Kamm J, Terhorst J, Durbin R and Song YS

    Journal of the American Statistical Association 2019;115;531;1472-1487

    PUBMED: 33012903; PMC: 7531012; DOI: 10.1080/01621459.2019.1635482

  • Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages.

    Beale MA, Marks M, Sahi SK, Tantalo LC, Nori AV, French P, Lukehart SA, Marra CM and Thomson NR

    Nature communications 2019;10;1;3255

    PUBMED: 31332179; PMC: 6646400; DOI: 10.1038/s41467-019-11216-7

  • ZRANB3 is an African-specific type 2 diabetes locus associated with beta-cell mass and insulin response.

    Adeyemo AA, Zaghloul NA, Chen G, Doumatey AP, Leitch CC, Hostelley TL, Nesmith JE, Zhou J, Bentley AR, Shriner D et al.

    Nature communications 2019;10;1;3195

    PUBMED: 31324766; PMC: 6642147; DOI: 10.1038/s41467-019-10967-7

  • Outcompeting p53-Mutant Cells in the Normal Esophagus by Redox Manipulation.

    Fernandez-Antoran D, Piedrafita G, Murai K, Ong SH, Herms A, Frezza C and Jones PH

    Cell stem cell 2019;25;3;329-341.e6

    PUBMED: 31327664; PMC: 6739485; DOI: 10.1016/j.stem.2019.06.011

  • Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets.

    Newell F, Kong Y, Wilmott JS, Johansson PA, Ferguson PM, Cui C, Li Z, Kazakoff SH, Burke H, Dodds TJ et al.

    Nature communications 2019;10;1;3163

    PUBMED: 31320640; PMC: 6639323; DOI: 10.1038/s41467-019-11107-x

  • Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.

    Romagnoni A, Jégou S, Van Steen K, Wainrib G, Hugot JP and International Inflammatory Bowel Disease Genetics Consortium (IIBDGC)

    Scientific reports 2019;9;1;10351

    PUBMED: 31316157; PMC: 6637191; DOI: 10.1038/s41598-019-46649-z

  • Establishment and equilibrium levels of deleterious mutations in large populations.

    Viljoen JW, de Villiers JP, van Zyl AJ, Mezzavilla M and Pepper MS

    Scientific reports 2019;9;1;10384

    PUBMED: 31316137; PMC: 6637196; DOI: 10.1038/s41598-019-46803-7

  • Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD.

    Seni J, Mshana SE, Msigwa F, Iddi S, Mazigo H, Parkhill J, Holmes MA and Paterson GK

    Journal of global antimicrobial resistance 2019

    PUBMED: 31323428; DOI: 10.1016/j.jgar.2019.07.006

  • Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India.

    Munir A, Kumar N, Ramalingam SB, Tamilzhalagan S, Shanmugam SK, Palaniappan AN, Nair D, Priyadarshini P, Natarajan M, Tripathy S et al.

    Scientific reports 2019;9;1;10283

    PUBMED: 31311987; PMC: 6635374; DOI: 10.1038/s41598-019-46756-x

  • PAPSS2-related brachyolmia: Clinical and radiological phenotype in 18 new cases.

    Bownass L, Abbs S, Armstrong R, Baujat G, Behzadi G, Berentsen RD, Burren C, Calder A, Cormier-Daire V, Newbury-Ecob R et al.

    American journal of medical genetics. Part A 2019;179;9;1884-1894

    PUBMED: 31313512; DOI: 10.1002/ajmg.a.61282

  • Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow.

    Walker JA, Clark PA, Crisp A, Barlow JL, Szeto A, Ferreira ACF, Rana BMJ, Jolin HE, Rodriguez-Rodriguez N, Sivasubramaniam M et al.

    Immunity 2019;51;1;104-118.e7

    PUBMED: 31128961; PMC: 6642165; DOI: 10.1016/j.immuni.2019.05.002

  • Genome-wide CRISPR-Cas9 screening in mammalian cells.

    Yu JSL and Yusa K

    Methods (San Diego, Calif.) 2019;164-165;29-35

    PUBMED: 31034882; DOI: 10.1016/j.ymeth.2019.04.015

  • The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria.

    Zhu SJ, Hendry JA, Almagro-Garcia J, Pearson RD, Amato R, Miles A, Weiss DJ, Lucas TC, Nguyen M, Gething PW et al.

    eLife 2019;8

    PUBMED: 31298657; PMC: 6684230; DOI: 10.7554/eLife.40845

  • Viral coinfection analysis using a MinHash toolkit.

    Dawson ET, Wagner S, Roberson D, Yeager M, Boland J, Garrison E, Chanock S, Schiffman M, Raine-Bennett T, Lorey T et al.

    BMC bioinformatics 2019;20;1;389

    PUBMED: 31299914; PMC: 6626348; DOI: 10.1186/s12859-019-2918-y

  • Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.

    Agoti CN, Phan MVT, Munywoki PK, Githinji G, Medley GF, Cane PA, Kellam P, Cotten M and Nokes DJ

    Scientific reports 2019;9;1;10076

    PUBMED: 31296922; PMC: 6624209; DOI: 10.1038/s41598-019-46509-w

  • Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.

    Colonna V, D'Agostino N, Garrison E, Albrechtsen A, Meisner J, Facchiano A, Cardi T and Tripodi P

    Scientific reports 2019;9;1;10067

    PUBMED: 31296904; PMC: 6624249; DOI: 10.1038/s41598-019-46136-5

  • Mechanisms of Progression of Myeloid Preleukemia to Transformed Myeloid Leukemia in Children with Down Syndrome.

    Labuhn M, Perkins K, Matzk S, Varghese L, Garnett C, Papaemmanuil E, Metzner M, Kennedy A, Amstislavskiy V, Risch T et al.

    Cancer cell 2019;36;2;123-138.e10

    PUBMED: 31303423; PMC: 6863161; DOI: 10.1016/j.ccell.2019.06.007

  • Novel Methicillin-Resistant Staphylococcus aureus CC8 Clone Identified in a Hospital Setting in Armenia.

    Jamrozy D, Misra R, Xu Z, Ter-Stepanyan MM, Kocharyan KS, Cave R, Hambardzumyan AD and Mkrtchyan HV

    Frontiers in microbiology 2019;10;1592

    PUBMED: 31354680; PMC: 6635598; DOI: 10.3389/fmicb.2019.01592

  • IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.

    Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT and de la Roche M

    EMBO reports 2019;e47379

    PUBMED: 31283095; DOI: 10.15252/embr.201847379

  • A practical guide for mutational signature analysis in hematological malignancies.

    Maura F, Degasperi A, Nadeu F, Leongamornlert D, Davies H, Moore L, Royo R, Ziccheddu B, Puente XS, Avet-Loiseau H et al.

    Nature communications 2019;10;1;2969

    PUBMED: 31278357; PMC: 6611883; DOI: 10.1038/s41467-019-11037-8

  • Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data.

    Wright CF, Prigmore E, Rajan D, Handsaker J, McRae J, Kaplanis J, Fitzgerald TW, FitzPatrick DR, Firth HV and Hurles ME

    Nature communications 2019;10;1;2985

    PUBMED: 31278258; PMC: 6611863; DOI: 10.1038/s41467-019-11059-2

  • High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

    Pensar J, Xu Y, Puranen S, Pesonen M, Kabashima Y and Corander J

    Computational Statistics & Data Analysis 2019;141;62-76

    DOI: 10.1016/j.csda.2019.06.012

  • NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs.

    Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaitė L, Garone C, Shin S, Kim JS, Frye M et al.

    Nucleic acids research 2019

    PUBMED: 31276587; DOI: 10.1093/nar/gkz559

  • Application of single-cell RNA sequencing methodologies in understanding haematopoiesis and immunology.

    Ranzoni AM, Strzelecka PM and Cvejic A

    Essays in biochemistry 2019;63;2;217-225

    PUBMED: 31186287; PMC: 6610449; DOI: 10.1042/EBC20180072

  • Complete Whole-Genome Sequences of Two Raoultella terrigena Strains, NCTC 13097 and NCTC 13098, Isolated from Human Cases.

    Fazal MA, Alexander S, Grayson NE, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J and Russell JE

    Microbiology resource announcements 2019;8;27

    PUBMED: 31270187; PMC: 6606901; DOI: 10.1128/MRA.00239-19

  • Genes for Good: Engaging the Public in Genetics Research via Social Media.

    Brieger K, Zajac GJM, Pandit A, Foerster JR, Li KW, Annis AC, Schmidt EM, Clark CP, McMorrow K, Zhou W et al.

    American journal of human genetics 2019;105;1;65-77

    PUBMED: 31204010; PMC: 6612519; DOI: 10.1016/j.ajhg.2019.05.006

  • Determining antimicrobial susceptibility in Salmonella enterica serovar Typhimurium through whole genome sequencing: a comparison against multiple phenotypic susceptibility testing methods.

    Mensah N, Tang Y, Cawthraw S, AbuOun M, Fenner J, Thomson NR, Mather AE and Petrovska-Holmes L

    BMC microbiology 2019;19;1;148

    PUBMED: 31266463; PMC: 6604184; DOI: 10.1186/s12866-019-1520-9

  • The clinical application of gene editing: ethical and social issues.

    Ormond KE, Bombard Y, Bonham VL, Hoffman-Andrews L, Howard H, Isasi R, Musunuru K, Riggan KA, Michie M and Allyse M

    Personalized medicine 2019;16;4;337-350

    PUBMED: 31331245; DOI: 10.2217/pme-2018-0155

  • The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.

    Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga FA, Timens W, Koppelman GH, Budinger GRS et al.

    American journal of respiratory cell and molecular biology 2019;61;1;31-41

    PUBMED: 30995076; PMC: 6604220; DOI: 10.1165/rcmb.2018-0416TR

  • A novel framework for MR image segmentation and quantification by using MedGA.

    Rundo L, Tangherloni A, Cazzaniga P, Nobile MS, Russo G, Gilardi MC, Vitabile S, Mauri G, Besozzi D and Militello C

    Computer methods and programs in biomedicine 2019;176;159-172

    PUBMED: 31200903; DOI: 10.1016/j.cmpb.2019.04.016

  • A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans.

    Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L et al.

    Science advances 2019;5;7;eaax0396

    PUBMED: 31392275; PMC: 6669018; DOI: 10.1126/sciadv.aax0396

  • A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort.

    Telele NF, Kalu AW, Gebre-Selassie S, Fekade D, Marrone G, Grossmann S, Neogi U, Tegbaru B and Sönnerborg A

    BMC infectious diseases 2019;19;1;569

    PUBMED: 31262272; PMC: 6604127; DOI: 10.1186/s12879-019-4196-8

  • Antibody Reactivity to Merozoite Antigens in Ghanaian Adults Correlates With Growth Inhibitory Activity Against Plasmodium falciparum in Culture.

    Mensah-Brown HE, Aspeling-Jones H, Delimini RK, Asante KP, Amlabu E, Bah SY, Beeson JG, Wright GJ, Conway DJ and Awandare GA

    Open forum infectious diseases 2019;6;7;ofz254

    PUBMED: 31294045; PMC: 6611546; DOI: 10.1093/ofid/ofz254

  • Cardiac disorders and structural brain abnormalities are commonly associated with hypospadias in children with neurodevelopmental disorders.

    Gazdagh GE, Wang C, McGowan R, Tobias ES, Ahmed SF and DDD Study

    Clinical dysmorphology 2019;28;3;114-119

    PUBMED: 30921090; DOI: 10.1097/MCD.0000000000000275

  • CRISPR-Knockout Screen Identifies Dmap1 as a Regulator of Chemically Induced Reprogramming and Differentiation of Cardiac Progenitors.

    Yu JSL, Palano G, Lim C, Moggio A, Drowley L, Plowright AT, Bohlooly-Y M, Rosen BS, Hansson EM, Wang QD and Yusa K

    Stem cells (Dayton, Ohio) 2019;37;7;958-972

    PUBMED: 30932271; DOI: 10.1002/stem.3012

  • Differences in Signaling Patterns on PI3K Inhibition Reveal Context Specificity in KRAS-Mutant Cancers.

    Stewart A, Coker EA, Pölsterl S, Georgiou A, Minchom AR, Carreira S, Cunningham D, O'Brien ME, Raynaud FI, de Bono JS et al.

    Molecular cancer therapeutics 2019;18;8;1396-1404

    PUBMED: 31262731; PMC: 6679718; DOI: 10.1158/1535-7163.MCT-18-0727

  • Domestication of Campylobacter jejuni NCTC 11168.

    Pascoe B, Williams LK, Calland JK, Meric G, Hitchings MD, Dyer M, Ryder J, Shaw S, Lopes BS, Chintoan-Uta C et al.

    Microbial genomics 2019;5;7

    PUBMED: 31310201; DOI: 10.1099/mgen.0.000279

  • Dual diagnosis causing severe phenotype in a patient with Angelman syndrome.

    Kanani F, Mordekar S, Parker MJ, Balasubramanian M and DDD Study

    Clinical dysmorphology 2019;28;3;160-163

    PUBMED: 30998607; DOI: 10.1097/MCD.0000000000000280

  • Exome sequencing identifies a novel missense variant in CTSC causing nonsyndromic aggressive periodontitis.

    Molitor A, Prud'homme T, Miao Z, Conrad S, Bloch-Zupan A, Pichot A, Hanauer A, Isidor B, Bahram S and Carapito R

    Journal of human genetics 2019;64;7;689-694

    PUBMED: 31068678; DOI: 10.1038/s10038-019-0615-3

  • Genome-wide Association Study of Change in Fasting Glucose over time in 13,807 non-diabetic European Ancestry Individuals.

    Liu CT, Merino J, Rybin D, DiCorpo D, Benke KS, Bragg-Gresham JL, Canouil M, Corre T, Grallert H, Isaacs A et al.

    Scientific reports 2019;9;1;9439

    PUBMED: 31263163; PMC: 6602949; DOI: 10.1038/s41598-019-45823-7

  • Genome-wide association study of type 2 diabetes in Africa.

    Chen J, Sun M, Adeyemo A, Pirie F, Carstensen T, Pomilla C, Doumatey AP, Chen G, Young EH, Sandhu M et al.

    Diabetologia 2019;62;7;1204-1211

    PUBMED: 31049640; PMC: 6560001; DOI: 10.1007/s00125-019-4880-7

  • Genomics: the power, potential and pitfalls of the new technologies and how they are transforming healthcare.

    Josephs KS, Berner A, George A, Scott RH, Health Education England's Genomic Education Programme, Firth HV and Tatton-Brown K

    Clinical medicine (London, England) 2019;19;4;269-272

    PUBMED: 31308101; PMC: 6752247; DOI: 10.7861/clinmedicine.19-4-269

  • How well do we understand the basis of classic selective sweeps in humans?

    Szpak M, Xue Y, Ayub Q and Tyler-Smith C

    FEBS letters 2019;593;13;1431-1448

    PUBMED: 31116407; DOI: 10.1002/1873-3468.13447

  • Identification and validation of two peptide markers for the recognition of Clostridioides difficile MLST-1 and MLST-11 by MALDI-MS.

    Corver J, Sen J, Hornung BVH, Mertens BJ, Berssenbrugge EKL, Harmanus C, Sanders IMJG, Kumar N, Lawley TD, Kuijper EJ et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019;25;7;904.e1-904.e7

    PUBMED: 31130255; DOI: 10.1016/j.cmi.2018.10.008

  • Identification of a new panel of reference genes to study pairing-dependent gene expression in Schistosoma mansoni.

    Haeberlein S, Angrisano A, Quack T, Lu Z, Kellershohn J, Blohm A, Grevelding CG and Hahnel SR

    International journal for parasitology 2019;49;8;615-624

    PUBMED: 31136746; DOI: 10.1016/j.ijpara.2019.01.006

  • Infection by Brucella melitensis or Brucella papionis modifies essential physiological functions of human trophoblasts.

    García-Méndez KB, Hielpos SM, Soler-Llorens PF, Arce-Gorvel V, Hale C, Gorvel JP, O'Callaghan D and Keriel A

    Cellular microbiology 2019;21;7;e13019

    PUBMED: 30817085; DOI: 10.1111/cmi.13019

  • Investigation of the role of typhoid toxin in acute typhoid fever in a human challenge model.

    Gibani MM, Jones E, Barton A, Jin C, Meek J, Camara S, Galal U, Heinz E, Rosenberg-Hasson Y, Obermoser G et al.

    Nature medicine 2019;25;7;1082-1088

    PUBMED: 31270506; PMC: 6892374; DOI: 10.1038/s41591-019-0505-4

  • Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.

    Renaud G, Hanghøj K, Korneliussen TS, Willerslev E and Orlando L

    Genetics 2019;212;3;587-614

    PUBMED: 31088861; PMC: 6614887; DOI: 10.1534/genetics.119.302057

  • Mendelian Randomization Analysis of Hemoglobin A1c as a Risk Factor for Coronary Artery Disease.

    Leong A, Chen J, Wheeler E, Hivert MF, Liu CT, Merino J, Dupuis J, Tai ES, Rotter JI, Florez JC et al.

    Diabetes care 2019;42;7;1202-1208

    PUBMED: 30659074; DOI: 10.2337/dc18-1712

  • Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010-2018.

    Arana A, Jere KC, Chaguza C, Montes M, Alkorta M, Iturriza-Gomara M and Cilla G

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2019;71;67-75

    PUBMED: 30905774; DOI: 10.1016/j.meegid.2019.03.016

  • POT1 germline mutations but not TERT promoter mutations are implicated in melanoma susceptibility in a large cohort of Spanish melanoma families.

    Potrony M, Puig-Butille JA, Ribera-Sola M, Iyer V, Robles-Espinoza CD, Aguilera P, Carrera C, Malvehy J, Badenas C, Landi MT et al.

    The British journal of dermatology 2019;181;1;105-113

    PUBMED: 30451293; PMC: 6526091; DOI: 10.1111/bjd.17443

  • Relationship between disease biology and clinical phenotype in myeloproliferative neoplasms

    Nangalia, J.

    HemaSphere 2019;1;S2;146-148

    PMC: 8925713; DOI: 10.1097/HS9.0000000000000207

  • HNF4A Haploinsufficiency in MODY1 Abrogates Liver and Pancreas Differentiation from Patient-Derived Induced Pluripotent Stem Cells.

    Ng NHJ, Jasmen JB, Lim CS, Lau HH, Krishnan VG, Kadiwala J, Kulkarni RN, Ræder H, Vallier L, Hoon S and Teo AKK

    iScience 2019;16;192-205

    PUBMED: 31195238; PMC: 6562146; DOI: 10.1016/j.isci.2019.05.032

  • Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies.

    Alanine DGW, Quinkert D, Kumarasingha R, Mehmood S, Donnellan FR, Minkah NK, Dadonaite B, Diouf A, Galaway F, Silk SE et al.

    Cell 2019;178;1;216-228.e21

    PUBMED: 31204103; PMC: 6602525; DOI: 10.1016/j.cell.2019.05.025

  • Common and distinct transcriptional signatures of mammalian embryonic lethality.

    Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E et al.

    Nature communications 2019;10;1;2792

    PUBMED: 31243271; PMC: 6594971; DOI: 10.1038/s41467-019-10642-x

  • CTCF variants in 39 individuals with a variable neurodevelopmental disorder broaden the mutational and clinical spectrum.

    Konrad EDH, Nardini N, Caliebe A, Nagel I, Young D, Horvath G, Santoro SL, Shuss C, Ziegler A, Bonneau D et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;12;2723-2733

    PUBMED: 31239556; PMC: 6892744; DOI: 10.1038/s41436-019-0585-z

  • Evaluating 18s-rRNA LAMP and selective whole genome amplification (sWGA) assay in detecting asymptomatic Plasmodium falciparum infections in blood donors.

    Aninagyei E, Smith-Graham S, Boye A, Egyir-Yawson A and Acheampong DO

    Malaria journal 2019;18;1;214

    PUBMED: 31234871; PMC: 6591871; DOI: 10.1186/s12936-019-2850-7

  • Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus.

    Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamrozy D, Reuter S, Lovering A et al.

    Nature microbiology 2019;4;10;1680-1691

    PUBMED: 31235959; PMC: 7611363; DOI: 10.1038/s41564-019-0471-0

  • SOCS2 is part of a highly prognostic 4-gene signature in AML and promotes disease aggressiveness.

    Nguyen CH, Glüxam T, Schlerka A, Bauer K, Grandits AM, Hackl H, Dovey O, Zöchbauer-Müller S, Cooper JL, Vassiliou GS et al.

    Scientific reports 2019;9;1;9139

    PUBMED: 31235852; PMC: 6591510; DOI: 10.1038/s41598-019-45579-0

  • Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations.

    Kaplanis J, Akawi N, Gallone G, McRae JF, Prigmore E, Wright CF, Fitzpatrick DR, Firth HV, Barrett JC, Hurles ME and Deciphering Developmental Disorders study

    Genome research 2019;29;7;1047-1056

    PUBMED: 31227601; PMC: 6633265; DOI: 10.1101/gr.239756.118

  • Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839.

    Fazal MA, Alexander S, Grayson NE, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J and Russell JE

    Microbiology resource announcements 2019;8;25

    PUBMED: 31221642; PMC: 6588363; DOI: 10.1128/MRA.00232-19

  • Fast hierarchical Bayesian analysis of population structure.

    Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW and Corander J

    Nucleic acids research 2019;47;11;5539-5549

    PUBMED: 31076776; PMC: 6582336; DOI: 10.1093/nar/gkz361

  • Development of Personalized Therapeutic Strategies by Targeting Actionable Vulnerabilities in Metastatic and Chemotherapy-Resistant Breast Cancer PDXs.

    Punzi S, Meliksetian M, Riva L, Marocchi F, Pruneri G, Criscitiello C, Orsi F, Spaggiari L, Casiraghi M, Della Vigna P et al.

    Cells 2019;8;6

    PUBMED: 31216647; PMC: 6627522; DOI: 10.3390/cells8060605

  • Genetic Risk Score for Coronary Disease Identifies Predispositions to Cardiovascular and Noncardiovascular Diseases.

    Ntalla I, Kanoni S, Zeng L, Giannakopoulou O, Danesh J, Watkins H, Samani NJ, Deloukas P, Schunkert H and UK Biobank CardioMetabolic Consortium CHD Working Group

    Journal of the American College of Cardiology 2019;73;23;2932-2942

    PUBMED: 31196449; DOI: 10.1016/j.jacc.2019.03.512

  • Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

    Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R et al.

    Nature communications 2019;10;1;2674

    PUBMED: 31209238; PMC: 6572829; DOI: 10.1038/s41467-019-09799-2

  • Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns.

    Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA et al.

    Nature communications 2019;10;1;2665

    PUBMED: 31209259; PMC: 6572796; DOI: 10.1038/s41467-019-10121-3

  • A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa.

    Haber M, Jones AL, Connell BA, Asan, Arciero E, Yang H, Thomas MG, Xue Y and Tyler-Smith C

    Genetics 2019;212;4;1421-1428

    PUBMED: 31196864; PMC: 6707464; DOI: 10.1534/genetics.119.302368

  • DNA methylation profiling allows for characterization of atrial and ventricular cardiac tissues and hiPSC-CMs.

    Hoff K, Lemme M, Kahlert AK, Runde K, Audain E, Schuster D, Scheewe J, Attmann T, Pickardt T, Caliebe A et al.

    Clinical epigenetics 2019;11;1;89

    PUBMED: 31186048; PMC: 6560887; DOI: 10.1186/s13148-019-0679-0

  • Putative novel cps loci in a large global collection of pneumococci.

    van Tonder AJ, Gladstone RA, Lo SW, Nahm MH, du Plessis M, Cornick J, Kwambana-Adams B, Madhi SA, Hawkins PA, Benisty R et al.

    Microbial genomics 2019;5;7

    PUBMED: 31184299; PMC: 6700660; DOI: 10.1099/mgen.0.000274

  • Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study.

    Lo SW, Gladstone RA, van Tonder AJ, Lees JA, du Plessis M, Benisty R, Givon-Lavi N, Hawkins PA, Cornick JE, Kwambana-Adams B et al.

    The Lancet. Infectious diseases 2019;19;7;759-769

    PUBMED: 31196809; PMC: 7641901; DOI: 10.1016/S1473-3099(19)30297-X

  • A novel NAA10 p.(R83H) variant with impaired acetyltransferase activity identified in two boys with ID and microcephaly.

    Ree R, Geithus AS, Tørring PM, Sørensen KP, Damkjær M, DDD study, Lynch SA and Arnesen T

    BMC medical genetics 2019;20;1;101

    PUBMED: 31174490; PMC: 6554967; DOI: 10.1186/s12881-019-0803-1

  • An unusual Burkholderia gladioli double chain-initiating nonribosomal peptide synthetase assembles 'fungal' icosalide antibiotics.

    Jenner M, Jian X, Dashti Y, Masschelein J, Hobson C, Roberts DM, Jones C, Harris S, Parkhill J, Raja HA et al.

    Chemical science 2019;10;21;5489-5494

    PUBMED: 31293732; PMC: 6553374; DOI: 10.1039/c8sc04897e

  • ZMYM2 inhibits NANOG-mediated reprogramming.

    Lawrence M, Theunissen TW, Lombard P, Adams DJ and Silva JCR

    Wellcome open research 2019;4;88

    PUBMED: 31363497; PMC: 6640293; DOI: 10.12688/wellcomeopenres.15250.1

  • The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.

    Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X et al.

    G3 (Bethesda, Md.) 2019;9;6;1795-1805

    PUBMED: 30996023; PMC: 6553538; DOI: 10.1534/g3.119.400071

  • The population history of northeastern Siberia since the Pleistocene.

    Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G et al.

    Nature 2019;570;7760;182-188

    PUBMED: 31168093; DOI: 10.1038/s41586-019-1279-z

  • Derivation and maintenance of mouse haploid embryonic stem cells.

    Elling U, Woods M, Forment JV, Fu B, Yang F, Ng BL, Vicente JR, Adams DJ, Doe B, Jackson SP et al.

    Nature protocols 2019;14;7;1991-2014

    PUBMED: 31160788; PMC: 6997032; DOI: 10.1038/s41596-019-0169-z

  • Establishment of porcine and human expanded potential stem cells.

    Gao X, Nowak-Imialek M, Chen X, Chen D, Herrmann D, Ruan D, Chen ACH, Eckersley-Maslin MA, Ahmad S, Lee YL et al.

    Nature cell biology 2019;21;6;687-699

    PUBMED: 31160711; PMC: 7035105; DOI: 10.1038/s41556-019-0333-2

  • The gene regulatory basis of genetic compensation during neural crest induction.

    Dooley CM, Wali N, Sealy IM, White RJ, Stemple DL, Collins JE and Busch-Nentwich EM

    PLoS genetics 2019;15;6;e1008213

    PUBMED: 31199790; PMC: 6594659; DOI: 10.1371/journal.pgen.1008213

  • Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

    Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA, Towers RJ, Duchêne S, Smeesters PR, Frost HR, Price DJ et al.

    Nature genetics 2019;51;6;1035-1043

    PUBMED: 31133745; PMC: 6650292; DOI: 10.1038/s41588-019-0417-8

  • Best Practices for Illumina Library Preparation.

    Bronner IF and Quail MA

    Current protocols in human genetics 2019;102;1;e86

    PUBMED: 31216112; DOI: 10.1002/cphg.86

  • Characterization of paralogous uncx transcription factor encoding genes in zebrafish.

    Nittoli V, Fortunato AE, Fasano G, Coppola U, Gentile A, Maiella S, Langellotto F, Porreca I, De Paolo R, Marino R et al.

    Gene: X 2019;2;100011

    PUBMED: 31193955; PMC: 6543554; DOI: 10.1016/j.gene.2019.100011

  • Clinical Implications of Identifying Pathogenic Variants in Individuals With Thoracic Aortic Dissection.

    Wolford BN, Hornsby WE, Guo D, Zhou W, Lin M, Farhat L, McNamara J, Driscoll A, Wu X, Schmidt EM et al.

    Circulation. Genomic and precision medicine 2019;12;6;e002476

    PUBMED: 31211624; PMC: 6582991; DOI: 10.1161/CIRCGEN.118.002476

  • Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.

    Czechowska K, Lannigan J, Wang L, Arcidiacono J, Ashhurst TM, Barnard RM, Bauer S, Bispo C, Bonilla DL, Brinkman RR et al.

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2019;95;6;598-644

    PUBMED: 31207046; DOI: 10.1002/cyto.a.23777

  • Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana.

    Aldrich C, Hartman H, Feasey N, Chattaway MA, Dekker D, Al-Emran HM, Larkin L, McCormick J, Sarpong N, Le Hello S et al.

    PLoS neglected tropical diseases 2019;13;6;e0007485

    PUBMED: 31220112; PMC: 6605661; DOI: 10.1371/journal.pntd.0007485

  • Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls.

    Flannick J, Mercader JM, Fuchsberger C, Udler MS, Mahajan A, Wessel J, Teslovich TM, Caulkins L, Koesterer R, Barajas-Olmos F et al.

    Nature 2019;570;7759;71-76

    PUBMED: 31118516; PMC: 6699738; DOI: 10.1038/s41586-019-1231-2

  • Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria.

    Mullins AJ, Murray JAH, Bull MJ, Jenner M, Jones C, Webster G, Green AE, Neill DR, Connor TR, Parkhill J et al.

    Nature microbiology 2019;4;6;996-1005

    PUBMED: 30833726; PMC: 6544543; DOI: 10.1038/s41564-019-0383-z

  • Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648.

    Schaufler K, Semmler T, Wieler LH, Trott DJ, Pitout J, Peirano G, Bonnedahl J, Dolejska M, Literak I, Fuchs S et al.

    Antimicrobial agents and chemotherapy 2019;63;6

    PUBMED: 30885899; PMC: 6535536; DOI: 10.1128/AAC.00243-19

  • Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex.

    Chiner-Oms Á, Sánchez-Busó L, Corander J, Gagneux S, Harris SR, Young D, González-Candelas F and Comas I

    Science advances 2019;5;6;eaaw3307

    PUBMED: 31448322; PMC: 6691555; DOI: 10.1126/sciadv.aaw3307

  • High-throughput elucidation of thrombus formation reveals sources of platelet function variability.

    van Geffen JP, Brouns SLN, Batista J, McKinney H, Kempster C, Nagy M, Sivapalaratnam S, Baaten CCFMJ, Bourry N, Frontini M et al.

    Haematologica 2019;104;6;1256-1267

    PUBMED: 30545925; PMC: 6545858; DOI: 10.3324/haematol.2018.198853

  • Inherited missense variants that affect GFI1B function do not necessarily cause bleeding diatheses.

    van Oorschot R, Marneth AE, Bergevoet SM, van Bergen MGJM, Peerlinck K, Lentaigne CE, Millar CM, Westbury SK, Favier R, Erber WN et al.

    Haematologica 2019;104;6;e260-e264

    PUBMED: 30573501; PMC: 6545829; DOI: 10.3324/haematol.2018.207712

  • Letter to the editor: Chlamydia trachomatis samples testing falsely negative in the Aptima Combo 2 test in Finland, 2019.

    Unemo M, Getman D, Hadad R, Cole M, Thomson N, Puolakkainen M and Spiteri G

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019;24;24

    PUBMED: 31213219; PMC: 6582517; DOI: 10.2807/1560-7917.ES.2019.24.24.1900354

  • DUOX2/DUOXA2 Mutations Frequently Cause Congenital Hypothyroidism that Evades Detection on Newborn Screening in the United Kingdom.

    Peters C, Nicholas AK, Schoenmakers E, Lyons G, Langham S, Serra EG, Sebire NJ, Muzza M, Fugazzola L and Schoenmakers N

    Thyroid : official journal of the American Thyroid Association 2019;29;6;790-801

    PUBMED: 31044655; PMC: 6588112; DOI: 10.1089/thy.2018.0587

  • Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory.

    Raven KE, Blane B, Leek D, Churcher C, Kokko-Gonzales P, Pugazhendhi D, Fraser L, Betley J, Parkhill J and Peacock SJ

    Journal of clinical microbiology 2019;57;6

    PUBMED: 30894439; PMC: 6535593; DOI: 10.1128/JCM.00180-19

  • Plasmodium knowlesi as a model system for characterising Plasmodium vivax drug resistance candidate genes.

    Verzier LH, Coyle R, Singh S, Sanderson T and Rayner JC

    PLoS neglected tropical diseases 2019;13;6;e0007470

    PUBMED: 31158222; PMC: 6564043; DOI: 10.1371/journal.pntd.0007470

  • Slc20a2, Encoding the Phosphate Transporter PiT2, Is an Important Genetic Determinant of Bone Quality and Strength.

    Beck-Cormier S, Lelliott CJ, Logan JG, Lafont DT, Merametdjian L, Leitch VD, Butterfield NC, Protheroe HJ, Croucher PI, Baldock PA et al.

    Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2019;34;6;1101-1114

    PUBMED: 30721528; PMC: 6618161; DOI: 10.1002/jbmr.3691

  • A catalog of genetic loci associated with kidney function from analyses of a million individuals.

    Wuttke M, Li Y, Li M, Sieber KB, Feitosa MF, Gorski M, Tin A, Wang L, Chu AY, Hoppmann A et al.

    Nature genetics 2019;51;6;957-972

    PUBMED: 31152163; PMC: 6698888; DOI: 10.1038/s41588-019-0407-x

  • Best practice for CRISPR design using current tools and resources.

    Thomas M, Parry-Smith D and Iyer V

    Methods (San Diego, Calif.) 2019;164-165;3-17

    PUBMED: 31152780; DOI: 10.1016/j.ymeth.2019.05.019

  • Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.

    Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, Dunlop MG et al.

    Nature communications 2019;10;1;2373

    PUBMED: 31147538; PMC: 6542828; DOI: 10.1038/s41467-019-10016-3

  • The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

    De Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B et al.

    Cell reports 2019;27;9;2690-2708.e10

    PUBMED: 31141692; PMC: 6546974; DOI: 10.1016/j.celrep.2019.04.098

  • Progression of the canonical reference malaria parasite genome from 2002-2019.

    Böhme U, Otto TD, Sanders M, Newbold CI and Berriman M

    Wellcome open research 2019;4;58

    PUBMED: 31080894; PMC: 6484455; DOI: 10.12688/wellcomeopenres.15194.2

  • Somatic mutation and clonal expansions in human tissues.

    Martincorena I

    Genome medicine 2019;11;1;35

    PUBMED: 31138277; PMC: 6537184; DOI: 10.1186/s13073-019-0648-4

  • Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.

    Schroeder H, Margaryan A, Szmyt M, Theulot B, Włodarczak P, Rasmussen S, Gopalakrishnan S, Szczepanek A, Konopka T, Jensen TZT et al.

    Proceedings of the National Academy of Sciences of the United States of America 2019;116;22;10705-10710

    PUBMED: 31061125; PMC: 6561172; DOI: 10.1073/pnas.1820210116

  • Essential role of inverted repeat in Epstein-Barr virus IR-1 in B cell transformation; geographical variation of the viral genome.

    Bridges R, Correia S, Wegner F, Venturini C, Palser A, White RE, Kellam P, Breuer J and Farrell PJ

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2019;374;1773;20180299

    PUBMED: 30955492; PMC: 6501908; DOI: 10.1098/rstb.2018.0299

  • Germline selection shapes human mitochondrial DNA diversity.

    Wei W, Tuna S, Keogh MJ, Smith KR, Aitman TJ, Beales PL, Bennett DL, Gale DP, Bitner-Glindzicz MAK, Black GC et al.

    Science (New York, N.Y.) 2019;364;6442

    PUBMED: 31123110; DOI: 10.1126/science.aau6520

  • Malta (MYH9 Associated Elastin Aggregation) Syndrome: Germline Variants in MYH9 Cause Rare Sweat Duct Proliferations and Irregular Elastin Aggregations.

    Fewings E, Ziemer M, Hörtnagel K, Reicherter K, Larionov A, Redman J, Goldgraben MA, Pepler A, Hearn T, Firth H et al.

    The Journal of investigative dermatology 2019

    PUBMED: 31125547; DOI: 10.1016/j.jid.2019.03.1151

  • Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees.

    Li L, Koh CC, Reker D, Brown JB, Wang H, Lee NK, Liow HH, Dai H, Fan HM, Chen L and Wei DQ

    Scientific reports 2019;9;1;7703

    PUBMED: 31118426; PMC: 6531441; DOI: 10.1038/s41598-019-43125-6

  • ALPK1 hotspot mutation as a driver of human spiradenoma and spiradenocarcinoma.

    Rashid M, van der Horst M, Mentzel T, Butera F, Ferreira I, Pance A, Rütten A, Luzar B, Marusic Z, de Saint Aubain N et al.

    Nature communications 2019;10;1;2213

    PUBMED: 31101826; PMC: 6525246; DOI: 10.1038/s41467-019-09979-0

  • Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design

    Tangherloni A, Spolaor S, Cazzaniga P, Besozzi D, Rundo L, Mauri G and Nobile MS

    Applied Soft Computing 2019;81;105494

    DOI: 10.1016/j.asoc.2019.105494

  • Identification of a regeneration-organizing cell in the Xenopus tail.

    Aztekin C, Hiscock TW, Marioni JC, Gurdon JB, Simons BD and Jullien J

    Science (New York, N.Y.) 2019;364;6441;653-658

    PUBMED: 31097661; PMC: 6986927; DOI: 10.1126/science.aav9996

  • Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening.

    Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E et al.

    Nature communications 2019;10;1;2198

    PUBMED: 31097696; PMC: 6522557; DOI: 10.1038/s41467-019-09940-1

  • Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.

    Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV, Croucher NJ, Gladstone RA, Bootsma HJ, Rots NY, Wijmega-Monsuur AJ et al.

    Nature communications 2019;10;1;2176

    PUBMED: 31092817; PMC: 6520353; DOI: 10.1038/s41467-019-09976-3

  • The clinical presentation caused by truncating CHD8 variants.

    Douzgou S, Liang HW, Metcalfe K, Somarathi S, Tischkowitz M, Mohamed W, Kini U, McKee S, Yates L, Bertoli M et al.

    Clinical genetics 2019;96;1;72-84

    PUBMED: 31001818; DOI: 10.1111/cge.13554

  • Using Human Induced Pluripotent Stem Cell-derived Intestinal Organoids to Study and Modify Epithelial Cell Protection Against Salmonella and Other Pathogens.

    Lees EA, Forbester JL, Forrest S, Kane L, Goulding D and Dougan G

    Journal of visualized experiments : JoVE 2019;147

    PUBMED: 31132035; DOI: 10.3791/59478

  • Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.

    O'Donnell-Luria AH, Pais LS, Faundes V, Wood JC, Sveden A, Luria V, Abou Jamra R, Accogli A, Amburgey K, Anderlid BM et al.

    American journal of human genetics 2019;104;6;1210-1222

    PUBMED: 31079897; PMC: 6556837; DOI: 10.1016/j.ajhg.2019.03.021

  • Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts.

    Decano AG, Ludden C, Feltwell T, Judge K, Parkhill J and Downing T

    mSphere 2019;4;3

    PUBMED: 31068432; PMC: 6506616; DOI: 10.1128/mSphere.00130-19

  • Karyotype, evolution and phylogenetic reconstruction in Micronycterinae bats with implications for the ancestral karyotype of Phyllostomidae.

    Benathar TCM, Nagamachi CY, Rodrigues LRR, O'Brien PCM, Ferguson-Smith MA, Yang F and Pieczarka JC

    BMC evolutionary biology 2019;19;1;98

    PUBMED: 31064342; PMC: 6505122; DOI: 10.1186/s12862-019-1421-4

  • GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures.

    Styrkarsdottir U, Stefansson OA, Gunnarsdottir K, Thorleifsson G, Lund SH, Stefansdottir L, Juliusson K, Agustsdottir AB, Zink F, Halldorsson GH et al.

    Nature communications 2019;10;1;2054

    PUBMED: 31053729; PMC: 6499783; DOI: 10.1038/s41467-019-09860-0

  • A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly.

    Maori E, Navarro IC, Boncristiani H, Seilly DJ, Rudolph KLM, Sapetschnig A, Lin CC, Ladbury JE, Evans JD, Heeney JL and Miska EA

    Molecular cell 2019;74;3;598-608.e6

    PUBMED: 31051140; PMC: 6509358; DOI: 10.1016/j.molcel.2019.03.010

  • A Specific CNOT1 Mutation Results in a Novel Syndrome of Pancreatic Agenesis and Holoprosencephaly through Impaired Pancreatic and Neurological Development.

    De Franco E, Watson RA, Weninger WJ, Wong CC, Flanagan SE, Caswell R, Green A, Tudor C, Lelliott CJ, Geyer SH et al.

    American journal of human genetics 2019;104;5;985-989

    PUBMED: 31006513; PMC: 6506862; DOI: 10.1016/j.ajhg.2019.03.018

  • A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences.

    Haber M, Doumet-Serhal C, Scheib CL, Xue Y, Mikulski R, Martiniano R, Fischer-Genz B, Schutkowski H, Kivisild T and Tyler-Smith C

    American journal of human genetics 2019;104;5;977-984

    PUBMED: 31006515; PMC: 6506814; DOI: 10.1016/j.ajhg.2019.03.015

  • MEK1/2 inhibitor withdrawal reverses acquired resistance driven by BRAFV600E amplification whereas KRASG13D amplification promotes EMT-chemoresistance.

    Sale MJ, Balmanno K, Saxena J, Ozono E, Wojdyla K, McIntyre RE, Gilley R, Woroniuk A, Howarth KD, Hughes G et al.

    Nature communications 2019;10;1;2030

    PUBMED: 31048689; PMC: 6497655; DOI: 10.1038/s41467-019-09438-w

  • Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans.

    Ashton PM, Thanh LT, Trieu PH, Van Anh D, Trinh NM, Beardsley J, Kibengo F, Chierakul W, Dance DAB, Rattanavong S et al.

    Nature communications 2019;10;1;2035

    PUBMED: 31048698; PMC: 6497710; DOI: 10.1038/s41467-019-10092-5

  • An open resource for accurately benchmarking small variant and reference calls.

    Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY et al.

    Nature biotechnology 2019;37;5;561-566

    PUBMED: 30936564; PMC: 6500473; DOI: 10.1038/s41587-019-0074-6

  • Association of the POT1 Germline Missense Variant p.I78T With Familial Melanoma.

    Wong K, Robles-Espinoza CD, Rodriguez D, Rudat SS, Puig S, Potrony M, Wong CC, Hewinson J, Aguilera P, Puig-Butille JA et al.

    JAMA dermatology 2019;155;5;604-609

    PUBMED: 30586141; PMC: 6506889; DOI: 10.1001/jamadermatol.2018.3662

  • Attitudes of publics who are unwilling to donate DNA data for research.

    Middleton A, Milne R, Thorogood A, Kleiderman E, Niemiec E, Prainsack B, Farley L, Bevan P, Steed C, Smith J et al.

    European journal of medical genetics 2019;62;5;316-323

    PUBMED: 30476628; PMC: 6582635; DOI: 10.1016/j.ejmg.2018.11.014

  • Australians' perspectives on support around use of personal genomic testing: Findings from the Genioz study.

    Metcalfe SA, Hickerton C, Savard J, Stackpoole E, Tytherleigh R, Tutty E, Terrill B, Turbitt E, Gray K, Middleton A et al.

    European journal of medical genetics 2019;62;5;290-299

    PUBMED: 30439534; DOI: 10.1016/j.ejmg.2018.11.002

  • Australians' views and experience of personal genomic testing: survey findings from the Genioz study.

    Savard J, Hickerton C, Tytherleigh R, Terrill B, Turbitt E, Newson AJ, Wilson B, Gray K, Gaff C, Middleton A et al.

    European journal of human genetics : EJHG 2019;27;5;711-720

    PUBMED: 30666046; PMC: 6461785; DOI: 10.1038/s41431-018-0325-x

  • Caribbean multi-centre study of Klebsiella pneumoniae: whole-genome sequencing, antimicrobial resistance and virulence factors.

    Heinz E, Brindle R, Morgan-McCalla A, Peters K and Thomson NR

    Microbial genomics 2019;5;5

    PUBMED: 31038449; PMC: 6562249; DOI: 10.1099/mgen.0.000266

  • Challenges in unsupervised clustering of single-cell RNA-seq data.

    Kiselev VY, Andrews TS and Hemberg M

    Nature reviews. Genetics 2019;20;5;273-282

    PUBMED: 30617341; DOI: 10.1038/s41576-018-0088-9

  • Collecting and exploiting data to understand a nation's sexual health needs: Implications for the British National Surveys of Sexual Attitudes and Lifestyles (Natsal).

    Mercer CH, Clifton S, Prior G, Aldridge RW, Bonell C, Copas AJ, Field N, Gibbs J, Macdowall W, Mitchell KR et al.

    Sexually transmitted infections 2019;95;3;159-161

    PUBMED: 30890634; PMC: 6580741; DOI: 10.1136/sextrans-2018-053571

  • Construction of an Escherichia coli genome with fewer codons sets records.

    Blount BA and Ellis T

    Nature 2019;569;7757;492-494

    PUBMED: 31097820; DOI: 10.1038/d41586-019-01584-x

  • Genome-wide association study in Finnish twins highlights the connection between nicotine addiction and neurotrophin signaling pathway.

    Hällfors J, Palviainen T, Surakka I, Gupta R, Buchwald J, Raevuori A, Ripatti S, Korhonen T, Jousilahti P, Madden PAF et al.

    Addiction biology 2019;24;3;549-561

    PUBMED: 29532581; PMC: 6519128; DOI: 10.1111/adb.12618

  • Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages.

    Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ et al.

    The Journal of antimicrobial chemotherapy 2019;74;5;1223-1232

    PUBMED: 30778540; PMC: 6477993; DOI: 10.1093/jac/dkz032

  • Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.

    Raven KE, Ludden C, Gouliouris T, Blane B, Naydenova P, Brown NM, Parkhill J and Peacock SJ

    Microbial genomics 2019;5;5

    PUBMED: 31107200; PMC: 6562247; DOI: 10.1099/mgen.0.000267

  • High-resolution mapping reveals that microniches in the gastric glands control Helicobacter pylori colonization of the stomach.

    Fung C, Tan S, Nakajima M, Skoog EC, Camarillo-Guerrero LF, Klein JA, Lawley TD, Solnick JV, Fukami T and Amieva MR

    PLoS biology 2019;17;5;e3000231

    PUBMED: 31048876; PMC: 6497225; DOI: 10.1371/journal.pbio.3000231

  • How to Find a Resident Kidney Macrophage: the Single-Cell Sequencing Solution.

    Clatworthy MR

    Journal of the American Society of Nephrology : JASN 2019;30;5;715-716

    PUBMED: 30948628; PMC: 6493991; DOI: 10.1681/ASN.2019030245

  • Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma.

    Hoffman M, Gillmor AH, Kunz DJ, Johnston MJ, Nikolic A, Narta K, Zarrei M, King J, Ellestad K, Dang NH et al.

    Cancer research 2019;79;9;2111-2123

    PUBMED: 30877103; DOI: 10.1158/0008-5472.CAN-18-3441

  • Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors.

    Warrington NM, Beaumont RN, Horikoshi M, Day FR, Helgeland Ø, Laurin C, Bacelis J, Peng S, Hao K, Feenstra B et al.

    Nature genetics 2019;51;5;804-814

    PUBMED: 31043758; PMC: 6522365; DOI: 10.1038/s41588-019-0403-1

  • Molecular autopsy by trio exome sequencing (ES) and postmortem examination in fetuses and neonates with prenatally identified structural anomalies.

    Quinlan-Jones E, Lord J, Williams D, Hamilton S, Marton T, Eberhardt RY, Rinck G, Prigmore E, Keelagher R, McMullan DJ et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;5;1065-1073

    PUBMED: 30293990; PMC: 6752266; DOI: 10.1038/s41436-018-0298-8

  • Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage.

    van Praagh JB, de Goffau MC, Bakker IS, van Goor H, Harmsen HJM, Olinga P and Havenga K

    Annals of surgery 2019;269;5;911-916

    PUBMED: 29303807; DOI: 10.1097/SLA.0000000000002651

  • Rare Protein-Truncating Variants in APOB, Lower Low-Density Lipoprotein Cholesterol, and Protection Against Coronary Heart Disease.

    Peloso GM, Nomura A, Khera AV, Chaffin M, Won HH, Ardissino D, Danesh J, Schunkert H, Wilson JG, Samani N et al.

    Circulation. Genomic and precision medicine 2019;12;5;e002376

    PUBMED: 30939045; PMC: 7044908; DOI: 10.1161/CIRCGEN.118.002376

  • Reasonable expectations of privacy in non-disclosure of familial genetic risk: What is it reasonable to expect?

    Chico V

    European journal of medical genetics 2019;62;5;308-315

    PUBMED: 30521983; PMC: 6588831; DOI: 10.1016/j.ejmg.2018.11.013

  • Response to Comment on "Mucus Microbiome of Anastomotic Tissue During Surgery Has Predictive Value for Colorectal Anastomotic Leakage".

    van Praagh JB, de Goffau MC, Harmsen HJM and Havenga K

    Annals of surgery 2019;269;5;e69-e70

    PUBMED: 30985361; DOI: 10.1097/SLA.0000000000002857

  • Tracing outbreaks with machine learning.

    Wheeler NE

    Nature reviews. Microbiology 2019;17;5;269

    PUBMED: 30742026; DOI: 10.1038/s41579-019-0153-1

  • Truncation of GdpP mediates β-lactam resistance in clinical isolates of Staphylococcus aureus.

    Ba X, Kalmar L, Hadjirin NF, Kerschner H, Apfalter P, Morgan FJ, Paterson GK, Girvan SL, Zhou R, Harrison EM and Holmes MA

    The Journal of antimicrobial chemotherapy 2019;74;5;1182-1191

    PUBMED: 30759229; DOI: 10.1093/jac/dkz013

  • Whole genome sequence of Vibrio cholerae directly from dried spotted filter paper.

    Bénard AHM, Guenou E, Fookes M, Ateudjieu J, Kasambara W, Siever M, Rebaudet S, Boncy J, Adrien P, Piarroux R et al.

    PLoS neglected tropical diseases 2019;13;5;e0007330

    PUBMED: 31145741; PMC: 6559667; DOI: 10.1371/journal.pntd.0007330

  • World congress on genetic counselling.

    Middleton A, Patch C and Biesecker B

    European journal of medical genetics 2019;62;5;287

    PUBMED: 31004824; DOI: 10.1016/j.ejmg.2019.04.011

  • Xist Intron 1 Repression by Transcriptional-Activator-Like Effectors Designer Transcriptional Factor Improves Somatic Cell Reprogramming in Mice.

    Zhang J, Gao X, Yang J, Fan X, Wang W, Liang Y, Fan L, Han H, Xu X, Tang F et al.

    Stem cells (Dayton, Ohio) 2019;37;5;599-608

    PUBMED: 30353613; DOI: 10.1002/stem.2928

  • Environmental DNA for improved detection and environmental surveillance of schistosomiasis.

    Sengupta ME, Hellström M, Kariuki HC, Olsen A, Thomsen PF, Mejer H, Willerslev E, Mwanje MT, Madsen H, Kristensen TK et al.

    Proceedings of the National Academy of Sciences of the United States of America 2019;116;18;8931-8940

    PUBMED: 30975758; PMC: 6500138; DOI: 10.1073/pnas.1815046116

  • Automating the Shared Resource Laboratory Using Computer Scripts: A Case Report.

    Hall C, Brown L, Graham J, Thompson S and Ng BL

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2019;95;7;797-802

    PUBMED: 31034711; PMC: 6767128; DOI: 10.1002/cyto.a.23775

  • A defined mechanistic correlate of protection against Plasmodium falciparum malaria in non-human primates.

    Douglas AD, Baldeviano GC, Jin J, Miura K, Diouf A, Zenonos ZA, Ventocilla JA, Silk SE, Marshall JM, Alanine DGW et al.

    Nature communications 2019;10;1;1953

    PUBMED: 31028254; PMC: 6486575; DOI: 10.1038/s41467-019-09894-4

  • Improved spatial ecological sampling using open data and standardization: an example from malaria mosquito surveillance.

    Sedda L, Lucas ER, Djogbénou LS, Edi AVC, Egyir-Yawson A, Kabula BI, Midega J, Ochomo E, Weetman D and Donnelly MJ

    Journal of the Royal Society, Interface 2019;16;153;20180941

    PUBMED: 30966952; PMC: 6505554; DOI: 10.1098/rsif.2018.0941

  • Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313.

    Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA and MacLennan CA

    Wellcome open research 2019;4;74

    PUBMED: 31231691; PMC: 6560496; DOI: 10.12688/wellcomeopenres.15059.1

  • Persistence of Nasopharyngeal Pneumococcal Vaccine Serotypes and Increase of Nonvaccine Serotypes Among Vaccinated Infants and Their Mothers 5 Years After Introduction of Pneumococcal Conjugate Vaccine 13 in The Gambia.

    Usuf E, Bottomley C, Bojang E, Cox I, Bojang A, Gladstone R, Kampmann B, Hill PC and Roca A

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019;68;9;1512-1521

    PUBMED: 30165376; PMC: 6481996; DOI: 10.1093/cid/ciy726

  • Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

    McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM, Horner C, Peacock SJ, Parkhill J, Croucher NJ and Corander J

    mBio 2019;10;2

    PUBMED: 31015329; PMC: 6479005; DOI: 10.1128/mBio.00644-19

  • Notch Signaling Mediates Secondary Senescence.

    Teo YV, Rattanavirotkul N, Olova N, Salzano A, Quintanilla A, Tarrats N, Kiourtis C, Müller M, Green AR, Adams PD et al.

    Cell reports 2019;27;4;997-1007.e5

    PUBMED: 31018144; PMC: 6486482; DOI: 10.1016/j.celrep.2019.03.104

  • Felodipine induces autophagy in mouse brains with pharmacokinetics amenable to repurposing.

    Siddiqi FH, Menzies FM, Lopez A, Stamatakou E, Karabiyik C, Ureshino R, Ricketts T, Jimenez-Sanchez M, Esteban MA, Lai L et al.

    Nature communications 2019;10;1;1817

    PUBMED: 31000720; PMC: 6472390; DOI: 10.1038/s41467-019-09494-2

  • Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis.

    Castro-Dopico T, Dennison TW, Ferdinand JR, Mathews RJ, Fleming A, Clift D, Stewart BJ, Jing C, Strongili K, Labzin LI et al.

    Immunity 2019;50;4;1099-1114.e10

    PUBMED: 30876876; PMC: 6477154; DOI: 10.1016/j.immuni.2019.02.006

  • International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.

    Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, Corander J, Page AJ, Marttinen P, Bentley LJ, Ochoa TJ et al.

    EBioMedicine 2019;43;338-346

    PUBMED: 31003929; PMC: 6557916; DOI: 10.1016/j.ebiom.2019.04.021

  • Gimpute: an efficient genetic data imputation pipeline.

    Chen J, Lippold D, Frank J, Rayner W, Meyer-Lindenberg A and Schwarz E

    Bioinformatics (Oxford, England) 2019;35;8;1433-1435

    PUBMED: 30239591; DOI: 10.1093/bioinformatics/bty814

  • Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation.

    Brinkman AB, Nik-Zainal S, Simmer F, Rodríguez-González FG, Smid M, Alexandrov LB, Butler A, Martin S, Davies H, Glodzik D et al.

    Nature communications 2019;10;1;1749

    PUBMED: 30988298; PMC: 6465362; DOI: 10.1038/s41467-019-09828-0

  • CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification.

    Djoumbou-Feunang Y, Pon A, Karu N, Zheng J, Li C, Arndt D, Gautam M, Allen F and Wishart DS

    Metabolites 2019;9;4

    PUBMED: 31013937; PMC: 6523630; DOI: 10.3390/metabo9040072

  • Point of View: An evolution from genetic counselling to genomic counselling.

    Patch C and Middleton A

    European journal of medical genetics 2019;62;5;288-289

    PUBMED: 30991113; DOI: 10.1016/j.ejmg.2019.04.010

  • PIGT-CDG, a disorder of the glycosylphosphatidylinositol anchor: description of 13 novel patients and expansion of the clinical characteristics.

    Bayat A, Knaus A, Juul AW, Dukic D, Gardella E, Charzewska A, Clement E, Hjalgrim H, Hoffman-Zacharska D, Horn D et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;10;2216-2223

    PUBMED: 30976099; DOI: 10.1038/s41436-019-0512-3

  • Steroid receptor coactivator-1 modulates the function of Pomc neurons and energy homeostasis.

    Yang Y, van der Klaauw AA, Zhu L, Cacciottolo TM, He Y, Stadler LKJ, Wang C, Xu P, Saito K, Hinton A et al.

    Nature communications 2019;10;1;1718

    PUBMED: 30979869; PMC: 6461669; DOI: 10.1038/s41467-019-08737-6

  • TET3 prevents terminal differentiation of adult NSCs by a non-catalytic action at Snrpn.

    Montalbán-Loro R, Lozano-Ureña A, Ito M, Krueger C, Reik W, Ferguson-Smith AC and Ferrón SR

    Nature communications 2019;10;1;1726

    PUBMED: 30979904; PMC: 6461695; DOI: 10.1038/s41467-019-09665-1

  • A Compendium of Mutational Signatures of Environmental Agents.

    Kucab JE, Zou X, Morganella S, Joel M, Nanda AS, Nagy E, Gomez C, Degasperi A, Harris R, Jackson SP et al.

    Cell 2019;177;4;821-836.e16

    PUBMED: 30982602; PMC: 6506336; DOI: 10.1016/j.cell.2019.03.001

  • Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

    Gorman KM, Meyer E, Grozeva D, Spinelli E, McTague A, Sanchis-Juan A, Carss KJ, Bryant E, Reich A, Schneider AL et al.

    American journal of human genetics 2019;104;5;948-956

    PUBMED: 30982612; PMC: 6507039; DOI: 10.1016/j.ajhg.2019.03.005

  • The history, genome and biology of NCTC 30: a non-pandemic Vibrio cholerae isolate from World War One.

    Dorman MJ, Kane L, Domman D, Turnbull JD, Cormie C, Fazal MA, Goulding DA, Russell JE, Alexander S and Thomson NR

    Proceedings. Biological sciences 2019;286;1900;20182025

    PUBMED: 30966987; PMC: 6501683; DOI: 10.1098/rspb.2018.2025

  • High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139.

    Dorman MJ, Domman D, Uddin MI, Sharmin S, Afrad MH, Begum YA, Qadri F and Thomson NR

    Scientific reports 2019;9;1;5865

    PUBMED: 30971707; PMC: 6458141; DOI: 10.1038/s41598-019-41883-x

  • Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.

    Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, Santos R, Rao Y, Sassi F, Pinnelli M et al.

    Nature 2019;568;7753;511-516

    PUBMED: 30971826; DOI: 10.1038/s41586-019-1103-9

  • Comparative analysis of sequencing technologies for single-cell transcriptomics.

    Natarajan KN, Miao Z, Jiang M, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L et al.

    Genome biology 2019;20;1;70

    PUBMED: 30961669; PMC: 6454680; DOI: 10.1186/s13059-019-1676-5

  • Genome-Scale CRISPRa Screen Identifies Novel Factors for Cellular Reprogramming.

    Yang J, Rajan SS, Friedrich MJ, Lan G, Zou X, Ponstingl H, Garyfallos DA, Liu P, Bradley A and Metzakopian E

    Stem cell reports 2019;12;4;757-771

    PUBMED: 30905739; PMC: 6450436; DOI: 10.1016/j.stemcr.2019.02.010

  • Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3.

    Bassano I, Ong SH, Sanz-Hernandez M, Vinkler M, Kebede A, Hanotte O, Onuigbo E, Fife M and Kellam P

    BMC genomics 2019;20;1;272

    PUBMED: 30952207; PMC: 6451222; DOI: 10.1186/s12864-019-5621-5

  • Convergent regulatory evolution and loss of flight in paleognathous birds.

    Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M and Edwards SV

    Science (New York, N.Y.) 2019;364;6435;74-78

    PUBMED: 30948549; DOI: 10.1126/science.aat7244

  • Enhanced β-adrenergic signalling underlies an age-dependent beneficial metabolic effect of PI3K p110α inactivation in adipose tissue.

    Araiz C, Yan A, Bettedi L, Samuelson I, Virtue S, McGavigan AK, Dani C, Vidal-Puig A and Foukas LC

    Nature communications 2019;10;1;1546

    PUBMED: 30948720; PMC: 6449391; DOI: 10.1038/s41467-019-09514-1

  • Delineation of dominant and recessive forms of LZTR1-associated Noonan syndrome.

    Pagnamenta AT, Kaisaki PJ, Bennett F, Burkitt-Wright E, Martin HC, Ferla MP, Taylor JM, Gompertz L, Lahiri N, Tatton-Brown K et al.

    Clinical genetics 2019;95;6;693-703

    PUBMED: 30859559; PMC: 6563422; DOI: 10.1111/cge.13533

  • Mapping imported malaria in Bangladesh using parasite genetic and human mobility data.

    Chang HH, Wesolowski A, Sinha I, Jacob CG, Mahmud A, Uddin D, Zaman SI, Hossain MA, Faiz MA, Ghose A et al.

    eLife 2019;8

    PUBMED: 30938289; PMC: 6478433; DOI: 10.7554/eLife.43481

  • The genetic changes of Wilms tumour.

    Treger TD, Chowdhury T, Pritchard-Jones K and Behjati S

    Nature reviews. Nephrology 2019;15;4;240-251

    PUBMED: 30705419; DOI: 10.1038/s41581-019-0112-0

  • Association of Plasma Vitamin D Metabolites With Incident Type 2 Diabetes: EPIC-InterAct Case-Cohort Study.

    Zheng JS, Imamura F, Sharp SJ, van der Schouw YT, Sluijs I, Gundersen TE, Ardanaz E, Boeing H, Bonet C, Gómez JH et al.

    The Journal of clinical endocrinology and metabolism 2019;104;4;1293-1303

    PUBMED: 30418614; PMC: 6397435; DOI: 10.1210/jc.2018-01522

  • CCL27/CCL28-CCR10 Chemokine Signaling Mediates Migration of Lymphatic Endothelial Cells.

    Karnezis T, Farnsworth RH, Harris NC, Williams SP, Caesar C, Byrne DJ, Herle P, Macheda ML, Shayan R, Zhang YF et al.

    Cancer research 2019;79;7;1558-1572

    PUBMED: 30709930; DOI: 10.1158/0008-5472.CAN-18-1858

  • Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer.

    Butler TM, Boniface CT, Johnson-Camacho K, Tabatabaei S, Melendez D, Kelley T, Gray J, Corless CL and Spellman PT

    Cold Spring Harbor molecular case studies 2019;5;2

    PUBMED: 30833418; PMC: 6549569; DOI: 10.1101/mcs.a003772

  • Deep phenotyping of 14 new patients with IQSEC2 variants, including monozygotic twins of discordant phenotype.

    Radley JA, O'Sullivan RBG, Turton SE, Cox H, Vogt J, Morton J, Jones E, Smithson S, Lachlan K, Rankin J et al.

    Clinical genetics 2019;95;4;496-506

    PUBMED: 30666632; DOI: 10.1111/cge.13507

  • Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment.

    Gouliouris T, Raven KE, Moradigaravand D, Ludden C, Coll F, Blane B, Naydenova P, Horner C, Brown NM, Corander J et al.

    Genome research 2019;29;4;626-634

    PUBMED: 30898881; PMC: 6442392; DOI: 10.1101/gr.232629.117

  • Dicer1 is required for pigment cell and craniofacial development in zebrafish.

    Weiner AMJ, Scampoli NL, Steeman TJ, Dooley CM, Busch-Nentwich EM, Kelsh RN and Calcaterra NB

    Biochimica et biophysica acta. Gene regulatory mechanisms 2019;1862;4;472-485

    PUBMED: 30840854; DOI: 10.1016/j.bbagrm.2019.02.005

  • Discovery of Salmonella trehalose phospholipids reveals functional convergence with mycobacteria.

    Reinink P, Buter J, Mishra VK, Ishikawa E, Cheng TY, Willemsen PTJ, Porwollik S, Brennan PJ, Heinz E, Mayfield JA et al.

    The Journal of experimental medicine 2019;216;4;757-771

    PUBMED: 30804000; PMC: 6446866; DOI: 10.1084/jem.20181812

  • DNA metabarcoding-Need for robust experimental designs to draw sound ecological conclusions.

    Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE et al.

    Molecular ecology 2019;28;8;1857-1862

    PUBMED: 31033079; DOI: 10.1111/mec.15060

  • Dysregulations of sonic hedgehog signaling in MED12-related X-linked intellectual disability disorders.

    Srivastava S, Niranjan T, May MM, Tarpey P, Allen W, Hackett A, Jouk PS, Raymond L, Briault S, Skinner C et al.

    Molecular genetics & genomic medicine 2019;7;4;e00569

    PUBMED: 30729724; PMC: 6465656; DOI: 10.1002/mgg3.569

  • Highly Diverse Hepatitis C Strains Detected in Sub-Saharan Africa Have Unknown Susceptibility to Direct-Acting Antiviral Treatments.

    Davis C, Mgomella GS, da Silva Filipe A, Frost EH, Giroux G, Hughes J, Hogan C, Kaleebu P, Asiki G, McLauchlan J et al.

    Hepatology (Baltimore, Md.) 2019;69;4;1426-1441

    PUBMED: 30387174; PMC: 6492010; DOI: 10.1002/hep.30342

  • In conversation with Sarah Teichmann.

    Dhillon P and Teichmann SA

    The FEBS journal 2019;286;8;1445-1450

    PUBMED: 31012289; DOI: 10.1111/febs.14806

  • Mature sperm small-RNA profile in the sparrow: implications for transgenerational effects of age on fitness.

    Matsushima W, Brink K, Schroeder J, Miska EA and Gapp K

    Environmental epigenetics 2019;5;2;dvz007

    PUBMED: 31139435; PMC: 6527922; DOI: 10.1093/eep/dvz007

  • Melanoma subtypes: genomic profiles, prognostic molecular markers and therapeutic possibilities.

    Rabbie R, Ferguson P, Molina-Aguilar C, Adams DJ and Robles-Espinoza CD

    The Journal of pathology 2019;247;5;539-551

    PUBMED: 30511391; PMC: 6492003; DOI: 10.1002/path.5213

  • Method for culturing Candidatus Ornithobacterium hominis.

    Lawrence KA, Harris TM, Salter SJ, Hall RW, Smith-Vaughan HC, Chang AB and Marsh RL

    Journal of microbiological methods 2019;159;157-160

    PUBMED: 30871998; DOI: 10.1016/j.mimet.2019.03.006

  • Mouse screen reveals multiple new genes underlying mouse and human hearing loss.

    Ingham NJ, Pearson SA, Vancollie VE, Rook V, Lewis MA, Chen J, Buniello A, Martelletti E, Preite L, Lam CC et al.

    PLoS biology 2019;17;4;e3000194

    PUBMED: 30973865; PMC: 6459510; DOI: 10.1371/journal.pbio.3000194

  • Myosin 10 is involved in murine pigmentation.

    Liakath-Ali K, Vancollie VE, Sequeira I, Lelliott CJ and Watt FM

    Experimental dermatology 2019;28;4;391-394

    PUBMED: 29509981; PMC: 6519374; DOI: 10.1111/exd.13528

  • PANINI: Pangenome Neighbour Identification for Bacterial Populations.

    Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ, Corander J and Aanensen DM

    Microbial genomics 2019;5;4

    PUBMED: 30465642; PMC: 6521588; DOI: 10.1099/mgen.0.000220

  • Reply to Bombard and Mighton.

    Carrieri D, Howard HC, Clarke AJ, Stefansdottir V, Cornel MC, van El CG and Forzano F

    European journal of human genetics : EJHG 2019;27;4;507-508

    PUBMED: 30659262; PMC: 6460587; DOI: 10.1038/s41431-018-0315-z

  • Resolving variant-to-function relationships in hematopoiesis.

    Tardaguila M and Soranzo N

    Nature genetics 2019;51;4;581-583

    PUBMED: 30926964; DOI: 10.1038/s41588-019-0386-y

  • Reverse GWAS: Using genetics to identify and model phenotypic subtypes.

    Dahl A, Cai N, Ko A, Laakso M, Pajukanta P, Flint J and Zaitlen N

    PLoS genetics 2019;15;4;e1008009

    PUBMED: 30951530; PMC: 6469799; DOI: 10.1371/journal.pgen.1008009

  • rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree.

    Wailan AM, Coll F, Heinz E, Tonkin-Hill G, Corander J, Feasey NA and Thomson NR

    Microbial genomics 2019;5;4

    PUBMED: 30920366; PMC: 6521585; DOI: 10.1099/mgen.0.000264

  • Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales.

    Li J, Vázquez-García I, Persson K, González A, Yue JX, Barré B, Hall MN, Long A, Warringer J, Mustonen V and Liti G

    Molecular biology and evolution 2019;36;4;691-708

    PUBMED: 30657986; PMC: 6445301; DOI: 10.1093/molbev/msz006

  • TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells.

    Rasmussen KD, Berest I, Keβler S, Nishimura K, Simón-Carrasco L, Vassiliou GS, Pedersen MT, Christensen J, Zaugg JB and Helin K

    Genome research 2019;29;4;564-575

    PUBMED: 30796038; PMC: 6442383; DOI: 10.1101/gr.239277.118

  • USP44 is dispensable for normal hematopoietic stem cell function, lymphocyte development, and B-cell-mediated immune response in a mouse model.

    Lin YH, Forster M, Liang Y, Yu M, Wang H, Robert F, Langlais D, Pelletier J, Clare S and Nijnik A

    Experimental hematology 2019;72;1-8

    PUBMED: 30639577; DOI: 10.1016/j.exphem.2019.01.001

  • Vaccination of Icelandic Children with the 10-Valent Pneumococcal Vaccine Leads to a Significant Herd Effect among Adults in Iceland.

    Quirk SJ, Haraldsson G, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Bentley SD, Haraldsson Á, Erlendsdóttir H, Brueggemann AB and Kristinsson KG

    Journal of clinical microbiology 2019;57;4

    PUBMED: 30651396; PMC: 6440763; DOI: 10.1128/JCM.01766-18

  • A natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis.

    Krimpenfort P, Snoek M, Lambooij JP, Song JY, van der Weide R, Bhaskaran R, Teunissen H, Adams DJ, de Wit E and Berns A

    Nature communications 2019;10;1;1425

    PUBMED: 30926782; PMC: 6441055; DOI: 10.1038/s41467-019-09321-8

  • Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids.

    Bentley AR, Sung YJ, Brown MR, Winkler TW, Kraja AT, Ntalla I, Schwander K, Chasman DI, Lim E, Deng X et al.

    Nature genetics 2019;51;4;636-648

    PUBMED: 30926973; PMC: 6467258; DOI: 10.1038/s41588-019-0378-y

  • PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice.

    Weber J, de la Rosa J, Grove CS, Schick M, Rad L, Baranov O, Strong A, Pfaus A, Friedrich MJ, Engleitner T et al.

    Nature communications 2019;10;1;1415

    PUBMED: 30926791; PMC: 6440946; DOI: 10.1038/s41467-019-09180-3

  • Translating insights into tumor evolution to clinical practice: promises and challenges.

    Fittall MW and Van Loo P

    Genome medicine 2019;11;1;20

    PUBMED: 30925887; PMC: 6440005; DOI: 10.1186/s13073-019-0632-z

  • The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

    Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L et al.

    Developmental cell 2019;49;1;10-29

    PUBMED: 30930166; PMC: 6616346; DOI: 10.1016/j.devcel.2019.03.001

  • EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

    Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st Human Cell Atlas Jamboree and Marioni JC

    Genome biology 2019;20;1;63

    PUBMED: 30902100; PMC: 6431044; DOI: 10.1186/s13059-019-1662-y

  • The Genetic Basis of Metabolic Disease.

    Barroso I and McCarthy MI

    Cell 2019;177;1;146-161

    PUBMED: 30901536; PMC: 6432945; DOI: 10.1016/j.cell.2019.02.024

  • De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder.

    Calpena E, Hervieu A, Kaserer T, Swagemakers SMA, Goos JAC, Popoola O, Ortiz-Ruiz MJ, Barbaro-Dieber T, Bownass L, Brilstra EH et al.

    American journal of human genetics 2019;104;4;709-720

    PUBMED: 30905399; PMC: 6451695; DOI: 10.1016/j.ajhg.2019.02.006

  • Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AML.

    Basheer F, Giotopoulos G, Meduri E, Yun H, Mazan M, Sasca D, Gallipoli P, Marando L, Gozdecka M, Asby R et al.

    The Journal of experimental medicine 2019;216;4;966-981

    PUBMED: 30890554; PMC: 6446874; DOI: 10.1084/jem.20181276

  • Integration of transcriptional and mutational data simplifies the stratification of peripheral T-cell lymphoma.

    Maura F, Agnelli L, Leongamornlert D, Bolli N, Chan WC, Dodero A, Carniti C, Heavican TB, Pellegrinelli A, Pruneri G et al.

    American journal of hematology 2019;94;6;628-634

    PUBMED: 30829413; PMC: 6684242; DOI: 10.1002/ajh.25450

  • Positive selection in Europeans and East-Asians at the ABCA12 gene.

    Sirica R, Buonaiuto M, Petrella V, Sticco L, Tramontano D, Antonini D, Missero C, Guardiola O, Andolfi G, Kumar H et al.

    Scientific reports 2019;9;1;4843

    PUBMED: 30890716; PMC: 6424970; DOI: 10.1038/s41598-019-40360-9

  • Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

    Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC and Odom DT

    Nature communications 2019;10;1;1251

    PUBMED: 30890697; PMC: 6424977; DOI: 10.1038/s41467-019-09182-1

  • Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways.

    Steele CD, Tarabichi M, Oukrif D, Webster AP, Ye H, Fittall M, Lombard P, Martincorena I, Tarpey PS, Collord G et al.

    Cancer cell 2019;35;3;441-456.e8

    PUBMED: 30889380; PMC: 6428691; DOI: 10.1016/j.ccell.2019.02.002

  • Interferon-Induced Transmembrane Protein 1 Restricts Replication of Viruses That Enter Cells via the Plasma Membrane.

    Smith SE, Busse DC, Binter S, Weston S, Diaz Soria C, Laksono BM, Clare S, Van Nieuwkoop S, Van den Hoogen BG, Clement M et al.

    Journal of virology 2019;93;6

    PUBMED: 30567988; PMC: 6401438; DOI: 10.1128/JVI.02003-18

  • Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus.

    Doyle SR, Illingworth CJR, Laing R, Bartley DJ, Redman E, Martinelli A, Holroyd N, Morrison AA, Rezansoff A, Tracey A et al.

    BMC genomics 2019;20;1;218

    PUBMED: 30876405; PMC: 6420744; DOI: 10.1186/s12864-019-5592-6

  • Collateral damage and CRISPR genome editing.

    Thomas M, Burgio G, Adams DJ and Iyer V

    PLoS genetics 2019;15;3;e1007994

    PUBMED: 30870431; PMC: 6417652; DOI: 10.1371/journal.pgen.1007994

  • An experimental human blood stage model for studying Plasmodium malariae infection.

    Woodford J, Collins KA, Odedra A, Wang C, Kyung JI, Domingo GJ, Watts R, Marquart L, Berriman M, Otto TD and McCarthy JS

    The Journal of infectious diseases 2019

    PUBMED: 30852586; DOI: 10.1093/infdis/jiz102

  • Antibiotic Resistance and Typhoid.

    Dyson ZA, Klemm EJ, Palmer S and Dougan G

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019;68;Suppl 2;S165-S170

    PUBMED: 30845331; PMC: 6405283; DOI: 10.1093/cid/ciy1111

  • Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis.

    Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC et al.

    Cell 2019;176;6;1282-1294.e20

    PUBMED: 30849372; PMC: 6424819; DOI: 10.1016/j.cell.2019.02.012

  • Salmonella Typhi From Blood Cultures in the Democratic Republic of the Congo: A 10-Year Surveillance.

    Tack B, Phoba MF, Van Puyvelde S, Kalonji LM, Hardy L, Barbé B, Van der Sande MAB, Monsieurs E, Deborggraeve S, Lunguya O and Jacobs J

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019;68;Supplement_2;S130-S137

    PUBMED: 30845337; PMC: 6405282; DOI: 10.1093/cid/ciy1116

  • Assessing the causal association of glycine with risk of cardio-metabolic diseases.

    Wittemans LBL, Lotta LA, Oliver-Williams C, Stewart ID, Surendran P, Karthikeyan S, Day FR, Koulman A, Imamura F, Zeng L et al.

    Nature communications 2019;10;1;1060

    PUBMED: 30837465; PMC: 6400990; DOI: 10.1038/s41467-019-08936-1

  • mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

    Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P et al.

    Analytical chemistry 2019;91;5;3302-3310

    PUBMED: 30688441; PMC: 6660005; DOI: 10.1021/acs.analchem.8b04310

  • Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements.

    Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ and Cleveland DW

    Nature genetics 2019;51;4;705-715

    PUBMED: 30833795; PMC: 6441390; DOI: 10.1038/s41588-019-0360-8

  • Factors Associated With Outcomes of Patients With Primary Sclerosing Cholangitis and Development and Validation of a Risk Scoring System.

    Goode EC, Clark AB, Mells GF, Srivastava B, Spiess K, Gelson WTH, Trivedi PJ, Lynch KD, Castren E, Vesterhus MN et al.

    Hepatology (Baltimore, Md.) 2019;69;5;2120-2135

    PUBMED: 30566748; PMC: 6519245; DOI: 10.1002/hep.30479

  • Microbial abundance, activity and population genomic profiling with mOTUs2.

    Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP et al.

    Nature communications 2019;10;1;1014

    PUBMED: 30833550; PMC: 6399450; DOI: 10.1038/s41467-019-08844-4

  • The circular RNome of primary breast cancer.

    Smid M, Wilting SM, Uhr K, Rodríguez-González FG, de Weerd V, Prager-Van der Smissen WJC, van der Vlugt-Daane M, van Galen A, Nik-Zainal S, Butler A et al.

    Genome research 2019;29;3;356-366

    PUBMED: 30692147; PMC: 6396421; DOI: 10.1101/gr.238121.118

  • A lentiviral vector-based insertional mutagenesis screen identifies mechanisms of resistance to MAPK inhibitors in melanoma.

    Ranzani M, Alifrangis C, Thompson NA, Rust AG, Allahyar A, Iyer V, Price S, Ellis P, Turner G, de Ridder J et al.

    Pigment cell & melanoma research 2019;32;2;332-335

    PUBMED: 30218636; DOI: 10.1111/pcmr.12737

  • A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC.

    MacFadyen AC, Harrison EM, Drigo I, Parkhill J, Holmes MA and Paterson GK

    The Journal of antimicrobial chemotherapy 2019;74;3;547-552

    PUBMED: 30590583; PMC: 6484881; DOI: 10.1093/jac/dky502

  • An Orphan CpG Island Drives Expression of a let-7 miRNA Precursor with an Important Role in Mouse Development.

    Koerner MV, Chhatbar K, Webb S, Cholewa-Waclaw J, Selfridge J, De Sousa D, Skarnes B, Rosen B, Thomas M, Bottomley J et al.

    Epigenomes 2019;3;1;7

    PUBMED: 31354981; PMC: 6660310; DOI: 10.3390/epigenomes3010007

  • A proteomic time course through the differentiation of human induced pluripotent stem cells into hepatocyte-like cells.

    Hurrell T, Segeritz CP, Vallier L, Lilley KS and Cromarty AD

    Scientific reports 2019;9;1;3270

    PUBMED: 30824743; PMC: 6397265; DOI: 10.1038/s41598-019-39400-1

  • BRN2 suppresses apoptosis, reprograms DNA damage repair, and is associated with a high somatic mutation burden in melanoma.

    Herbert K, Binet R, Lambert JP, Louphrasitthiphol P, Kalkavan H, Sesma-Sanz L, Robles-Espinoza CD, Sarkar S, Suer E, Andrews S et al.

    Genes & development 2019;33;5-6;310-332

    PUBMED: 30804224; PMC: 6411009; DOI: 10.1101/gad.314633.118

  • C9orf72 arginine-rich dipeptide proteins interact with ribosomal proteins in vivo to induce a toxic translational arrest that is rescued by eIF1A.

    Moens TG, Niccoli T, Wilson KM, Atilano ML, Birsa N, Gittings LM, Holbling BV, Dyson MC, Thoeng A, Neeves J et al.

    Acta neuropathologica 2019;137;3;487-500

    PUBMED: 30604225; PMC: 6514073; DOI: 10.1007/s00401-018-1946-4

  • Characterization of mecC gene-carrying coagulase-negative Staphylococcus spp. isolated from various animals.

    Loncaric I, Kübber-Heiss A, Posautz A, Ruppitsch W, Lepuschitz S, Schauer B, Feßler AT, Krametter-Frötscher R, Harrison EM, Holmes MA et al.

    Veterinary microbiology 2019;230;138-144

    PUBMED: 30827379; DOI: 10.1016/j.vetmic.2019.02.014

  • Evaluation of a Dual Isolation Width Acquisition Method for Isobaric Labeling Ratio Decompression.

    Roumeliotis TI, Weisser H and Choudhary JS

    Journal of proteome research 2019;18;3;1433-1440

    PUBMED: 30576155; PMC: 6399672; DOI: 10.1021/acs.jproteome.8b00870

  • Federated discovery and sharing of genomic data using Beacons.

    Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P et al.

    Nature biotechnology 2019;37;3;220-224

    PUBMED: 30833764; PMC: 6728157; DOI: 10.1038/s41587-019-0046-x

  • Genetic determinants of risk in pulmonary arterial hypertension: international genome-wide association studies and meta-analysis.

    Rhodes CJ, Batai K, Bleda M, Haimel M, Southgate L, Germain M, Pauciulo MW, Hadinnapola C, Aman J, Girerd B et al.

    The Lancet. Respiratory medicine 2019;7;3;227-238

    PUBMED: 30527956; PMC: 6391516; DOI: 10.1016/S2213-2600(18)30409-0

  • Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations.

    Sakornsakolpat P, Prokopenko D, Lamontagne M, Reeve NF, Guyatt AL, Jackson VE, Shrine N, Qiao D, Bartz TM, Kim DK et al.

    Nature genetics 2019;51;3;494-505

    PUBMED: 30804561; PMC: 6546635; DOI: 10.1038/s41588-018-0342-2

  • Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing.

    Kunkle BW, Grenier-Boley B, Sims R, Bis JC, Damotte V, Naj AC, Boland A, Vronskaya M, van der Lee SJ, Amlie-Wolf A et al.

    Nature genetics 2019;51;3;414-430

    PUBMED: 30820047; PMC: 6463297; DOI: 10.1038/s41588-019-0358-2

  • How elusive can a malaria vaccine be?

    Pance A

    Nature reviews. Microbiology 2019;17;3;129

    PUBMED: 30626910; DOI: 10.1038/s41579-018-0148-3

  • Human biology and ancient DNA: exploring disease, domestication and movement.

    Houldcroft CJ, Rifkin RF and Underdown SJ

    Annals of human biology 2019;46;2;95-98

    PUBMED: 31303107; DOI: 10.1080/03014460.2019.1629536

  • Identification and expression profiling of microRNAs in Hymenolepis.

    Macchiaroli N, Cucher M, Kamenetzky L, Yones C, Bugnon L, Berriman M, Olson PD and Rosenzvit MC

    International journal for parasitology 2019;49;3-4;211-223

    PUBMED: 30677390; DOI: 10.1016/j.ijpara.2018.07.005

  • Identification of common genetic risk variants for autism spectrum disorder.

    Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R et al.

    Nature genetics 2019;51;3;431-444

    PUBMED: 30804558; PMC: 6454898; DOI: 10.1038/s41588-019-0344-8

  • Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.

    Nguyen VT, Jamrozy D, Matamoros S, Carrique-Mas JJ, Ho HM, Thai QH, Nguyen TNM, Wagenaar JA, Thwaites G, Parkhill J et al.

    The Journal of antimicrobial chemotherapy 2019;74;3;561-570

    PUBMED: 30629197; PMC: 6376849; DOI: 10.1093/jac/dky506

  • Nasal carriage of Staphylococcus pseudintermedius in patients with granulomatosis with polyangiitis.

    Kronbichler A, Blane B, Holmes MA, Wagner J, Parkhill J, Peacock SJ, Jayne DRW and Harrison EM

    Rheumatology (Oxford, England) 2019;58;3;548-550

    PUBMED: 30412252; PMC: 6381761; DOI: 10.1093/rheumatology/key317

  • New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

    Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P et al.

    Nature genetics 2019;51;3;481-493

    PUBMED: 30804560; PMC: 6397078; DOI: 10.1038/s41588-018-0321-7

  • Oral delivery of the anti-tumor necrosis factor α domain antibody, V565, results in high intestinal and fecal concentrations with minimal systemic exposure in cynomolgus monkeys.

    Crowe JS, Roberts KJ, Carlton TM, Maggiore L, Cubitt MF, Ray KP, Donnelly MC, Wahlich JC, Humphreys JI, Robinson JR et al.

    Drug development and industrial pharmacy 2019;45;3;387-394

    PUBMED: 30395728; DOI: 10.1080/03639045.2018.1542708

  • Using a Systems Biology Approach To Study Host-Pathogen Interactions.

    Yeung A, Hale C, Clare S, Palmer S, Bartholdson Scott J, Baker S and Dougan G

    Microbiology spectrum 2019;7;2

    PUBMED: 30953425; DOI: 10.1128/microbiolspec.BAI-0021-2019

  • Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea.

    Greenhill AR, Mutreja A, Bulach D, Belousoff MJ, Jonduo MH, Collins DA, Kas MP, Wapling J, Seemann T, Lafana A et al.

    Microbial genomics 2019;5;3

    PUBMED: 30810520; PMC: 6487313; DOI: 10.1099/mgen.0.000256

  • The golden death bacillus Chryseobacterium nematophagum is a novel matrix digesting pathogen of nematodes.

    Page AP, Roberts M, Félix MA, Pickard D, Page A and Weir W

    BMC biology 2019;17;1;10

    PUBMED: 30813925; PMC: 6394051; DOI: 10.1186/s12915-019-0632-x

  • De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome.

    Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W et al.

    Genome medicine 2019;11;1;12

    PUBMED: 30819258; PMC: 6393995; DOI: 10.1186/s13073-019-0623-0

  • Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability.

    Cogné B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR et al.

    American journal of human genetics 2019;104;3;530-541

    PUBMED: 30827496; PMC: 6407527; DOI: 10.1016/j.ajhg.2019.01.010

  • Inactivation of Ppp1r15a minimises weight gain and insulin resistance during caloric excess in female mice.

    Patel V, Bidault G, Chambers JE, Carobbio S, Everden AJT, Garcés C, Dalton LE, Gribble FM, Vidal-Puig A and Marciniak SJ

    Scientific reports 2019;9;1;2903

    PUBMED: 30814564; PMC: 6393541; DOI: 10.1038/s41598-019-39562-y

  • Association of Genetic Variants in NUDT15 With Thiopurine-Induced Myelosuppression in Patients With Inflammatory Bowel Disease.

    Walker GJ, Harrison JW, Heap GA, Voskuil MD, Andersen V, Anderson CA, Ananthakrishnan AN, Barrett JC, Beaugerie L, Bewshea CM et al.

    JAMA 2019;321;8;773-785

    PUBMED: 30806694; PMC: 6439872; DOI: 10.1001/jama.2019.0709

  • Genome-wide association study suggests impact of chromosome 10 rs139401390 on kidney function in patients with coronary artery disease.

    Schmitz B, Kleber ME, Lenders M, Delgado GE, Engelbertz C, Huang J, Pavenstädt H, Breithardt G, Brand SM, März W and Brand E

    Scientific reports 2019;9;1;2750

    PUBMED: 30809046; PMC: 6391429; DOI: 10.1038/s41598-019-39055-y

  • A single-cell molecular map of mouse gastrulation and early organogenesis.

    Pijuan-Sala B, Griffiths JA, Guibentif C, Hiscock TW, Jawaid W, Calero-Nieto FJ, Mulas C, Ibarra-Soria X, Tyser RCV, Ho DLL et al.

    Nature 2019;566;7745;490-495

    PUBMED: 30787436; PMC: 6522369; DOI: 10.1038/s41586-019-0933-9

  • Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1.

    Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S, Pickard D, Wilksch J, Cao H, Haq IU, Dougan G and Strugnell RA

    Scientific reports 2019;9;1;2392

    PUBMED: 30787414; PMC: 6382945; DOI: 10.1038/s41598-019-38943-7

  • Compensatory growth renders Tcf7l1a dispensable for eye formation despite its requirement in eye field specification.

    Young RM, Hawkins TA, Cavodeassi F, Stickney HL, Schwarz Q, Lawrence LM, Wierzbicki C, Cheng BY, Luo J, Ambrosio EM et al.

    eLife 2019;8

    PUBMED: 30777146; PMC: 6380838; DOI: 10.7554/eLife.40093

  • Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

    Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A et al.

    Cell reports 2019;26;8;2078-2087.e3

    PUBMED: 30784590; PMC: 6381787; DOI: 10.1016/j.celrep.2019.01.094

  • Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation.

    Miragaia RJ, Gomes T, Chomka A, Jardine L, Riedel A, Hegazy AN, Whibley N, Tucci A, Chen X, Lindeman I et al.

    Immunity 2019;50;2;493-504.e7

    PUBMED: 30737144; PMC: 6382439; DOI: 10.1016/j.immuni.2019.01.001

  • Identification of functional long non-coding RNAs in C. elegans.

    Akay A, Jordan D, Navarro IC, Wrzesinski T, Ponting CP, Miska EA and Haerty W

    BMC biology 2019;17;1;14

    PUBMED: 30777050; PMC: 6378714; DOI: 10.1186/s12915-019-0635-7

  • Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.

    Justice AE, Karaderi T, Highland HM, Young KL, Graff M, Lu Y, Turcot V, Auer PL, Fine RS, Guo X et al.

    Nature genetics 2019;51;3;452-469

    PUBMED: 30778226; PMC: 6560635; DOI: 10.1038/s41588-018-0334-2

  • The epilepsy-associated protein TBC1D24 is required for normal development, survival and vesicle trafficking in mammalian neurons.

    Finelli MJ, Aprile D, Castroflorio E, Jeans A, Moschetta M, Chessum L, Degiacomi MT, Grasegger J, Lupien-Meilleur A, Bassett A et al.

    Human molecular genetics 2019;28;4;584-597

    PUBMED: 30335140; PMC: 6360273; DOI: 10.1093/hmg/ddy370

  • O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli.

    Sharp C, Boinett C, Cain A, Housden NG, Kumar S, Turner K, Parkhill J and Kleanthous C

    Journal of bacteriology 2019;201;4

    PUBMED: 30510143; PMC: 6351738; DOI: 10.1128/JB.00545-18

  • A new genomic blueprint of the human gut microbiota.

    Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD and Finn RD

    Nature 2019;568;7753;499-504

    PUBMED: 30745586; PMC: 6784870; DOI: 10.1038/s41586-019-0965-1

  • Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

    Linker SM, Urban L, Clark SJ, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O and Bonder MJ

    Genome biology 2019;20;1;30

    PUBMED: 30744673; PMC: 6371455; DOI: 10.1186/s13059-019-1644-0

  • Metastasis in the wild: investigating metastasis in non-laboratory animals.

    Abu-Helil B and van der Weyden L

    Clinical & experimental metastasis 2019;36;1;15-28

    PUBMED: 30739231; PMC: 6394581; DOI: 10.1007/s10585-019-09956-3

  • De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability.

    Nicola P, Blackburn PR, Rasmussen KJ, Bertsch NL, Klee EW, Hasadsri L, Pichurin PN, Rankin J, Raymond FL, DDD Study and Clayton-Smith J

    American journal of medical genetics. Part A 2019;179;4;570-578

    PUBMED: 30734472; DOI: 10.1002/ajmg.a.61061

  • Human Semaphorin 3 Variants Link Melanocortin Circuit Development and Energy Balance.

    van der Klaauw AA, Croizier S, Mendes de Oliveira E, Stadler LKJ, Park S, Kong Y, Banton MC, Tandon P, Hendricks AE, Keogh JM et al.

    Cell 2019;176;4;729-742.e18

    PUBMED: 30661757; PMC: 6370916; DOI: 10.1016/j.cell.2018.12.009

  • Clonal approaches to understanding the impact of mutations on hematologic disease development.

    Nangalia J, Mitchell E and Green AR

    Blood 2019;133;13;1436-1445

    PUBMED: 30728143; DOI: 10.1182/blood-2018-11-835405

  • Elevated apoptosis impairs epithelial cell turnover and shortens villi in TNF-driven intestinal inflammation.

    Parker A, Vaux L, Patterson AM, Modasia A, Muraro D, Fletcher AG, Byrne HM, Maini PK, Watson AJM and Pin C

    Cell death & disease 2019;10;2;108

    PUBMED: 30728350; PMC: 6365534; DOI: 10.1038/s41419-018-1275-5

  • Histone modifications underlie monocyte dysregulation in patients with systemic sclerosis, underlining the treatment potential of epigenetic targeting.

    van der Kroef M, Castellucci M, Mokry M, Cossu M, Garonzi M, Bossini-Castillo LM, Chouri E, Wichers CGK, Beretta L, Trombetta E et al.

    Annals of the rheumatic diseases 2019;78;4;529-538

    PUBMED: 30793699; DOI: 10.1136/annrheumdis-2018-214295

  • Mycobacterium ulcerans Population Genomics To Inform on the Spread of Buruli Ulcer across Central Africa.

    Vandelannoote K, Phanzu DM, Kibadi K, Eddyani M, Meehan CJ, Jordaens K, Leirs H, Portaels F, Stinear TP, Harris SR and de Jong BC

    mSphere 2019;4;1

    PUBMED: 30728280; PMC: 6365612; DOI: 10.1128/mSphere.00472-18

  • 'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs.

    Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC, Cormie C, Ochoa-Montaño B, Ling CL, Tangmanakit J, Turner P and Parkhill J

    Microbial genomics 2019;5;2

    PUBMED: 30720420; PMC: 6421346; DOI: 10.1099/mgen.0.000247

  • Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii.

    Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M et al.

    Microbial genomics 2019;5;2

    PUBMED: 30720421; PMC: 6421349; DOI: 10.1099/mgen.0.000246

  • Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

    Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F and Garnett MJ

    Genome biology 2019;20;1;27

    PUBMED: 30722791; PMC: 6362594; DOI: 10.1186/s13059-019-1637-z

  • A human gut bacterial genome and culture collection for improved metagenomic analyses.

    Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y et al.

    Nature biotechnology 2019;37;2;186-192

    PUBMED: 30718869; PMC: 6785715; DOI: 10.1038/s41587-018-0009-7

  • Genome-wide Approaches to Investigate Anthelmintic Resistance.

    Doyle SR and Cotton JA

    Trends in parasitology 2019;35;4;289-301

    PUBMED: 30733094; DOI: 10.1016/j.pt.2019.01.004

  • Genome-wide by environment interaction studies of depressive symptoms and psychosocial stress in UK Biobank and Generation Scotland.

    Arnau-Soler A, Macdonald-Dunlop E, Adams MJ, Clarke TK, MacIntyre DJ, Milburn K, Navrady L, Generation Scotland, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Hayward C et al.

    Translational psychiatry 2019;9;1;14

    PUBMED: 30718454; PMC: 6361928; DOI: 10.1038/s41398-018-0360-y

  • The 2018 Otto Aufranc Award: How Does Genome-wide Variation Affect Osteolysis Risk After THA?

    MacInnes SJ, Hatzikotoulas K, Fenstad AM, Shah K, Southam L, Tachmazidou I, Hallan G, Dale H, Panoutsopoulou K, Furnes O et al.

    Clinical orthopaedics and related research 2019;477;2;297-309

    PUBMED: 30794219; PMC: 6370091; DOI: 10.1097/01.blo.0000533629.49193.09

  • An atlas of genetic influences on osteoporosis in humans and mice.

    Morris JA, Kemp JP, Youlten SE, Laurent L, Logan JG, Chai RC, Vulpescu NA, Forgetta V, Kleinman A, Mohanty ST et al.

    Nature genetics 2019;51;2;258-266

    PUBMED: 30598549; PMC: 6358485; DOI: 10.1038/s41588-018-0302-x

  • The impact of targeted malaria elimination with mass drug administrations on falciparum malaria in Southeast Asia: A cluster randomised trial.

    von Seidlein L, Peto TJ, Landier J, Nguyen TN, Tripura R, Phommasone K, Pongvongsa T, Lwin KM, Keereecharoen L, Kajeechiwa L et al.

    PLoS medicine 2019;16;2;e1002745

    PUBMED: 30768615; PMC: 6377128; DOI: 10.1371/journal.pmed.1002745

  • A library of recombinant Babesia microti cell surface and secreted proteins for diagnostics discovery and reverse vaccinology.

    Elton CM, Rodriguez M, Ben Mamoun C, Lobo CA and Wright GJ

    International journal for parasitology 2019;49;2;115-125

    PUBMED: 30367868; PMC: 6406021; DOI: 10.1016/j.ijpara.2018.10.003

  • Deletion of myeloid IRS2 enhances adipose tissue sympathetic nerve function and limits obesity.

    Rached MT, Millership SJ, Pedroni SMA, Choudhury AI, Costa ASH, Hardy DG, Glegola JA, Irvine EE, Selman C, Woodberry MC et al.

    Molecular metabolism 2019;20;38-50

    PUBMED: 30553769; PMC: 6358539; DOI: 10.1016/j.molmet.2018.11.010

  • Disentangling the genetics of lean mass.

    Karasik D, Zillikens MC, Hsu YH, Aghdassi A, Akesson K, Amin N, Barroso I, Bennett DA, Bertram L, Bochud M et al.

    The American journal of clinical nutrition 2019;109;2;276-287

    PUBMED: 30721968; PMC: 6500901; DOI: 10.1093/ajcn/nqy272

  • DORA Editorial.

    Parish T, Harris M, Fry N, Mathee K, Trujillo ME, Bentley S and Thomson N

    Journal of medical microbiology 2019;68;2;117-118

    PUBMED: 30516466; DOI: 10.1099/jmm.0.000887

  • Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program.

    Eckersley-Maslin M, Alda-Catalinas C, Blotenburg M, Kreibich E, Krueger C and Reik W

    Genes & development 2019;33;3-4;194-208

    PUBMED: 30692203; PMC: 6362816; DOI: 10.1101/gad.321174.118

  • Endothelin receptor Aa regulates proliferation and differentiation of Erb-dependent pigment progenitors in zebrafish.

    Camargo-Sosa K, Colanesi S, Müller J, Schulte-Merker S, Stemple D, Patton EE and Kelsh RN

    PLoS genetics 2019;15;2;e1007941

    PUBMED: 30811380; PMC: 6392274; DOI: 10.1371/journal.pgen.1007941

  • FAM92A Underlies Nonsyndromic Postaxial Polydactyly in Humans and an Abnormal Limb and Digit Skeletal Phenotype in Mice.

    Schrauwen I, Giese AP, Aziz A, Lafont DT, Chakchouk I, Santos-Cortez RLP, Lee K, Acharya A, Khan FS, Ullah A et al.

    Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2019;34;2;375-386

    PUBMED: 30395363; PMC: 6489482; DOI: 10.1002/jbmr.3594

  • GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals.

    Iotchkova V, Ritchie GRS, Geihs M, Morganella S, Min JL, Walter K, Timpson NJ, UK10K Consortium, Dunham I, Birney E and Soranzo N

    Nature genetics 2019;51;2;343-353

    PUBMED: 30692680; DOI: 10.1038/s41588-018-0322-6

  • Genome-scale drop-out screens to identify cancer cell vulnerabilities in AML.

    Basheer FT and Vassiliou GS

    Current opinion in genetics & development 2019;54;83-87

    PUBMED: 31063922; DOI: 10.1016/j.gde.2019.04.004

  • Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.

    Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J, French NP, Savoian MS, Gardner PP and Biggs PJ

    Microbial genomics 2019;5;2

    PUBMED: 30777818; PMC: 6421344; DOI: 10.1099/mgen.0.000251

  • IL-33 Augments Virus-Specific Memory T Cell Inflation and Potentiates the Efficacy of an Attenuated Cytomegalovirus-Based Vaccine.

    McLaren JE, Clement M, Marsden M, Miners KL, Llewellyn-Lacey S, Grant EJ, Rubina A, Gimeno Brias S, Gostick E, Stacey MA et al.

    Journal of immunology (Baltimore, Md. : 1950) 2019;202;3;943-955

    PUBMED: 30635396; PMC: 6341181; DOI: 10.4049/jimmunol.1701757

  • Important Extracellular Interactions between Plasmodium Sporozoites and Host Cells Required for Infection.

    Dundas K, Shears MJ, Sinnis P and Wright GJ

    Trends in parasitology 2019;35;2;129-139

    PUBMED: 30583849; PMC: 6375296; DOI: 10.1016/j.pt.2018.11.008

  • In vitro establishment of expanded-potential stem cells from mouse pre-implantation embryos or embryonic stem cells.

    Yang J, Ryan DJ, Lan G, Zou X and Liu P

    Nature protocols 2019;14;2;350-378

    PUBMED: 30617351; DOI: 10.1038/s41596-018-0096-4

  • Interleukin-6 Receptor Signaling and Abdominal Aortic Aneurysm Growth Rates.

    Paige E, Clément M, Lareyre F, Sweeting M, Raffort J, Grenier C, Finigan A, Harrison J, Peters JE, Sun BB et al.

    Circulation. Genomic and precision medicine 2019;12;2;e002413

    PUBMED: 30657332; PMC: 6383754; DOI: 10.1161/CIRCGEN.118.002413

  • Mammalian Hbs1L deficiency causes congenital anomalies and developmental delay associated with Pelota depletion and 80S monosome accumulation.

    O'Connell AE, Gerashchenko MV, O'Donohue MF, Rosen SM, Huntzinger E, Gleeson D, Galli A, Ryder E, Cao S, Murphy Q et al.

    PLoS genetics 2019;15;2;e1007917

    PUBMED: 30707697; PMC: 6373978; DOI: 10.1371/journal.pgen.1007917

  • Meeting the discovery challenge of drug-resistant infections: progress and focusing resources.

    Dougan G, Dowson C, Overington J and Next Generation Antibiotic Discovery Symposium Participants

    Drug discovery today 2019;24;2;452-461

    PUBMED: 30476550; DOI: 10.1016/j.drudis.2018.11.015

  • Targeting MEK in vemurafenib-resistant hairy cell leukemia.

    Caeser R, Collord G, Yao WQ, Chen Z, Vassiliou GS, Beer PA, Du MQ, Scott MA, Follows GA and Hodson DJ

    Leukemia 2019;33;2;541-545

    PUBMED: 30341394; PMC: 6365378; DOI: 10.1038/s41375-018-0270-2

  • Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment.

    Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Schütz F, Gönczy P, Piano F, Gunsalus K, Miska EA and Keller L

    PLoS genetics 2019;15;2;e1007905

    PUBMED: 30735500; PMC: 6383947; DOI: 10.1371/journal.pgen.1007905

  • Using genomics to understand antimicrobial resistance and transmission in Neisseria gonorrhoeae.

    Sánchez-Busó L and Harris SR

    Microbial genomics 2019;5;2

    PUBMED: 30698520; PMC: 6421347; DOI: 10.1099/mgen.0.000239

  • Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs.

    Canuti M, Williams CV, Sagan SM, Oude Munnink BB, Gadi S, Verhoeven JTP, Kellam P, Cotten M, Lang AS, Junge RE et al.

    Archives of virology 2019;164;2;509-522

    PUBMED: 30460488; DOI: 10.1007/s00705-018-4099-9

  • Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study.

    Lord J, McMullan DJ, Eberhardt RY, Rinck G, Hamilton SJ, Quinlan-Jones E, Prigmore E, Keelagher R, Best SK, Carey GK et al.

    Lancet (London, England) 2019;393;10173;747-757

    PUBMED: 30712880; PMC: 6386638; DOI: 10.1016/S0140-6736(18)31940-8

  • scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling.

    Lush ME, Diaz DC, Koenecke N, Baek S, Boldt H, St Peter MK, Gaitan-Escudero T, Romero-Carvajal A, Busch-Nentwich EM, Perera AG et al.

    eLife 2019;8

    PUBMED: 30681411; PMC: 6363392; DOI: 10.7554/eLife.44431

  • Fast and flexible bacterial genomic epidemiology with PopPUNK.

    Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD and Croucher NJ

    Genome research 2019;29;2;304-316

    PUBMED: 30679308; PMC: 6360808; DOI: 10.1101/gr.241455.118

  • JACKS: joint analysis of CRISPR/Cas9 knockout screens.

    Allen F, Behan F, Khodak A, Iorio F, Yusa K, Garnett M and Parts L

    Genome research 2019;29;3;464-471

    PUBMED: 30674557; PMC: 6396427; DOI: 10.1101/gr.238923.118

  • One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock.

    Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B, Coll F, de Goffau M, Naydenova P, Horner C, Hernandez-Garcia J et al.

    mBio 2019;10;1

    PUBMED: 30670621; PMC: 6343043; DOI: 10.1128/mBio.02693-18

  • Sociodemographic patterns of health insurance coverage in Namibia.

    Allcock SH, Young EH and Sandhu MS

    International journal for equity in health 2019;18;1;16

    PUBMED: 30670031; PMC: 6341740; DOI: 10.1186/s12939-019-0915-4

  • Towards Closed-Loop Integration of Point-of-Care Technologies.

    Tan EKW, Au YZ, Moghaddam GK, Occhipinti LG and Lowe CR

    Trends in biotechnology 2019

    PUBMED: 30683459; DOI: 10.1016/j.tibtech.2018.12.004

  • Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

    Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H, Lun ATL, Marioni JC and Reik W

    Cell reports 2019;26;4;815-824.e4

    PUBMED: 30673604; PMC: 6344340; DOI: 10.1016/j.celrep.2018.12.099

  • Cross-species genomic landscape comparison of human mucosal melanoma with canine oral and equine melanoma.

    Wong K, van der Weyden L, Schott CR, Foote A, Constantino-Casas F, Smith S, Dobson JM, Murchison EP, Wu H, Yeh I et al.

    Nature communications 2019;10;1;353

    PUBMED: 30664638; PMC: 6341101; DOI: 10.1038/s41467-018-08081-1

  • Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions.

    Teixeira VH, Pipinikas CP, Pennycuick A, Lee-Six H, Chandrasekharan D, Beane J, Morris TJ, Karpathakis A, Feber A, Breeze CE et al.

    Nature medicine 2019;25;3;517-525

    PUBMED: 30664780; DOI: 10.1038/s41591-018-0323-0

  • Genomic analysis of Plasmodium vivax in southern Ethiopia reveals selective pressures in multiple parasite mechanisms.

    Auburn S, Getachew S, Pearson RD, Amato R, Miotto O, Trimarsanto H, Zhu SJ, Rumaseb A, Marfurt J, Noviyanti R et al.

    The Journal of infectious diseases 2019

    PUBMED: 30668735; DOI: 10.1093/infdis/jiz016

  • Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data.

    Tachmazidou I, Hatzikotoulas K, Southam L, Esparza-Gordillo J, Haberland V, Zheng J, Johnson T, Koprulu M, Zengini E, Steinberg J et al.

    Nature genetics 2019;51;2;230-236

    PUBMED: 30664745; PMC: 6400267; DOI: 10.1038/s41588-018-0327-1

  • Low-frequency variation in TP53 has large effects on head circumference and intracranial volume.

    Haworth S, Shapland CY, Hayward C, Prins BP, Felix JF, Medina-Gomez C, Rivadeneira F, Wang C, Ahluwalia TS, Vrijheid M et al.

    Nature communications 2019;10;1;357

    PUBMED: 30664637; PMC: 6341110; DOI: 10.1038/s41467-018-07863-x

  • Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures.

    Zweier M, Begemann A, McWalter K, Cho MT, Abela L, Banka S, Behring B, Berger A, Brown CW, Carneiro M et al.

    European journal of human genetics : EJHG 2019;27;5;747-759

    PUBMED: 30664714; PMC: 6461771; DOI: 10.1038/s41431-018-0331-z

  • A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing.

    Kingan SB, Heaton H, Cudini J, Lambert CC, Baybayan P, Galvin BD, Durbin R, Korlach J and Lawniczak MKN

    Genes 2019;10;1

    PUBMED: 30669388; PMC: 6357164; DOI: 10.3390/genes10010062

  • Antibiotics-induced monodominance of a novel gut bacterial order.

    Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MT, Gossmann TI, Huerta-Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A et al.

    Gut 2019;68;10;1781-1790

    PUBMED: 30658995; PMC: 6839795; DOI: 10.1136/gutjnl-2018-317715

  • More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells.

    Gomez-Valero L, Rusniok C, Carson D, Mondino S, Pérez-Cobas AE, Rolando M, Pasricha S, Reuter S, Demirtas J, Crumbach J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2019

    PUBMED: 30659146; DOI: 10.1073/pnas.1808016116

  • De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism.

    Zawerton A, Yao B, Yeager JP, Pippucci T, Haseeb A, Smith JD, Wischmann L, Kühl SJ, Dean JCS, Pilz DT et al.

    American journal of human genetics 2019;104;2;246-259

    PUBMED: 30661772; PMC: 6369454; DOI: 10.1016/j.ajhg.2018.12.014

  • Human blood vessel organoids as a model of diabetic vasculopathy.

    Wimmer RA, Leopoldi A, Aichinger M, Wick N, Hantusch B, Novatchkova M, Taubenschmid J, Hämmerle M, Esk C, Bagley JA et al.

    Nature 2019;565;7740;505-510

    PUBMED: 30651639; PMC: 7116578; DOI: 10.1038/s41586-018-0858-8

  • Crumble: reference free lossy compression of sequence quality values.

    Bonfield JK, McCarthy SA and Durbin R

    Bioinformatics (Oxford, England) 2019;35;2;337-339

    PUBMED: 29992288; PMC: 6330002; DOI: 10.1093/bioinformatics/bty608

  • Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni.

    Ittiprasert W, Mann VH, Karinshak SE, Coghlan A, Rinaldi G, Sankaranarayanan G, Chaidee A, Tanno T, Kumkhaek C, Prangtaworn P et al.

    eLife 2019;8

    PUBMED: 30644357; PMC: 6355194; DOI: 10.7554/eLife.41337

  • Exclusive dependence of IL-10Rα signalling on intestinal microbiota homeostasis and control of whipworm infection.

    Duque-Correa MA, Karp NA, McCarthy C, Forman S, Goulding D, Sankaranarayanan G, Jenkins TP, Reid AJ, Cambridge EL, Ballesteros Reviriego C et al.

    PLoS pathogens 2019;15;1;e1007265

    PUBMED: 30640950; PMC: 6347331; DOI: 10.1371/journal.ppat.1007265

  • Refining the Primrose syndrome phenotype: A study of five patients with ZBTB20 de novo variants and a review of the literature.

    Cleaver R, Berg J, Craft E, Foster A, Gibbons RJ, Hobson E, Lachlan K, Naik S, Sampson JR, Sharif S et al.

    American journal of medical genetics. Part A 2019;179;3;344-349

    PUBMED: 30637921; DOI: 10.1002/ajmg.a.61024

  • TP53 mutation status divides myelodysplastic syndromes with complex karyotypes into distinct prognostic subgroups.

    Haase D, Stevenson KE, Neuberg D, Maciejewski JP, Nazha A, Sekeres MA, Ebert BL, Garcia-Manero G, Haferlach C, Haferlach T et al.

    Leukemia 2019;33;7;1747-1758

    PUBMED: 30635634; PMC: 6609480; DOI: 10.1038/s41375-018-0351-2

  • Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.

    Rascovan N, Sjögren KG, Kristiansen K, Nielsen R, Willerslev E, Desnues C and Rasmussen S

    Cell 2019;176;1-2;295-305.e10

    PUBMED: 30528431; DOI: 10.1016/j.cell.2018.11.005

  • Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.

    Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R and Teichmann SA

    Cell 2019;176;4;882-896.e18

    PUBMED: 30639098; PMC: 6370901; DOI: 10.1016/j.cell.2018.11.044

  • ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder.

    Carapito R, Ivanova EL, Morlon A, Meng L, Molitor A, Erdmann E, Kieffer B, Pichot A, Naegely L, Kolmer A et al.

    American journal of human genetics 2019;104;2;319-330

    PUBMED: 30639322; PMC: 6369415; DOI: 10.1016/j.ajhg.2018.12.007

  • A maternally inherited frameshift CDKL5 variant in a male with global developmental delay and late-onset generalized epilepsy.

    Fraser H, Goldman A, Wright R, Deciphering Developmental Disorders Study and Banka S

    American journal of medical genetics. Part A 2019;179;3;507-511

    PUBMED: 30624022; DOI: 10.1002/ajmg.a.40661

  • The Gene Ontology Resource: 20 years and still GOing strong.

    The Gene Ontology Consortium

    Nucleic acids research 2019;47;D1;D330-D338

    PUBMED: 30395331; PMC: 6323945; DOI: 10.1093/nar/gky1055

  • The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019.

    Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E et al.

    Nucleic acids research 2019;47;D1;D1005-D1012

    PUBMED: 30445434; PMC: 6323933; DOI: 10.1093/nar/gky1120

  • ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks.

    Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M, Barros AC, Woods M, Fu B, Yang F, Chen E et al.

    Nature communications 2019;10;1;87

    PUBMED: 30622252; PMC: 6325118; DOI: 10.1038/s41467-018-07729-2

  • BACTOME-a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates.

    Hornischer K, Khaledi A, Pohl S, Schniederjans M, Pezoldt L, Casilag F, Muthukumarasamy U, Bruchmann S, Thöming J, Kordes A and Häussler S

    Nucleic acids research 2019;47;D1;D716-D720

    PUBMED: 30272193; PMC: 6324029; DOI: 10.1093/nar/gky895

  • Cell Model Passports-a hub for clinical, genetic and functional datasets of preclinical cancer models.

    van der Meer D, Barthorpe S, Yang W, Lightfoot H, Hall C, Gilbert J, Francies HE and Garnett MJ

    Nucleic acids research 2019;47;D1;D923-D929

    PUBMED: 30260411; PMC: 6324059; DOI: 10.1093/nar/gky872

  • COSMIC: the Catalogue Of Somatic Mutations In Cancer.

    Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E et al.

    Nucleic acids research 2019;47;D1;D941-D947

    PUBMED: 30371878; PMC: 6323903; DOI: 10.1093/nar/gky1015

  • GATA6 Cooperates with EOMES/SMAD2/3 to Deploy the Gene Regulatory Network Governing Human Definitive Endoderm and Pancreas Formation.

    Chia CY, Madrigal P, Denil SLIJ, Martinez I, Garcia-Bernardo J, El-Khairi R, Chhatriwala M, Shepherd MH, Hattersley AT, Dunn NR and Vallier L

    Stem cell reports 2019;12;1;57-70

    PUBMED: 30629940; PMC: 6335596; DOI: 10.1016/j.stemcr.2018.12.003

  • Genetic effects on promoter usage are highly context-specific and contribute to complex traits.

    Alasoo K, Rodrigues J, Danesh J, Freitag DF, Paul DS and Gaffney DJ

    eLife 2019;8

    PUBMED: 30618377; PMC: 6349408; DOI: 10.7554/eLife.41673

  • Open Targets Platform: new developments and updates two years on.

    Carvalho-Silva D, Pierleoni A, Pignatelli M, Ong C, Fumis L, Karamanis N, Carmona M, Faulconbridge A, Hercules A, McAuley E et al.

    Nucleic acids research 2019;47;D1;D1056-D1065

    PUBMED: 30462303; PMC: 6324073; DOI: 10.1093/nar/gky1133

  • PDX Finder: A portal for patient-derived tumor xenograft model discovery.

    Conte N, Mason JC, Halmagyi C, Neuhauser S, Mosaku A, Yordanova G, Chatzipli A, Begley DA, Krupke DM, Parkinson H et al.

    Nucleic acids research 2019;47;D1;D1073-D1079

    PUBMED: 30535239; PMC: 6323912; DOI: 10.1093/nar/gky984

  • Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle.

    Vohra P, Chaudhuri RR, Mayho M, Vrettou C, Chintoan-Uta C, Thomson NR, Hope JC, Hopkins J and Stevens MP

    BMC genomics 2019;20;1;20

    PUBMED: 30621582; PMC: 6325888; DOI: 10.1186/s12864-018-5319-0

  • Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci.

    Erzurumluoglu AM, Liu M, Jackson VE, Barnes DR, Datta G, Melbourne CA, Young R, Batini C, Surendran P, Jiang T et al.

    Molecular psychiatry 2019

    PUBMED: 30617275; DOI: 10.1038/s41380-018-0313-0

  • Separating Bacteria by Capsule Amount Using a Discontinuous Density Gradient.

    Feltwell T, Dorman MJ, Goulding DA, Parkhill J and Short FL

    Journal of visualized experiments : JoVE 2019;143

    PUBMED: 30663644; DOI: 10.3791/58679

  • Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders.

    Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, Lacerda DR, Solli A, Norstedt J, Reed K et al.

    Current biology : CB 2019;29;1;149-157.e3

    PUBMED: 30581024; DOI: 10.1016/j.cub.2018.11.029

  • A Toxicogenomic Approach Reveals a Novel Gene Regulatory Network Active in In Vitro and In Vivo Models of Thyroid Carcinogenesis.

    Reale C, Russo F, Credendino SC, Cuomo D, De Vita G, Mallardo M, Pennino F, Porreca I, Triassi M, De Felice M and Ambrosino C

    International journal of environmental research and public health 2019;16;1

    PUBMED: 30621213; PMC: 6338918; DOI: 10.3390/ijerph16010122

  • The BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC Differentiation.

    Zhang W, Chronis C, Chen X, Zhang H, Spalinskas R, Pardo M, Chen L, Wu G, Zhu Z, Yu Y et al.

    Cell stem cell 2019;24;1;138-152.e8

    PUBMED: 30609396; PMC: 6486830; DOI: 10.1016/j.stem.2018.12.001

  • Integrating Genomics into Healthcare: A Global Responsibility.

    Stark Z, Dolman L, Manolio TA, Ozenberger B, Hill SL, Caulfied MJ, Levy Y, Glazer D, Wilson J, Lawler M et al.

    American journal of human genetics 2019;104;1;13-20

    PUBMED: 30609404; PMC: 6323624; DOI: 10.1016/j.ajhg.2018.11.014

  • Genomic insights into the 2016-2017 cholera epidemic in Yemen.

    Weill FX, Domman D, Njamkepo E, Almesbahi AA, Naji M, Nasher SS, Rakesh A, Assiri AM, Sharma NC, Kariuki S et al.

    Nature 2019;565;7738;230-233

    PUBMED: 30602788; PMC: 6420076; DOI: 10.1038/s41586-018-0818-3

  • A cellular census of human lungs identifies novel cell states in health and in asthma

    Vieira Braga, Felipe A., Kar, Gozde, Berg, Marijn, Carpaij, Orestes A., Polanski, Krzysztof et al.

    Nature Medicine 2019;25;7;1153

    DOI: 10.1038/s41591-019-0468-5; URL: https://doi.org/10.1038/s41591-019-0468-5

  • The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.

    Cremers AJH, Mobegi FM, van der Gaast-de Jongh C, van Weert M, van Opzeeland FJ, Vehkala M, Knol MJ, Bootsma HJ, Välimäki N, Croucher NJ et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019;68;1;61-69

    PUBMED: 29788414; DOI: 10.1093/cid/ciy417

  • An iPSC-Derived Myeloid Lineage Model of Herpes Virus Latency and Reactivation.

    Poole E, Huang CJZ, Forbester J, Shnayder M, Nachshon A, Kweider B, Basaj A, Smith D, Jackson SE, Liu B et al.

    Frontiers in microbiology 2019;10;2233

    PUBMED: 31649625; PMC: 6795026; DOI: 10.3389/fmicb.2019.02233

  • The Life Cycle of the Acropora Coral-Eating Flatworm (AEFW), Prosthiostomum acroporae; The Influence of Temperature and Management Guidelines

    Barton, Jonathan A., Hutson, Kate S., Bourne, David G., Humphrey, Craig, Dybala, Cat and Rawlinson et al.

    Frontiers in Marine Science 2019;6

    DOI: 10.3389/fmars.2019.00524; URL: https://doi.org/10.3389/fmars.2019.00524

  • A linear mixed-model approach to study multivariate gene-environment interactions.

    Moore R, Casale FP, Jan Bonder M, Horta D, BIOS Consortium, Franke L, Barroso I and Stegle O

    Nature genetics 2019;51;1;180-186

    PUBMED: 30478441; PMC: 6354905; DOI: 10.1038/s41588-018-0271-0

  • The USTC co-opts an ancient machinery to drive piRNA transcription in C. elegans.

    Weng C, Kosalka J, Berkyurek AC, Stempor P, Feng X, Mao H, Zeng C, Li WJ, Yan YH, Dong MQ et al.

    Genes & development 2019;33;1-2;90-102

    PUBMED: 30567997; PMC: 6317315; DOI: 10.1101/gad.319293.118

  • Antigen Receptor Sequence Reconstruction and Clonality Inference from scRNA-Seq Data.

    Lindeman I and Stubbington MJT

    Methods in molecular biology (Clifton, N.J.) 2019;1935;223-249

    PUBMED: 30758830; DOI: 10.1007/978-1-4939-9057-3_15

  • Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals.

    Mellor KC, Petrovska L, Thomson NR, Harris K, Reid SWJ and Mather AE

    Frontiers in microbiology 2019;10;708

    PUBMED: 31031720; PMC: 6473194; DOI: 10.3389/fmicb.2019.00708

  • Assays for functionally defined normal and malignant mammary stem cells.

    Aalam SMM, Beer PA and Kannan N

    Advances in cancer research 2019;141;129-174

    PUBMED: 30691682; DOI: 10.1016/bs.acr.2018.12.004

  • Beating tumour drug resistance: "Lamarckian" induction in the spotlight.

    Robles-Espinoza CD

    Pigment cell & melanoma research 2019;32;1;6-8

    PUBMED: 30339326; DOI: 10.1111/pcmr.12744

  • Brown and beige fat: From molecules to physiology and pathophysiology.

    Carobbio S, Guénantin AC, Samuelson I, Bahri M and Vidal-Puig A

    Biochimica et biophysica acta. Molecular and cell biology of lipids 2019;1864;1;37-50

    PUBMED: 29852279; DOI: 10.1016/j.bbalip.2018.05.013

  • Characterisation and correlates of stunting among Malaysian children and adolescents aged 6-19 years.

    Partap U, Young EH, Allotey P, Sandhu MS and Reidpath DD

    Global health, epidemiology and genomics 2019;4;e2

    PUBMED: 30891249; PMC: 6415126; DOI: 10.1017/gheg.2019.1

  • ChIPmentation for Low-Input Profiling of In Vivo Protein-DNA Interactions.

    Kunowska N and Chen X

    Methods in molecular biology (Clifton, N.J.) 2019;1979;269-282

    PUBMED: 31028644; DOI: 10.1007/978-1-4939-9240-9_17

  • Combined Genome and Transcriptome (G&T) Sequencing of Single Cells.

    Bronner IF and Lorenz S

    Methods in molecular biology (Clifton, N.J.) 2019;1979;319-362

    PUBMED: 31028647; DOI: 10.1007/978-1-4939-9240-9_20

  • Comparative Analysis of Microfluidics Thrombus Formation in Multiple Genetically Modified Mice: Link to Thrombosis and Hemostasis.

    Nagy M, van Geffen JP, Stegner D, Adams DJ, Braun A, de Witt SM, Elvers M, Geer MJ, Kuijpers MJE, Kunzelmann K et al.

    Frontiers in cardiovascular medicine 2019;6;99

    PUBMED: 31417909; PMC: 6682619; DOI: 10.3389/fcvm.2019.00099

  • Complimentary Methods for Multivariate Genome-Wide Association Study Identify New Susceptibility Genes for Blood Cell Traits.

    Fatumo S, Carstensen T, Nashiru O, Gurdasani D, Sandhu M and Kaleebu P

    Frontiers in genetics 2019;10;334

    PUBMED: 31080455; PMC: 6497788; DOI: 10.3389/fgene.2019.00334

  • Conditional Gene Knockout in Human Cells with Inducible CRISPR/Cas9.

    Snijders KE, Cooper JD, Vallier L and Bertero A

    Methods in molecular biology (Clifton, N.J.) 2019;1961;185-209

    PUBMED: 30912047; DOI: 10.1007/978-1-4939-9170-9_12

  • Derivation of Intestinal Organoids from Human Induced Pluripotent Stem Cells for Use as an Infection System.

    Forbester JL, Hannan N, Vallier L and Dougan G

    Methods in molecular biology (Clifton, N.J.) 2019;1576;157-169

    PUBMED: 27576565; DOI: 10.1007/7651_2016_7

  • Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

    Merla C, Rodrigues C, Passet V, Corbella M, Thorpe HA, Kallonen TVS, Zong Z, Marone P, Bandi C, Sassera D et al.

    Frontiers in microbiology 2019;10;2360

    PUBMED: 31708881; PMC: 6824210; DOI: 10.3389/fmicb.2019.02360

  • DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.

    Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E et al.

    Gut 2019;68;1;49-61

    PUBMED: 29141958; PMC: 6839835; DOI: 10.1136/gutjnl-2017-314817

  • DNA Sequence Variation in ACVR1C Encoding the Activin Receptor-Like Kinase 7 Influences Body Fat Distribution and Protects Against Type 2 Diabetes.

    Emdin CA, Khera AV, Aragam K, Haas M, Chaffin M, Klarin D, Natarajan P, Bick A, Zekavat SM, Nomura A et al.

    Diabetes 2019;68;1;226-234

    PUBMED: 30389748; PMC: 6302541; DOI: 10.2337/db18-0857

  • DORA Editorial.

    Parish T, Harris M, Fry N, Mathee K, Trujillo ME, Bentley S and Thomson N

    The Journal of general virology 2019;100;1;1-2

    PUBMED: 30516467; DOI: 10.1099/jgv.0.001191

  • Drug Sensitivity Assays of Human Cancer Organoid Cultures.

    Francies HE, Barthorpe A, McLaren-Douglas A, Barendt WJ and Garnett MJ

    Methods in molecular biology (Clifton, N.J.) 2019;1576;339-351

    PUBMED: 27628132; PMC: 6527507; DOI: 10.1007/7651_2016_10

  • Editing the Genome of Human Induced Pluripotent Stem Cells Using CRISPR/Cas9 Ribonucleoprotein Complexes.

    Bruntraeger M, Byrne M, Long K and Bassett AR

    Methods in molecular biology (Clifton, N.J.) 2019;1961;153-183

    PUBMED: 30912046; DOI: 10.1007/978-1-4939-9170-9_11

  • Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative.

    Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FPJ, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B et al.

    Frontiers in genetics 2019;10;611

    PUBMED: 31417602; PMC: 6681681; DOI: 10.3389/fgene.2019.00611

  • Evidence for increased genetic risk load for major depression in patients assigned to electroconvulsive therapy.

    Foo JC, Streit F, Frank J, Witt SH, Treutlein J, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Baune BT, Moebus S, Jöckel KH, Forstner AJ et al.

    American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2019;180;1;35-45

    PUBMED: 30507021; DOI: 10.1002/ajmg.b.32700

  • Exploring Plasmodium falciparum Var Gene Expression to Assess Host Selection Pressure on Parasites During Infancy.

    Kivisi CA, Muthui M, Hunt M, Fegan G, Otto TD, Githinji G, Warimwe GM, Rance R, Marsh K, Bull PC and Abdi AI

    Frontiers in immunology 2019;10;2328

    PUBMED: 31681266; PMC: 6798654; DOI: 10.3389/fimmu.2019.02328

  • Fat storage-inducing transmembrane protein 2 (FIT2) is less abundant in type 2 diabetes, and regulates triglyceride accumulation and insulin sensitivity in adipocytes.

    Agrawal M, Yeo CR, Shabbir A, Chhay V, Silver DL, Magkos F, Vidal-Puig A and Toh SA

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2019;33;1;430-440

    PUBMED: 30020828; DOI: 10.1096/fj.201701321RR

  • FBXO7 sensitivity of phenotypic traits elucidated by a hypomorphic allele.

    Ballesteros Reviriego C, Clare S, Arends MJ, Cambridge EL, Swiatkowska A, Caetano S, Abu-Helil B, Kane L, Harcourt K, Goulding DA et al.

    PloS one 2019;14;3;e0212481

    PUBMED: 30840666; PMC: 6402633; DOI: 10.1371/journal.pone.0212481

  • Generation of gene-corrected human induced pluripotent stem cell lines derived from retinitis pigmentosa patient with Ser331Cysfs*5 mutation in MERTK.

    Artero Castro A, Long K, Bassett A, Machuca C, León M, Ávila-Fernandez A, Cortón M, Vidal-Puig T, Ayuso C, Lukovic D and Erceg S

    Stem cell research 2019;34;101341

    PUBMED: 30612079; DOI: 10.1016/j.scr.2018.11.003

  • Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3.

    Guzmán-Verri C, Suárez-Esquivel M, Ruíz-Villalobos N, Zygmunt MS, Gonnet M, Campos E, Víquez-Ruiz E, Chacón-Díaz C, Aragón-Aranda B, Conde-Álvarez R et al.

    Frontiers in veterinary science 2019;6;175

    PUBMED: 31231665; PMC: 6568212; DOI: 10.3389/fvets.2019.00175

  • Genetic architecture of human thinness compared to severe obesity.

    Riveros-McKay F, Mistry V, Bounds R, Hendricks A, Keogh JM, Thomas H, Henning E, Corbin LJ, Understanding Society Scientific Group, O'Rahilly S et al.

    PLoS genetics 2019;15;1;e1007603

    PUBMED: 30677029; PMC: 6345421; DOI: 10.1371/journal.pgen.1007603

  • Genome-Wide Epigenetic and Transcriptomic Characterization of Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Organoids.

    Kraiczy J, Ross ADB, Forbester JL, Dougan G, Vallier L and Zilbauer M

    Cellular and molecular gastroenterology and hepatology 2019;7;2;285-288

    PUBMED: 30704978; PMC: 6354438; DOI: 10.1016/j.jcmgh.2018.10.008

  • Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.

    van Tonder AJ, Bray JE, Jolley KA, Jansen van Rensburg M, Quirk SJ, Haraldsson G, Maiden MCJ, Bentley SD, Haraldsson Á, Erlendsdóttir H et al.

    Frontiers in microbiology 2019;10;317

    PUBMED: 30858837; PMC: 6398412; DOI: 10.3389/fmicb.2019.00317

  • Germline mutations in the transcription factor IKZF5 cause thrombocytopenia

    Lentaigne, Claire, Greene, Daniel, Sivapalaratnam, Suthesh, Favier, Remi, Seyres, Denis et al.

    Blood 2019;134;23;2070

    DOI: 10.1182/blood.2019000782; URL: https://doi.org/10.1182/blood.2019000782

  • GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats.

    Dawson ET and Durbin R

    Journal of open source software 2019;4;33

    PUBMED: 31535074; PMC: 6751074; DOI: 10.21105/joss.01083

  • GPR35 promotes glycolysis, proliferation, and oncogenic signaling by engaging with the sodium potassium pump.

    Schneditz G, Elias JE, Pagano E, Zaeem Cader M, Saveljeva S, Long K, Mukhopadhyay S, Arasteh M, Lawley TD, Dougan G et al.

    Science signaling 2019;12;562

    PUBMED: 30600262; PMC: 6364804; DOI: 10.1126/scisignal.aau9048

  • High-Throughput Single-Cell Real-Time Quantitative PCR Analysis.

    Haim-Vilmovsky L

    Methods in molecular biology (Clifton, N.J.) 2019;1979;177-183

    PUBMED: 31028638; DOI: 10.1007/978-1-4939-9240-9_11

  • htsget: a protocol for securely streaming genomic data.

    Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A et al.

    Bioinformatics (Oxford, England) 2019;35;1;119-121

    PUBMED: 29931085; PMC: 6298043; DOI: 10.1093/bioinformatics/bty492

  • IgG and Fcγ Receptors in Intestinal Immunity and Inflammation.

    Castro-Dopico T and Clatworthy MR

    Frontiers in immunology 2019;10;805

    PUBMED: 31031776; PMC: 6473071; DOI: 10.3389/fimmu.2019.00805

  • Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.

    Chung WSF, Walker AW, Vermeiren J, Sheridan PO, Bosscher D, Garcia-Campayo V, Parkhill J, Flint HJ and Duncan SH

    FEMS microbiology ecology 2019;95;1

    PUBMED: 30304332; PMC: 6238074; DOI: 10.1093/femsec/fiy201

  • Infection with carcinogenic helminth parasites and its production of metabolites induces the formation of DNA-adducts.

    Gouveia MJ, Brindley PJ, Rinaldi G, Gärtner F, da Costa JMC and Vale N

    Infectious agents and cancer 2019;14;41

    PUBMED: 31798678; PMC: 6884881; DOI: 10.1186/s13027-019-0257-2

  • Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator.

    Abdallah AM, Weerdenburg EM, Guan Q, Ummels R, Borggreve S, Adroub SA, Malas TB, Naeem R, Zhang H, Otto TD et al.

    PloS one 2019;14;1;e0211003

    PUBMED: 30673778; DOI: 10.1371/journal.pone.0211003

  • Isolation of five Enterobacteriaceae species harbouring blaNDM-1 and mcr-1 plasmids from a single paediatric patient.

    Martino F, Tijet N, Melano R, Petroni A, Heinz E, De Belder D, Faccone D, Rapoport M, Biondi E, Rodrigo V et al.

    PloS one 2019;14;9;e0221960

    PUBMED: 31498841; PMC: 6733481; DOI: 10.1371/journal.pone.0221960

  • Males, the Wrongly Neglected Partners of the Biologically Unprecedented Male-Female Interaction of Schistosomes.

    Lu Z, Spänig S, Weth O and Grevelding CG

    Frontiers in genetics 2019;10;796

    PUBMED: 31552097; PMC: 6743411; DOI: 10.3389/fgene.2019.00796

  • Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States.

    Mohamed N, Timofeyeva Y, Jamrozy D, Rojas E, Hao L, Silmon de Monerri NC, Hawkins J, Singh G, Cai B, Liberator P et al.

    PloS one 2019;14;1;e0208356

    PUBMED: 30641545; PMC: 6331205; DOI: 10.1371/journal.pone.0208356

  • Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.

    Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M, Osei-Wusu S, Asare P, Aboagye SY, Ekuban SA, Yahayah AI et al.

    PloS one 2019;14;3;e0209395

    PUBMED: 30830912; PMC: 6398925; DOI: 10.1371/journal.pone.0209395

  • Mutations in the MAB_2299c TetR Regulator Confer Cross-Resistance to Clofazimine and Bedaquiline in Mycobacterium abscessus.

    Richard M, Gutiérrez AV, Viljoen A, Rodriguez-Rincon D, Roquet-Baneres F, Blaise M, Everall I, Parkhill J, Floto RA and Kremer L

    Antimicrobial agents and chemotherapy 2019;63;1

    PUBMED: 30323043; PMC: 6325171; DOI: 10.1128/AAC.01316-18

  • NOTCH1 Represses MCL-1 Levels in GSI-resistant T-ALL, Making them Susceptible to ABT-263.

    Dastur A, Choi A, Costa C, Yin X, Williams A, McClanaghan J, Greenberg M, Roderick J, Patel NU, Boisvert J et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2019;25;1;312-324

    PUBMED: 30224339; PMC: 6320296; DOI: 10.1158/1078-0432.CCR-18-0867

  • Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring.

    Beal MA, Meier MJ, Williams A, Rowan-Carroll A, Gagné R, Lindsay SJ, Fitzgerald T, Hurles ME, Marchetti F and Yauk CL

    Communications biology 2019;2;228

    PUBMED: 31240266; PMC: 6586636; DOI: 10.1038/s42003-019-0476-5

  • Peptides Derived of Kunitz-Type Serine Protease Inhibitor as Potential Vaccine Against Experimental Schistosomiasis.

    Hernández-Goenaga J, López-Abán J, Protasio AV, Vicente Santiago B, Del Olmo E, Vanegas M, Fernández-Soto P, Patarroyo MA and Muro A

    Frontiers in immunology 2019;10;2498

    PUBMED: 31736947; PMC: 6838133; DOI: 10.3389/fimmu.2019.02498

  • PiggyBac Transposon-Based Insertional Mutagenesis in Mice.

    Friedrich MJ, Bronner IF, Liu P, Bradley A and Rad R

    Methods in molecular biology (Clifton, N.J.) 2019;1907;171-183

    PUBMED: 30543000; DOI: 10.1007/978-1-4939-8967-6_14

  • Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013.

    Toleman MS, Reuter S, Jamrozy D, Wilson HJ, Blane B, Harrison EM, Coll F, Hope RJ, Kearns A, Parkhill J et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019;24;4

    PUBMED: 30696529; PMC: 6351993; DOI: 10.2807/1560-7917.ES.2019.24.4.1800215

  • Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A.

    Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF et al.

    NPJ genomic medicine 2019;4;31

    PUBMED: 31814998; PMC: 6889285; DOI: 10.1038/s41525-019-0106-7

  • Repeated clinical malaria episodes are associated with modification of the immune system in children

    Bediako, Yaw, Adams, Rhys, Reid, Adam J., Valletta, John Joseph, Ndungu, Francis M. et al.

    BMC Medicine 2019;17;1;1

    DOI: 10.1186/s12916-019-1292-y; URL: https://doi.org/10.1186/s12916-019-1292-y

  • Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes.

    Ferwerda B, Maury MM, Brouwer MC, Hafner L, van der Ende A, Bentley S, Lecuit M and van de Beek D

    Frontiers in microbiology 2019;10;2702

    PUBMED: 31849867; PMC: 6901971; DOI: 10.3389/fmicb.2019.02702

  • Resolving the fibrotic niche of human liver cirrhosis at single-cell level

    Ramachandran, P., Dobie, R., Wilson-Kanamori, J. R., Dora, E. F., Henderson, B. E. P. et al.

    Nature 2019;575;7783;512

    DOI: 10.1038/s41586-019-1631-3; URL: https://doi.org/10.1038/s41586-019-1631-3

  • Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing.

    Aicher TP, Carroll S, Raddi G, Gierahn T, Wadsworth MH, Hughes TK, Love C and Shalek AK

    Methods in molecular biology (Clifton, N.J.) 2019;1979;111-132

    PUBMED: 31028635; DOI: 10.1007/978-1-4939-9240-9_8

  • Sequencing in the time of Ebola.

    Van Puyvelde S and Argimon S

    Nature reviews. Microbiology 2019;17;1;5

    PUBMED: 30504802; DOI: 10.1038/s41579-018-0130-0

  • Setting Up a Single-Cell Genomic Laboratory.

    Mamanova L

    Methods in molecular biology (Clifton, N.J.) 2019;1979;3-8

    PUBMED: 31028628; DOI: 10.1007/978-1-4939-9240-9_1

  • Single-Cell RNA Sequencing with Drop-Seq.

    Bageritz J and Raddi G

    Methods in molecular biology (Clifton, N.J.) 2019;1979;73-85

    PUBMED: 31028633; DOI: 10.1007/978-1-4939-9240-9_6

  • Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding.

    MacFadyen AC, Drigo I, Harrison EM, Parkhill J, Holmes MA and Paterson GK

    International journal of systematic and evolutionary microbiology 2019;69;1;82-86

    PUBMED: 30427304; DOI: 10.1099/ijsem.0.003098

  • Studying DNA Methylation in Single-Cell Format with scBS-seq.

    Kunowska N

    Methods in molecular biology (Clifton, N.J.) 2019;1979;235-250

    PUBMED: 31028642; DOI: 10.1007/978-1-4939-9240-9_15

  • Tissue Handling and Dissociation for Single-Cell RNA-Seq.

    Vieira Braga FA and Miragaia RJ

    Methods in molecular biology (Clifton, N.J.) 2019;1979;9-21

    PUBMED: 31028629; DOI: 10.1007/978-1-4939-9240-9_2

  • Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania

    Ehud Inbar, Jahangheer Shaik, Stefano A. Iantorno, Audrey Romano, Chukwunonso O. Nzelu, Katherine Owens, Mandy J. Sanders, Deborah Dobson, James A. Cotton, Michael E. Grigg et al.

    PLOS Genetics 2019;15;5;e1008042

    DOI: 10.1371/journal.pgen.1008042; URL: https://doi.org/10.1371/journal.pgen.1008042

2018

  • Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics.

    Yiangou L, Grandy RA, Morell CM, Tomaz RA, Osnato A, Kadiwala J, Muraro D, Garcia-Bernardo J, Nakanoh S, Bernard WG et al.

    Stem cell reports 2018;12;1;165-179

    PUBMED: 30595546; PMC: 6335580; DOI: 10.1016/j.stemcr.2018.11.020

  • Pathogenicity and selective constraint on variation near splice sites.

    Lord J, Gallone G, Short PJ, McRae JF, Ironfield H, Wynn EH, Gerety SS, He L, Kerr B, Johnson DS et al.

    Genome research 2018;29;2;159-170

    PUBMED: 30587507; PMC: 6360807; DOI: 10.1101/gr.238444.118

  • Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

    Giri A, Hellwege JN, Keaton JM, Park J, Qiu C, Warren HR, Torstenson ES, Kovesdy CP, Sun YV, Wilson OD et al.

    Nature genetics 2018;51;1;51-62

    PUBMED: 30578418; PMC: 6365102; DOI: 10.1038/s41588-018-0303-9

  • A test metric for assessing single-cell RNA-seq batch correction.

    Büttner M, Miao Z, Wolf FA, Teichmann SA and Theis FJ

    Nature methods 2018;16;1;43-49

    PUBMED: 30573817; DOI: 10.1038/s41592-018-0254-1

  • ALDH1 Bio-activates Nifuroxazide to Eradicate ALDHHigh Melanoma-Initiating Cells.

    Sarvi S, Crispin R, Lu Y, Zeng L, Hurley TD, Houston DR, von Kriegsheim A, Chen CH, Mochly-Rosen D, Ranzani M et al.

    Cell chemical biology 2018;25;12;1456-1469.e6

    PUBMED: 30293938; PMC: 6309505; DOI: 10.1016/j.chembiol.2018.09.005

  • Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations.

    Márquez A, Kerick M, Zhernakova A, Gutierrez-Achury J, Chen WM, Onengut-Gumuscu S, González-Álvaro I, Rodriguez-Rodriguez L, Rios-Fernández R, González-Gay MA et al.

    Genome medicine 2018;10;1;97

    PUBMED: 30572963; PMC: 6302306; DOI: 10.1186/s13073-018-0604-8

  • Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance.

    Chacón-Duque JC, Adhikari K, Fuentes-Guajardo M, Mendoza-Revilla J, Acuña-Alonzo V, Barquera R, Quinto-Sánchez M, Gómez-Valdés J, Everardo Martínez P, Villamil-Ramírez H et al.

    Nature communications 2018;9;1;5388

    PUBMED: 30568240; PMC: 6300600; DOI: 10.1038/s41467-018-07748-z

  • Single cell analysis of clonal architecture in acute myeloid leukaemia.

    Potter N, Miraki-Moud F, Ermini L, Titley I, Vijayaraghavan G, Papaemmanuil E, Campbell P, Gribben J, Taussig D and Greaves M

    Leukemia 2018;33;5;1113-1123

    PUBMED: 30568172; PMC: 6451634; DOI: 10.1038/s41375-018-0319-2

  • SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.

    Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M et al.

    Nature communications 2018;9;1;5378

    PUBMED: 30568163; PMC: 6300607; DOI: 10.1038/s41467-018-07620-0

  • Emergence of dominant multidrug-resistant bacterial clades: Lessons from history and whole-genome sequencing.

    Klemm EJ, Wong VK and Dougan G

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;51;12872-12877

    PUBMED: 30559200; DOI: 10.1073/pnas.1717162115

  • A rapid and robust method for single cell chromatin accessibility profiling.

    Chen X, Miragaia RJ, Natarajan KN and Teichmann SA

    Nature communications 2018;9;1;5345

    PUBMED: 30559361; PMC: 6297232; DOI: 10.1038/s41467-018-07771-0

  • Cerebrofaciothoracic dysplasia: Four new patients with a recurrent TMCO1 pathogenic variant.

    Michael Yates T, Ng OH, Offiah AC, Willoughby J, Berg JN, DDD Study and Johnson DS

    American journal of medical genetics. Part A 2018;179;1;43-49

    PUBMED: 30556256; DOI: 10.1002/ajmg.a.60678

  • Chromosome Analysis Using Benchtop Flow Analysers and High Speed Cell Sorters.

    Ng BL, Fu B, Graham J, Hall C and Thompson S

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2018;95;3;323-331

    PUBMED: 30556955; PMC: 6491968; DOI: 10.1002/cyto.a.23692

  • Bi-allelic mutations in MYL1 cause a severe congenital myopathy.

    Ravenscroft G, Zaharieva IT, Bortolotti CA, Lambrughi M, Pignataro M, Borsari M, Sewry CA, Phadke R, Haliloglu G, Ong R et al.

    Human molecular genetics 2018;27;24;4263-4272

    PUBMED: 30215711; PMC: 6540289; DOI: 10.1093/hmg/ddy320

  • pyseer: a comprehensive tool for microbial pangenome-wide association studies.

    Lees JA, Galardini M, Bentley SD, Weiser JN and Corander J

    Bioinformatics (Oxford, England) 2018;34;24;4310-4312

    PUBMED: 30535304; PMC: 6289128; DOI: 10.1093/bioinformatics/bty539

  • Visualising the Cardiovascular System of Embryos of Biomedical Model Organisms with High Resolution Episcopic Microscopy (HREM).

    Weninger WJ, Maurer-Gesek B, Reissig LF, Prin F, Wilson R, Galli A, Adams DJ, White JK, Mohun TJ and Geyer SH

    Journal of cardiovascular development and disease 2018;5;4

    PUBMED: 30558275; PMC: 6306920; DOI: 10.3390/jcdd5040058

  • Bayesian inference of ancestral dates on bacterial phylogenetic trees.

    Didelot X, Croucher NJ, Bentley SD, Harris SR and Wilson DJ

    Nucleic acids research 2018;46;22;e134

    PUBMED: 30184106; PMC: 6294524; DOI: 10.1093/nar/gky783

  • Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.

    Moradigaravand D, Palm M, Farewell A, Mustonen V, Warringer J and Parts L

    PLoS computational biology 2018;14;12;e1006258

    PUBMED: 30550564; PMC: 6310291; DOI: 10.1371/journal.pcbi.1006258

  • A synthesis approach of mouse studies to identify genes and proteins in arterial thrombosis and bleeding.

    Baaten CCFMJ, Meacham S, de Witt SM, Feijge MAH, Adams DJ, Akkerman JN, Cosemans JMEM, Grassi L, Jupe S, Kostadima M et al.

    Blood 2018;132;24;e35-e46

    PUBMED: 30275110; PMC: 6293874; DOI: 10.1182/blood-2018-02-831982

  • CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines.

    Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI et al.

    iScience 2018;10;247-264

    PUBMED: 30553813; PMC: 6302245; DOI: 10.1016/j.isci.2018.11.029

  • Chemical Synergy between Ionophore PBT2 and Zinc Reverses Antibiotic Resistance.

    Bohlmann L, De Oliveira DMP, El-Deeb IM, Brazel EB, Harbison-Price N, Ong CY, Rivera-Hernandez T, Ferguson SA, Cork AJ, Phan MD et al.

    mBio 2018;9;6

    PUBMED: 30538186; PMC: 6299484; DOI: 10.1128/mBio.02391-18

  • Robust adaptive immune response against Babesia microti infection marked by low parasitemia in a murine model of sickle cell disease.

    Yi W, Bao W, Rodriguez M, Liu Y, Singh M, Ramlall V, Cursino-Santos JR, Zhong H, Elton CM, Wright GJ et al.

    Blood advances 2018;2;23;3462-3478

    PUBMED: 30518538; PMC: 6290097; DOI: 10.1182/bloodadvances.2018026468

  • Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies.

    International League Against Epilepsy Consortium on Complex Epilepsies

    Nature communications 2018;9;1;5269

    PUBMED: 30531953; PMC: 6288131; DOI: 10.1038/s41467-018-07524-z

  • Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum.

    Tarr SJ, Díaz-Ingelmo O, Stewart LB, Hocking SE, Murray L, Duffy CW, Otto TD, Chappell L, Rayner JC, Awandare GA and Conway DJ

    BMC genomics 2018;19;1;894

    PUBMED: 30526479; PMC: 6288915; DOI: 10.1186/s12864-018-5257-x

  • Early human dispersals within the Americas.

    Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T et al.

    Science (New York, N.Y.) 2018;362;6419

    PUBMED: 30409807; DOI: 10.1126/science.aav2621

  • Cyclosporine H Overcomes Innate Immune Restrictions to Improve Lentiviral Transduction and Gene Editing In Human Hematopoietic Stem Cells.

    Petrillo C, Thorne LG, Unali G, Schiroli G, Giordano AMS, Piras F, Cuccovillo I, Petit SJ, Ahsan F, Noursadeghi M et al.

    Cell stem cell 2018;23;6;820-832.e9

    PUBMED: 30416070; PMC: 6292841; DOI: 10.1016/j.stem.2018.10.008

  • Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern.

    Lin JW, Reid AJ, Cunningham D, Böhme U, Tumwine I, Keller-Mclaughlin S, Sanders M, Berriman M and Langhorne J

    Wellcome open research 2018;3;142

    PUBMED: 30542666; PMC: 6259598; DOI: 10.12688/wellcomeopenres.14797.2

  • DORA Editorial.

    Parish T, Harris M, Fry N, Mathee K, Trujillo ME, Bentley S and Thomson N

    International journal of systematic and evolutionary microbiology 2018

    PUBMED: 30516461; DOI: 10.1099/ijsem.0.003172

  • DORA Editorial.

    Parish T, Harris M, Fry N, Mathee K, Trujillo ME, Bentley S and Thomson N

    Microbiology (Reading, England) 2018

    PUBMED: 30516468; DOI: 10.1099/mic.0.000751

  • The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background.

    Zhu L, Tripathi J, Rocamora FM, Miotto O, van der Pluijm R, Voss TS, Mok S, Kwiatkowski DP, Nosten F, Day NPJ et al.

    Nature communications 2018;9;1;5158

    PUBMED: 30514877; PMC: 6279830; DOI: 10.1038/s41467-018-07588-x

  • Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer.

    Golparian D, Donà V, Sánchez-Busó L, Foerster S, Harris S, Endimiani A, Low N and Unemo M

    Scientific reports 2018;8;1;17596

    PUBMED: 30514867; PMC: 6279828; DOI: 10.1038/s41598-018-35750-4

  • A highly conserved mecC-encoding SCCmec type XI in a bovine isolate of methicillin-resistant Staphylococcus xylosus.

    MacFadyen AC, Harrison EM, Ellington MJ, Parkhill J, Holmes MA and Paterson GK

    The Journal of antimicrobial chemotherapy 2018;73;12;3516-3518

    PUBMED: 30165441; PMC: 6292145; DOI: 10.1093/jac/dky333

  • A novel IGSF1 mutation in a large Irish kindred highlights the need for familial screening in the IGSF1 deficiency syndrome.

    Roche EF, McGowan A, Koulouri O, Turgeon MO, Nicholas AK, Heffernan E, El-Khairi R, Abid N, Lyons G, Halsall D et al.

    Clinical endocrinology 2018;89;6;813-823

    PUBMED: 30086211; PMC: 6282842; DOI: 10.1111/cen.13827

  • 5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells.

    Raiber EA, Portella G, Martínez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D et al.

    Nature chemistry 2018;10;12;1258-1266

    PUBMED: 30349137; DOI: 10.1038/s41557-018-0149-x

  • Amino acid residues in five separate HLA genes can explain most of the known associations between the MHC and primary biliary cholangitis.

    Darlay R, Ayers KL, Mells GF, Hall LS, Liu JZ, Almarri MA, Alexander GJ, Jones DE, Sandford RN, Anderson CA and Cordell HJ

    PLoS genetics 2018;14;12;e1007833

    PUBMED: 30507971; PMC: 6292650; DOI: 10.1371/journal.pgen.1007833

  • Analysis of novel missense ATR mutations reveals new splicing defects underlying Seckel syndrome.

    Llorens-Agost M, Luessing J, van Beneden A, Eykelenboom J, O'Reilly D, Bicknell LS, Reynolds JJ, van Koegelenberg M, Hurles ME, Brady AF et al.

    Human mutation 2018;39;12;1847-1853

    PUBMED: 30199583; DOI: 10.1002/humu.23648

  • Ancient nuclear genomes enable repatriation of Indigenous human remains.

    Wright JL, Wasef S, Heupink TH, Westaway MC, Rasmussen S, Pardoe C, Fourmile GG, Young M, Johnson T, Slade J et al.

    Science advances 2018;4;12;eaau5064

    PUBMED: 30585290; PMC: 6300400; DOI: 10.1126/sciadv.aau5064

  • Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide.

    Walpole S, Pritchard AL, Cebulla CM, Pilarski R, Stautberg M, Davidorf FH, de la Fouchardière A, Cabaret O, Golmard L, Stoppa-Lyonnet D et al.

    Journal of the National Cancer Institute 2018;110;12;1328-1341

    PUBMED: 30517737; PMC: 6292796; DOI: 10.1093/jnci/djy171

  • DORA Editorial.

    Parish T, Harris M, Fry N, Mathee K, Trujillo ME, Bentley S and Thomson N

    Microbial genomics 2018;4;12

    PUBMED: 30516464; PMC: 6412037; DOI: 10.1099/mgen.0.000238

  • Genome-wide haplotyping embryos developing from 0PN and 1PN zygotes increases transferrable embryos in PGT-M.

    Destouni A, Dimitriadou E, Masset H, Debrock S, Melotte C, Van Den Bogaert K, Zamani Esteki M, Ding J, Voet T, Denayer E et al.

    Human reproduction (Oxford, England) 2018;33;12;2302-2311

    PUBMED: 30383227; PMC: 6238370; DOI: 10.1093/humrep/dey325

  • Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex.

    Sanoussi CN, de Jong BC, Odoun M, Arekpa K, Ali Ligali M, Bodi O, Harris S, Ofori-Anyinam B, Yeboah-Manu D, Otchere ID et al.

    Journal of medical microbiology 2018;67;12;1718-1727

    PUBMED: 30388066; DOI: 10.1099/jmm.0.000846

  • Neutral tumor evolution?

    Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC and Van Loo P

    Nature genetics 2018;50;12;1630-1633

    PUBMED: 30374075; PMC: 6548558; DOI: 10.1038/s41588-018-0258-x

  • The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

    Park SE, Pham DT, Boinett C, Wong VK, Pak GD, Panzner U, Espinoza LMC, von Kalckreuth V, Im J, Schütt-Gerowitt H et al.

    Nature communications 2018;9;1;5094

    PUBMED: 30504848; PMC: 6269545; DOI: 10.1038/s41467-018-07370-z

  • Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.

    Kwun MJ, Oggioni MR, De Ste Croix M, Bentley SD and Croucher NJ

    Nucleic acids research 2018;46;21;11438-11453

    PUBMED: 30321375; PMC: 6265443; DOI: 10.1093/nar/gky906

  • SLING: a tool to search for linked genes in bacterial datasets.

    Horesh G, Harms A, Fino C, Parts L, Gerdes K, Heinz E and Thomson NR

    Nucleic acids research 2018;46;21;e128

    PUBMED: 30124998; PMC: 6265476; DOI: 10.1093/nar/gky738

  • Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution.

    Atack JM, Weinert LA, Tucker AW, Husna AU, Wileman TM, F Hadjirin N, Hoa NT, Parkhill J, Maskell DJ, Blackall PJ and Jennings MP

    Nucleic acids research 2018;46;21;11466-11476

    PUBMED: 30304532; PMC: 6265453; DOI: 10.1093/nar/gky913

  • A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways.

    Campino S, Marin-Menendez A, Kemp A, Cross N, Drought L, Otto TD, Benavente ED, Ravenhall M, Schwach F, Girling G et al.

    PLoS pathogens 2018;14;11;e1007436

    PUBMED: 30496294; PMC: 6289454; DOI: 10.1371/journal.ppat.1007436

  • DNA Polymerase Epsilon Deficiency Causes IMAGe Syndrome with Variable Immunodeficiency.

    Logan CV, Murray JE, Parry DA, Robertson A, Bellelli R, Tarnauskaitė Ž, Challis R, Cleal L, Borel V, Fluteau A et al.

    American journal of human genetics 2018;103;6;1038-1044

    PUBMED: 30503519; PMC: 6288413; DOI: 10.1016/j.ajhg.2018.10.024

  • Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.

    Méric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S et al.

    Nature communications 2018;9;1;5034

    PUBMED: 30487573; PMC: 6261936; DOI: 10.1038/s41467-018-07368-7

  • A guideline for the diagnosis and management of polycythaemia vera. A British Society for Haematology Guideline.

    McMullin MF, Harrison CN, Ali S, Cargo C, Chen F, Ewing J, Garg M, Godfrey A, S SK, McLornan DP et al.

    British journal of haematology 2018;184;2;176-191

    PUBMED: 30478826; DOI: 10.1111/bjh.15648

  • Metabolomic Consequences of Genetic Inhibition of PCSK9 Compared With Statin Treatment

    Sliz E, Kettunen J, Holmes MV, Williams CO, Boachie C, Wang Q, Männikkö M, Sebert S, Walters R, Lin K et al.

    Circulation 2018;138;22;2499–2512

    PUBMED: 30525347; PMC: 6254781; DOI: 10.1161/CIRCULATIONAHA.118.034942

  • Predicting the mutations generated by repair of Cas9-induced double-strand breaks.

    Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, De Angeli P, Páleníková P, Khodak A, Kiselev V, Kosicki M et al.

    Nature biotechnology 2018

    PUBMED: 30480667; PMC: 6949135; DOI: 10.1038/nbt.4317

  • Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue.

    Pellegrinelli V, Peirce VJ, Howard L, Virtue S, Türei D, Senzacqua M, Frontini A, Dalley JW, Horton AR, Bidault G et al.

    Nature communications 2018;9;1;4974

    PUBMED: 30478315; PMC: 6255810; DOI: 10.1038/s41467-018-07453-x

  • High-resolution genetic mapping of putative causal interactions between regions of open chromatin.

    Kumasaka N, Knights AJ and Gaffney DJ

    Nature genetics 2018;51;1;128-137

    PUBMED: 30478436; PMC: 6330062; DOI: 10.1038/s41588-018-0278-6

  • Pooled extracellular receptor-ligand interaction screening using CRISPR activation.

    Chong ZS, Ohnishi S, Yusa K and Wright GJ

    Genome biology 2018;19;1;205

    PUBMED: 30477585; PMC: 6258485; DOI: 10.1186/s13059-018-1581-3

  • Evidence for genetic contribution to the increased risk of type 2 diabetes in schizophrenia.

    Hackinger S, Prins B, Mamakou V, Zengini E, Marouli E, Brčić L, Serafetinidis I, Lamnissou K, Kontaxakis V, Dedoussis G et al.

    Translational psychiatry 2018;8;1;252

    PUBMED: 30470734; PMC: 6251918; DOI: 10.1038/s41398-018-0304-6

  • Sphingolipid dysregulation due to lack of functional KDSR impairs proplatelet formation causing thrombocytopenia.

    Bariana TK, Labarque V, Heremans J, Thys C, De Reys M, Greene D, Jenkins B, Grassi L, Seyres D, Burden F et al.

    Haematologica 2018

    PUBMED: 30467204; DOI: 10.3324/haematol.2018.204784

  • Approaches to identify extracellular receptor-ligand interactions.

    Wood L and Wright GJ

    Current opinion in structural biology 2018;56;28-36

    PUBMED: 30469141; DOI: 10.1016/j.sbi.2018.10.002

  • The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort.

    Dorman MJ, Feltwell T, Goulding DA, Parkhill J and Short FL

    mBio 2018;9;6

    PUBMED: 30459193; PMC: 6247091; DOI: 10.1128/mBio.01863-18

  • Dual-stressor selection alters eco-evolutionary dynamics in experimental communities.

    Hiltunen T, Cairns J, Frickel J, Jalasvuori M, Laakso J, Kaitala V, Künzel S, Karakoc E and Becks L

    Nature ecology & evolution 2018;2;12;1974-1981

    PUBMED: 30455439; DOI: 10.1038/s41559-018-0701-5

  • Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement.

    Jia G, Preussner J, Chen X, Guenther S, Yuan X, Yekelchyk M, Kuenne C, Looso M, Zhou Y, Teichmann S and Braun T

    Nature communications 2018;9;1;4877

    PUBMED: 30451828; PMC: 6242939; DOI: 10.1038/s41467-018-07307-6

  • Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

    Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ, Turner GF and Durbin R

    Nature ecology & evolution 2018;2;12;1940-1955

    PUBMED: 30455444; PMC: 6443041; DOI: 10.1038/s41559-018-0717-x

  • Single-cell transcriptional analysis reveals ILC-like cells in zebrafish.

    Hernández PP, Strzelecka PM, Athanasiadis EI, Hall D, Robalo AF, Collins CM, Boudinot P, Levraud JP and Cvejic A

    Science immunology 2018;3;29

    PUBMED: 30446505; PMC: 6258902; DOI: 10.1126/sciimmunol.aau5265

  • Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance.

    Kazachenka A, Bertozzi TM, Sjoberg-Herrera MK, Walker N, Gardner J, Gunning R, Pahita E, Adams S, Adams D and Ferguson-Smith AC

    Cell 2018;175;5;1259-1271.e13

    PUBMED: 30454646; PMC: 6242299; DOI: 10.1016/j.cell.2018.09.043

  • Single-cell reconstruction of the early maternal-fetal interface in humans.

    Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A et al.

    Nature 2018;563;7731;347-353

    PUBMED: 30429548; DOI: 10.1038/s41586-018-0698-6

  • A guideline for the management of specific situations in polycythaemia vera and secondary erythrocytosis: A British Society for Haematology Guideline.

    McMullin MFF, Mead AJ, Ali S, Cargo C, Chen F, Ewing J, Garg M, Godfrey A, Knapper S, McLornan DP et al.

    British journal of haematology 2018;184;2;161-175

    PUBMED: 30426472; PMC: 6519221; DOI: 10.1111/bjh.15647

  • Identification and Mechanistic Understanding of Dihydroorotate Dehydrogenase Point Mutations in Plasmodium falciparum that Confer in Vitro Resistance to the Clinical Candidate DSM265.

    White J, Dhingra SK, Deng X, El Mazouni F, Lee MCS, Afanador GA, Lawong A, Tomchick DR, Ng CL, Bath J et al.

    ACS infectious diseases 2018;5;1;90-101

    PUBMED: 30375858; PMC: 6467762; DOI: 10.1021/acsinfecdis.8b00211

  • IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation.

    Yánez DC, Sahni H, Ross S, Solanki A, Lau CI, Papaioannou E, Barbarulo A, Powell R, Lange UC, Adams DJ et al.

    European journal of immunology 2018;49;1;66-78

    PUBMED: 30365177; PMC: 6396086; DOI: 10.1002/eji.201847692

  • Quantifying the contribution of recessive coding variation to developmental disorders.

    Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M et al.

    Science (New York, N.Y.) 2018;362;6419;1161-1164

    PUBMED: 30409806; PMC: 6726470; DOI: 10.1126/science.aar6731

  • Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits.

    Gilly A, Suveges D, Kuchenbaecker K, Pollard M, Southam L, Hatzikotoulas K, Farmaki AE, Bjornland T, Waples R, Appel EVR et al.

    Nature communications 2018;9;1;4674

    PUBMED: 30405126; PMC: 6220258; DOI: 10.1038/s41467-018-07070-8

  • Complement Susceptibility in Relation to Genome Sequence of Recent Klebsiella pneumoniae Isolates from Thai Hospitals.

    Loraine J, Heinz E, De Sousa Almeida J, Milevskyy O, Voravuthikunchai SP, Srimanote P, Kiratisin P, Thomson NR and Taylor PW

    mSphere 2018;3;6

    PUBMED: 30404929; PMC: 6222052; DOI: 10.1128/mSphere.00537-18

  • Simulation-based benchmarking of isoform quantification in single-cell RNA-seq.

    Westoby J, Herrera MS, Ferguson-Smith AC and Hemberg M

    Genome biology 2018;19;1;191

    PUBMED: 30404663; PMC: 6223048; DOI: 10.1186/s13059-018-1571-5

  • Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.

    Gouliouris T, Raven KE, Ludden C, Blane B, Corander J, Horner CS, Hernandez-Garcia J, Wood P, Hadjirin NF, Radakovic M et al.

    mBio 2018;9;6

    PUBMED: 30401778; PMC: 6222123; DOI: 10.1128/mBio.01780-18

  • Comparative genomics of the major parasitic worms.

    International Helminth Genomes Consortium

    Nature genetics 2018;51;1;163-174

    PUBMED: 30397333; PMC: 6349046; DOI: 10.1038/s41588-018-0262-1

  • Dissecting human disease with single-cell omics: application in model systems and in the clinic.

    Strzelecka PM, Ranzoni AM and Cvejic A

    Disease models & mechanisms 2018;11;11

    PUBMED: 30401698; PMC: 6262815; DOI: 10.1242/dmm.036525

  • The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers.

    Sondka Z, Bamford S, Cole CG, Ward SA, Dunham I and Forbes SA

    Nature reviews. Cancer 2018;18;11;696-705

    PUBMED: 30293088; PMC: 6450507; DOI: 10.1038/s41568-018-0060-1

  • A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa.

    Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J and Cain AK

    Microbial genomics 2018;4;11

    PUBMED: 30383525; PMC: 6321873; DOI: 10.1099/mgen.0.000229

  • A large impact crater beneath Hiawatha Glacier in northwest Greenland.

    Kjær KH, Larsen NK, Binder T, Bjørk AA, Eisen O, Fahnestock MA, Funder S, Garde AA, Haack H, Helm V et al.

    Science advances 2018;4;11;eaar8173

    PUBMED: 30443592; PMC: 6235527; DOI: 10.1126/sciadv.aar8173

  • The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels.

    Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA and Hollox EJ

    American journal of human genetics 2018;103;5;769-776

    PUBMED: 30388403; PMC: 6218809; DOI: 10.1016/j.ajhg.2018.10.008

  • Chromosome assembly of large and complex genomes using multiple references.

    Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D et al.

    Genome research 2018;28;11;1720-1732

    PUBMED: 30341161; PMC: 6211643; DOI: 10.1101/gr.236273.118

  • Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.

    Mahajan A, Taliun D, Thurner M, Robertson NR, Torres JM, Rayner NW, Payne AJ, Steinthorsdottir V, Scott RA, Grarup N et al.

    Nature genetics 2018;50;11;1505-1513

    PUBMED: 30297969; PMC: 6287706; DOI: 10.1038/s41588-018-0241-6

  • Functional analysis of Salmonella Typhi adaptation to survival in water.

    Kingsley RA, Langridge G, Smith SE, Makendi C, Fookes M, Wileman TM, El Ghany MA, Keith Turner A, Dyson ZA, Sridhar S et al.

    Environmental microbiology 2018;20;11;4079-4090

    PUBMED: 30450829; PMC: 6282856; DOI: 10.1111/1462-2920.14458

  • Functional characterization of common BCL11B gene desert variants suggests a lymphocyte-mediated association of BCL11B with aortic stiffness.

    Maskari RA, Hardege I, Cleary S, Figg N, Li Y, Siew K, Khir A, Yu Y, Liu P, Wilkinson I et al.

    European journal of human genetics : EJHG 2018;26;11;1648-1657

    PUBMED: 30089823; PMC: 6189060; DOI: 10.1038/s41431-018-0226-z

  • Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders.

    Ligthart S, Vaez A, Võsa U, Stathopoulou MG, de Vries PS, Prins BP, Van der Most PJ, Tanaka T, Naderi E, Rose LM et al.

    American journal of human genetics 2018;103;5;691-706

    PUBMED: 30388399; PMC: 6218410; DOI: 10.1016/j.ajhg.2018.09.009

  • Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci.

    Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A, Pollard AJ, von Gottberg A, du Plessis M, Antonio M, Kwambana-Adams BA et al.

    PLoS pathogens 2018;14;11;e1007438

    PUBMED: 30475919; PMC: 6283594; DOI: 10.1371/journal.ppat.1007438

  • Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity.

    Hahn O, Stubbs TM, Reik W, Grönke S, Beyer A and Partridge L

    PLoS genetics 2018;14;11;e1007766

    PUBMED: 30462643; PMC: 6281273; DOI: 10.1371/journal.pgen.1007766

  • Inducible developmental reprogramming redefines commitment to sexual development in the malaria parasite Plasmodium berghei.

    Kent RS, Modrzynska KK, Cameron R, Philip N, Billker O and Waters AP

    Nature microbiology 2018;3;11;1206-1213

    PUBMED: 30177743; PMC: 6317699; DOI: 10.1038/s41564-018-0223-6

  • mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species.

    Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL and Schürch AC

    Microbial genomics 2018;4;11

    PUBMED: 30383524; PMC: 6321875; DOI: 10.1099/mgen.0.000224

  • Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers.

    Glodzik D, Purdie C, Rye IH, Simpson PT, Staaf J, Span PN, Russnes HG and Nik-Zainal S

    Annals of oncology : official journal of the European Society for Medical Oncology 2018;29;11;2223-2231

    PUBMED: 30252041; PMC: 6290883; DOI: 10.1093/annonc/mdy404

  • PPM1D Mutations Drive Clonal Hematopoiesis in Response to Cytotoxic Chemotherapy.

    Hsu JI, Dayaram T, Tovy A, De Braekeleer E, Jeong M, Wang F, Zhang J, Heffernan TP, Gera S, Kovacs JJ et al.

    Cell stem cell 2018;23;5;700-713.e6

    PUBMED: 30388424; PMC: 6224657; DOI: 10.1016/j.stem.2018.10.004

  • Quantitative mass spectrometry for human melanocortin peptides in vitro and in vivo suggests prominent roles for β-MSH and desacetyl α-MSH in energy homeostasis.

    Kirwan P, Kay RG, Brouwers B, Herranz-Pérez V, Jura M, Larraufie P, Jerber J, Pembroke J, Bartels T, White A et al.

    Molecular metabolism 2018;17;82-97

    PUBMED: 30201275; PMC: 6197775; DOI: 10.1016/j.molmet.2018.08.006

  • Small diameter helical vascular scaffolds support endothelial cell survival.

    Parikh V, Kadiwala J, Hidalgo Bastida A, Holt C, Sanami M, Miraftab M, Shakur R and Azzawi M

    Nanomedicine : nanotechnology, biology, and medicine 2018;14;8;2598-2608

    PUBMED: 30172863; DOI: 10.1016/j.nano.2018.08.005

  • Staphylococcus cornubiensis sp. nov., a member of the Staphylococcus intermedius Group (SIG).

    Murray AK, Lee J, Bendall R, Zhang L, Sunde M, Schau Slettemeås J, Gaze W, Page AJ and Vos M

    International journal of systematic and evolutionary microbiology 2018;68;11;3404-3408

    PUBMED: 30204583; DOI: 10.1099/ijsem.0.002992

  • Updated recommendation for the benign stand-alone ACMG/AMP criterion.

    Ghosh R, Harrison SM, Rehm HL, Plon SE, Biesecker LG and ClinGen Sequence Variant Interpretation Working Group

    Human mutation 2018;39;11;1525-1530

    PUBMED: 30311383; PMC: 6188666; DOI: 10.1002/humu.23642

  • Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma.

    Gapp K, van Steenwyk G, Germain PL, Matsushima W, Rudolph KLM, Manuella F, Roszkowski M, Vernaz G, Ghosh T, Pelczar P et al.

    Molecular psychiatry 2018;25;9;2162-2174

    PUBMED: 30374190; PMC: 7473836; DOI: 10.1038/s41380-018-0271-6

  • Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.

    Laumer CE, Gruber-Vodicka H, Hadfield MG, Pearse VB, Riesgo A, Marioni JC and Giribet G

    eLife 2018;7

    PUBMED: 30373720; PMC: 6277202; DOI: 10.7554/eLife.36278

  • A single nucleotide polymorphism in the Plasmodium falciparum atg18 gene associates with artemisinin resistance and confers enhanced parasite survival under nutrient deprivation.

    Breglio KF, Amato R, Eastman R, Lim P, Sa JM, Guha R, Ganesan S, Dorward DW, Klumpp-Thomas C, McKnight C et al.

    Malaria journal 2018;17;1;391

    PUBMED: 30367653; PMC: 6204056; DOI: 10.1186/s12936-018-2532-x

  • Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation.

    Teumer A, Chaker L, Groeneweg S, Li Y, Di Munno C, Barbieri C, Schultheiss UT, Traglia M, Ahluwalia TS, Akiyama M et al.

    Nature communications 2018;9;1;4455

    PUBMED: 30367059; PMC: 6203810; DOI: 10.1038/s41467-018-06356-1

  • The phenotypic spectrum of WWOX-related disorders: 20 additional cases of WOREE syndrome and review of the literature.

    Piard J, Hawkes L, Milh M, Villard L, Borgatti R, Romaniello R, Fradin M, Capri Y, Héron D, Nougues MC et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2018;21;6;1308-1318

    PUBMED: 30356099; PMC: 6752669; DOI: 10.1038/s41436-018-0339-3

  • Exploring the association between SRPX2 variants and neurodevelopment: How causal is it?

    Schirwani S, McConnell V, Willoughby J, DDD Study and Balasubramanian M

    Gene 2018;685;50-54

    PUBMED: 30393191; DOI: 10.1016/j.gene.2018.10.067

  • GNE variants causing autosomal recessive macrothrombocytopenia without associated muscle wasting.

    Revel-Vilk S, Shai E, Turro E, Jahshan N, Hi-Am E, Spectre G, Daum H, Kalish Y, Althaus K, Greinacher A et al.

    Blood 2018;132;17;1851-1854

    PUBMED: 30171045; PMC: 6202914; DOI: 10.1182/blood-2018-04-845545

  • Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development.

    Duffy CW, Amambua-Ngwa A, Ahouidi AD, Diakite M, Awandare GA, Ba H, Tarr SJ, Murray L, Stewart LB, D'Alessandro U et al.

    Scientific reports 2018;8;1;15763

    PUBMED: 30361631; PMC: 6202401; DOI: 10.1038/s41598-018-34078-3

  • Gene expression variability across cells and species shapes innate immunity.

    Hagai T, Chen X, Miragaia RJ, Rostom R, Gomes T, Kunowska N, Henriksson J, Park JE, Proserpio V, Donati G et al.

    Nature 2018;563;7730;197-202

    PUBMED: 30356220; PMC: 6347972; DOI: 10.1038/s41586-018-0657-2

  • Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.

    Pramanik J, Chen X, Kar G, Henriksson J, Gomes T, Park JE, Natarajan K, Meyer KB, Miao Z, McKenzie ANJ et al.

    Genome medicine 2018;10;1;76

    PUBMED: 30355343; PMC: 6199730; DOI: 10.1186/s13073-018-0589-3

  • Novel KAT6B proximal familial variant expands genotypic and phenotypic spectrum.

    Yates TM, Langley CLM, DDD Study, Grozeva D, Raymond FL and Johnson DS

    Clinical genetics 2018;95;2;334-335

    PUBMED: 30353918; DOI: 10.1111/cge.13456

  • The Developmental Shift of NMDA Receptor Composition Proceeds Independently of GluN2 Subunit-Specific GluN2 C-Terminal Sequences.

    McKay S, Ryan TJ, McQueen J, Indersmitten T, Marwick KFM, Hasel P, Kopanitsa MV, Baxter PS, Martel MA, Kind PC et al.

    Cell reports 2018;25;4;841-851.e4

    PUBMED: 30355491; PMC: 6218242; DOI: 10.1016/j.celrep.2018.09.089

  • Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance.

    Bruske E, Otto TD and Frank M

    Malaria journal 2018;17;1;376

    PUBMED: 30348135; PMC: 6198375; DOI: 10.1186/s12936-018-2503-2

  • Genome-Wide Sequence Analysis of Kaposi Sarcoma-Associated Herpesvirus Shows Diversification Driven by Recombination.

    Sallah N, Palser AL, Watson SJ, Labo N, Asiki G, Marshall V, Newton R, Whitby D, Kellam P and Barroso I

    The Journal of infectious diseases 2018;218;11;1700-1710

    PUBMED: 30010810; PMC: 6195662; DOI: 10.1093/infdis/jiy427

  • De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias.

    Helbig KL, Lauerer RJ, Bahr JC, Souza IA, Myers CT, Uysal B, Schwarz N, Gandini MA, Huang S, Keren B et al.

    American journal of human genetics 2018;103;5;666-678

    PUBMED: 30343943; PMC: 6216110; DOI: 10.1016/j.ajhg.2018.09.006

  • Homozygous loss-of-function mutations in SLC26A7 cause goitrous congenital hypothyroidism.

    Cangul H, Liao XH, Schoenmakers E, Kero J, Barone S, Srichomkwun P, Iwayama H, Serra EG, Saglam H, Eren E et al.

    JCI insight 2018;3;20

    PUBMED: 30333321; PMC: 6237461; DOI: 10.1172/jci.insight.99631

  • Missense Mutations of the Pro65 Residue of PCGF2 Cause a Recognizable Syndrome Associated with Craniofacial, Neurological, Cardiovascular, and Skeletal Features.

    Turnpenny PD, Wright MJ, Sloman M, Caswell R, van Essen AJ, Gerkes E, Pfundt R, White SM, Shaul-Lotan N, Carpenter L et al.

    American journal of human genetics 2018;103;5;786-793

    PUBMED: 30343942; PMC: 6218713; DOI: 10.1016/j.ajhg.2018.09.012

  • RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing.

    Nojima T, Rebelo K, Gomes T, Grosso AR, Proudfoot NJ and Carmo-Fonseca M

    Molecular cell 2018;72;2;369-379.e4

    PUBMED: 30340024; PMC: 6201815; DOI: 10.1016/j.molcel.2018.09.004

  • Somatic mutant clones colonize the human esophagus with age.

    Martincorena I, Fowler JC, Wabik A, Lawson ARJ, Abascal F, Hall MWJ, Cagan A, Murai K, Mahbubani K, Stratton MR et al.

    Science (New York, N.Y.) 2018;362;6417;911-917

    PUBMED: 30337457; PMC: 6298579; DOI: 10.1126/science.aau3879

  • Genome organization and DNA accessibility control antigenic variation in trypanosomes.

    Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S et al.

    Nature 2018;563;7729;121-125

    PUBMED: 30333624; PMC: 6784898; DOI: 10.1038/s41586-018-0619-8

  • Genomic Risk Prediction of Coronary Artery Disease in 480,000 Adults: Implications for Primary Prevention.

    Inouye M, Abraham G, Nelson CP, Wood AM, Sweeting MJ, Dudbridge F, Lai FY, Kaptoge S, Brozynska M, Wang T et al.

    Journal of the American College of Cardiology 2018;72;16;1883-1893

    PUBMED: 30309464; PMC: 6176870; DOI: 10.1016/j.jacc.2018.07.079

  • Integrative Molecular Characterization of Malignant Pleural Mesothelioma.

    Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, Tarpey P, Danilova L, Drill E, Gibb EA et al.

    Cancer discovery 2018;8;12;1548-1565

    PUBMED: 30322867; PMC: 6310008; DOI: 10.1158/2159-8290.CD-18-0804

  • Mutational Analysis Identifies Therapeutic Biomarkers in Inflammatory Bowel Disease-Associated Colorectal Cancers.

    Din S, Wong K, Mueller MF, Oniscu A, Hewinson J, Black CJ, Miller ML, Jiménez-Sánchez A, Rabbie R, Rashid M et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2018;24;20;5133-5142

    PUBMED: 29950348; PMC: 6193541; DOI: 10.1158/1078-0432.CCR-17-3713

  • Drug repurposing: progress, challenges and recommendations.

    Pushpakom S, Iorio F, Eyers PA, Escott KJ, Hopper S, Wells A, Doig A, Guilliams T, Latimer J, McNamee C et al.

    Nature reviews. Drug discovery 2018;18;1;41-58

    PUBMED: 30310233; DOI: 10.1038/nrd.2018.168

  • Epistasis studies reveal redundancy among calcium-dependent protein kinases in motility and invasion of malaria parasites.

    Fang H, Gomes AR, Klages N, Pino P, Maco B, Walker EM, Zenonos ZA, Angrisano F, Baum J, Doerig C et al.

    Nature communications 2018;9;1;4248

    PUBMED: 30315162; PMC: 6185908; DOI: 10.1038/s41467-018-06733-w

  • Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building.

    David S, Mentasti M, Lai S, Vaghji L, Ready D, Chalker VJ and Parkhill J

    Microbial genomics 2018;4;10

    PUBMED: 30312149; PMC: 6249432; DOI: 10.1099/mgen.0.000226

  • Comparative immunogenicity and efficacy of equivalent outer membrane vesicle and glycoconjugate vaccines against nontyphoidal Salmonella.

    Micoli F, Rondini S, Alfini R, Lanzilao L, Necchi F, Negrea A, Rossi O, Brandt C, Clare S, Mastroeni P et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;41;10428-10433

    PUBMED: 30262653; PMC: 6187145; DOI: 10.1073/pnas.1807655115

  • EROS/CYBC1 mutations: Decreased NADPH oxidase function and chronic granulomatous disease.

    Thomas DC, Charbonnier LM, Schejtman A, Aldhekri H, Coomber EL, Dufficy ER, Beenken AE, Lee JC, Clare S, Speak AO et al.

    The Journal of allergy and clinical immunology 2018;143;2;782-785.e1

    PUBMED: 30312704; PMC: 6490677; DOI: 10.1016/j.jaci.2018.09.019

  • Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability.

    Verheije R, Kupchik GS, Isidor B, Kroes HY, Lynch SA, Hawkes L, Hempel M, Gelb BD, Ghoumid J, D'Amours G et al.

    European journal of human genetics : EJHG 2018;27;2;278-290

    PUBMED: 30291340; PMC: 6336847; DOI: 10.1038/s41431-018-0281-5

  • Addressing Diversity and Inclusion in Human Genetics Research.

    No authors listed

    Cell 2018;175;2;303-305

    PUBMED: 30290134; DOI: 10.1016/j.cell.2018.09.034

  • XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data.

    Kluin RJC, Kemper K, Kuilman T, de Ruiter JR, Iyer V, Forment JV, Cornelissen-Steijger P, de Rink I, Ter Brugge P, Song JY et al.

    BMC bioinformatics 2018;19;1;366

    PUBMED: 30286710; PMC: 6172735; DOI: 10.1186/s12859-018-2353-5

  • Homozygosity mapping provides supporting evidence of pathogenicity in recessive Mendelian disease.

    Wakeling MN, Laver TW, Wright CF, De Franco E, Stals KL, Patch AM, Hattersley AT, Flanagan SE, Ellard S and DDD Study

    Genetics in medicine : official journal of the American College of Medical Genetics 2018;21;4;982-986

    PUBMED: 30279471; PMC: 6330071; DOI: 10.1038/s41436-018-0281-4

  • The evolutionary landscape of colorectal tumorigenesis.

    Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C et al.

    Nature ecology & evolution 2018;2;10;1661-1672

    PUBMED: 30177804; PMC: 6152905; DOI: 10.1038/s41559-018-0642-z

  • A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid.

    Britto CD, Wong VK, Dougan G and Pollard AJ

    PLoS neglected tropical diseases 2018;12;10;e0006779

    PUBMED: 30307935; PMC: 6198998; DOI: 10.1371/journal.pntd.0006779

  • Beating the odds to secure a permanent contract.

    Smaglik P

    Nature 2018;562;7725;S49-S51

    PUBMED: 30283115; DOI: 10.1038/d41586-018-06873-5

  • Comparative genomics of Czech vaccine strains of Bordetella pertussis.

    Dienstbier A, Pouchnik D, Wildung M, Amman F, Hofacker IL, Parkhill J, Holubova J, Sebo P and Vecerek B

    Pathogens and disease 2018;76;7

    PUBMED: 30184175; DOI: 10.1093/femspd/fty071

  • COMRADES determines in vivo RNA structures and interactions.

    Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ et al.

    Nature methods 2018;15;10;785-788

    PUBMED: 30202058; PMC: 6168409; DOI: 10.1038/s41592-018-0121-0

  • Genome-wide association study identifies inversion in the CTRB1-CTRB2 locus to modify risk for alcoholic and non-alcoholic chronic pancreatitis.

    Rosendahl J, Kirsten H, Hegyi E, Kovacs P, Weiss FU, Laumen H, Lichtner P, Ruffert C, Chen JM, Masson E et al.

    Gut 2018;67;10;1855-1863

    PUBMED: 28754779; PMC: 6145291; DOI: 10.1136/gutjnl-2017-314454

  • hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in α1-antitrypsin deficiency.

    Segeritz CP, Rashid ST, de Brito MC, Serra MP, Ordonez A, Morell CM, Kaserman JE, Madrigal P, Hannan NRF, Gatto L et al.

    Journal of hepatology 2018;69;4;851-860

    PUBMED: 29879455; PMC: 6562205; DOI: 10.1016/j.jhep.2018.05.028

  • Lysogenic conversion of atypical enteropathogenic Escherichia coli (aEPEC) from human, murine, and bovine origin with bacteriophage Φ3538 Δstx2::cat proves their enterohemorrhagic E. coli (EHEC) progeny.

    Eichhorn I, Heidemanns K, Ulrich RG, Schmidt H, Semmler T, Fruth A, Bethe A, Goulding D, Pickard D, Karch H and Wieler LH

    International journal of medical microbiology : IJMM 2018;308;7;890-898

    PUBMED: 29937391; DOI: 10.1016/j.ijmm.2018.06.005

  • Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence.

    Smet A, Yahara K, Rossi M, Tay A, Backert S, Armin E, Fox JG, Flahou B, Ducatelle R, Haesebrouck F and Corander J

    The ISME journal 2018;12;10;2518-2531

    PUBMED: 29942073; PMC: 6154992; DOI: 10.1038/s41396-018-0199-5

  • P465L-PPARγ mutation confers partial resistance to the hypolipidaemic action of fibrates.

    Rodriguez-Cuenca S, Carobbio S, Barceló-Coblijn G, Prieur X, Relat J, Amat R, Campbell M, Dias AR, Bahri M, Gray SL and Vidal-Puig A

    Diabetes, obesity & metabolism 2018;20;10;2339-2350

    PUBMED: 29790245; PMC: 6589924; DOI: 10.1111/dom.13370

  • Population genetic analysis of Chadian Guinea worms reveals that human and non-human hosts share common parasite populations.

    Thiele EA, Eberhard ML, Cotton JA, Durrant C, Berg J, Hamm K and Ruiz-Tiben E

    PLoS neglected tropical diseases 2018;12;10;e0006747

    PUBMED: 30286084; DOI: 10.1371/journal.pntd.0006747

  • ProxECAT: Proxy External Controls Association Test. A new case-control gene region association test using allele frequencies from public controls.

    Hendricks AE, Billups SC, Pike HNC, Farooqi IS, Zeggini E, Santorico SA, Barroso I and Dupuis J

    PLoS genetics 2018;14;10;e1007591

    PUBMED: 30325923; PMC: 6191077; DOI: 10.1371/journal.pgen.1007591

  • Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

    Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A et al.

    Nature genetics 2018;50;11;1574-1583

    PUBMED: 30275530; PMC: 6205630; DOI: 10.1038/s41588-018-0223-8

  • Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells.

    Ellis DA, Mustonen V, Rodríguez-López M, Rallis C, Malecki M, Jeffares DC and Bähler J

    Genetics 2018;210;2;733-744

    PUBMED: 30072377; PMC: 6216586; DOI: 10.1534/genetics.118.301262

  • Congenital macrothrombocytopenia with focal myelofibrosis due to mutations in human G6b-B is rescued in humanized mice.

    Hofmann I, Geer MJ, Vögtle T, Crispin A, Campagna DR, Barr A, Calicchio ML, Heising S, van Geffen JP, Kuijpers MJE et al.

    Blood 2018;132;13;1399-1412

    PUBMED: 29898956; PMC: 6161765; DOI: 10.1182/blood-2017-08-802769

  • Epidermal Tissue Adapts to Restrain Progenitors Carrying Clonal p53 Mutations.

    Murai K, Skrupskelyte G, Piedrafita G, Hall M, Kostiou V, Ong SH, Nagy T, Cagan A, Goulding D, Klein AM et al.

    Cell stem cell 2018;23;5;687-699.e8

    PUBMED: 30269904; PMC: 6224607; DOI: 10.1016/j.stem.2018.08.017

  • Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.

    Niemi MEK, Martin HC, Rice DL, Gallone G, Gordon S, Kelemen M, McAloney K, McRae J, Radford EJ, Yu S et al.

    Nature 2018;562;7726;268-271

    PUBMED: 30258228; PMC: 6726472; DOI: 10.1038/s41586-018-0566-4

  • Effect of vaccination on pneumococci isolated from the nasopharynx of healthy children and the middle ear of children with otitis media in Iceland.

    Quirk SJ, Haraldsson G, Erlendsdóttir H, Hjálmarsdóttir MÁ, van Tonder AJ, Hrafnkelsson B, Sigurðsson S, Bentley SD, Haraldsson Á, Brueggemann AB and Kristinsson KG

    Journal of clinical microbiology 2018

    PUBMED: 30257906; DOI: 10.1128/JCM.01046-18

  • Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis.

    Tiwari S, van Tonder AJ, Vilchèze C, Mendes V, Thomas SE, Malek A, Chen B, Chen M, Kim J, Blundell TL et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;39;9779-9784

    PUBMED: 30143580; PMC: 6166831; DOI: 10.1073/pnas.1808874115

  • Phenotype description and response to thrombopoietin receptor agonist in DIAPH1-related disorder.

    Westbury SK, Downes K, Burney C, Lozano ML, Obaji SG, Toh CH, Sevivas T, Morgan NV, Erber WN, Kempster C et al.

    Blood advances 2018;2;18;2341-2346

    PUBMED: 30232087; PMC: 6156883; DOI: 10.1182/bloodadvances.2018020370

  • Identification of novel adenovirus genotype 90 in children from Bangladesh.

    Houldcroft CJ, Beale MA, Sayeed MA, Qadri F, Dougan G and Mutreja A

    Microbial genomics 2018;4;10

    PUBMED: 30248001; PMC: 6249435; DOI: 10.1099/mgen.0.000221

  • KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants.

    Kennedy J, Goudie D, Blair E, Chandler K, Joss S, McKay V, Green A, Armstrong R, Lees M, Kamien B et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2018;21;4;850-860

    PUBMED: 30245513; PMC: 6634310; DOI: 10.1038/s41436-018-0259-2

  • Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance.

    Stringer JM, Forster SC, Qu Z, Prokopuk L, O'Bryan MK, Gardner DK, White SJ, Adelson D and Western PS

    BMC biology 2018;16;1;104

    PUBMED: 30236109; PMC: 6149058; DOI: 10.1186/s12915-018-0569-5

  • Pulmonary metastatic colonisation and granulomas in NOX2-deficient mice.

    van der Weyden L, Speak AO, Swiatkowska A, Clare S, Schejtman A, Santilli G, Arends MJ and Adams DJ

    The Journal of pathology 2018;246;3;300-310

    PUBMED: 30062795; PMC: 6221033; DOI: 10.1002/path.5140

  • Alpha kinase 1 controls intestinal inflammation by suppressing the IL-12/Th1 axis.

    Ryzhakov G, West NR, Franchini F, Clare S, Ilott NE, Sansom SN, Bullers SJ, Pearson C, Costain A, Vaughan-Jackson A et al.

    Nature communications 2018;9;1;3797

    PUBMED: 30228258; PMC: 6143560; DOI: 10.1038/s41467-018-06085-5

  • Genome-Wide Association Study Reveals Genetic Link between Diarrhea-Associated Entamoeba histolytica Infection and Inflammatory Bowel Disease.

    Wojcik GL, Marie C, Abhyankar MM, Yoshida N, Watanabe K, Mentzer AJ, Carstensen T, Mychaleckyj J, Kirkpatrick BD, Rich SS et al.

    mBio 2018;9;5

    PUBMED: 30228239; PMC: 6143743; DOI: 10.1128/mBio.01668-18

  • Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits.

    Evangelou E, Warren HR, Mosen-Ansorena D, Mifsud B, Pazoki R, Gao H, Ntritsos G, Dimou N, Cabrera CP, Karaman I et al.

    Nature genetics 2018;50;10;1412-1425

    PUBMED: 30224653; PMC: 6284793; DOI: 10.1038/s41588-018-0205-x

  • Interleukin-22 promotes phagolysosomal fusion to induce protection against Salmonella enterica Typhimurium in human epithelial cells.

    Forbester JL, Lees EA, Goulding D, Forrest S, Yeung A, Speak A, Clare S, Coomber EL, Mukhopadhyay S, Kraiczy J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;40;10118-10123

    PUBMED: 30217896; PMC: 6176607; DOI: 10.1073/pnas.1811866115

  • The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature.

    Inman GJ, Wang J, Nagano A, Alexandrov LB, Purdie KJ, Taylor RG, Sherwood V, Thomson J, Hogan S, Spender LC et al.

    Nature communications 2018;9;1;3667

    PUBMED: 30202019; PMC: 6131170; DOI: 10.1038/s41467-018-06027-1

  • An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.

    Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD et al.

    Scientific reports 2018;8;1;13537

    PUBMED: 30202034; PMC: 6131140; DOI: 10.1038/s41598-018-31659-0

  • Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles.

    Croucher NJ, Løchen A and Bentley SD

    Annual review of microbiology 2018;72;521-549

    PUBMED: 30200849; DOI: 10.1146/annurev-micro-090817-062338

  • Refining the phenotype associated with GNB1 mutations: Clinical data on 18 newly identified patients and review of the literature.

    Hemati P, Revah-Politi A, Bassan H, Petrovski S, Bilancia CG, Ramsey K, Griffin NG, Bier L, Cho MT, Rosello M et al.

    American journal of medical genetics. Part A 2018;176;11;2259-2275

    PUBMED: 30194818; DOI: 10.1002/ajmg.a.40472

  • Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion.

    Abou Tayoun AN, Pesaran T, DiStefano MT, Oza A, Rehm HL, Biesecker LG, Harrison SM and ClinGen Sequence Variant Interpretation Working Group (ClinGen SVI)

    Human mutation 2018

    PUBMED: 30192042; DOI: 10.1002/humu.23626

  • Population dynamics of normal human blood inferred from somatic mutations.

    Lee-Six H, Øbro NF, Shepherd MS, Grossmann S, Dawson K, Belmonte M, Osborne RJ, Huntly BJP, Martincorena I, Anderson E et al.

    Nature 2018;561;7724;473-478

    PUBMED: 30185910; PMC: 6163040; DOI: 10.1038/s41586-018-0497-0

  • Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils.

    Grassi L, Pourfarzad F, Ullrich S, Merkel A, Were F, Carrillo-de-Santa-Pau E, Yi G, Hiemstra IH, Tool ATJ, Mul E et al.

    Cell reports 2018;24;10;2784-2794

    PUBMED: 30184510; PMC: 6326331; DOI: 10.1016/j.celrep.2018.08.018

  • Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites.

    Loy DE, Plenderleith LJ, Sundararaman SA, Liu W, Gruszczyk J, Chen YJ, Trimboli S, Learn GH, MacLean OA, Morgan ALK et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;36;E8450-E8459

    PUBMED: 30127015; PMC: 6130405; DOI: 10.1073/pnas.1810053115

  • New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam.

    Mather AE, Phuong TLT, Gao Y, Clare S, Mukhopadhyay S, Goulding DA, Hoang NTD, Tuyen HT, Lan NPH, Thompson CN et al.

    mBio 2018;9;5

    PUBMED: 30181247; PMC: 6123440; DOI: 10.1128/mBio.01056-18

  • Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes.

    Lewis MA, Nolan LS, Cadge BA, Matthews LJ, Schulte BA, Dubno JR, Steel KP and Dawson SJ

    BMC medical genomics 2018;11;1;77

    PUBMED: 30180840; PMC: 6123954; DOI: 10.1186/s12920-018-0395-1

  • An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis.

    Torres VVL, Heinz E, Stubenrauch CJ, Wilksch JJ, Cao H, Yang J, Clements A, Dunstan RA, Alcock F, Webb CT et al.

    Molecular microbiology 2018;109;5;584-599

    PUBMED: 29873128; DOI: 10.1111/mmi.13990

  • The return of Pfeiffer's bacillus: Rising incidence of ampicillin resistance in Haemophilus influenzae.

    Heinz E

    Microbial genomics 2018;4;9

    PUBMED: 30207515; PMC: 6202453; DOI: 10.1099/mgen.0.000214

  • Cold-induced epigenetic programming of the sperm enhances brown adipose tissue activity in the offspring.

    Sun W, Dong H, Becker AS, Dapito DH, Modica S, Grandl G, Opitz L, Efthymiou V, Straub LG, Sarker G et al.

    Nature medicine 2018;24;9;1372-1383

    PUBMED: 29988127; DOI: 10.1038/s41591-018-0102-y

  • COSMIC-3D provides structural perspectives on cancer genetics for drug discovery.

    Jubb HC, Saini HK, Verdonk ML and Forbes SA

    Nature genetics 2018;50;9;1200-1202

    PUBMED: 30158682; PMC: 6159874; DOI: 10.1038/s41588-018-0214-9

  • Detecting archaic introgression using an unadmixed outgroup.

    Skov L, Hui R, Shchur V, Hobolth A, Scally A, Schierup MH and Durbin R

    PLoS genetics 2018;14;9;e1007641

    PUBMED: 30226838; PMC: 6161914; DOI: 10.1371/journal.pgen.1007641

  • Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.

    Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Charnock-Jones DS and Smith GCS

    Microbiome 2018;6;1;151

    PUBMED: 30172254; PMC: 6119588; DOI: 10.1186/s40168-018-0529-x

  • Genome-scale identification of cellular pathways required for cell surface recognition.

    Sharma S, Bartholdson SJ, Couch ACM, Yusa K and Wright GJ

    Genome research 2018;28;9;1372-1382

    PUBMED: 29914970; PMC: 6120632; DOI: 10.1101/gr.231183.117

  • Naturally occurring polymorphisms in the virulence regulator Rsp modulate Staphylococcus aureus survival in blood and antibiotic susceptibility.

    Krishna A, Holden MTG, Peacock SJ, Edwards AM and Wigneshweraraj S

    Microbiology (Reading, England) 2018;164;9;1189-1195

    PUBMED: 30028663; PMC: 6230762; DOI: 10.1099/mic.0.000695

  • Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis.

    Georgakopoulos-Soares I, Morganella S, Jain N, Hemberg M and Nik-Zainal S

    Genome research 2018;28;9;1264-1271

    PUBMED: 30104284; PMC: 6120622; DOI: 10.1101/gr.231688.117

  • Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae.

    Cleary D, Devine V, Morris D, Osman K, Gladstone R, Bentley S, Faust S and Clarke S

    Microbial genomics 2018;4;9

    PUBMED: 30080135; PMC: 6202451; DOI: 10.1099/mgen.0.000209

  • Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements.

    Kosicki M, Tomberg K and Bradley A

    Nature biotechnology 2018;36;8;765-771

    PUBMED: 30010673; PMC: 6390938; DOI: 10.1038/nbt.4192

  • scanPAV: a pipeline for extracting presence-absence variations in genome pairs.

    Giordano F, Stammnitz MR, Murchison EP and Ning Z

    Bioinformatics (Oxford, England) 2018;34;17;3022-3024

    PUBMED: 29608694; PMC: 6129304; DOI: 10.1093/bioinformatics/bty189

  • Terminal uridylyltransferases target RNA viruses as part of the innate immune system.

    Le Pen J, Jiang H, Di Domenico T, Kneuss E, Kosałka J, Leung C, Morgan M, Much C, Rudolph KLM, Enright AJ et al.

    Nature structural & molecular biology 2018;25;9;778-786

    PUBMED: 30104661; PMC: 6130846; DOI: 10.1038/s41594-018-0106-9

  • Variant antigen repertoires in Trypanosoma congolense populations and experimental infections can be profiled from deep sequence data using universal protein motifs.

    Silva Pereira S, Casas-Sánchez A, Haines LR, Ogugo M, Absolomon K, Sanders M, Kemp S, Acosta-Serrano Á, Noyes H, Berriman M and Jackson AP

    Genome research 2018;28;9;1383-1394

    PUBMED: 30006414; PMC: 6120623; DOI: 10.1101/gr.234146.118

  • Rare-Variant Studies to Complement Genome-Wide Association Studies.

    Sazonovs A and Barrett JC

    Annual review of genomics and human genetics 2018;19;97-112

    PUBMED: 29801418; DOI: 10.1146/annurev-genom-083117-021641

  • Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors.

    Anderson ND, de Borja R, Young MD, Fuligni F, Rosic A, Roberts ND, Hajjar S, Layeghifard M, Novokmet A, Kowalski PE et al.

    Science (New York, N.Y.) 2018;361;6405

    PUBMED: 30166462; PMC: 6176908; DOI: 10.1126/science.aam8419

  • The opium poppy genome and morphinan production.

    Guo L, Winzer T, Yang X, Li Y, Ning Z, He Z, Teodor R, Lu Y, Bowser TA, Graham IA and Ye K

    Science (New York, N.Y.) 2018;362;6412;343-347

    PUBMED: 30166436; DOI: 10.1126/science.aat4096

  • Circulating tumor DNA in patients with colorectal adenomas: assessment of detectability and genetic heterogeneity.

    Myint NNM, Verma AM, Fernandez-Garcia D, Sarmah P, Tarpey PS, Al-Aqbi SS, Cai H, Trigg R, West K, Howells LM et al.

    Cell death & disease 2018;9;9;894

    PUBMED: 30166531; PMC: 6117318; DOI: 10.1038/s41419-018-0934-x

  • Hydroxycarbamide Plus Aspirin Versus Aspirin Alone in Patients With Essential Thrombocythemia Age 40 to 59 Years Without High-Risk Features.

    Godfrey AL, Campbell PJ, MacLean C, Buck G, Cook J, Temple J, Wilkins BS, Wheatley K, Nangalia J, Grinfeld J et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2018;36;34;3361-3369

    PUBMED: 30153096; PMC: 6269131; DOI: 10.1200/JCO.2018.78.8414

  • The germline genetic component of drug sensitivity in cancer cell lines.

    Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J and Stegle O

    Nature communications 2018;9;1;3385

    PUBMED: 30139972; PMC: 6107640; DOI: 10.1038/s41467-018-05811-3

  • Fitness Loss under Amino Acid Starvation in Artemisinin-Resistant Plasmodium falciparum Isolates from Cambodia.

    Bunditvorapoom D, Kochakarn T, Kotanan N, Modchang C, Kümpornsin K, Loesbanluechai D, Krasae T, Cui L, Chotivanich K, White NJ et al.

    Scientific reports 2018;8;1;12622

    PUBMED: 30135481; PMC: 6105667; DOI: 10.1038/s41598-018-30593-5

  • Genomic patterns of progression in smoldering multiple myeloma.

    Bolli N, Maura F, Minvielle S, Gloznik D, Szalat R, Fullam A, Martincorena I, Dawson KJ, Samur MK, Zamora J et al.

    Nature communications 2018;9;1;3363

    PUBMED: 30135448; PMC: 6105687; DOI: 10.1038/s41467-018-05058-y

  • Loose ends: almost one in five human genes still have unresolved coding status.

    Abascal F, Juan D, Jungreis I, Martinez L, Rigau M, Rodriguez JM, Vazquez J and Tress ML

    Nucleic acids research 2018;46;14;7070-7084

    PUBMED: 29982784; PMC: 6101605; DOI: 10.1093/nar/gky587

  • Peroxisome Proliferator-Activated Receptor γ2 Controls the Rate of Adipose Tissue Lipid Storage and Determines Metabolic Flexibility.

    Virtue S, Petkevicius K, Moreno-Navarrete JM, Jenkins B, Hart D, Dale M, Koulman A, Fernández-Real JM and Vidal-Puig A

    Cell reports 2018;24;8;2005-2012.e7

    PUBMED: 30134163; DOI: 10.1016/j.celrep.2018.07.063

  • BCL11A interacts with SOX2 to control the expression of epigenetic regulators in lung squamous carcinoma.

    Lazarus KA, Hadi F, Zambon E, Bach K, Santolla MF, Watson JK, Correia LL, Das M, Ugur R, Pensa S et al.

    Nature communications 2018;9;1;3327

    PUBMED: 30127402; PMC: 6102279; DOI: 10.1038/s41467-018-05790-5

  • Natural Genetic Variation in a Multigenerational Phenotype in C. elegans.

    Frézal L, Demoinet E, Braendle C, Miska E and Félix MA

    Current biology : CB 2018;28;16;2588-2596.e8

    PUBMED: 30078564; DOI: 10.1016/j.cub.2018.05.091

  • Variation graph toolkit improves read mapping by representing genetic variation in the reference.

    Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF et al.

    Nature biotechnology 2018;36;9;875-879

    PUBMED: 30125266; PMC: 6126949; DOI: 10.1038/nbt.4227

  • Genome-wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease.

    Yao C, Chen G, Song C, Keefe J, Mendelson M, Huan T, Sun BB, Laser A, Maranville JC, Wu H et al.

    Nature communications 2018;9;1;3268

    PUBMED: 30111768; PMC: 6093935; DOI: 10.1038/s41467-018-05512-x

  • Sequence variation of Epstein-Barr virus: viral types, geography, codon usage and diseases.

    Correia S, Bridges R, Wegner F, Venturini C, Palser A, Middeldorp JM, Cohen JI, Lorenzetti MA, Bassano I, White RE et al.

    Journal of virology 2018

    PUBMED: 30111570; DOI: 10.1128/JVI.01132-18

  • Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data.

    Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R et al.

    BMC genomics 2018;19;1;613

    PUBMED: 30107785; PMC: 6092779; DOI: 10.1186/s12864-018-4988-z

  • Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota.

    Jenkins TP, Peachey LE, Ajami NJ, MacDonald AS, Hsieh MH, Brindley PJ, Cantacessi C and Rinaldi G

    Scientific reports 2018;8;1;12072

    PUBMED: 30104612; PMC: 6089957; DOI: 10.1038/s41598-018-30412-x

  • Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.

    Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P et al.

    BMC genomics 2018;19;1;604

    PUBMED: 30103702; PMC: 6088408; DOI: 10.1186/s12864-018-4989-y

  • Genomics and clinical correlates of renal cell carcinoma.

    Mitchell TJ, Rossi SH, Klatte T and Stewart GD

    World journal of urology 2018;36;12;1899-1911

    PUBMED: 30099580; PMC: 6280817; DOI: 10.1007/s00345-018-2429-x

  • Biology and genome of a newly discovered sibling species of Caenorhabditis elegans.

    Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Liu D, Tsuyama K, Maeda Y, Namai S, Kumagai R, Tracey A et al.

    Nature communications 2018;9;1;3216

    PUBMED: 30097582; PMC: 6086898; DOI: 10.1038/s41467-018-05712-5

  • Combined Influence of B-Cell Receptor Rearrangement and Somatic Hypermutation on B-Cell Class-Switch Fate in Health and in Chronic Lymphocytic Leukemia.

    Petrova VN, Muir L, McKay PF, Vassiliou GS, Smith KGC, Lyons PA, Russell CA, Anderson CA, Kellam P and Bashford-Rogers RJM

    Frontiers in immunology 2018;9;1784

    PUBMED: 30147686; PMC: 6095981; DOI: 10.3389/fimmu.2018.01784

  • Microevolution of epidemiological highly relevant non-O157 enterohemorrhagic Escherichia coli of serogroups O26 and O111.

    Eichhorn I, Semmler T, Mellmann A, Pickard D, Anjum MF, Fruth A, Karch H and Wieler LH

    International journal of medical microbiology : IJMM 2018;308;8;1085-1095

    PUBMED: 30115547; DOI: 10.1016/j.ijmm.2018.08.003

  • Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes.

    Makunin AI, Romanenko SA, Beklemisheva VR, Perelman PL, Druzhkova AS, Petrova KO, Prokopov DY, Chernyaeva EN, Johnson JL, Kukekova AV et al.

    Genes 2018;9;8

    PUBMED: 30103445; PMC: 6116037; DOI: 10.3390/genes9080405

  • Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.

    Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW et al.

    Science (New York, N.Y.) 2018;361;6402;594-599

    PUBMED: 30093597; PMC: 6104812; DOI: 10.1126/science.aat1699

  • Inter-homologue repair in fertilized human eggs?

    Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A and Jasin M

    Nature 2018;560;7717;E5-E7

    PUBMED: 30089924; DOI: 10.1038/s41586-018-0379-5

  • CTCF maintains regulatory homeostasis of cancer pathways.

    Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC and Odom DT

    Genome biology 2018;19;1;106

    PUBMED: 30086769; DOI: 10.1186/s13059-018-1484-3

  • Dietary stearic acid regulates mitochondria in vivo in humans.

    Senyilmaz-Tiebe D, Pfaff DH, Virtue S, Schwarz KV, Fleming T, Altamura S, Muckenthaler MU, Okun JG, Vidal-Puig A, Nawroth P and Teleman AA

    Nature communications 2018;9;1;3129

    PUBMED: 30087348; PMC: 6081440; DOI: 10.1038/s41467-018-05614-6

  • Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System.

    Liu MM, Boinett CJ, Chan ACK, Parkhill J, Murphy MEP and Gaynor EC

    mBio 2018;9;4

    PUBMED: 30087169; PMC: 6083913; DOI: 10.1128/mBio.01347-18

  • Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging.

    Severo MS, Landry JJM, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA and Levashina EA

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;32;E7568-E7577

    PUBMED: 30038005; PMC: 6094101; DOI: 10.1073/pnas.1803062115

  • Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.

    Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK et al.

    Current biology : CB 2018;28;15;2420-2428.e10

    PUBMED: 30033331; PMC: 6089836; DOI: 10.1016/j.cub.2018.05.058

  • Combination therapy as a potential risk factor for the development of type 2 diabetes in patients with schizophrenia: the GOMAP study.

    Mamakou V, Hackinger S, Zengini E, Tsompanaki E, Marouli E, Serafetinidis I, Prins B, Karabela A, Glezou E, Southam L et al.

    BMC psychiatry 2018;18;1;249

    PUBMED: 30071838; PMC: 6090901; DOI: 10.1186/s12888-018-1826-4

  • Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates.

    Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A, Mahasirimongkol S, Yanai H, Yamada N, Nedsuwan S, Imasanguan W et al.

    Scientific reports 2018;8;1;11597

    PUBMED: 30072734; PMC: 6072702; DOI: 10.1038/s41598-018-29986-3

  • Registered access: authorizing data access.

    Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J et al.

    European journal of human genetics : EJHG 2018;26;12;1721-1731

    PUBMED: 30069064; PMC: 6244209; DOI: 10.1038/s41431-018-0219-y

  • An enhanced CRISPR repressor for targeted mammalian gene regulation.

    Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A et al.

    Nature methods 2018;15;8;611-616

    PUBMED: 30013045; PMC: 6129399; DOI: 10.1038/s41592-018-0048-5

  • The murine hepatic sequelae of long-term ethanol consumption are sex-specific and exacerbated by Aldh1b1 loss.

    Müller MF, Kendall TJ, Adams DJ, Zhou Y and Arends MJ

    Experimental and molecular pathology 2018;105;1;63-70

    PUBMED: 29859945; DOI: 10.1016/j.yexmp.2018.05.008

  • Antibodies to Intercellular Adhesion Molecule 1-Binding Plasmodium falciparum Erythrocyte Membrane Protein 1-DBLβ Are Biomarkers of Protective Immunity to Malaria in a Cohort of Young Children from Papua New Guinea.

    Tessema SK, Utama D, Chesnokov O, Hodder AN, Lin CS, Harrison GLA, Jespersen JS, Petersen B, Tavul L, Siba P et al.

    Infection and immunity 2018;86;8

    PUBMED: 29784862; PMC: 6056858; DOI: 10.1128/IAI.00485-17

  • BCL11B mutations in patients affected by a neurodevelopmental disorder with reduced type 2 innate lymphoid cells.

    Lessel D, Gehbauer C, Bramswig NC, Schluth-Bolard C, Venkataramanappa S, van Gassen KLI, Hempel M, Haack TB, Baresic A, Genetti CA et al.

    Brain : a journal of neurology 2018;141;8;2299-2311

    PUBMED: 29985992; PMC: 6061686; DOI: 10.1093/brain/awy173

  • Bisphenol a and mesenchymal stem cells: Recent insights.

    Nunes HC, Scarano WR, Deffune E, Felisbino SL, Porreca I and Delella FK

    Life sciences 2018;206;22-28

    PUBMED: 29778805; DOI: 10.1016/j.lfs.2018.05.023

  • BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq.

    Lindeman I, Emerton G, Mamanova L, Snir O, Polanski K, Qiao SW, Sollid LM, Teichmann SA and Stubbington MJT

    Nature methods 2018;15;8;563-565

    PUBMED: 30065371; DOI: 10.1038/s41592-018-0082-3

  • Chronic TNFα-driven injury delays cell migration to villi in the intestinal epithelium.

    Muraro D, Parker A, Vaux L, Filippi S, Almet AA, Fletcher AG, Watson AJM, Pin C, Maini PK and Byrne HM

    Journal of the Royal Society, Interface 2018;15;145

    PUBMED: 30068555; PMC: 6127161; DOI: 10.1098/rsif.2018.0037

  • Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk.

    Minchin JEN, Scahill CM, Staudt N, Busch-Nentwich EM and Rawls JF

    Journal of lipid research 2018;59;8;1536-1545

    PUBMED: 29794036; PMC: 6071777; DOI: 10.1194/jlr.D084525

  • Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations.

    Arciero E, Kraaijenbrink T, Asan, Haber M, Mezzavilla M, Ayub Q, Wang W, Pingcuo Z, Yang H, Wang J et al.

    Molecular biology and evolution 2018;35;8;1916-1933

    PUBMED: 29796643; PMC: 6063301; DOI: 10.1093/molbev/msy094

  • Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

    Scerri EML, Thomas MG, Manica A, Gunz P, Stock JT, Stringer C, Grove M, Groucutt HS, Timmermann A, Rightmire GP et al.

    Trends in ecology & evolution 2018;33;8;582-594

    PUBMED: 30007846; PMC: 6092560; DOI: 10.1016/j.tree.2018.05.005

  • Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions.

    Tuck AC, Natarajan KN, Rice GM, Borawski J, Mohn F, Rankova A, Flemr M, Wenger A, Nutiu R, Teichmann S and Bühler M

    Life science alliance 2018;1;4;e201800124

    PUBMED: 30456373; PMC: 6238598; DOI: 10.26508/lsa.201800124

  • Draft Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Typhimurium Clinical Isolates from Uruguay.

    Cordeiro NF, D'Alessandro B, Iriarte A, Pickard D, Yim L, Chabalgoity JA, Betancor L and Vignoli R

    Microbiology resource announcements 2018;7;4

    PUBMED: 30533879; PMC: 6256424; DOI: 10.1128/MRA.00917-18

  • Ecto-5'-nucleotidase (CD73) regulates peripheral chemoreceptor activity and cardiorespiratory responses to hypoxia.

    Holmes AP, Ray CJ, Pearson SA, Coney AM and Kumar P

    The Journal of physiology 2018;596;15;3137-3148

    PUBMED: 28560821; PMC: 6068227; DOI: 10.1113/JP274498

  • FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.

    Grinter R, Hay ID, Song J, Wang J, Teng D, Dhanesakaran V, Wilksch JJ, Davies MR, Littler D, Beckham SA et al.

    PLoS biology 2018;16;8;e2006026

    PUBMED: 30071011; PMC: 6071955; DOI: 10.1371/journal.pbio.2006026

  • Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study.

    Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N, Ojal J, Shebe M, Awuondo KO, Mturi N, Tsofa B et al.

    The Lancet. Haematology 2018;5;8;e333-e345

    PUBMED: 30033078; PMC: 6069675; DOI: 10.1016/S2352-3026(18)30107-8

  • Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent.

    Cuypers B, Berg M, Imamura H, Dumetz F, De Muylder G, Domagalska MA, Rijal S, Bhattarai NR, Maes I, Sanders M et al.

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2018;62;170-178

    PUBMED: 29679745; PMC: 6261844; DOI: 10.1016/j.meegid.2018.04.021

  • Long reads: their purpose and place.

    Pollard MO, Gurdasani D, Mentzer AJ, Porter T and Sandhu MS

    Human molecular genetics 2018;27;R2;R234-R241

    PUBMED: 29767702; PMC: 6061690; DOI: 10.1093/hmg/ddy177

  • Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck.

    Lamelas A, Hamid AM, Dangy JP, Hauser J, Jud M, Röltgen K, Hodgson A, Junghanss T, Harris SR, Parkhill J et al.

    Genome biology and evolution 2018;10;8;2102-2109

    PUBMED: 30060167; PMC: 6110524; DOI: 10.1093/gbe/evy152

  • Molecular genetic overlap between migraine and major depressive disorder.

    Yang Y, Zhao H, Boomsma DI, Ligthart L, Belin AC, Smith GD, Esko T, Freilinger TM, Hansen TF, Ikram MA et al.

    European journal of human genetics : EJHG 2018;26;8;1202-1216

    PUBMED: 29995844; PMC: 6057914; DOI: 10.1038/s41431-018-0150-2

  • Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution.

    Gilabert A, Otto TD, Rutledge GG, Franzon B, Ollomo B, Arnathau C, Durand P, Moukodoum ND, Okouga AP, Ngoubangoye B et al.

    PLoS biology 2018;16;8;e2006035

    PUBMED: 30142149; PMC: 6130868; DOI: 10.1371/journal.pbio.2006035

  • Recognizing the reagent microbiome.

    de Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A, Charnock-Jones DS, Peacock SJ, Smith GCS and Parkhill J

    Nature microbiology 2018;3;8;851-853

    PUBMED: 30046175; DOI: 10.1038/s41564-018-0202-y

  • Reply to Dookie et al., "Whole-Genome Sequencing To Guide the Selection of Treatment for Drug-Resistant Tuberculosis".

    Köser CU, Heyckendorf J, Andres S, Olaru ID, Schön T, Sturegård E, Beckert P, Schleusener V, Kohl TA, Hillemann D et al.

    Antimicrobial agents and chemotherapy 2018;62;8

    PUBMED: 30054377; PMC: 6105783; DOI: 10.1128/AAC.00616-18

  • Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures.

    Sozen B, Amadei G, Cox A, Wang R, Na E, Czukiewska S, Chappell L, Voet T, Michel G, Jing N et al.

    Nature cell biology 2018;20;8;979-989

    PUBMED: 30038254; DOI: 10.1038/s41556-018-0147-7

  • Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells.

    Dev H, Chiang TW, Lescale C, de Krijger I, Martin AG, Pilger D, Coates J, Sczaniecka-Clift M, Wei W, Ostermaier M et al.

    Nature cell biology 2018;20;8;954-965

    PUBMED: 30022119; PMC: 6145444; DOI: 10.1038/s41556-018-0140-1

  • Surveying what's flushed away.

    Iraola G and Kumar N

    Nature reviews. Microbiology 2018;16;8;456

    PUBMED: 29930288; DOI: 10.1038/s41579-018-0047-7

  • T cell cytolytic capacity is independent of initial stimulation strength.

    Richard AC, Lun ATL, Lau WWY, Göttgens B, Marioni JC and Griffiths GM

    Nature immunology 2018;19;8;849-858

    PUBMED: 30013148; PMC: 6300116; DOI: 10.1038/s41590-018-0160-9

  • Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus.

    Page AJ and Keane JA

    PeerJ 2018;6;e5233

    PUBMED: 30083440; PMC: 6074768; DOI: 10.7717/peerj.5233

  • Organoid cultures recapitulate esophageal adenocarcinoma heterogeneity providing a model for clonality studies and precision therapeutics.

    Li X, Francies HE, Secrier M, Perner J, Miremadi A, Galeano-Dalmau N, Barendt WJ, Letchford L, Leyden GM, Goffin EK et al.

    Nature communications 2018;9;1;2983

    PUBMED: 30061675; PMC: 6065407; DOI: 10.1038/s41467-018-05190-9

  • RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

    Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW and Corander J

    Wellcome open research 2018;3;93

    PUBMED: 30345380; PMC: 6178908; DOI: 10.12688/wellcomeopenres.14694.1

  • Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.

    Peacock SJ, Parkhill J and Brown NM

    Microbiology (Reading, England) 2018

    PUBMED: 30052172; DOI: 10.1099/mic.0.000700

  • Developmental Sensitivity in Schistosoma mansoni to Puromycin To Establish Drug Selection of Transgenic Schistosomes.

    Yan HB, Smout MJ, Ju C, Folley AE, Skinner DE, Mann VH, Loukas A, Hu W, Brindley PJ and Rinaldi G

    Antimicrobial agents and chemotherapy 2018;62;8

    PUBMED: 29760143; PMC: 6105839; DOI: 10.1128/AAC.02568-17

  • Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches.

    Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D, Loiseau C, Meehan C, Osei-Wusu S, Forson A, Laryea C et al.

    Scientific reports 2018;8;1;11269

    PUBMED: 30050166; PMC: 6062541; DOI: 10.1038/s41598-018-29620-2

  • De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder.

    Gregor A, Sadleir LG, Asadollahi R, Azzarello-Burri S, Battaglia A, Ousager LB, Boonsawat P, Bruel AL, Buchert R, Calpena E et al.

    American journal of human genetics 2018;103;2;305-316

    PUBMED: 30057029; PMC: 6080769; DOI: 10.1016/j.ajhg.2018.07.003

  • Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis.

    Wyllie S, Thomas M, Patterson S, Crouch S, De Rycker M, Lowe R, Gresham S, Urbaniak MD, Otto TD, Stojanovski L et al.

    Nature 2018;560;7717;192-197

    PUBMED: 30046105; PMC: 6402543; DOI: 10.1038/s41586-018-0356-z

  • Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.

    Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA, Krueger F, Mohammed H, Dean W, Nichols J, Rugg-Gunn P et al.

    Cell systems 2018;7;1;63-76.e12

    PUBMED: 30031774; PMC: 6066359; DOI: 10.1016/j.cels.2018.06.012

  • The First Norovirus Longitudinal Seroepidemiological Study From Sub-Saharan Africa Reveals High Seroprevalence of Diverse Genotypes Associated With Host Susceptibility Factors.

    Thorne L, Nalwoga A, Mentzer AJ, de Rougemont A, Hosmillo M, Webb E, Nampiija M, Muhwezi A, Carstensen T, Gurdasani D et al.

    The Journal of infectious diseases 2018;218;5;716-725

    PUBMED: 29912471; PMC: 6057498; DOI: 10.1093/infdis/jiy219

  • Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157.

    Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C and Cain AK

    mBio 2018;9;4

    PUBMED: 30042196; PMC: 6058288; DOI: 10.1128/mBio.00705-18

  • Gene exchange drives the ecological success of a multi-host bacterial pathogen.

    Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ et al.

    Nature ecology & evolution 2018;2;9;1468-1478

    PUBMED: 30038246; PMC: 7610605; DOI: 10.1038/s41559-018-0617-0

  • PPARs and Metabolic Disorders Associated with Challenged Adipose Tissue Plasticity.

    Corrales P, Vidal-Puig A and Medina-Gómez G

    International journal of molecular sciences 2018;19;7

    PUBMED: 30037087; DOI: 10.3390/ijms19072124

  • Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans.

    Mühlemann B, Margaryan A, Damgaard PB, Allentoft ME, Vinner L, Hansen AJ, Weber A, Bazaliiskii VI, Molak M, Arneborg J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;29;7557-7562

    PUBMED: 29967156; PMC: 6055166; DOI: 10.1073/pnas.1804921115

  • A cross-sectional analysis of ITN and IRS coverage in Namibia in 2013.

    Allcock SH, Young EH and Sandhu MS

    Malaria journal 2018;17;1;264

    PUBMED: 30012154; PMC: 6048889; DOI: 10.1186/s12936-018-2417-z

  • Clonal heterogeneity of acute myeloid leukemia treated with the IDH2 inhibitor enasidenib.

    Quek L, David MD, Kennedy A, Metzner M, Amatangelo M, Shih A, Stoilova B, Quivoron C, Heiblig M, Willekens C et al.

    Nature medicine 2018;24;8;1167-1177

    PUBMED: 30013198; PMC: 6925974; DOI: 10.1038/s41591-018-0115-6

  • Eradication genomics-lessons for parasite control.

    Cotton JA, Berriman M, Dalén L and Barnes I

    Science (New York, N.Y.) 2018;361;6398;130-131

    PUBMED: 30002241; DOI: 10.1126/science.aar6609

  • Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles.

    Dumont BL, Williams CL, Ng BL, Horncastle V, Chambers CL, McGraw LA, Adams D, Mackay TFC and Breen M

    Genetics 2018;210;1;83-97

    PUBMED: 30002081; PMC: 6116968; DOI: 10.1534/genetics.118.301182

  • A Requirement for Zic2 in the Regulation of Nodal Expression Underlies the Establishment of Left-Sided Identity.

    Dykes IM, Szumska D, Kuncheria L, Puliyadi R, Chen CM, Papanayotou C, Lockstone H, Dubourg C, David V, Schneider JE et al.

    Scientific reports 2018;8;1;10439

    PUBMED: 29992973; PMC: 6041270; DOI: 10.1038/s41598-018-28714-1

  • Malaria Vaccines: Recent Advances and New Horizons.

    Draper SJ, Sack BK, King CR, Nielsen CM, Rayner JC, Higgins MK, Long CA and Seder RA

    Cell host & microbe 2018;24;1;43-56

    PUBMED: 30001524; PMC: 6054918; DOI: 10.1016/j.chom.2018.06.008

  • SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.

    Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL and Miska EA

    Development (Cambridge, England) 2018;145;13

    PUBMED: 29945865; PMC: 6053661; DOI: 10.1242/dev.164640

  • Detection and removal of barcode swapping in single-cell RNA-seq data.

    Griffiths JA, Richard AC, Bach K, Lun ATL and Marioni JC

    Nature communications 2018;9;1;2667

    PUBMED: 29991676; PMC: 6039488; DOI: 10.1038/s41467-018-05083-x

  • Genome-wide CRISPR-KO Screen Uncovers mTORC1-Mediated Gsk3 Regulation in Naive Pluripotency Maintenance and Dissolution.

    Li M, Yu JSL, Tilgner K, Ong SH, Koike-Yusa H and Yusa K

    Cell reports 2018;24;2;489-502

    PUBMED: 29996108; PMC: 6057492; DOI: 10.1016/j.celrep.2018.06.027

  • No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice.

    Iyer V, Boroviak K, Thomas M, Doe B, Riva L, Ryder E and Adams DJ

    PLoS genetics 2018;14;7;e1007503

    PUBMED: 29985941; PMC: 6057650; DOI: 10.1371/journal.pgen.1007503

  • Prediction of acute myeloid leukaemia risk in healthy individuals.

    Abelson S, Collord G, Ng SWK, Weissbrod O, Mendelson Cohen N, Niemeyer E, Barda N, Zuzarte PC, Heisler L, Sundaravadanam Y et al.

    Nature 2018;559;7714;400-404

    PUBMED: 29988082; PMC: 6485381; DOI: 10.1038/s41586-018-0317-6

  • Single-cell biology: resolving biological complexity, one cell at a time.

    Ranzoni AM and Cvejic A

    Development (Cambridge, England) 2018;145;13

    PUBMED: 29986899; DOI: 10.1242/dev.163972

  • The prehistoric peopling of Southeast Asia.

    McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C et al.

    Science (New York, N.Y.) 2018;361;6397;88-92

    PUBMED: 29976827; DOI: 10.1126/science.aat3628

  • Increasing nursing capacity in genomics: Overview of existing global genomics resources.

    Calzone KA, Kirk M, Tonkin E, Badzek L, Benjamin C and Middleton A

    Nurse education today 2018;69;53-59

    PUBMED: 30007148; PMC: 6112149; DOI: 10.1016/j.nedt.2018.06.032

  • Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

    Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F and Odom DT

    Nucleic acids research 2018;46;12;5950-5966

    PUBMED: 29860520; PMC: 6093183; DOI: 10.1093/nar/gky437

  • Expanding the phenotype of the X-linked BCOR microphthalmia syndromes.

    Ragge N, Isidor B, Bitoun P, Odent S, Giurgea I, Cogné B, Deb W, Vincent M, Le Gall J, Morton J et al.

    Human genetics 2018;138;8-9;1051-1069

    PUBMED: 29974297; DOI: 10.1007/s00439-018-1896-x

  • Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics.

    Auburn S, Benavente ED, Miotto O, Pearson RD, Amato R, Grigg MJ, Barber BE, William T, Handayuni I, Marfurt J et al.

    Nature communications 2018;9;1;2585

    PUBMED: 29968722; PMC: 6030216; DOI: 10.1038/s41467-018-04965-4

  • Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital.

    Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018;67;2;161-170

    PUBMED: 29340588; PMC: 6030810; DOI: 10.1093/cid/ciy027

  • Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

    Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM et al.

    Nucleic acids research 2018;46;W1;W186-W193

    PUBMED: 29873782; PMC: 6030976; DOI: 10.1093/nar/gky474

  • Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

    Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S et al.

    Nucleic acids research 2018;46;W1;W25-W29

    PUBMED: 29788132; PMC: 6030932; DOI: 10.1093/nar/gky329

  • Itraconazole targets cell cycle heterogeneity in colorectal cancer.

    Buczacki SJA, Popova S, Biggs E, Koukorava C, Buzzelli J, Vermeulen L, Hazelwood L, Francies H, Garnett MJ and Winton DJ

    The Journal of experimental medicine 2018;215;7;1891-1912

    PUBMED: 29853607; PMC: 6028508; DOI: 10.1084/jem.20171385

  • RSAT 2018: regulatory sequence analysis tools 20th anniversary.

    Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D et al.

    Nucleic acids research 2018;46;W1;W209-W214

    PUBMED: 29722874; PMC: 6030903; DOI: 10.1093/nar/gky317

  • Whole Genome Sequence and Comparative Genomics Analysis of Multi-drug Resistant Environmental Staphylococcus epidermidis ST59.

    Xu Z, Misra R, Jamrozy D, Paterson GK, Cutler RR, Holmes MA, Gharbia S and Mkrtchyan HV

    G3 (Bethesda, Md.) 2018;8;7;2225-2230

    PUBMED: 29716961; PMC: 6027886; DOI: 10.1534/g3.118.200314

  • A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes.

    van Zuydam NR, Ahlqvist E, Sandholm N, Deshmukh H, Rayner NW, Abdalla M, Ladenvall C, Ziemek D, Fauman E, Robertson NR et al.

    Diabetes 2018;67;7;1414-1427

    PUBMED: 29703844; PMC: 6014557; DOI: 10.2337/db17-0914

  • A graph-based approach to diploid genome assembly.

    Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R and Marschall T

    Bioinformatics (Oxford, England) 2018;34;13;i105-i114

    PUBMED: 29949989; PMC: 6022571; DOI: 10.1093/bioinformatics/bty279

  • The Human Cell Atlas: Technical approaches and challenges.

    Hon CC, Shin JW, Carninci P and Stubbington MJT

    Briefings in functional genomics 2018;17;4;283-294

    PUBMED: 29092000; PMC: 6063304; DOI: 10.1093/bfgp/elx029

  • An outbreak of a rare Shiga-toxin-producing Escherichia coli serotype (O117:H7) among men who have sex with men.

    Baker KS, Dallman TJ, Thomson NR and Jenkins C

    Microbial genomics 2018;4;7

    PUBMED: 29781799; PMC: 6113874; DOI: 10.1099/mgen.0.000181

  • AP-1 Takes Centre Stage in Enhancer Chromatin Dynamics.

    Madrigal P and Alasoo K

    Trends in cell biology 2018;28;7;509-511

    PUBMED: 29778529; DOI: 10.1016/j.tcb.2018.04.009

  • Association of LPA Variants With Risk of Coronary Disease and the Implications for Lipoprotein(a)-Lowering Therapies: A Mendelian Randomization Analysis.

    Burgess S, Ference BA, Staley JR, Freitag DF, Mason AM, Nielsen SF, Willeit P, Young R, Surendran P, Karthikeyan S et al.

    JAMA cardiology 2018;3;7;619-627

    PUBMED: 29926099; PMC: 6481553; DOI: 10.1001/jamacardio.2018.1470

  • Can Wolbachia save the day?

    Pance A

    Nature reviews. Microbiology 2018;16;7;396

    PUBMED: 29720706; DOI: 10.1038/s41579-018-0021-4

  • Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses.

    Napolitani G, Kurupati P, Teng KWW, Gibani MM, Rei M, Aulicino A, Preciado-Llanes L, Wong MT, Becht E, Howson L et al.

    Nature immunology 2018;19;7;742-754

    PUBMED: 29925993; DOI: 10.1038/s41590-018-0133-z

  • Comparative sequence analysis of the capsular polysaccharide loci of Actinobacillus pleuropneumoniae serovars 1-18, and development of two multiplex PCRs for comprehensive capsule typing.

    Bossé JT, Li Y, Fernandez Crespo R, Lacouture S, Gottschalk M, Sárközi R, Fodor L, Casas Amoribieta M, Angen Ø, Nedbalcova K et al.

    Veterinary microbiology 2018;220;83-89

    PUBMED: 29885806; PMC: 6008488; DOI: 10.1016/j.vetmic.2018.05.011

  • Consequences of Identifying XIAP Deficiency in an Adult Patient With Inflammatory Bowel Disease.

    Quaranta M, Wilson R, Gonçalves Serra E, Pandey S, Schwerd T, Gilmour K, Klenerman P, Powrie F, Keshav S, Travis SPL et al.

    Gastroenterology 2018;155;1;231-234

    PUBMED: 29894681; DOI: 10.1053/j.gastro.2018.03.069

  • De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses.

    Olsson S, Pinosio S, González-Martínez SC, Abascal F, Mayol M, Grivet D and Vendramin GG

    Plant molecular biology 2018;97;4-5;337-345

    PUBMED: 29850988; DOI: 10.1007/s11103-018-0742-9

  • Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Assay for Diagnosis of Cutaneous and Visceral Leishmaniasis.

    Adams ER, Schoone G, Versteeg I, Gomez MA, Diro E, Mori Y, Perlee D, Downing T, Saravia N, Assaye A et al.

    Journal of clinical microbiology 2018;56;7

    PUBMED: 29695527; PMC: 6018344; DOI: 10.1128/JCM.00386-18

  • Dynamics of the epigenetic landscape during the maternal-to-zygotic transition.

    Eckersley-Maslin MA, Alda-Catalinas C and Reik W

    Nature reviews. Molecular cell biology 2018;19;7;436-450

    PUBMED: 29686419; DOI: 10.1038/s41580-018-0008-z

  • Farewell Stan Stanley Falkow: 1934-2018.

    Cabello FC, Cohen SN, Curtiss R, Dougan G, van Embden J, Finlay BB, Heffron F, Helinski D, Hull R, Hull S et al.

    Environmental microbiology 2018;20;7;2322-2333

    PUBMED: 30146753; DOI: 10.1111/1462-2920.14308

  • Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing.

    Cuypers WL, Jacobs J, Wong V, Klemm EJ, Deborggraeve S and Van Puyvelde S

    Microbial genomics 2018;4;7

    PUBMED: 29975627; PMC: 6113872; DOI: 10.1099/mgen.0.000195

  • Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.

    Savage JE, Jansen PR, Stringer S, Watanabe K, Bryois J, de Leeuw CA, Nagel M, Awasthi S, Barr PB, Coleman JRI et al.

    Nature genetics 2018;50;7;912-919

    PUBMED: 29942086; PMC: 6411041; DOI: 10.1038/s41588-018-0152-6

  • Genome-wide association study of response to methotrexate in early rheumatoid arthritis patients.

    Taylor JC, Bongartz T, Massey J, Mifsud B, Spiliopoulou A, Scott IC, Wang J, Morgan M, Plant D, Colombo M et al.

    The pharmacogenomics journal 2018;18;4;528-538

    PUBMED: 29795407; DOI: 10.1038/s41397-018-0025-5

  • Global and targeted approaches to single-cell transcriptome characterization.

    Kolodziejczyk AA and Lönnberg T

    Briefings in functional genomics 2018;17;4;209-219

    PUBMED: 29028866; PMC: 6063303; DOI: 10.1093/bfgp/elx025

  • Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains.

    Phan MVT, Ngo Tri T, Hong Anh P, Baker S, Kellam P and Cotten M

    Virus evolution 2018;4;2;vey035

    PUBMED: 30568804; PMC: 6295324; DOI: 10.1093/ve/vey035

  • Microevolution and Patterns of Transmission of Shigella sonnei within Cyclic Outbreaks Shigellosis, Israel.

    Behar A, Baker KS, Bassal R, Ezernitchi A, Valinsky L, Thomson NR and Cohen D

    Emerging infectious diseases 2018;24;7;1335-1339

    PUBMED: 29912703; PMC: 6038740; DOI: 10.3201/eid2407.171313

  • Multiplex genomewide association analysis of breast milk fatty acid composition extends the phenotypic association and potential selection of FADS1 variants to arachidonic acid, a critical infant micronutrient.

    Mychaleckyj JC, Nayak U, Colgate ER, Zhang D, Carstensen T, Ahmed S, Ahmed T, Mentzer AJ, Alam M, Kirkpatrick BD et al.

    Journal of medical genetics 2018;55;7;459-468

    PUBMED: 29514873; PMC: 6047159; DOI: 10.1136/jmedgenet-2017-105134

  • RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics.

    Claessens A, Harris LM, Stanojcic S, Chappell L, Stanton A, Kuk N, Veneziano-Broccia P, Sterkers Y, Rayner JC and Merrick CJ

    PLoS genetics 2018;14;7;e1007490

    PUBMED: 29965959; PMC: 6044543; DOI: 10.1371/journal.pgen.1007490

  • SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.

    Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ and Keane JA

    Microbial genomics 2018;4;7

    PUBMED: 29870330; PMC: 6113868; DOI: 10.1099/mgen.0.000186

  • Single-cell genomics.

    Hemberg M

    Briefings in functional genomics 2018;17;4;207-208

    PUBMED: 30060035; PMC: 6063269; DOI: 10.1093/bfgp/ely025

  • Superbubbles, Ultrabubbles, and Cacti.

    Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E and Hickey G

    Journal of computational biology : a journal of computational molecular cell biology 2018;25;7;649-663

    PUBMED: 29461862; PMC: 6067107; DOI: 10.1089/cmb.2017.0251

  • Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

    Otieno JR, Kamau EM, Oketch JW, Ngoi JM, Gichuki AM, Binter Š, Otieno GP, Ngama M, Agoti CN, Cane PA et al.

    Virus evolution 2018;4;2;vey027

    PUBMED: 30271623; PMC: 6153471; DOI: 10.1093/ve/vey027

  • Point-prevalence survey of carbapenemase-producing Enterobacteriaceae and vancomycin-resistant enterococci in adult inpatients in a university teaching hospital in the UK.

    Wilson HJ, Khokhar F, Enoch DA, Brown NM, Ahluwalia J, Dougan G and Török ME

    The Journal of hospital infection 2018;100;1;35-39

    PUBMED: 29969691; DOI: 10.1016/j.jhin.2018.06.024

  • Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

    Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR et al.

    Scientific reports 2018;8;1;9868

    PUBMED: 29959380; PMC: 6026146; DOI: 10.1038/s41598-018-28199-y

  • Cryo-EM structure of an essential Plasmodium vivax invasion complex.

    Gruszczyk J, Huang RK, Chan LJ, Menant S, Hong C, Murphy JM, Mok YF, Griffin MDW, Pearson RD, Wong W et al.

    Nature 2018;559;7712;135-139

    PUBMED: 29950717; DOI: 10.1038/s41586-018-0249-1

  • Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria.

    Lee HJ, Georgiadou A, Walther M, Nwakanma D, Stewart LB, Levin M, Otto TD, Conway DJ, Coin LJ and Cunnington AJ

    Science translational medicine 2018;10;447

    PUBMED: 29950443; PMC: 6326353; DOI: 10.1126/scitranslmed.aar3619

  • Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia.

    Amambua-Ngwa A, Jeffries D, Amato R, Worwui A, Karim M, Ceesay S, Nyang H, Nwakanma D, Okebe J, Kwiatkowski D et al.

    Scientific reports 2018;8;1;9687

    PUBMED: 29946063; PMC: 6018809; DOI: 10.1038/s41598-018-28017-5

  • CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

    Morgan MD and Marioni JC

    Genome biology 2018;19;1;81

    PUBMED: 29945659; PMC: 6020341; DOI: 10.1186/s13059-018-1461-x

  • The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections.

    Pimenoff VN, Houldcroft CJ, Rifkin RF and Underdown S

    Genes 2018;9;7

    PUBMED: 29941858; PMC: 6070984; DOI: 10.3390/genes9070317

  • Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh.

    Domman D, Chowdhury F, Khan AI, Dorman MJ, Mutreja A, Uddin MI, Paul A, Begum YA, Charles RC, Calderwood SB et al.

    Nature genetics 2018;50;7;951-955

    PUBMED: 29942084; PMC: 6283067; DOI: 10.1038/s41588-018-0150-8

  • Global Distribution of Invasive Serotype 35D Streptococcus pneumoniae Isolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine.

    Lo SW, Gladstone RA, van Tonder AJ, Hawkins PA, Kwambana-Adams B, Cornick JE, Madhi SA, Nzenze SA, du Plessis M, Kandasamy R et al.

    Journal of clinical microbiology 2018;56;7

    PUBMED: 29720431; PMC: 6018339; DOI: 10.1128/JCM.00228-18

  • Analysis of shared heritability in common disorders of the brain.

    Brainstorm Consortium, Anttila V, Bulik-Sullivan B, Finucane HK, Walters RK, Bras J, Duncan L, Escott-Price V, Falcone GJ, Gormley P et al.

    Science (New York, N.Y.) 2018;360;6395

    PUBMED: 29930110; PMC: 6097237; DOI: 10.1126/science.aap8757

  • IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.

    Momozawa Y, Dmitrieva J, Théâtre E, Deffontaine V, Rahmouni S, Charloteaux B, Crins F, Docampo E, Elansary M, Gori AS et al.

    Nature communications 2018;9;1;2427

    PUBMED: 29930244; PMC: 6013502; DOI: 10.1038/s41467-018-04365-8

  • Ancient Biomolecules and Evolutionary Inference.

    Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S et al.

    Annual review of biochemistry 2018;87;1029-1060

    PUBMED: 29709200; DOI: 10.1146/annurev-biochem-062917-012002

  • Genetic Diversity of Cryptosporidium hominis in a Bangladeshi Community as Revealed by Whole-Genome Sequencing.

    Gilchrist CA, Cotton JA, Burkey C, Arju T, Gilmartin A, Lin Y, Ahmed E, Steiner K, Alam M, Ahmed S et al.

    The Journal of infectious diseases 2018;218;2;259-264

    PUBMED: 29514308; PMC: 6009673; DOI: 10.1093/infdis/jiy121

  • Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

    Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W and Stegle O

    Molecular systems biology 2018;14;6;e8124

    PUBMED: 29925568; PMC: 6010767; DOI: 10.15252/msb.20178124

  • Vitamin D and risk of pregnancy related hypertensive disorders: mendelian randomisation study.

    Magnus MC, Miliku K, Bauer A, Engel SM, Felix JF, Jaddoe VWV, Lawlor DA, London SJ, Magnus P, McGinnis R et al.

    BMJ (Clinical research ed.) 2018;361;k2167

    PUBMED: 29925546; PMC: 6008987; DOI: 10.1136/bmj.k2167

  • Inhibition of somatosensory mechanotransduction by annexin A6.

    Raouf R, Lolignier S, Sexton JE, Millet Q, Santana-Varela S, Biller A, Fuller AM, Pereira V, Choudhary JS, Collins MO et al.

    Science signaling 2018;11;535

    PUBMED: 29921656; DOI: 10.1126/scisignal.aao2060

  • Tissue-Restricted Adaptive Type 2 Immunity Is Orchestrated by Expression of the Costimulatory Molecule OX40L on Group 2 Innate Lymphoid Cells.

    Halim TYF, Rana BMJ, Walker JA, Kerscher B, Knolle MD, Jolin HE, Serrao EM, Haim-Vilmovsky L, Teichmann SA, Rodewald HR et al.

    Immunity 2018;48;6;1195-1207.e6

    PUBMED: 29907525; PMC: 6015114; DOI: 10.1016/j.immuni.2018.05.003

  • Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants.

    Wegert J, Vokuhl C, Collord G, Del Castillo Velasco-Herrera M, Farndon SJ, Guzzo C, Jorgensen M, Anderson J, Slater O, Duncan C et al.

    Nature communications 2018;9;1;2378

    PUBMED: 29915264; PMC: 6006309; DOI: 10.1038/s41467-018-04650-6

  • Kpax3: Bayesian bi-clustering of large sequence datasets.

    Pessia A and Corander J

    Bioinformatics (Oxford, England) 2018;34;12;2132-2133

    PUBMED: 29425273; DOI: 10.1093/bioinformatics/bty056

  • SET de novo frameshift variants associated with developmental delay and intellectual disabilities.

    Richardson R, Splitt M, Newbury-Ecob R, Hulbert A, Kennedy J, Weber A and DDD Study

    European journal of human genetics : EJHG 2018;26;9;1306-1311

    PUBMED: 29907757; PMC: 6117329; DOI: 10.1038/s41431-018-0199-y

  • Genomic evidence that the live Chlamydia abortus vaccine strain 1B is not attenuated and has the potential to cause disease.

    Longbottom D, Sait M, Livingstone M, Laroucau K, Sachse K, Harris SR, Thomson NR and Seth-Smith HMB

    Vaccine 2018;36;25;3593-3598

    PUBMED: 29759381; PMC: 6005232; DOI: 10.1016/j.vaccine.2018.05.042

  • MAN1B-CDG: Novel variants with a distinct phenotype and review of literature.

    Balasubramanian M, Johnson DS and DDD Study

    European journal of medical genetics 2018;62;2;109-114

    PUBMED: 29908352; DOI: 10.1016/j.ejmg.2018.06.011

  • A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes.

    Papachristou EK, Kishore K, Holding AN, Harvey K, Roumeliotis TI, Chilamakuri CSR, Omarjee S, Chia KM, Swarbrick A, Lim E et al.

    Nature communications 2018;9;1;2311

    PUBMED: 29899353; PMC: 5998130; DOI: 10.1038/s41467-018-04619-5

  • Eavesdropping and crosstalk between secreted quorum sensing peptide signals that regulate bacteriocin production in Streptococcus pneumoniae.

    Miller EL, Kjos M, Abrudan MI, Roberts IS, Veening JW and Rozen DE

    The ISME journal 2018;12;10;2363-2375

    PUBMED: 29899510; PMC: 6155019; DOI: 10.1038/s41396-018-0178-x

  • Flaviviruses Exploit the Lipid Droplet Protein AUP1 to Trigger Lipophagy and Drive Virus Production.

    Zhang J, Lan Y, Li MY, Lamers MM, Fusade-Boyer M, Klemm E, Thiele C, Ashour J and Sanyal S

    Cell host & microbe 2018;23;6;819-831.e5

    PUBMED: 29902443; DOI: 10.1016/j.chom.2018.05.005

  • Cancer-mutation network and the number and specificity of driver mutations.

    Iranzo J, Martincorena I and Koonin EV

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;26;E6010-E6019

    PUBMED: 29895694; PMC: 6042135; DOI: 10.1073/pnas.1803155115

  • Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants.

    Dadaev T, Saunders EJ, Newcombe PJ, Anokian E, Leongamornlert DA, Brook MN, Cieza-Borrella C, Mijuskovic M, Wakerell S, Olama AAA et al.

    Nature communications 2018;9;1;2256

    PUBMED: 29892050; PMC: 5995836; DOI: 10.1038/s41467-018-04109-8

  • Compensation between CSF1R+ macrophages and Foxp3+ Treg cells drives resistance to tumor immunotherapy.

    Gyori D, Lim EL, Grant FM, Spensberger D, Roychoudhuri R, Shuttleworth SJ, Okkenhaug K, Stephens LR and Hawkins PT

    JCI insight 2018;3;11

    PUBMED: 29875321; PMC: 6124419; DOI: 10.1172/jci.insight.120631

  • Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum.

    Ganna A, Satterstrom FK, Zekavat SM, Das I, Kurki MI, Churchhouse C, Alfoldi J, Martin AR, Havulinna AS, Byrnes A et al.

    American journal of human genetics 2018;102;6;1204-1211

    PUBMED: 29861106; PMC: 5992130; DOI: 10.1016/j.ajhg.2018.05.002

  • Genomic atlas of the human plasma proteome.

    Sun BB, Maranville JC, Peters JE, Stacey D, Staley JR, Blackshaw J, Burgess S, Jiang T, Paige E, Surendran P et al.

    Nature 2018;558;7708;73-79

    PUBMED: 29875488; PMC: 6697541; DOI: 10.1038/s41586-018-0175-2

  • The genomics of insecticide resistance: insights from recent studies in African malaria vectors.

    Clarkson CS, Temple HJ and Miles A

    Current opinion in insect science 2018;27;111-115

    PUBMED: 30025626; PMC: 6060083; DOI: 10.1016/j.cois.2018.05.017

  • 'Your DNA, Your Say': global survey gathering attitudes toward genomics: design, delivery and methods.

    Middleton A, Niemiec E, Prainsack B, Bobe J, Farley L, Steed C, Smith J, Bevan P, Bonhomme N, Kleiderman E et al.

    Personalized medicine 2018;15;4;311-318

    PUBMED: 29856292; DOI: 10.2217/pme-2018-0032

  • Ancient human parallel lineages within North America contributed to a coastal expansion.

    Scheib CL, Li H, Desai T, Link V, Kendall C, Dewar G, Griffith PW, Mörseburg A, Johnson JR, Potter A et al.

    Science (New York, N.Y.) 2018;360;6392;1024-1027

    PUBMED: 29853687; DOI: 10.1126/science.aar6851

  • Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

    Haghverdi L, Lun ATL, Morgan MD and Marioni JC

    Nature biotechnology 2018;36;5;421-427

    PUBMED: 29608177; PMC: 6152897; DOI: 10.1038/nbt.4091

  • Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core.

    Segawa T, Takeuchi N, Fujita K, Aizen VB, Willerslev E and Yonezawa T

    Heredity 2018;120;6;562-573

    PUBMED: 29302050; PMC: 5943335; DOI: 10.1038/s41437-017-0040-3

  • Designing an intuitive web application for drug discovery scientists.

    Karamanis N, Pignatelli M, Carvalho-Silva D, Rowland F, Cham JA and Dunham I

    Drug discovery today 2018;23;6;1169-1174

    PUBMED: 29337199; DOI: 10.1016/j.drudis.2018.01.032

  • Editorial overview: Molecular and genetic basis of [metabolic] disease: Genes, glucose, glycerol and girth: metabolism in our DNA.

    Barroso I and Florez JC

    Current opinion in genetics & development 2018;50;iv-vi

    PUBMED: 30100123; DOI: 10.1016/j.gde.2018.07.001

  • Editorial overview: Sequences and topology: Dynamic sequences and topologies of proteins.

    Marsh JA and Teichmann SA

    Current opinion in structural biology 2018;50;vii-viii

    PUBMED: 30080482; DOI: 10.1016/j.sbi.2018.07.005

  • Genetics of HbA1c: a case study in clinical translation.

    Leong A and Wheeler E

    Current opinion in genetics & development 2018;50;79-85

    PUBMED: 29522974; DOI: 10.1016/j.gde.2018.02.008

  • Implications of insecticide resistance for malaria vector control with long-lasting insecticidal nets: a WHO-coordinated, prospective, international, observational cohort study.

    Kleinschmidt I, Bradley J, Knox TB, Mnzava AP, Kafy HT, Mbogo C, Ismail BA, Bigoga JD, Adechoubou A, Raghavendra K et al.

    The Lancet. Infectious diseases 2018;18;6;640-649

    PUBMED: 29650424; PMC: 5968369; DOI: 10.1016/S1473-3099(18)30172-5

  • Juggling resistance mutations.

    Rutledge GG and Amato R

    Nature reviews. Microbiology 2018;16;6;332

    PUBMED: 29703939; DOI: 10.1038/s41579-018-0008-1

  • Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.

    Wick RR, Heinz E, Holt KE and Wyres KL

    Journal of clinical microbiology 2018;56;6

    PUBMED: 29618504; PMC: 5971559; DOI: 10.1128/JCM.00197-18

  • Long- and short-term outcomes in renal allografts with deceased donors: A large recipient and donor genome-wide association study.

    Hernandez-Fuentes MP, Franklin C, Rebollo-Mesa I, Mollon J, Delaney F, Perucha E, Stapleton C, Borrows R, Byrne C, Cavalleri G et al.

    American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2018;18;6;1370-1379

    PUBMED: 29392897; PMC: 6001640; DOI: 10.1111/ajt.14594

  • Neisseria gonorrhoeae molecular typing for understanding sexual networks and antimicrobial resistance transmission: A systematic review.

    Town K, Bolt H, Croxford S, Cole M, Harris S, Field N and Hughes G

    The Journal of infection 2018;76;6;507-514

    PUBMED: 29698633; PMC: 5999358; DOI: 10.1016/j.jinf.2018.02.011

  • Recurrent rearrangements of FOS and FOSB define osteoblastoma.

    Fittall MW, Mifsud W, Pillay N, Ye H, Strobl AC, Verfaillie A, Demeulemeester J, Zhang L, Berisha F, Tarabichi M et al.

    Nature communications 2018;9;1;2150

    PUBMED: 29858576; PMC: 5984627; DOI: 10.1038/s41467-018-04530-z

  • Single-cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukemia.

    De Bie J, Demeyer S, Alberti-Servera L, Geerdens E, Segers H, Broux M, De Keersmaecker K, Michaux L, Vandenberghe P, Voet T et al.

    Leukemia 2018;32;6;1358-1369

    PUBMED: 29740158; PMC: 5990522; DOI: 10.1038/s41375-018-0127-8

  • SuperDCA for genome-wide epistasis analysis.

    Puranen S, Pesonen M, Pensar J, Xu YY, Lees JA, Bentley SD, Croucher NJ and Corander J

    Microbial genomics 2018;4;6

    PUBMED: 29813016; PMC: 6096938; DOI: 10.1099/mgen.0.000184

  • De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder.

    Reijnders MRF, Miller KA, Alvi M, Goos JAC, Lees MM, de Burca A, Henderson A, Kraus A, Mikat B, de Vries BBA et al.

    American journal of human genetics 2018;102;6;1195-1203

    PUBMED: 29861108; PMC: 5992133; DOI: 10.1016/j.ajhg.2018.04.014

  • Generating CRISPR/Cas9-Derived Mutant Mice by Zygote Cytoplasmic Injection Using an Automatic Microinjector

    Brendan Doe, Ellen Brown and Katharina Boroviak

    Methods and Protocols 2018;1;1;5

    DOI: 10.3390/mps1010005

  • Polycythaemia Vera, Essential Thrombocythaemia and Myelofibrosis

    Godfrey, Anna L., Vassiliou,George S. and Green, Anthony R.

    ABC of Clinical Haematology 2018;21

    URL: https://books.google.co.uk/books?...hl=en&lr=&id=DjdJDwAAQBAJ&oi=fnd&pg=PA21&dq=Polycythaemia+Vera,+Essential+Thrombocythaemia+and+Myelofibrosis&ots=0Jcec3PI10&sig=_KkGpttypLWE489V2gxJPYyyNPA#v=onepage&q=Polycythaemia%20Vera%2C%20Essential%20Thrombocythaemia%20and%20Myelofibrosis&f=false

  • Polycythaemia Vera, Essential Thrombocythaemia and Myelofibrosis

    Godfrey, A.L, VASSILIOU,G.S and Green,A.R

    ABC of Clinical Haematology 2018;21

    URL: https://bit.ly/2LIGc1m

  • Proteomic profiling of the brain of mice with experimental cerebral malaria.

    Moussa E, Huang H, Ahras M, Lall A, Thezenas ML, Fischer R, Kessler BM, Pain A, Billker O and Casals-Pascual C

    Journal of proteomics 2018;180;61-69

    PUBMED: 28602553; DOI: 10.1016/j.jprot.2017.06.002

  • Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

    Davies G, Lam M, Harris SE, Trampush JW, Luciano M, Hill WD, Hagenaars SP, Ritchie SJ, Marioni RE, Fawns-Ritchie C et al.

    Nature communications 2018;9;1;2098

    PUBMED: 29844566; PMC: 5974083; DOI: 10.1038/s41467-018-04362-x

  • An in vitro erythrocyte preference assay reveals that Plasmodium falciparum parasites prefer Type O over Type A erythrocytes.

    Theron M, Cross N, Cawkill P, Bustamante LY and Rayner JC

    Scientific reports 2018;8;1;8133

    PUBMED: 29802282; PMC: 5970199; DOI: 10.1038/s41598-018-26559-2

  • Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans.

    Fleurbaaij F, Henneman AA, Corver J, Knetsch CW, Smits WK, Nauta ST, Giera M, Dragan I, Kumar N, Lawley TD et al.

    Scientific reports 2018;8;1;8181

    PUBMED: 29802257; PMC: 5970244; DOI: 10.1038/s41598-018-26079-z

  • A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.

    Schlaffner CN, Pirklbauer GJ, Bender A, Steen JAJ and Choudhary JS

    Journal of visualized experiments : JoVE 2018;135

    PUBMED: 29889196; PMC: 6101353; DOI: 10.3791/57633

  • Early lineage segregation of multipotent embryonic mammary gland progenitors.

    Wuidart A, Sifrim A, Fioramonti M, Matsumura S, Brisebarre A, Brown D, Centonze A, Dannau A, Dubois C, Van Keymeulen A et al.

    Nature cell biology 2018;20;6;666-676

    PUBMED: 29784918; PMC: 5985933; DOI: 10.1038/s41556-018-0095-2

  • Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.

    Otto TD, Gilabert A, Crellen T, Böhme U, Arnathau C, Sanders M, Oyola SO, Okouga AP, Boundenga L, Willaume E et al.

    Nature microbiology 2018;3;6;687-697

    PUBMED: 29784978; PMC: 5985962; DOI: 10.1038/s41564-018-0162-2

  • Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

    Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH et al.

    Virus evolution 2018;4;1;vey007

    PUBMED: 29876136; PMC: 5961307; DOI: 10.1093/ve/vey007

  • Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens.

    Baker S, Thomson N, Weill FX and Holt KE

    Science (New York, N.Y.) 2018;360;6390;733-738

    PUBMED: 29773743; PMC: 6510332; DOI: 10.1126/science.aar3777

  • Automated typing of red blood cell and platelet antigens: a whole-genome sequencing study.

    Lane WJ, Westhoff CM, Gleadall NS, Aguad M, Smeland-Wagman R, Vege S, Simmons DP, Mah HH, Lebo MS, Walter K et al.

    The Lancet. Haematology 2018;5;6;e241-e251

    PUBMED: 29780001; PMC: 6438177; DOI: 10.1016/S2352-3026(18)30053-X

  • Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi.

    Fisher MC, Ghosh P, Shelton JMG, Bates K, Brookes L, Wierzbicki C, Rosa GM, Farrer RA, Aanensen DM, Alvarado-Rybak M et al.

    Scientific reports 2018;8;1;7772

    PUBMED: 29773857; PMC: 5958081; DOI: 10.1038/s41598-018-24472-2

  • Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action.

    Fukuda K, Limmathurotsakul D, Okeke IN, Shetty N, van Doorn R, Feasey NA, Chiara F, Zoubiane G, Jinks T, Parkhill J et al.

    Wellcome open research 2018;3;59

    PUBMED: 29904730; PMC: 5989141; DOI: 10.12688/wellcomeopenres.14586.2

  • Fed-EXosome: extracellular vesicles and cell-cell communication in metabolic regulation.

    Samuelson I and Vidal-Puig AJ

    Essays in biochemistry 2018;62;2;165-175

    PUBMED: 29717059; DOI: 10.1042/EBC20170087

  • Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey.

    Harris SR, Cole MJ, Spiteri G, Sánchez-Busó L, Golparian D, Jacobsson S, Goater R, Abudahab K, Yeats CA, Bercot B et al.

    The Lancet. Infectious diseases 2018;18;7;758-768

    PUBMED: 29776807; PMC: 6010626; DOI: 10.1016/S1473-3099(18)30225-1

  • Recent Asian origin of chytrid fungi causing global amphibian declines.

    O'Hanlon SJ, Rieux A, Farrer RA, Rosa GM, Waldman B, Bataille A, Kosch TA, Murray KA, Brankovics B, Fumagalli M et al.

    Science (New York, N.Y.) 2018;360;6389;621-627

    PUBMED: 29748278; PMC: 6311102; DOI: 10.1126/science.aar1965

  • Genome-wide and high-density CRISPR-Cas9 screens identify point mutations in PARP1 causing PARP inhibitor resistance.

    Pettitt SJ, Krastev DB, Brandsma I, Dréan A, Song F, Aleksandrov R, Harrell MI, Menon M, Brough R, Campbell J et al.

    Nature communications 2018;9;1;1849

    PUBMED: 29748565; PMC: 5945626; DOI: 10.1038/s41467-018-03917-2

  • The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

    de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N et al.

    Science (New York, N.Y.) 2018;360;6396

    PUBMED: 29743352; PMC: 6748862; DOI: 10.1126/science.aar7711

  • 137 ancient human genomes from across the Eurasian steppes.

    Damgaard PB, Marchi N, Rasmussen S, Peyrot M, Renaud G, Korneliussen T, Moreno-Mayar JV, Pedersen MW, Goldberg A, Usmanova E et al.

    Nature 2018;557;7705;369-374

    PUBMED: 29743675; DOI: 10.1038/s41586-018-0094-2

  • Ancient hepatitis B viruses from the Bronze Age to the Medieval period.

    Mühlemann B, Jones TC, Damgaard PB, Allentoft ME, Shevnina I, Logvin A, Usmanova E, Panyushkina IP, Boldgiv B, Bazartseren T et al.

    Nature 2018;557;7705;418-423

    PUBMED: 29743673; DOI: 10.1038/s41586-018-0097-z

  • Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance.

    Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G et al.

    Scientific reports 2018;8;1;7389

    PUBMED: 29743642; PMC: 5943296; DOI: 10.1038/s41598-018-25764-3

  • CRISPR/Cas9 editing in human pluripotent stem cell-cardiomyocytes highlights arrhythmias, hypocontractility, and energy depletion as potential therapeutic targets for hypertrophic cardiomyopathy.

    Mosqueira D, Mannhardt I, Bhagwan JR, Lis-Slimak K, Katili P, Scott E, Hassan M, Prondzynski M, Harmer SC, Tinker A et al.

    European heart journal 2018

    PUBMED: 29741611; DOI: 10.1093/eurheartj/ehy249

  • De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder.

    Snijders Blok L, Hiatt SM, Bowling KM, Prokop JW, Engel KL, Cochran JN, Bebin EM, Bijlsma EK, Ruivenkamp CAL, Terhal P et al.

    Human genetics 2018;137;5;375-388

    PUBMED: 29740699; PMC: 5973976; DOI: 10.1007/s00439-018-1887-y

  • HIV treatment is associated with a two-fold higher probability of raised triglycerides: Pooled Analyses in 21 023 individuals in sub-Saharan Africa.

    Ekoru K, Young EH, Dillon DG, Gurdasani D, Stehouwer N, Faurholt-Jepsen D, Levitt NS, Crowther NJ, Nyirenda M, Njelekela MA et al.

    Global health, epidemiology and genomics 2018;3

    PUBMED: 29881632; PMC: 5985947; DOI: 10.1017/gheg.2018.7

  • Meeting report: 31st International Mammalian Genome Conference, Mammalian Genetics and Genomics: From Molecular Mechanisms to Translational Applications.

    Sánchez-Andrade G, Moskowitz J, Howe S and Gunn TM

    Mammalian genome : official journal of the International Mammalian Genome Society 2018

    PUBMED: 29740698; DOI: 10.1007/s00335-018-9747-6

  • Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis.

    Steinberg J, Brooks RA, Southam L, Bhatnagar S, Roumeliotis TI, Hatzikotoulas K, Zengini E, Wilkinson JM, Choudhary JS, McCaskie AW and Zeggini E

    Rheumatology (Oxford, England) 2018

    PUBMED: 29741735; DOI: 10.1093/rheumatology/key101

  • Human Genetics: Busy Subway Networks in Remote Oceania?

    Bergström A and Tyler-Smith C

    Current biology : CB 2018;28;9;R549-R551

    PUBMED: 29738726; DOI: 10.1016/j.cub.2018.03.033

  • UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs.

    Gozdecka M, Meduri E, Mazan M, Tzelepis K, Dudek M, Knights AJ, Pardo M, Yu L, Choudhary JS, Metzakopian E et al.

    Nature genetics 2018;50;6;883-894

    PUBMED: 29736013; PMC: 6029661; DOI: 10.1038/s41588-018-0114-z

  • The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from Atopic Dermatitis patients.

    Harkins CP, McAleer MA, Bennett D, McHugh M, Fleury OM, Pettigrew KA, Oravcová K, Parkhill J, Proby CM, Dawe RS et al.

    The British journal of dermatology 2018

    PUBMED: 29729180; DOI: 10.1111/bjd.16722

  • Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya.

    Kiyuka PK, Agoti CN, Munywoki PK, Njeru R, Bett A, Otieno JR, Otieno GP, Kamau E, Clark TG, van der Hoek L et al.

    The Journal of infectious diseases 2018;217;11;1728-1739

    PUBMED: 29741740; DOI: 10.1093/infdis/jiy098

  • A CRISPR knockout screen Identifies SETDB1-target retroelement silencing factors in embryonic stem cells.

    Fukuda K, Okuda A, Yusa K and Shinkai Y

    Genome research 2018

    PUBMED: 29728365; DOI: 10.1101/gr.227280.117

  • Single-Cell (Multi)omics Technologies.

    Chappell L, Russell AJC and Voet T

    Annual review of genomics and human genetics 2018;19;15-41

    PUBMED: 29727584; DOI: 10.1146/annurev-genom-091416-035324

  • Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis.

    Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Bronner IF, Casandra D, Mayho M et al.

    Science (New York, N.Y.) 2018;360;6388

    PUBMED: 29724925; PMC: 6360947; DOI: 10.1126/science.aap7847

  • Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres.

    Otto TD, Böhme U, Sanders M, Reid A, Bruske EI, Duffy CW, Bull PC, Pearson RD, Abdi A, Dimonte S et al.

    Wellcome open research 2018;3;52

    PUBMED: 29862326; PMC: 5964635; DOI: 10.12688/wellcomeopenres.14571.1

  • Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.

    Almeida A, Mitchell AL, Tarkowska A and Finn RD

    GigaScience 2018;7;5

    PUBMED: 29762668; PMC: 5967554; DOI: 10.1093/gigascience/giy054

  • Clonal haematopoiesis is not prevalent in survivors of childhood cancer.

    Collord G, Park N, Podestà M, Dagnino M, Cilloni D, Jones D, Varela I, Frassoni F and Vassiliou GS

    British journal of haematology 2018;181;4;537-539

    PUBMED: 28369776; PMC: 6001539; DOI: 10.1111/bjh.14630

  • Defective germline reprogramming rewires the spermatogonial transcriptome.

    Vasiliauskaitė L, Berrens RV, Ivanova I, Carrieri C, Reik W, Enright AJ and O'Carroll D

    Nature structural & molecular biology 2018;25;5;394-404

    PUBMED: 29728652; DOI: 10.1038/s41594-018-0058-0

  • Expanding the molecular basis and phenotypic spectrum of ZDHHC9-associated X-linked intellectual disability.

    Schirwani S, Wakeling E, Smith K, DDD Study and Balasubramanian M

    American journal of medical genetics. Part A 2018;176;5;1238-1244

    PUBMED: 29681091; DOI: 10.1002/ajmg.a.38683

  • Functional mRNA analysis reveals aberrant splicing caused by novel intronic mutation in WDR45 in NBIA patient.

    Willoughby J, Duff-Farrier C, Desurkar A, Kurian M, Raghavan A, DDD Study and Balasubramanian M

    American journal of medical genetics. Part A 2018;176;5;1049-1054

    PUBMED: 29681108; DOI: 10.1002/ajmg.a.38656

  • Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

    Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF et al.

    Nature genetics 2018;50;5;668-681

    PUBMED: 29700475; PMC: 5934326; DOI: 10.1038/s41588-018-0090-3

  • Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni.

    Roquis D, Taudt A, Geyer KK, Padalino G, Hoffmann KF, Holroyd N, Berriman M, Aliaga B, Chaparro C, Grunau C and Augusto RC

    PLoS pathogens 2018;14;5;e1007066

    PUBMED: 29782530; PMC: 5983875; DOI: 10.1371/journal.ppat.1007066

  • Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.

    Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A et al.

    PLoS genetics 2018;14;5;e1007329

    PUBMED: 29795570; PMC: 5967709; DOI: 10.1371/journal.pgen.1007329

  • Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa.

    Huckins LM, Hatzikotoulas K, Southam L, Thornton LM, Steinberg J, Aguilera-McKay F, Treasure J, Schmidt U, Gunasinghe C, Romero A et al.

    Molecular psychiatry 2018;23;5;1169-1180

    PUBMED: 29155802; PMC: 5828108; DOI: 10.1038/mp.2017.88

  • Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

    Wheeler NE, Gardner PP and Barquist L

    PLoS genetics 2018;14;5;e1007333

    PUBMED: 29738521; PMC: 5940178; DOI: 10.1371/journal.pgen.1007333

  • RADpainter and fineRADstructure: Population Inference from RADseq Data.

    Malinsky M, Trucchi E, Lawson DJ and Falush D

    Molecular biology and evolution 2018;35;5;1284-1290

    PUBMED: 29474601; PMC: 5913677; DOI: 10.1093/molbev/msy023

  • Society and personal genome data.

    Middleton A

    Human molecular genetics 2018;27;R1;R8-R13

    PUBMED: 29522190; PMC: 5946868; DOI: 10.1093/hmg/ddy084

  • SpatialDE: identification of spatially variable genes.

    Svensson V, Teichmann SA and Stegle O

    Nature methods 2018;15;5;343-346

    PUBMED: 29553579; PMC: 6350895; DOI: 10.1038/nmeth.4636

  • Validating the concept of mutational signatures with isogenic cell models.

    Zou X, Owusu M, Harris R, Jackson SP, Loizou JI and Nik-Zainal S

    Nature communications 2018;9;1;1744

    PUBMED: 29717121; PMC: 5931590; DOI: 10.1038/s41467-018-04052-8

  • Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.

    Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC and Arendt D

    Molecular biology and evolution 2018;35;5;1047-1062

    PUBMED: 29373712; PMC: 5913682; DOI: 10.1093/molbev/msx336

  • Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.

    Iorio F, Garcia-Alonso L, Brammeld JS, Martincorena I, Wille DR, McDermott U and Saez-Rodriguez J

    Scientific reports 2018;8;1;6713

    PUBMED: 29713020; PMC: 5928049; DOI: 10.1038/s41598-018-25076-6

  • Population size changes and selection drive patterns of parallel evolution in a host-virus system.

    Frickel J, Feulner PGD, Karakoc E and Becks L

    Nature communications 2018;9;1;1706

    PUBMED: 29703896; PMC: 5923231; DOI: 10.1038/s41467-018-03990-7

  • Targeting of NAT10 enhances healthspan in a mouse model of human accelerated aging syndrome.

    Balmus G, Larrieu D, Barros AC, Collins C, Abrudan M, Demir M, Geisler NJ, Lelliott CJ, White JK, Karp NA et al.

    Nature communications 2018;9;1;1700

    PUBMED: 29703891; PMC: 5923383; DOI: 10.1038/s41467-018-03770-3

  • RTS,S/AS01 malaria vaccine mismatch observed among Plasmodium falciparum isolates from southern and central Africa and globally.

    Pringle JC, Carpi G, Almagro-Garcia J, Zhu SJ, Kobayashi T, Mulenga M, Bobanga T, Chaponda M, Moss WJ and Norris DE

    Scientific reports 2018;8;1;6622

    PUBMED: 29700348; PMC: 5920075; DOI: 10.1038/s41598-018-24585-8

  • Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional chromosome painting.

    Gomes AJB, Nagamachi CY, Rodrigues LRR, Ferguson-Smith MA, Yang F, O'Brien PCM and Pieczarka JC

    BMC evolutionary biology 2018;18;1;62

    PUBMED: 29699485; PMC: 5921544; DOI: 10.1186/s12862-018-1176-3

  • Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus.

    Coughlan S, Taylor AS, Feane E, Sanders M, Schonian G, Cotton JA and Downing T

    Royal Society open science 2018;5;4;172212

    PUBMED: 29765675; PMC: 5936940; DOI: 10.1098/rsos.172212

  • Two complement receptor one alleles have opposing associations with cerebral malaria and interact with α+thalassaemia.

    Opi DH, Swann O, Macharia A, Uyoga S, Band G, Ndila CM, Harrison EM, Thera MA, Kone AK, Diallo DA et al.

    eLife 2018;7

    PUBMED: 29690995; PMC: 5953541; DOI: 10.7554/eLife.31579

  • Alpha-v-containing integrins are host receptors for the Plasmodium falciparum sporozoite surface protein, TRAP.

    Dundas K, Shears MJ, Sun Y, Hopp CS, Crosnier C, Metcalf T, Girling G, Sinnis P, Billker O and Wright GJ

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;17;4477-4482

    PUBMED: 29632205; PMC: 5924908; DOI: 10.1073/pnas.1719660115

  • Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease.

    Emdin CA, Khera AV, Chaffin M, Klarin D, Natarajan P, Aragam K, Haas M, Bick A, Zekavat SM, Nomura A et al.

    Nature communications 2018;9;1;1613

    PUBMED: 29691411; PMC: 5915445; DOI: 10.1038/s41467-018-03911-8

  • Earth BioGenome Project: Sequencing life for the future of life.

    Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J, Crandall KA, Durbin R, Edwards SV, Forest F, Gilbert MTP et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;17;4325-4333

    PUBMED: 29686065; PMC: 5924910; DOI: 10.1073/pnas.1720115115

  • The Tatton-Brown-Rahman Syndrome: A clinical study of 55 individuals with de novo constitutive DNMT3A variants.

    Tatton-Brown K, Zachariou A, Loveday C, Renwick A, Mahamdallie S, Aksglaede L, Baralle D, Barge-Schaapveld D, Blyth M, Bouma M et al.

    Wellcome open research 2018;3;46

    PUBMED: 29900417; PMC: 5964628; DOI: 10.12688/wellcomeopenres.14430.1

  • Extending the clinical and genetic spectrum of ARID2 related intellectual disability. A case series of 7 patients.

    Gazdagh G, Blyth M, Scurr I, Turnpenny PD, Mehta SG, Armstrong R, McEntagart M, Newbury-Ecob R, Tobias ES, DDD Study and Joss S

    European journal of medical genetics 2018;62;1;27-34

    PUBMED: 29698805; DOI: 10.1016/j.ejmg.2018.04.014

  • Children with cerebral malaria or severe malarial anaemia lack immunity to distinct variant surface antigen subsets.

    Travassos MA, Niangaly A, Bailey JA, Ouattara A, Coulibaly D, Lyke KE, Laurens MB, Pablo J, Jasinskas A, Nakajima R et al.

    Scientific reports 2018;8;1;6281

    PUBMED: 29674705; PMC: 5908851; DOI: 10.1038/s41598-018-24462-4

  • Culturing of female bladder bacteria reveals an interconnected urogenital microbiota.

    Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, Stares MD, Hilt EE, Price TK, Wolfe AJ and Lawley TD

    Nature communications 2018;9;1;1557

    PUBMED: 29674608; PMC: 5908796; DOI: 10.1038/s41467-018-03968-5

  • Novel GPR34 and CCR6 mutation and distinct genetic profiles in MALT lymphomas of different sites.

    Moody S, Thompson JS, Chuang SS, Liu H, Raderer M, Vassiliou G, Wlodarska I, Wu F, Cogliatti S, Robson A et al.

    Haematologica 2018;103;8;1329-1336

    PUBMED: 29674500; PMC: 6068028; DOI: 10.3324/haematol.2018.191601

  • Physiological and Genetic Adaptations to Diving in Sea Nomads.

    Ilardo MA, Moltke I, Korneliussen TS, Cheng J, Stern AJ, Racimo F, de Barros Damgaard P, Sikora M, Seguin-Orlando A, Rasmussen S et al.

    Cell 2018;173;3;569-580.e15

    PUBMED: 29677510; DOI: 10.1016/j.cell.2018.03.054

  • Identification of the tumour transition states occurring during EMT.

    Pastushenko I, Brisebarre A, Sifrim A, Fioramonti M, Revenco T, Boumahdi S, Van Keymeulen A, Brown D, Moers V, Lemaire S et al.

    Nature 2018;556;7702;463-468

    PUBMED: 29670281; DOI: 10.1038/s41586-018-0040-3

  • Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

    Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z et al.

    Nature genetics 2018;50;5;682-692

    PUBMED: 29662167; PMC: 6372064; DOI: 10.1038/s41588-018-0086-z

  • Using single-cell genomics to understand developmental processes and cell fate decisions.

    Griffiths JA, Scialdone A and Marioni JC

    Molecular systems biology 2018;14;4;e8046

    PUBMED: 29661792; PMC: 5900446; DOI: 10.15252/msb.20178046

  • Discovery of Potent and Selective MRCK Inhibitors with Therapeutic Effect on Skin Cancer.

    Unbekandt M, Belshaw S, Bower J, Clarke M, Cordes J, Crighton D, Croft DR, Drysdale MJ, Garnett MJ, Gill K et al.

    Cancer research 2018;78;8;2096-2114

    PUBMED: 29382705; PMC: 5901721; DOI: 10.1158/0008-5472.CAN-17-2870

  • Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.

    Baker KS, Dallman TJ, Field N, Childs T, Mitchell H, Day M, Weill FX, Lefèvre S, Tourdjman M, Hughes G et al.

    Nature communications 2018;9;1;1462

    PUBMED: 29654279; PMC: 5899146; DOI: 10.1038/s41467-018-03949-8

  • Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

    Turajlic S, Xu H, Litchfield K, Rowan A, Horswell S, Chambers T, O'Brien T, Lopez JI, Watkins TBK, Nicol D et al.

    Cell 2018;173;3;595-610.e11

    PUBMED: 29656894; PMC: 5938372; DOI: 10.1016/j.cell.2018.03.043

  • Glutaminolysis is a metabolic dependency in FLT3ITD acute myeloid leukemia unmasked by FLT3 tyrosine kinase inhibition.

    Gallipoli P, Giotopoulos G, Tzelepis K, Costa ASH, Vohra S, Medina-Perez P, Basheer F, Marando L, Di Lisio L, Dias JML et al.

    Blood 2018;131;15;1639-1653

    PUBMED: 29463564; PMC: 6061932; DOI: 10.1182/blood-2017-12-820035

  • Identification of rare sequence variation underlying heritable pulmonary arterial hypertension.

    Gräf S, Haimel M, Bleda M, Hadinnapola C, Southgate L, Li W, Hodgson J, Liu B, Salmon RM, Southwood M et al.

    Nature communications 2018;9;1;1416

    PUBMED: 29650961; PMC: 5897357; DOI: 10.1038/s41467-018-03672-4

  • Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal.

    Mitchell TJ, Turajlic S, Rowan A, Nicol D, Farmery JHR, O'Brien T, Martincorena I, Tarpey P, Angelopoulos N, Yates LR et al.

    Cell 2018;173;3;611-623.e17

    PUBMED: 29656891; PMC: 5927631; DOI: 10.1016/j.cell.2018.02.020

  • The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.

    van der Kuyl AC, Vink M, Zorgdrager F, Bakker M, Wymant C, Hall M, Gall A, Blanquart F, Berkhout B, Fraser C et al.

    Virus research 2018;250;51-64

    PUBMED: 29654800; DOI: 10.1016/j.virusres.2018.04.008

  • Intra-tumour diversification in colorectal cancer at the single-cell level.

    Roerink SF, Sasaki N, Lee-Six H, Young MD, Alexandrov LB, Behjati S, Mitchell TJ, Grossmann S, Lightfoot H, Egan DA et al.

    Nature 2018;556;7702;457-462

    PUBMED: 29643510; DOI: 10.1038/s41586-018-0024-3

  • Delineating the HMGB1 and HMGB2 interactome in prostate and ovary epithelial cells and its relationship with cancer.

    Barreiro-Alonso A, Lamas-Maceiras M, García-Díaz R, Rodríguez-Belmonte E, Yu L, Pardo M, Choudhary JS and Cerdán ME

    Oncotarget 2018;9;27;19050-19064

    PUBMED: 29721183; PMC: 5922377; DOI: 10.18632/oncotarget.24887

  • Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers.

    Meier B, Volkova NV, Hong Y, Schofield P, Campbell PJ, Gerstung M and Gartner A

    Genome research 2018;28;5;666-675

    PUBMED: 29636374; PMC: 5932607; DOI: 10.1101/gr.226845.117

  • The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils.

    Stammnitz MR, Coorens THH, Gori KC, Hayes D, Fu B, Wang J, Martin-Herranz DE, Alexandrov LB, Baez-Ortega A, Barthorpe S et al.

    Cancer cell 2018;33;4;607-619.e15

    PUBMED: 29634948; PMC: 5896245; DOI: 10.1016/j.ccell.2018.03.013

  • Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia.

    de la Fuente C, Ávila-Arcos MC, Galimany J, Carpenter ML, Homburger JR, Blanco A, Contreras P, Cruz Dávalos D, Reyes O, San Roman M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018

    PUBMED: 29632188; DOI: 10.1073/pnas.1715688115

  • Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

    Mahajan A, Wessel J, Willems SM, Zhao W, Robertson NR, Chu AY, Gan W, Kitajima H, Taliun D, Rayner NW et al.

    Nature genetics 2018;50;4;559-571

    PUBMED: 29632382; PMC: 5898373; DOI: 10.1038/s41588-018-0084-1

  • Human Pluripotent Stem Cell-Derived Endoderm for Modeling Development and Clinical Applications.

    Yiangou L, Ross ADB, Goh KJ and Vallier L

    Cell stem cell 2018;22;4;485-499

    PUBMED: 29625066; DOI: 10.1016/j.stem.2018.03.016

  • Effects of Environmental and Management-Associated Factors on Prevalence and Diversity of Streptococcus suis in Clinically Healthy Pig Herds in China and the United Kingdom.

    Zou G, Zhou J, Xiao R, Zhang L, Cheng Y, Jin H, Li L, Zhang L, Wu B, Qian P et al.

    Applied and environmental microbiology 2018;84;8

    PUBMED: 29427423; PMC: 5881051; DOI: 10.1128/AEM.02590-17

  • Genetic counselling in the era of genomic medicine.

    Patch C and Middleton A

    British medical bulletin 2018

    PUBMED: 29617718; DOI: 10.1093/bmb/ldy008

  • scmap: projection of single-cell RNA-seq data across data sets.

    Kiselev VY, Yiu A and Hemberg M

    Nature methods 2018;15;5;359-362

    PUBMED: 29608555; DOI: 10.1038/nmeth.4644

  • The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

    Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD et al.

    PLoS pathogens 2018;14;4;e1006966

    PUBMED: 29617440; PMC: 5902063; DOI: 10.1371/journal.ppat.1006966

  • Advances in the generation of bioengineered bile ducts.

    Justin AW, Saeb-Parsy K, Markaki AE, Vallier L and Sampaziotis F

    Biochimica et biophysica acta. Molecular basis of disease 2018;1864;4 Pt B;1532-1538

    PUBMED: 29097260; DOI: 10.1016/j.bbadis.2017.10.034

  • Are commercial providers a viable option for clinical bacterial sequencing?

    Raven K, Blane B, Churcher C, Parkhill J and Peacock SJ

    Microbial genomics 2018;4;4

    PUBMED: 29620501; PMC: 5989584; DOI: 10.1099/mgen.0.000173

  • CADM1 is essential for KSHV-encoded vGPCR-and vFLIP-mediated chronic NF-κB activation.

    Hunte R, Alonso P, Thomas R, Bazile CA, Ramos JC, van der Weyden L, Dominguez-Bendala J, Khan WN and Shembade N

    PLoS pathogens 2018;14;4;e1006968

    PUBMED: 29698475; PMC: 5919438; DOI: 10.1371/journal.ppat.1006968

  • Chemical Profiling of Primary Mesothelioma Cultures Defines Subtypes with Different Expression Profiles and Clinical Responses.

    Schunselaar LM, Quispel-Janssen JMMF, Kim Y, Alifrangis C, Zwart W, Baas P and Neefjes J

    Clinical cancer research : an official journal of the American Association for Cancer Research 2018;24;7;1761-1770

    PUBMED: 29066506; DOI: 10.1158/1078-0432.CCR-17-1345

  • Commensal Koch's postulates: establishing causation in human microbiota research.

    Neville BA, Forster SC and Lawley TD

    Current opinion in microbiology 2018;42;47-52

    PUBMED: 29112885; DOI: 10.1016/j.mib.2017.10.001

  • Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci.

    Martin J, Ponstingl H, Lefranc MP, Archer J, Sargan D and Bradley A

    Immunogenetics 2018;70;4;223-236

    PUBMED: 28924718; PMC: 5871656; DOI: 10.1007/s00251-017-1028-0

  • Direct Whole-Genome Sequencing of Cutaneous Strains of Haemophilus ducreyi.

    Marks M, Fookes M, Wagner J, Ghinai R, Sokana O, Sarkodie YA, Solomon AW, Mabey DCW and Thomson NR

    Emerging infectious diseases 2018;24;4;786-789

    PUBMED: 29553314; PMC: 5875288; DOI: 10.3201/eid2404.171726

  • Dynamics of cholera epidemics from Benin to Mauritania.

    Moore S, Dongdem AZ, Opare D, Cottavoz P, Fookes M, Sadji AY, Dzotsi E, Dogbe M, Jeddi F, Bidjada B et al.

    PLoS neglected tropical diseases 2018;12;4;e0006379

    PUBMED: 29630632; PMC: 5908202; DOI: 10.1371/journal.pntd.0006379

  • GDSCTools for mining pharmacogenomic interactions in cancer.

    Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J and Garnett MJ

    Bioinformatics (Oxford, England) 2018;34;7;1226-1228

    PUBMED: 29186349; PMC: 6031019; DOI: 10.1093/bioinformatics/btx744

  • High-throughput DNA methylation analysis in anorexia nervosa confirms TNXB hypermethylation.

    Kesselmeier M, Pütter C, Volckmar AL, Baurecht H, Grallert H, Illig T, Ismail K, Ollikainen M, Silén Y, Keski-Rahkonen A et al.

    The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry 2018;19;3;187-199

    PUBMED: 27367046; DOI: 10.1080/15622975.2016.1190033

  • Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy.

    Britto CD, Dyson ZA, Duchene S, Carter MJ, Gurung M, Kelly DF, Murdoch DR, Ansari I, Thorson S, Shrestha S et al.

    PLoS neglected tropical diseases 2018;12;4;e0006408

    PUBMED: 29684021; PMC: 5933809; DOI: 10.1371/journal.pntd.0006408

  • Maternal and fetal genetic contribution to gestational weight gain.

    Warrington NM, Richmond R, Fenstra B, Myhre R, Gaillard R, Paternoster L, Wang CA, Beaumont RN, Das S, Murcia M et al.

    International journal of obesity (2005) 2018;42;4;775-784

    PUBMED: 28990592; PMC: 5784805; DOI: 10.1038/ijo.2017.248

  • Proposal of serovars 17 and 18 of Actinobacillus pleuropneumoniae based on serological and genotypic analysis.

    Bossé JT, Li Y, Sárközi R, Fodor L, Lacouture S, Gottschalk M, Casas Amoribieta M, Angen Ø, Nedbalcova K, Holden MTG et al.

    Veterinary microbiology 2018;217;1-6

    PUBMED: 29615241; PMC: 5901230; DOI: 10.1016/j.vetmic.2018.02.019

  • Transcriptomic profiling of nematode parasites surviving vaccine exposure.

    Sallé G, Laing R, Cotton JA, Maitland K, Martinelli A, Holroyd N, Tracey A, Berriman M, Smith WD, Newlands GFJ et al.

    International journal for parasitology 2018;48;5;395-402

    PUBMED: 29534987; PMC: 5909036; DOI: 10.1016/j.ijpara.2018.01.004

  • Whole-exome sequencing of a meningeal melanocytic tumour reveals activating CYSLTR2 and EIF1AX hotspot mutations and similarities to uveal melanoma.

    Küsters-Vandevelde HVN, Germans MR, Rabbie R, Rashid M, Ten Broek R, Blokx WAM, Prinsen CFM, Adams DJ and Ter Laan M

    Brain tumor pathology 2018;35;2;127-130

    PUBMED: 29476293; DOI: 10.1007/s10014-018-0308-1

  • A homozygous variant disrupting the PIGH start-codon is associated with developmental delay, epilepsy, and microcephaly.

    Pagnamenta AT, Murakami Y, Anzilotti C, Titheradge H, Oates AJ, Morton J, DDD Study, Kinoshita T, Kini U and Taylor JC

    Human mutation 2018;39;6;822-826

    PUBMED: 29573052; PMC: 6001798; DOI: 10.1002/humu.23420

  • Binding of ISRIB reveals a regulatory site in the nucleotide exchange factor eIF2B.

    Zyryanova AF, Weis F, Faille A, Alard AA, Crespillo-Casado A, Sekine Y, Harding HP, Allen F, Parts L, Fromont C et al.

    Science (New York, N.Y.) 2018;359;6383;1533-1536

    PUBMED: 29599245; PMC: 5889100; DOI: 10.1126/science.aar5129

  • Recurrent histone mutations in T-cell acute lymphoblastic leukaemia.

    Collord G, Martincorena I, Young MD, Foroni L, Bolli N, Stratton MR, Vassiliou GS, Campbell PJ and Behjati S

    British journal of haematology 2018;184;4;676-679

    PUBMED: 29602208; PMC: 6766952; DOI: 10.1111/bjh.15155

  • Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris.

    Rhodes J, Abdolrasouli A, Farrer RA, Cuomo CA, Aanensen DM, Armstrong-James D, Fisher MC and Schelenz S

    Emerging microbes & infections 2018;7;1;43

    PUBMED: 29593275; PMC: 5874254; DOI: 10.1038/s41426-018-0045-x

  • Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance.

    Isaacs AT, Mawejje HD, Tomlinson S, Rigden DJ and Donnelly MJ

    BMC genomics 2018;19;1;225

    PUBMED: 29587635; PMC: 5870100; DOI: 10.1186/s12864-018-4605-1

  • Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.

    Reid AJ, Talman AM, Bennett HM, Gomes AR, Sanders MJ, Illingworth CJR, Billker O, Berriman M and Lawniczak MK

    eLife 2018;7

    PUBMED: 29580379; PMC: 5871331; DOI: 10.7554/eLife.33105

  • Breaking the code of antibiotic resistance.

    Lo SW, Kumar N and Wheeler NE

    Nature reviews. Microbiology 2018;16;5;262

    PUBMED: 29576619; DOI: 10.1038/nrmicro.2018.33

  • Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

    Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD and Harris SR

    Wellcome open research 2018;3;33

    PUBMED: 29774245; PMC: 5930550; DOI: 10.12688/wellcomeopenres.14265.2

  • Application of CRISPR-Cas9 Based Genome-Wide Screening Approaches to Study Cellular Signalling Mechanisms.

    Sharma S and Petsalaki E

    International journal of molecular sciences 2018;19;4

    PUBMED: 29561791; PMC: 5979383; DOI: 10.3390/ijms19040933

  • De novo mutations in regulatory elements in neurodevelopmental disorders.

    Short PJ, McRae JF, Gallone G, Sifrim A, Won H, Geschwind DH, Wright CF, Firth HV, FitzPatrick DR, Barrett JC and Hurles ME

    Nature 2018;555;7698;611-616

    PUBMED: 29562236; PMC: 5912909; DOI: 10.1038/nature25983

  • Preclinical Development of a Novel, Orally-Administered Anti-Tumour Necrosis Factor Domain Antibody for the Treatment of Inflammatory Bowel Disease.

    Crowe JS, Roberts KJ, Carlton TM, Maggiore L, Cubitt MF, Clare S, Harcourt K, Reckless J, MacDonald TT, Ray KP et al.

    Scientific reports 2018;8;1;4941

    PUBMED: 29563546; PMC: 5862986; DOI: 10.1038/s41598-018-23277-7

  • Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

    Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W et al.

    Genome research 2018;28;4;448-459

    PUBMED: 29563166; PMC: 5880236; DOI: 10.1101/gr.234096.117

  • Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni.

    Wendt GR, Collins JN, Pei J, Pearson MS, Bennett HM, Loukas A, Berriman M, Grishin NV and Collins JJ

    eLife 2018;7

    PUBMED: 29557781; PMC: 5927768; DOI: 10.7554/eLife.33221

  • Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis.

    Zengini E, Hatzikotoulas K, Tachmazidou I, Steinberg J, Hartwig FP, Southam L, Hackinger S, Boer CG, Styrkarsdottir U, Gilly A et al.

    Nature genetics 2018;50;4;549-558

    PUBMED: 29559693; PMC: 5896734; DOI: 10.1038/s41588-018-0079-y

  • Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis.

    Bergiers I, Andrews T, Vargel Bölükbaşı Ö, Buness A, Janosz E, Lopez-Anguita N, Ganter K, Kosim K, Celen C, Itır Perçin G et al.

    eLife 2018;7

    PUBMED: 29555020; PMC: 5860872; DOI: 10.7554/eLife.29312

  • Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

    Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR and Reik W

    Genome biology 2018;19;1;33

    PUBMED: 29544553; PMC: 5856372; DOI: 10.1186/s13059-018-1408-2

  • Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

    Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Pandolfini L, Zhang A, Pluchino S et al.

    Genome biology 2018;19;1;32

    PUBMED: 29540241; PMC: 5853149; DOI: 10.1186/s13059-018-1405-5

  • Placentation defects are highly prevalent in embryonic lethal mouse mutants.

    Perez-Garcia V, Fineberg E, Wilson R, Murray A, Mazzeo CI, Tudor C, Sienerth A, White JK, Tuck E, Ryder EJ et al.

    Nature 2018;555;7697;463-468

    PUBMED: 29539633; PMC: 5866719; DOI: 10.1038/nature26002

  • A comprehensive genomic history of extinct and living elephants.

    Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, Baleka S, Karpinski E, Ivancevic AM, To TH, Kortschak RD et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;11;E2566-E2574

    PUBMED: 29483247; PMC: 5856550; DOI: 10.1073/pnas.1720554115

  • A history of male migration in and out of the Green Sahara.

    Xue Y

    Genome biology 2018;19;1;30

    PUBMED: 29534762; PMC: 5851091; DOI: 10.1186/s13059-018-1410-8

  • Low genomic diversity of Legionella pneumophila within clinical specimens.

    David S, Mentasti M, Parkhill J and Chalker VJ

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018;24;9;1020.e1-1020.e4

    PUBMED: 29549055; PMC: 6123502; DOI: 10.1016/j.cmi.2018.03.004

  • SvABA: genome-wide detection of structural variants and indels by local assembly.

    Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X et al.

    Genome research 2018;28;4;581-591

    PUBMED: 29535149; PMC: 5880247; DOI: 10.1101/gr.221028.117

  • Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

    Malik R, Chauhan G, Traylor M, Sargurupremraj M, Okada Y, Mishra A, Rutten-Jacobs L, Giese AK, van der Laan SW, Gretarsdottir S et al.

    Nature genetics 2018;50;4;524-537

    PUBMED: 29531354; PMC: 5968830; DOI: 10.1038/s41588-018-0058-3

  • PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data.

    Page AJ, Wailan A, Shao Y, Judge K, Dougan G, Klemm EJ, Thomson NR and Keane JA

    Microbial genomics 2018;4;3

    PUBMED: 29533742; PMC: 5885016; DOI: 10.1099/mgen.0.000164

  • The Chlamydia muridarum plasmid revisited : new insights into growth kinetics.

    Skilton RJ, Wang Y, O'Neill C, Filardo S, Marsh P, Bénard A, Thomson NR, Ramsey KH and Clarke IN

    Wellcome open research 2018;3;25

    PUBMED: 29657985; PMC: 5871946; DOI: 10.12688/wellcomeopenres.13905.1

  • Origins and genetic legacies of the Caribbean Taino.

    Schroeder H, Sikora M, Gopalakrishnan S, Cassidy LM, Maisano Delser P, Sandoval Velasco M, Schraiber JG, Rasmussen S, Homburger JR, Ávila-Arcos MC et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;10;2341-2346

    PUBMED: 29463742; PMC: 5877975; DOI: 10.1073/pnas.1716839115

  • Phenotype of CNTNAP1: a study of patients demonstrating a specific severe congenital hypomyelinating neuropathy with survival beyond infancy.

    Low KJ, Stals K, Caswell R, Wakeling M, Clayton-Smith J, Donaldson A, Foulds N, Norman A, Splitt M, Urankar K et al.

    European journal of human genetics : EJHG 2018;26;6;796-807

    PUBMED: 29511323; PMC: 5974240; DOI: 10.1038/s41431-018-0110-x

  • Diagnostics for Yaws Eradication: Insights From Direct Next-Generation Sequencing of Cutaneous Strains of Treponema pallidum.

    Marks M, Fookes M, Wagner J, Butcher R, Ghinai R, Sokana O, Sarkodie YA, Lukehart SA, Solomon AW, Mabey DCW and Thomson N

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2018;66;6;818-824

    PUBMED: 29045605; PMC: 5848336; DOI: 10.1093/cid/cix892

  • Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals.

    Böhme U, Otto TD, Cotton JA, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C et al.

    Genome research 2018;28;4;547-560

    PUBMED: 29500236; PMC: 5880244; DOI: 10.1101/gr.218123.116

  • Molecular Genetic Analysis Subdivided by Adversity Exposure Suggests Etiologic Heterogeneity in Major Depression.

    Peterson RE, Cai N, Dahl AW, Bigdeli TB, Edwards AC, Webb BT, Bacanu SA, Zaitlen N, Flint J and Kendler KS

    The American journal of psychiatry 2018;175;6;545-554

    PUBMED: 29495898; PMC: 5988935; DOI: 10.1176/appi.ajp.2017.17060621

  • A novel prophage identified in strains from Salmonella enterica serovar Enteritidis is a phylogenetic signature of the lineage ST-1974.

    D'Alessandro B, Pérez Escanda V, Balestrazzi L, Iriarte A, Pickard D, Yim L, Chabalgoity JA and Betancor L

    Microbial genomics 2018;4;3

    PUBMED: 29509137; PMC: 5885013; DOI: 10.1099/mgen.0.000161

  • Ancient pathogen DNA in human teeth and petrous bones.

    Margaryan A, Hansen HB, Rasmussen S, Sikora M, Moiseyev V, Khoklov A, Epimakhov A, Yepiskoposyan L, Kriiska A, Varul L et al.

    Ecology and evolution 2018;8;6;3534-3542

    PUBMED: 29607044; PMC: 5869295; DOI: 10.1002/ece3.3924

  • Comparison of Salmonella enterica Serovars Typhi and Typhimurium Reveals Typhoidal Serovar-Specific Responses to Bile.

    Johnson R, Ravenhall M, Pickard D, Dougan G, Byrne A and Frankel G

    Infection and immunity 2018;86;3

    PUBMED: 29229736; PMC: 5820949; DOI: 10.1128/IAI.00490-17

  • Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism.

    Méric G, McNally A, Pessia A, Mourkas E, Pascoe B, Mageiros L, Vehkala M, Corander J and Sheppard SK

    Genome biology and evolution 2018;10;3;763-774

    PUBMED: 29452359; PMC: 5841378; DOI: 10.1093/gbe/evy026

  • Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins.

    Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G, Hopper JTS, Kintses B, Horvath P, Daruka L, Fekete G et al.

    Nature structural & molecular biology 2018;25;3;279-288

    PUBMED: 29434345; PMC: 5995306; DOI: 10.1038/s41594-018-0029-5

  • Exponential scaling of single-cell RNA-seq in the past decade.

    Svensson V, Vento-Tormo R and Teichmann SA

    Nature protocols 2018;13;4;599-604

    PUBMED: 29494575; DOI: 10.1038/nprot.2017.149

  • Genome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection.

    Raven KE, Gouliouris T, Parkhill J and Peacock SJ

    Journal of clinical microbiology 2018;56;3

    PUBMED: 29263205; PMC: 5824064; DOI: 10.1128/JCM.01520-17

  • Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.

    Moradigaravand D, Gouliouris T, Ludden C, Reuter S, Jamrozy D, Blane B, Naydenova P, Judge K, H Aliyu S, F Hadjirin N et al.

    Microbial genomics 2018;4;3

    PUBMED: 29498619; PMC: 5885014; DOI: 10.1099/mgen.0.000162

  • Investigation of Multiple Resistance Mechanisms in Voriconazole-Resistant Aspergillus flavus Clinical Isolates from a Chest Hospital Surveillance in Delhi, India.

    Sharma C, Kumar R, Kumar N, Masih A, Gupta D and Chowdhary A

    Antimicrobial agents and chemotherapy 2018;62;3

    PUBMED: 29311090; PMC: 5826139; DOI: 10.1128/AAC.01928-17

  • miR-96 is required for normal development of the auditory hindbrain.

    Schlüter T, Berger C, Rosengauer E, Fieth P, Krohs C, Ushakov K, Steel KP, Avraham KB, Hartmann AK, Felmy F and Nothwang HG

    Human molecular genetics 2018;27;5;860-874

    PUBMED: 29325119; DOI: 10.1093/hmg/ddy007

  • Nbeal2 interacts with Dock7, Sec16a, and Vac14.

    Mayer L, Jasztal M, Pardo M, Aguera de Haro S, Collins J, Bariana TK, Smethurst PA, Grassi L, Petersen R, Nurden P et al.

    Blood 2018;131;9;1000-1011

    PUBMED: 29187380; PMC: 5877783; DOI: 10.1182/blood-2017-08-800359

  • Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis.

    Deo P, Chow SH, Hay ID, Kleifeld O, Costin A, Elgass KD, Jiang JH, Ramm G, Gabriel K, Dougan G et al.

    PLoS pathogens 2018;14;3;e1006945

    PUBMED: 29601598; PMC: 5877877; DOI: 10.1371/journal.ppat.1006945

  • Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

    Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R et al.

    PLoS computational biology 2018;14;3;e1005934

    PUBMED: 29494619; PMC: 5849332; DOI: 10.1371/journal.pcbi.1005934

  • Strategies for managing rival bacterial communities: Lessons from burying beetles.

    Duarte A, Welch M, Swannack C, Wagner J and Kilner RM

    The Journal of animal ecology 2018;87;2;414-427

    PUBMED: 28682460; PMC: 5836980; DOI: 10.1111/1365-2656.12725

  • Toll-like receptor 2 costimulation potentiates the antitumor efficacy of CAR T Cells.

    Lai Y, Weng J, Wei X, Qin L, Lai P, Zhao R, Jiang Z, Li B, Lin S, Wang S et al.

    Leukemia 2018;32;3;801-808

    PUBMED: 28841215; DOI: 10.1038/leu.2017.249

  • Whole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel.

    Rew V, Mook P, Trienekens S, Baker KS, Dallman TJ, Jenkins C, Crook PD and Thomson NR

    Microbial genomics 2018;4;3

    PUBMED: 29583113; PMC: 5885021; DOI: 10.1099/mgen.0.000170

  • The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency.

    Bertero A, Brown S, Madrigal P, Osnato A, Ortmann D, Yiangou L, Kadiwala J, Hubner NC, de Los Mozos IR, Sadée C et al.

    Nature 2018;555;7695;256-259

    PUBMED: 29489750; PMC: 5951268; DOI: 10.1038/nature25784

  • Conditional Manipulation of Gene Function in Human Cells with Optimized Inducible shRNA.

    Bertero A, Yiangou L, Brown S, Ortmann D, Pawlowski M and Vallier L

    Current protocols in stem cell biology 2018;44;5C.4.1-5C.4.48

    PUBMED: 29512130; DOI: 10.1002/cpsc.45

  • Exome Sequencing and Genotyping Identify a Rare Variant in NLRP7 Gene Associated With Ulcerative Colitis.

    Onoufriadis A, Stone K, Katsiamides A, Amar A, Omar Y, de Lange KM, Taylor K, Barrett JC, Pollok R, Hayee B et al.

    Journal of Crohn's & colitis 2018;12;3;321-326

    PUBMED: 29211899; PMC: 6290881; DOI: 10.1093/ecco-jcc/jjx157

  • The contribution of CACNA1A, ATP1A2 and SCN1A mutations in hemiplegic migraine: A clinical and genetic study in Finnish migraine families.

    Hiekkala ME, Vuola P, Artto V, Häppölä P, Häppölä E, Vepsäläinen S, Cuenca-León E, Lal D, Gormley P, Hämäläinen E et al.

    Cephalalgia : an international journal of headache 2018;38;12;1849-1863

    PUBMED: 29486580; DOI: 10.1177/0333102418761041

  • Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity.

    Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J et al.

    Genome medicine 2018;10;1;15

    PUBMED: 29482619; PMC: 5828069; DOI: 10.1186/s13073-018-0521-x

  • scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

    Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC et al.

    Nature communications 2018;9;1;781

    PUBMED: 29472610; PMC: 5823944; DOI: 10.1038/s41467-018-03149-4

  • Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.

    Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T et al.

    Journal of clinical microbiology 2018;56;3

    PUBMED: 29237792; PMC: 5824051; DOI: 10.1128/JCM.01384-17

  • Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins.

    Klemm EJ, Shakoor S, Page AJ, Qamar FN, Judge K, Saeed DK, Wong VK, Dallman TJ, Nair S, Baker S et al.

    mBio 2018;9;1

    PUBMED: 29463654; PMC: 5821095; DOI: 10.1128/mBio.00105-18

  • Further delineation of an entity caused by CREBBP and EP300 mutations but not resembling Rubinstein-Taybi syndrome.

    Menke LA, DDD study, Gardeitchik T, Hammond P, Heimdal KR, Houge G, Hufnagel SB, Ji J, Johansson S, Kant SG et al.

    American journal of medical genetics. Part A 2018;176;4;862-876

    PUBMED: 29460469; DOI: 10.1002/ajmg.a.38626

  • Gut microbiota trajectory in early life may predict development of celiac disease.

    Olivares M, Walker AW, Capilla A, Benítez-Páez A, Palau F, Parkhill J, Castillejo G and Sanz Y

    Microbiome 2018;6;1;36

    PUBMED: 29458413; PMC: 5819212; DOI: 10.1186/s40168-018-0415-6

  • New GJA8 variants and phenotypes highlight its critical role in a broad spectrum of eye anomalies.

    Ceroni F, Aguilera-Garcia D, Chassaing N, Bax DA, Blanco-Kelly F, Ramos P, Tarilonte M, Villaverde C, da Silva LRJ, Ballesta-Martínez MJ et al.

    Human genetics 2018;138;8-9;1027-1042

    PUBMED: 29464339; DOI: 10.1007/s00439-018-1875-2

  • Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells.

    Hu G, Cui K, Fang D, Hirose S, Wang X, Wangsa D, Jin W, Ried T, Liu P, Zhu J et al.

    Immunity 2018;48;2;227-242.e8

    PUBMED: 29466755; PMC: 5847274; DOI: 10.1016/j.immuni.2018.01.013

  • Formalising recall by genotype as an efficient approach to detailed phenotyping and causal inference.

    Corbin LJ, Tan VY, Hughes DA, Wade KH, Paul DS, Tansey KE, Butcher F, Dudbridge F, Howson JM, Jallow MW et al.

    Nature communications 2018;9;1;711

    PUBMED: 29459775; PMC: 5818506; DOI: 10.1038/s41467-018-03109-y

  • In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum.

    Carrington E, Otto TD, Szestak T, Lennartz F, Higgins MK, Newbold CI and Craig AG

    Scientific reports 2018;8;1;3282

    PUBMED: 29459671; PMC: 5818487; DOI: 10.1038/s41598-018-21591-8

  • APPLaUD: access for patients and participants to individual level uninterpreted genomic data.

    Thorogood A, Bobe J, Prainsack B, Middleton A, Scott E, Nelson S, Corpas M, Bonhomme N, Rodriguez LL, Murtagh M et al.

    Human genomics 2018;12;1;7

    PUBMED: 29454384; PMC: 5816450; DOI: 10.1186/s40246-018-0139-5

  • The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.

    Kennedy NA, Lamb CA, Berry SH, Walker AW, Mansfield J, Parkes M, Simpkins R, Tremelling M, Nutland S, UK IBD Genetics Consortium et al.

    Inflammatory bowel diseases 2018;24;3;583-592

    PUBMED: 29462388; PMC: 6176884; DOI: 10.1093/ibd/izx061

  • Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort.

    Viñuela A, Brown AA, Buil A, Tsai PC, Davies MN, Bell JT, Dermitzakis ET, Spector TD and Small KS

    Human molecular genetics 2018;27;4;732-741

    PUBMED: 29228364; PMC: 5886097; DOI: 10.1093/hmg/ddx424

  • Heritable contributions versus genetic architecture.

    Timpson NJ, Greenwood CMT, Soranzo N, Lawson DJ and Richards JB

    Nature reviews. Genetics 2018;19;3;185

    PUBMED: 29440744; DOI: 10.1038/nrg.2018.7

  • Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae.

    Weetman D, Wilding CS, Neafsey DE, Müller P, Ochomo E, Isaacs AT, Steen K, Rippon EJ, Morgan JC, Mawejje HD et al.

    Scientific reports 2018;8;1;2920

    PUBMED: 29440767; PMC: 5811533; DOI: 10.1038/s41598-018-21265-5

  • APOBEC3A/B deletion polymorphism and cancer risk.

    Gansmo LB, Romundstad P, Hveem K, Vatten L, Nik-Zainal S, Lønning PE and Knappskog S

    Carcinogenesis 2018;39;2;118-124

    PUBMED: 29140415; PMC: 5862322; DOI: 10.1093/carcin/bgx131

  • Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome.

    Naumenko FM, Abnizova II, Beka N, Genaev MA and Orlov YL

    BMC genomics 2018;19;Suppl 3;92

    PUBMED: 29504893; PMC: 5836841; DOI: 10.1186/s12864-018-4475-6

  • Mapping human development at single-cell resolution.

    Behjati S, Lindsay S, Teichmann SA and Haniffa M

    Development (Cambridge, England) 2018;145;3

    PUBMED: 29439135; DOI: 10.1242/dev.152561

  • Mutant calreticulin knockin mice develop thrombocytosis and myelofibrosis without a stem cell self-renewal advantage.

    Li J, Prins D, Park HJ, Grinfeld J, Gonzalez-Arias C, Loughran S, Dovey OM, Klampfl T, Bennett C, Hamilton TL et al.

    Blood 2018;131;6;649-661

    PUBMED: 29282219; DOI: 10.1182/blood-2017-09-806356

  • Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome.

    Vasileiou G, Vergarajauregui S, Endele S, Popp B, Büttner C, Ekici AB, Gerard M, Bramswig NC, Albrecht B, Clayton-Smith J et al.

    American journal of human genetics 2018;102;3;468-479

    PUBMED: 29429572; PMC: 5985265; DOI: 10.1016/j.ajhg.2018.01.014

  • A novel variant in GLIS3 is associated with osteoarthritis.

    Casalone E, Tachmazidou I, Zengini E, Hatzikotoulas K, Hackinger S, Suveges D, Steinberg J, Rayner NW, arcOGEN Consortium, Wilkinson JM et al.

    Annals of the rheumatic diseases 2018;77;4;620-623

    PUBMED: 29436472; PMC: 5890630; DOI: 10.1136/annrheumdis-2017-211848

  • Paediatric genomics: diagnosing rare disease in children.

    Wright CF, FitzPatrick DR and Firth HV

    Nature reviews. Genetics 2018;19;5;253-268

    PUBMED: 29398702; DOI: 10.1038/nrg.2017.116

  • Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study.

    Amato R, Pearson RD, Almagro-Garcia J, Amaratunga C, Lim P, Suon S, Sreng S, Drury E, Stalker J, Miotto O et al.

    The Lancet. Infectious diseases 2018;18;3;337-345

    PUBMED: 29398391; PMC: 5835763; DOI: 10.1016/S1473-3099(18)30068-9

  • A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry.

    Doyle SR, Laing R, Bartley DJ, Britton C, Chaudhry U, Gilleard JS, Holroyd N, Mable BK, Maitland K, Morrison AA et al.

    Genome biology and evolution 2018;10;2;396-409

    PUBMED: 29267942; PMC: 5793844; DOI: 10.1093/gbe/evx269

  • A method for single pair mating in an obligate parasitic nematode.

    Sargison ND, Redman E, Morrison AA, Bartley DJ, Jackson F, Naghra-van Gijzel H, Holroyd N, Berriman M, Cotton JA and Gilleard JS

    International journal for parasitology 2018;48;2;159-165

    PUBMED: 29111440; DOI: 10.1016/j.ijpara.2017.08.010

  • The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare.

    Harkins CP, Pettigrew KA, Oravcová K, Gardner J, Hearn RMR, Rice D, Mather AE, Parkhill J, Brown SJ, Proby CM and Holden MTG

    The Journal of investigative dermatology 2018;138;2;336-343

    PUBMED: 28951239; PMC: 5780352; DOI: 10.1016/j.jid.2017.09.023

  • ADCY3, neuronal primary cilia and obesity.

    Barroso I

    Nature genetics 2018;50;2;166-167

    PUBMED: 29374254; DOI: 10.1038/s41588-018-0043-x

  • Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

    Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J et al.

    Nature cell biology 2018;20;2;127-134

    PUBMED: 29311656; PMC: 5787369; DOI: 10.1038/s41556-017-0013-z

  • DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

    Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T et al.

    Gastroenterology 2018;154;3;585-598

    PUBMED: 29031501; PMC: 6381389; DOI: 10.1053/j.gastro.2017.10.007

  • Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity.

    Ecker S, Pancaldi V, Valencia A, Beck S and Paul DS

    BioEssays : news and reviews in molecular, cellular and developmental biology 2018;40;2

    PUBMED: 29251357; DOI: 10.1002/bies.201700148

  • Genetic architecture: the shape of the genetic contribution to human traits and disease.

    Timpson NJ, Greenwood CMT, Soranzo N, Lawson DJ and Richards JB

    Nature reviews. Genetics 2018;19;2;110-124

    PUBMED: 29225335; DOI: 10.1038/nrg.2017.101

  • Genome watch: Microbial diversity knows no borders.

    Pike LJ, Viciani E and Kumar N

    Nature reviews. Microbiology 2018;16;2;66

    PUBMED: 29292388; DOI: 10.1038/nrmicro.2017.166

  • Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

    Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO et al.

    Nature genetics 2018;50;2;307-316

    PUBMED: 29358649; DOI: 10.1038/s41588-017-0029-0

  • Hepatitis E in southern Vietnam: Seroepidemiology in humans and molecular epidemiology in pigs.

    Berto A, Pham HA, Thao TTN, Vy NHT, Caddy SL, Hiraide R, Tue NT, Goodfellow I, Carrique-Mas JJ, Thwaites GE et al.

    Zoonoses and public health 2018;65;1;43-50

    PUBMED: 28598034; PMC: 6645987; DOI: 10.1111/zph.12364

  • Identifying cell populations with scRNASeq.

    Andrews TS and Hemberg M

    Molecular aspects of medicine 2018;59;114-122

    PUBMED: 28712804; DOI: 10.1016/j.mam.2017.07.002

  • Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes.

    Grarup N, Moltke I, Andersen MK, Dalby M, Vitting-Seerup K, Kern T, Mahendran Y, Jørsboe E, Larsen CVL, Dahl-Petersen IK et al.

    Nature genetics 2018;50;2;172-174

    PUBMED: 29311636; PMC: 5828106; DOI: 10.1038/s41588-017-0022-7

  • Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans.

    Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat-Carotta S, Hansen AH, Tripathy R, Traunbauer AK, Hochstoeger T et al.

    Nature neuroscience 2018;21;2;207-217

    PUBMED: 29311744; PMC: 5897053; DOI: 10.1038/s41593-017-0053-5

  • Response to Giem.

    Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M et al.

    American journal of human genetics 2018;102;2;331

    PUBMED: 29395077; PMC: 5985535; DOI: 10.1016/j.ajhg.2018.01.002

  • Separate and combined associations of obesity and metabolic health with coronary heart disease: a pan-European case-cohort analysis.

    Lassale C, Tzoulaki I, Moons KGM, Sweeting M, Boer J, Johnson L, Huerta JM, Agnoli C, Freisling H, Weiderpass E et al.

    European heart journal 2018;39;5;397-406

    PUBMED: 29020414; PMC: 6198928; DOI: 10.1093/eurheartj/ehx448

  • What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis.

    Heyckendorf J, Andres S, Köser CU, Olaru ID, Schön T, Sturegård E, Beckert P, Schleusener V, Kohl TA, Hillemann D et al.

    Antimicrobial agents and chemotherapy 2018;62;2

    PUBMED: 29133554; PMC: 5786814; DOI: 10.1128/AAC.01550-17

  • Why the antibiotic resistance crisis requires a One Health approach.

    Van Puyvelde S, Deborggraeve S and Jacobs J

    The Lancet. Infectious diseases 2018;18;2;132-134

    PUBMED: 29198739; DOI: 10.1016/S1473-3099(17)30704-1

  • Widespread spontaneous hyperproliferation, melanosis and melanoma in Hgf-Cdk4R24C mice.

    van der Weyden L, Arends MJ, Brenn T, Tuting T and Adams DJ

    Melanoma research 2018;28;1;76-78

    PUBMED: 29200095; PMC: 5739287; DOI: 10.1097/CMR.0000000000000414

  • A novel PIGA variant associated with severe X-linked epilepsy and profound developmental delay.

    Low KJ, James M, Sharples PM, Eaton M, Jenkinson S, Study DDD and Smithson SF

    Seizure 2018;56;1-3

    PUBMED: 29414593; DOI: 10.1016/j.seizure.2018.01.013

  • Extending the phenotype associated with the CSNK2A1-related Okur-Chung syndrome-A clinical study of 11 individuals.

    Owen CI, Bowden R, Parker MJ, Patterson J, Patterson J, Price S, Sarkar A, Castle B, Deshpande C, Splitt M et al.

    American journal of medical genetics. Part A 2018;176;5;1108-1114

    PUBMED: 29383814; DOI: 10.1002/ajmg.a.38610

  • Genome watch: Keeping tally in the microbiome.

    Almeida A and Shao Y

    Nature reviews. Microbiology 2018;16;3;124

    PUBMED: 29379216; DOI: 10.1038/nrmicro.2018.13

  • Limited Impact of Adolescent Meningococcal ACWY Vaccination on Neisseria meningitidis Serogroup W Carriage in University Students.

    Oldfield NJ, Green LR, Parkhill J, Bayliss CD and Turner DPJ

    The Journal of infectious diseases 2018;217;4;608-616

    PUBMED: 29155998; PMC: 5853931; DOI: 10.1093/infdis/jix596

  • Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

    Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K, HIPSCI Consortium, Hale C, Dougan G and Gaffney DJ

    Nature genetics 2018;50;3;424-431

    PUBMED: 29379200; PMC: 6548559; DOI: 10.1038/s41588-018-0046-7

  • Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes.

    Mueller S, Engleitner T, Maresch R, Zukowska M, Lange S, Kaltenbacher T, Konukiewitz B, Öllinger R, Zwiebel M, Strong A et al.

    Nature 2018;554;7690;62-68

    PUBMED: 29364867; PMC: 6097607; DOI: 10.1038/nature25459

  • Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control.

    Soares ML, Edwards CA, Dearden FL, Ferrón SR, Curran S, Corish JA, Rancourt RC, Allen SE, Charalambous M, Ferguson-Smith MA et al.

    Genome research 2018

    PUBMED: 29367313; PMC: 5848613; DOI: 10.1101/gr.221366.117

  • Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

    Farmery JHR, Smith ML, NIHR BioResource - Rare Diseases and Lynch AG

    Scientific reports 2018;8;1;1300

    PUBMED: 29358629; PMC: 5778012; DOI: 10.1038/s41598-017-14403-y

  • Evaluating genetic drift in time-series evolutionary analysis.

    R Nené N, Mustonen V and J R Illingworth C

    Journal of theoretical biology 2018;437;51-57

    PUBMED: 28958783; PMC: 5703635; DOI: 10.1016/j.jtbi.2017.09.021

  • A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination.

    León-Ortiz AM, Panier S, Sarek G, Vannier JB, Patel H, Campbell PJ and Boulton SJ

    Molecular cell 2018;69;2;292-305.e6

    PUBMED: 29351848; PMC: 5783719; DOI: 10.1016/j.molcel.2017.12.014

  • Dietary trehalose enhances virulence of epidemic Clostridium difficile.

    Collins J, Robinson C, Danhof H, Knetsch CW, van Leeuwen HC, Lawley TD, Auchtung JM and Britton RA

    Nature 2018;553;7688;291-294

    PUBMED: 29310122; PMC: 5984069; DOI: 10.1038/nature25178

  • Identification of genetic elements in metabolism by high-throughput mouse phenotyping.

    Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R et al.

    Nature communications 2018;9;1;288

    PUBMED: 29348434; PMC: 5773596; DOI: 10.1038/s41467-017-01995-2

  • Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.

    Kolluri KK, Alifrangis C, Kumar N, Ishii Y, Price S, Michaut M, Williams S, Barthorpe S, Lightfoot H, Busacca S et al.

    eLife 2018;7

    PUBMED: 29345617; PMC: 5773178; DOI: 10.7554/eLife.30224

  • FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations.

    Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y and Tyler-Smith C

    Genome biology 2018;19;1;5

    PUBMED: 29343290; PMC: 5771147; DOI: 10.1186/s13059-017-1380-2

  • Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.

    Jiang X, O'Reilly PF, Aschard H, Hsu YH, Richards JB, Dupuis J, Ingelsson E, Karasik D, Pilz S, Berry D et al.

    Nature communications 2018;9;1;260

    PUBMED: 29343764; PMC: 5772647; DOI: 10.1038/s41467-017-02662-2

  • Phenotypic Consequences of a Genetic Predisposition to Enhanced Nitric Oxide Signaling.

    Emdin CA, Khera AV, Klarin D, Natarajan P, Zekavat SM, Nomura A, Haas M, Aragam K, Ardissino D, Wilson JG et al.

    Circulation 2018;137;3;222-232

    PUBMED: 28982690; PMC: 5771958; DOI: 10.1161/CIRCULATIONAHA.117.028021

  • Rapid HIV disease progression following superinfection in an HLA-B*27:05/B*57:01-positive transmission recipient.

    Brener J, Gall A, Hurst J, Batorsky R, Lavandier N, Chen F, Edwards A, Bolton C, Dsouza R, Allen T et al.

    Retrovirology 2018;15;1;7

    PUBMED: 29338738; PMC: 5771019; DOI: 10.1186/s12977-018-0390-9

  • Phandango: an interactive viewer for bacterial population genomics.

    Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM and Harris SR

    Bioinformatics (Oxford, England) 2018;34;2;292-293

    PUBMED: 29028899; PMC: 5860215; DOI: 10.1093/bioinformatics/btx610

  • Mapping the malaria parasite druggable genome by using in vitro evolution and chemogenomics.

    Cowell AN, Istvan ES, Lukens AK, Gomez-Lorenzo MG, Vanaerschot M, Sakata-Kato T, Flannery EL, Magistrado P, Owen E, Abraham M et al.

    Science (New York, N.Y.) 2018;359;6372;191-199

    PUBMED: 29326268; PMC: 5925756; DOI: 10.1126/science.aan4472

  • Meta-analysis of exome array data identifies six novel genetic loci for lung function.

    Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B et al.

    Wellcome open research 2018;3;4

    PUBMED: 30175238; PMC: 6081985; DOI: 10.12688/wellcomeopenres.12583.3

  • Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.

    Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G and Lönnberg T

    Scientific reports 2018;8;1;685

    PUBMED: 29330484; PMC: 5766627; DOI: 10.1038/s41598-017-19100-4

  • Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells.

    Garaycoechea JI, Crossan GP, Langevin F, Mulderrig L, Louzada S, Yang F, Guilbaud G, Park N, Roerink S, Nik-Zainal S et al.

    Nature 2018;553;7687;171-177

    PUBMED: 29323295; PMC: 6047743; DOI: 10.1038/nature25154

  • Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders.

    Wright CF, McRae JF, Clayton S, Gallone G, Aitken S, FitzGerald TW, Jones P, Prigmore E, Rajan D, Lord J et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2018;20;10;1216-1223

    PUBMED: 29323667; PMC: 5912505; DOI: 10.1038/gim.2017.246

  • Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.

    Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M et al.

    Nature 2018;553;7687;203-207

    PUBMED: 29323294; DOI: 10.1038/nature25173

  • A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells.

    Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J et al.

    Stem cell reports 2018;10;1;1-6

    PUBMED: 29320760; PMC: 5768986; DOI: 10.1016/j.stemcr.2017.12.002

  • Transplantation of schistosome sporocysts between host snails: A video guide.

    Mouahid G, Rognon A, de Carvalho Augusto R, Driguez P, Geyer K, Karinshak S, Luviano N, Mann V, Quack T, Rawlinson K et al.

    Wellcome open research 2018;3;3

    PUBMED: 29487916; PMC: 5806052; DOI: 10.12688/wellcomeopenres.13488.1

  • Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis.

    Del Castillo Velasco-Herrera M, van der Weyden L, Nsengimana J, Speak AO, Sjöberg MK, Bishop DT, Jönsson G, Newton-Bishop J and Adams DJ

    Molecular oncology 2018;12;2;239-255

    PUBMED: 29193607; PMC: 5792739; DOI: 10.1002/1878-0261.12161

  • Transferrin receptor 1 is a reticulocyte-specific receptor for Plasmodium vivax.

    Gruszczyk J, Kanjee U, Chan LJ, Menant S, Malleret B, Lim NTY, Schmidt CQ, Mok YF, Lin KM, Pearson RD et al.

    Science (New York, N.Y.) 2018;359;6371;48-55

    PUBMED: 29302006; PMC: 5788258; DOI: 10.1126/science.aan1078

  • The Reactome Pathway Knowledgebase.

    Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B et al.

    Nucleic acids research 2018;46;D1;D649-D655

    PUBMED: 29145629; PMC: 5753187; DOI: 10.1093/nar/gkx1132

  • Ensembl 2018.

    Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG et al.

    Nucleic acids research 2018;46;D1;D754-D761

    PUBMED: 29155950; PMC: 5753206; DOI: 10.1093/nar/gkx1098

  • WormBase 2017: molting into a new stage.

    Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Davis P, Gao S, Grove C et al.

    Nucleic acids research 2018;46;D1;D869-D874

    PUBMED: 29069413; PMC: 5753391; DOI: 10.1093/nar/gkx998

  • Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children.

    The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE et al.

    Gut microbes 2018;9;1;38-54

    PUBMED: 28767339; PMC: 5914913; DOI: 10.1080/19490976.2017.1361093

  • nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

    Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K et al.

    Analytical chemistry 2018;90;1;649-656

    PUBMED: 29035042; DOI: 10.1021/acs.analchem.7b02795

  • Perturbation-response genes reveal signaling footprints in cancer gene expression.

    Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N and Saez-Rodriguez J

    Nature communications 2018;9;1;20

    PUBMED: 29295995; PMC: 5750219; DOI: 10.1038/s41467-017-02391-6

  • A biomarker feasibility study in the South East Asia Community Observatory health and demographic surveillance system.

    Partap U, Young EH, Allotey P, Sandhu MS and Reidpath DD

    Global health, epidemiology and genomics 2018;3;e14

    PUBMED: 30263138; PMC: 6152490; DOI: 10.1017/gheg.2018.13

  • The European Society for Medical Oncology (ESMO) Precision Medicine Glossary.

    Yates LR, Seoane J, Le Tourneau C, Siu LL, Marais R, Michiels S, Soria JC, Campbell P, Normanno N, Scarpa A et al.

    Annals of oncology : official journal of the European Society for Medical Oncology 2018;29;1;30-35

    PUBMED: 29140430; DOI: 10.1093/annonc/mdx707

  • A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals.

    Donkor ES, Jamrozy D, Mills RO, Dankwah T, Amoo PK, Egyir B, Badoe EV, Twasam J and Bentley SD

    Infection and drug resistance 2018;11;1757-1765

    PUBMED: 30349333; PMC: 6188180; DOI: 10.2147/IDR.S167639

  • The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation.

    Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M et al.

    Conservation genetics (Print) 2018;19;4;995-1005

    PUBMED: 30100824; PMC: 6061128; DOI: 10.1007/s10592-018-1072-9

  • The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei.

    Kelner A, Tinti M, Guther MLS, Foth BJ, Chappell L, Berriman M, Cowling VH and Ferguson MAJ

    PloS one 2018;13;7;e0201263

    PUBMED: 30040830; PMC: 6057678; DOI: 10.1371/journal.pone.0201263

  • A Simple Multistep Protocol for Differentiating Human Induced Pluripotent Stem Cells into Functional Macrophages.

    Mukherjee C, Hale C and Mukhopadhyay S

    Methods in molecular biology (Clifton, N.J.) 2018;1784;13-28

    PUBMED: 29761384; DOI: 10.1007/978-1-4939-7837-3_2

  • Ancient DNA from latrines in Northern Europe and the Middle East (500 BC-1700 AD) reveals past parasites and diet.

    Søe MJ, Nejsum P, Seersholm FV, Fredensborg BL, Habraken R, Haase K, Hald MM, Simonsen R, Højlund F, Blanke L et al.

    PloS one 2018;13;4;e0195481

    PUBMED: 29694397; PMC: 5918799; DOI: 10.1371/journal.pone.0195481

  • Applying polygenic risk scoring for psychiatric disorders to a large family with bipolar disorder and major depressive disorder.

    de Jong S, Diniz MJA, Saloma A, Gadelha A, Santoro ML, Ota VK, Noto C, Major Depressive Disorder and Bipolar Disorder Working Groups of the Psychiatric Genomics Consortium, Curtis C, Newhouse SJ et al.

    Communications biology 2018;1;163

    PUBMED: 30320231; PMC: 6175827; DOI: 10.1038/s42003-018-0155-y

  • Assessing Rare Variation in Complex Traits.

    Kuchenbaecker K and Appel EVR

    Methods in molecular biology (Clifton, N.J.) 2018;1793;51-71

    PUBMED: 29876891; DOI: 10.1007/978-1-4939-7868-7_5

  • Association between early life antibiotic use and childhood overweight and obesity: a narrative review.

    Partap U, Allcock SH, Parker E, Gurdasani D, Young EH and Sandhu MS

    Global health, epidemiology and genomics 2018;3;e18

    PUBMED: 30410780; PMC: 6218928; DOI: 10.1017/gheg.2018.16

  • Chromosome painting in Glyphorynchus spirurus (Vieillot, 1819) detects a new fission in Passeriformes.

    Ribas TFA, Nagamachi CY, Aleixo A, Pinheiro MLS, O Brien PCM, Ferguson-Smith MA, Yang F, Suarez P and Pieczarka JC

    PloS one 2018;13;8;e0202040

    PUBMED: 30138388; PMC: 6107148; DOI: 10.1371/journal.pone.0202040

  • Classification and Personalized Prognosis in Myeloproliferative Neoplasms

    No authors listed

    New England Journal of Medicine 2018

    DOI: 10.1056/NEJMoa1716614; URL: https://doi.org/10.1056/NEJMoa1716614

  • Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.

    Berthelot C, Villar D, Horvath JE, Odom DT and Flicek P

    Nature ecology & evolution 2018;2;1;152-163

    PUBMED: 29180706; PMC: 5733139; DOI: 10.1038/s41559-017-0377-2

  • Computational pan-genomics: status, promises and challenges.

    Computational Pan-Genomics Consortium

    Briefings in bioinformatics 2018;19;1;118-135

    PUBMED: 27769991; PMC: 5862344; DOI: 10.1093/bib/bbw089

  • Copy number variation arising from gene conversion on the human Y chromosome.

    Shi W, Massaia A, Louzada S, Banerjee R, Hallast P, Chen Y, Bergström A, Gu Y, Leonard S, Quail MA et al.

    Human genetics 2018;137;1;73-83

    PUBMED: 29209947; DOI: 10.1007/s00439-017-1857-9

  • Dairy Consumption and Body Mass Index Among Adults: Mendelian Randomization Analysis of 184802 Individuals from 25 Studies.

    Mendelian Randomization of Dairy Consumption Working Group

    Clinical chemistry 2018;64;1;183-191

    PUBMED: 29187356; PMC: 5837824; DOI: 10.1373/clinchem.2017.280701

  • Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data.

    Zhu SJ, Almagro-Garcia J and McVean G

    Bioinformatics (Oxford, England) 2018;34;1;9-15

    PUBMED: 28961721; DOI: 10.1093/bioinformatics/btx530

  • ESBL-plasmid carriage in E. coli enhances in vitro bacterial competition fitness and serum resistance in some strains of pandemic sequence types without overall fitness cost.

    Ranjan A, Scholz J, Semmler T, Wieler LH, Ewers C, Müller S, Pickard DJ, Schierack P, Tedin K, Ahmed N et al.

    Gut pathogens 2018;10;24

    PUBMED: 29983750; PMC: 6003029; DOI: 10.1186/s13099-018-0243-z

  • Evaluation of Protein-Ligand Docking by Cyscore.

    Cao Y, Dai W and Miao Z

    Methods in molecular biology (Clifton, N.J.) 2018;1762;233-243

    PUBMED: 29594775; DOI: 10.1007/978-1-4939-7756-7_12

  • False signals induced by single-cell imputation.

    Andrews TS and Hemberg M

    F1000Research 2018;7;1740

    PUBMED: 30906525; PMC: 6415334; DOI: 10.12688/f1000research.16613.2

  • Gene-level association analysis of systemic sclerosis: A comparison of African-Americans and White populations.

    Gorlova OY, Li Y, Gorlov I, Ying J, Chen WV, Assassi S, Reveille JD, Arnett FC, Zhou X, Bossini-Castillo L et al.

    PloS one 2018;13;1;e0189498

    PUBMED: 29293537; PMC: 5749683; DOI: 10.1371/journal.pone.0189498

  • Genetic Association in the HLA Region.

    Moutsianas L and Gutierrez-Achury J

    Methods in molecular biology (Clifton, N.J.) 2018;1793;111-134

    PUBMED: 29876894; DOI: 10.1007/978-1-4939-7868-7_8

  • Genome-wide association study of developmental dysplasia of the hip identifies an association with GDF5.

    Hatzikotoulas K, Roposch A, DDH Case Control Consortium, Shah KM, Clark MJ, Bratherton S, Limbani V, Steinberg J, Zengini E, Warsame K et al.

    Communications biology 2018;1;56

    PUBMED: 30273415; PMC: 6123669; DOI: 10.1038/s42003-018-0052-4

  • Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival.

    Zackay A, Cotton JA, Sanders M, Hailu A, Nasereddin A, Warburg A and Jaffe CL

    PLoS genetics 2018;14;1;e1007133

    PUBMED: 29315303; PMC: 5777657; DOI: 10.1371/journal.pgen.1007133

  • Genome-wide interaction study of a proxy for stress-sensitivity and its prediction of major depressive disorder.

    Arnau-Soler A, Adams MJ, Generation Scotland, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Hayward C and Thomson PA

    PloS one 2018;13;12;e0209160

    PUBMED: 30571770; PMC: 6301766; DOI: 10.1371/journal.pone.0209160

  • Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms.

    Olson PD, Zarowiecki M, James K, Baillie A, Bartl G, Burchell P, Chellappoo A, Jarero F, Tan LY, Holroyd N and Berriman M

    EvoDevo 2018;9;21

    PUBMED: 30455861; PMC: 6225667; DOI: 10.1186/s13227-018-0110-5

  • Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.

    van Hal SJ, Steinig EJ, Andersson P, Holden MTG, Harris SR, Nimmo GR, Williamson DA, Heffernan H, Ritchie SR, Kearns AM et al.

    Frontiers in microbiology 2018;9;1453

    PUBMED: 30038600; PMC: 6047344; DOI: 10.3389/fmicb.2018.01453

  • H3Africa: current perspectives.

    Mulder N, Abimiku A, Adebamowo SN, de Vries J, Matimba A, Olowoyo P, Ramsay M, Skelton M and Stein DJ

    Pharmacogenomics and personalized medicine 2018;11;59-66

    PUBMED: 29692621; PMC: 5903476; DOI: 10.2147/PGPM.S141546

  • Identification of genes required for eye development by high-throughput screening of mouse knockouts.

    Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM et al.

    Communications biology 2018;1;236

    PUBMED: 30588515; PMC: 6303268; DOI: 10.1038/s42003-018-0226-0

  • Immune Cell Dynamics Unfolded by Single-Cell Technologies.

    Kunz DJ, Gomes T and James KR

    Frontiers in immunology 2018;9;1435

    PUBMED: 29997618; PMC: 6028612; DOI: 10.3389/fimmu.2018.01435

  • Improving communication for interdisciplinary teams working on storage of digital information in DNA.

    Hesketh EE, Sayir J and Goldman N

    F1000Research 2018;7;39

    PUBMED: 29707196; PMC: 5883387; DOI: 10.12688/f1000research.13482.1

  • Insular Celtic population structure and genomic footprints of migration.

    Byrne RP, Martiniano R, Cassidy LM, Carrigan M, Hellenthal G, Hardiman O, Bradley DG and McLaughlin RL

    PLoS genetics 2018;14;1;e1007152

    PUBMED: 29370172; PMC: 5784891; DOI: 10.1371/journal.pgen.1007152

  • Interaction between hormone-sensitive lipase and ChREBP in fat cells controls insulin sensitivity

    Pauline Morigny, Marianne Houssier, Aline Mairal, Claire Ghilain, Etienne Mouisel, Fadila Benhamed, Bernard Masri, Emeline Recazens, Pierre-Damien Denechaud, Genevi&#232;ve Tavernier et al.

    Nature Metabolism 2018;1;1;133

    DOI: 10.1038/s42255-018-0007-6; URL: https://doi.org/10.1038/s42255-018-0007-6

  • Interferon lambda is required for interferon gamma-expressing NK cell responses but does not afford antiviral protection during acute and persistent murine cytomegalovirus infection.

    Gimeno Brias S, Marsden M, Forbester J, Clement M, Brandt C, Harcourt K, Kane L, Chapman L, Clare S and Humphreys IR

    PloS one 2018;13;5;e0197596

    PUBMED: 29768502; PMC: 5955543; DOI: 10.1371/journal.pone.0197596

  • Invasive Disease Caused Simultaneously by Dual Serotypes of Streptococcus pneumoniae.

    Ndlangisa K, du Plessis M, Allam M, Wolter N, de Gouveia L, Klugman KP, Cohen C, Gladstone RA and von Gottberg A

    Journal of clinical microbiology 2018;56;1

    PUBMED: 29118167; PMC: 5744228; DOI: 10.1128/JCM.01149-17

  • Key Concepts in Genetic Epidemiology.

    Panoutsopoulou K and Wheeler E

    Methods in molecular biology (Clifton, N.J.) 2018;1793;7-24

    PUBMED: 29876888; DOI: 10.1007/978-1-4939-7868-7_2

  • KILchip v1.0: A Novel Plasmodium falciparum Merozoite Protein Microarray to Facilitate Malaria Vaccine Candidate Prioritization.

    Kamuyu G, Tuju J, Kimathi R, Mwai K, Mburu J, Kibinge N, Chong Kwan M, Hawkings S, Yaa R, Chepsat E et al.

    Frontiers in immunology 2018;9;2866

    PUBMED: 30619257; PMC: 6298441; DOI: 10.3389/fimmu.2018.02866

  • Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens.

    Fergusson JR, Morgan MD, Bruchard M, Huitema L, Heesters BA, van Unen V, van Hamburg JP, van der Wel NN, Picavet D, Koning F et al.

    Frontiers in immunology 2018;9;2902

    PUBMED: 30692988; PMC: 6340304; DOI: 10.3389/fimmu.2018.02902

  • Molecular assays for antimalarial drug resistance surveillance: A target product profile.

    Nsanzabana C, Ariey F, Beck HP, Ding XC, Kamau E, Krishna S, Legrand E, Lucchi N, Miotto O, Nag S et al.

    PloS one 2018;13;9;e0204347

    PUBMED: 30235327; PMC: 6147503; DOI: 10.1371/journal.pone.0204347

  • Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

    Chabbert CD, Adjalley SH, Steinmetz LM and Pelechano V

    Methods in molecular biology (Clifton, N.J.) 2018;1689;177-194

    PUBMED: 29027175; DOI: 10.1007/978-1-4939-7380-4_16

  • Multiplexing for Oxidative Bisulfite Sequencing (oxBS-seq).

    Kirschner K, Krueger F, Green AR and Chandra T

    Methods in molecular biology (Clifton, N.J.) 2018;1708;665-678

    PUBMED: 29224169; DOI: 10.1007/978-1-4939-7481-8_34

  • Novel viral vectors in infectious diseases.

    Humphreys IR and Sebastian S

    Immunology 2018;153;1;1-9

    PUBMED: 28869761; PMC: 5721250; DOI: 10.1111/imm.12829

  • Objective measurement of physical activity: improving the evidence base to address non-communicable diseases in Africa.

    Barr AL, Young EH and Sandhu MS

    BMJ global health 2018;3;5;e001044

    PUBMED: 30364334; PMC: 6195142; DOI: 10.1136/bmjgh-2018-001044

  • Parasitic infections and resource economy of Danish Iron Age settlement through ancient DNA sequencing.

    Tams KW, Jensen Søe M, Merkyte I, Valeur Seersholm F, Henriksen PS, Klingenberg S, Willerslev E, Kjær KH, Hansen AJ and Kapel CMO

    PloS one 2018;13;6;e0197399

    PUBMED: 29924800; PMC: 6010210; DOI: 10.1371/journal.pone.0197399

  • Pre-clinical evaluation of a P. berghei-based whole-sporozoite malaria vaccine candidate.

    Mendes AM, Reuling IJ, Andrade CM, Otto TD, Machado M, Teixeira F, Pissarra J, Gonçalves-Rosa N, Bonaparte D, Sinfrónio J et al.

    NPJ vaccines 2018;3;54

    PUBMED: 30510775; PMC: 6258718; DOI: 10.1038/s41541-018-0091-3

  • Protein-mediated gelation and nano-scale assembly of unfunctionalized hyaluronic acid and chondroitin sulfate.

    Tabet A, Park JY, Shilts J, Sokolowski K, Rana VK, Kamp M, Warner N, Hoogland D and Scherman OA

    F1000Research 2018;7;1827

    PUBMED: 31448078; PMC: 6688722; DOI: 10.12688/f1000research.16929.3

  • Quality Control of Common and Rare Variants.

    Panoutsopoulou K and Walter K

    Methods in molecular biology (Clifton, N.J.) 2018;1793;25-36

    PUBMED: 29876889; DOI: 10.1007/978-1-4939-7868-7_3

  • Reactome graph database: Efficient access to complex pathway data.

    Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P and Hermjakob H

    PLoS computational biology 2018;14;1;e1005968

    PUBMED: 29377902; PMC: 5805351; DOI: 10.1371/journal.pcbi.1005968

  • Regulatory Hierarchies Controlling Virulence Gene Expression in Shigella flexneri and Vibrio cholerae.

    Dorman MJ and Dorman CJ

    Frontiers in microbiology 2018;9;2686

    PUBMED: 30473684; PMC: 6237886; DOI: 10.3389/fmicb.2018.02686

  • Signal Distortion: How Intracellular Pathogens Alter Host Cell Fate by Modulating NF-κB Dynamics.

    Nelson RH and Nelson DE

    Frontiers in immunology 2018;9;2962

    PUBMED: 30619320; PMC: 6302744; DOI: 10.3389/fimmu.2018.02962

  • Single agent and synergistic combinatorial efficacy of first-in-class small molecule imipridone ONC201 in hematological malignancies.

    Prabhu VV, Talekar MK, Lulla AR, Kline CLB, Zhou L, Hall J, Van den Heuvel APJ, Dicker DT, Babar J, Grupp SA et al.

    Cell cycle (Georgetown, Tex.) 2018;17;4;468-478

    PUBMED: 29157092; PMC: 5927637; DOI: 10.1080/15384101.2017.1403689

  • Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart.

    Massaia A, Chaves P, Samari S, Miragaia RJ, Meyer K, Teichmann SA and Noseda M

    Frontiers in cardiovascular medicine 2018;5;167

    PUBMED: 30525044; PMC: 6258739; DOI: 10.3389/fcvm.2018.00167

  • Split-Read Indel and Structural Variant Calling Using PINDEL.

    Ye K, Guo L, Yang X, Lamijer EW, Raine K and Ning Z

    Methods in molecular biology (Clifton, N.J.) 2018;1833;95-105

    PUBMED: 30039366; DOI: 10.1007/978-1-4939-8666-8_7

  • SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

    Do DV, Strauss B, Cukuroglu E, Macaulay I, Wee KB, Hu TX, Igor RLM, Lee C, Harrison A, Butler R et al.

    Cell discovery 2018;4;33

    PUBMED: 29928511; PMC: 6006335; DOI: 10.1038/s41421-018-0032-3

  • Steps forward for cancer precision medicine.

    Salgado R, Moore H, Martens JWM, Lively T, Malik S, McDermott U, Michiels S, Moscow JA, Tejpar S, McKee T et al.

    Nature reviews. Drug discovery 2018;17;1;1-2

    PUBMED: 29170471; DOI: 10.1038/nrd.2017.218

  • Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis.

    de Vries SPW, Hadjirin NF, Lay EM, Zadoks RN, Peacock SJ, Parkhill J, Grant AJ, McDougall S and Holmes MA

    International journal of systematic and evolutionary microbiology 2018;68;1;21-27

    PUBMED: 29099353; DOI: 10.1099/ijsem.0.002321

  • Tissue-specific transcriptome analyses provide new insights into GPCR signalling in adult Schistosoma mansoni.

    Hahnel S, Wheeler N, Lu Z, Wangwiwatsin A, McVeigh P, Maule A, Berriman M, Day T, Ribeiro P and Grevelding CG

    PLoS pathogens 2018;14;1;e1006718

    PUBMED: 29346437; PMC: 5773224; DOI: 10.1371/journal.ppat.1006718

  • Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.

    Bolt BJ, Rodgers FH, Shafie M, Kersey PJ, Berriman M and Howe KL

    Methods in molecular biology (Clifton, N.J.) 2018;1757;471-491

    PUBMED: 29761467; DOI: 10.1007/978-1-4939-7737-6_15

  • Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand.

    Price-Carter M, Brauning R, de Lisle GW, Livingstone P, Neill M, Sinclair J, Paterson B, Atkinson G, Knowles G, Crews K et al.

    Frontiers in veterinary science 2018;5;272

    PUBMED: 30425997; PMC: 6218598; DOI: 10.3389/fvets.2018.00272

2017

  • A pilot study to understand feasibility and acceptability of stool and cord blood sample collection for a large-scale longitudinal birth cohort.

    Bailey SR, Townsend CL, Dent H, Mallet C, Tsaliki E, Riley EM, Noursadeghi M, Lawley TD, Rodger AJ, Brocklehurst P and Field N

    BMC pregnancy and childbirth 2017;17;1;439

    PUBMED: 29282072; PMC: 5745976; DOI: 10.1186/s12884-017-1627-7

  • Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

    Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA et al.

    PLoS pathogens 2017;13;12;e1006749

    PUBMED: 29284042; PMC: 5790164; DOI: 10.1371/journal.ppat.1006749

  • KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis.

    Gueneau L, Fish RJ, Shamseldin HE, Voisin N, Tran Mau-Them F, Preiksaitiene E, Monroe GR, Lai A, Putoux A, Allias F et al.

    American journal of human genetics 2017;102;1;116-132

    PUBMED: 29290337; PMC: 5777449; DOI: 10.1016/j.ajhg.2017.12.002

  • Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure.

    Fookes MC, Hadfield J, Harris S, Parmar S, Unemo M, Jensen JS and Thomson NR

    BMC genomics 2017;18;1;993

    PUBMED: 29281972; PMC: 5745988; DOI: 10.1186/s12864-017-4399-6

  • The TBR1-related autistic-spectrum-disorder phenotype and its clinical spectrum.

    McDermott JH, Study DDD, Clayton-Smith J and Briggs TA

    European journal of medical genetics 2017;61;5;253-256

    PUBMED: 29288087; DOI: 10.1016/j.ejmg.2017.12.009

  • High throughput automated analysis of big flow cytometry data.

    Rahim A, Meskas J, Drissler S, Yue A, Lorenc A, Laing A, Saran N, White J, Abeler-Dörner L, Hayday A and Brinkman RR

    Methods (San Diego, Calif.) 2017;134-135;164-176

    PUBMED: 29287915; PMC: 5815930; DOI: 10.1016/j.ymeth.2017.12.015

  • Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients.

    Moradigaravand D, Gouliouris T, Blane B, Naydenova P, Ludden C, Crawley C, Brown NM, Török ME, Parkhill J and Peacock SJ

    Genome medicine 2017;9;1;119

    PUBMED: 29282103; PMC: 5744393; DOI: 10.1186/s13073-017-0507-0

  • Impact of insecticide resistance in Anopheles arabiensis on malaria incidence and prevalence in Sudan and the costs of mitigation.

    Kafy HT, Ismail BA, Mnzava AP, Lines J, Abdin MSE, Eltaher JS, Banaga AO, West P, Bradley J, Cook J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;52;E11267-E11275

    PUBMED: 29229808; PMC: 5748194; DOI: 10.1073/pnas.1713814114

  • Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

    Turcot V, Lu Y, Highland HM, Schurmann C, Justice AE, Fine RS, Bradfield JP, Esko T, Giri A, Graff M et al.

    Nature genetics 2017;50;1;26-41

    PUBMED: 29273807; PMC: 5945951; DOI: 10.1038/s41588-017-0011-x

  • Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders.

    Faundes V, Newman WG, Bernardini L, Canham N, Clayton-Smith J, Dallapiccola B, Davies SJ, Demos MK, Goldman A, Gill H et al.

    American journal of human genetics 2017;102;1;175-187

    PUBMED: 29276005; PMC: 5778085; DOI: 10.1016/j.ajhg.2017.11.013

  • Missense Variants in RHOBTB2 Cause a Developmental and Epileptic Encephalopathy in Humans, and Altered Levels Cause Neurological Defects in Drosophila.

    Straub J, Konrad EDH, Grüner J, Toutain A, Bok LA, Cho MT, Crawford HP, Dubbs H, Douglas G, Jobling R et al.

    American journal of human genetics 2017;102;1;44-57

    PUBMED: 29276004; PMC: 5777381; DOI: 10.1016/j.ajhg.2017.11.008

  • Phenotypic spectrum associated with de novo mutations in QRICH1 gene.

    Ververi A, Splitt M, Dean JCS, DDD Study and Brady AF

    Clinical genetics 2017;93;2;286-292

    PUBMED: 28692176; DOI: 10.1111/cge.13096

  • Lyplal1 is dispensable for normal fat deposition in mice.

    Watson RA, Gates AS, Wynn EH, Calvert FE, Girousse A, Lelliott CJ and Barroso I

    Disease models & mechanisms 2017;10;12;1481-1488

    PUBMED: 29084768; PMC: 5769613; DOI: 10.1242/dmm.031864

  • Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

    Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, Caulkins L, Koesterer R, Ma C, Moutsianas L et al.

    Scientific data 2017;4;170179

    PUBMED: 29257133; PMC: 5735917; DOI: 10.1038/sdata.2017.179

  • The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma.

    Cooke SL, Ennis D, Evers L, Dowson S, Chan MY, Paul J, Hirschowitz L, Glasspool RM, Singh N, Bell S et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2017;23;24;7633-7640

    PUBMED: 28954785; DOI: 10.1158/1078-0432.CCR-17-1789

  • IgG1 Is Required for Optimal Protection after Immunization with the Purified Porin OmpD from Salmonella Typhimurium.

    Zhang Y, Dominguez-Medina C, Cumley NJ, Heath JN, Essex SJ, Bobat S, Schager A, Goodall M, Kracker S, Buckley CD et al.

    Journal of immunology (Baltimore, Md. : 1950) 2017;199;12;4103-4109

    PUBMED: 29127147; PMC: 5713499; DOI: 10.4049/jimmunol.1700952

  • The metabolic syndrome- associated small G protein ARL15 plays a role in adipocyte differentiation and adiponectin secretion.

    Rocha N, Payne F, Huang-Doran I, Sleigh A, Fawcett K, Adams C, Stears A, Saudek V, O'Rahilly S, Barroso I and Semple RK

    Scientific reports 2017;7;1;17593

    PUBMED: 29242557; PMC: 5730586; DOI: 10.1038/s41598-017-17746-8

  • Observation of Cleft Palate in an Individual with SOX11 Mutation: Indication of a Role for SOX11 in Human Palatogenesis.

    Khan U, Study D, Baker E and Clayton-Smith J

    The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association 2017;55;3;456-461

    PUBMED: 29437512; DOI: 10.1177/1055665617739312

  • Sharing and reuse of individual participant data from clinical trials: principles and recommendations.

    Ohmann C, Banzi R, Canham S, Battaglia S, Matei M, Ariyo C, Becnel L, Bierer B, Bowers S, Clivio L et al.

    BMJ open 2017;7;12;e018647

    PUBMED: 29247106; PMC: 5736032; DOI: 10.1136/bmjopen-2017-018647

  • In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.

    Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR et al.

    Nature communications 2017;8;1;2109

    PUBMED: 29235467; PMC: 5727397; DOI: 10.1038/s41467-017-00686-2

  • Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.

    Bach K, Pensa S, Grzelak M, Hadfield J, Adams DJ, Marioni JC and Khaled WT

    Nature communications 2017;8;1;2128

    PUBMED: 29225342; PMC: 5723634; DOI: 10.1038/s41467-017-02001-5

  • Loss of PBRM1 rescues VHL dependent replication stress to promote renal carcinogenesis.

    Espana-Agusti J, Warren A, Chew SK, Adams DJ and Matakidou A

    Nature communications 2017;8;1;2026

    PUBMED: 29229903; PMC: 5725450; DOI: 10.1038/s41467-017-02245-1

  • Molecular and functional variation in iPSC-derived sensory neurons.

    Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL et al.

    Nature genetics 2017;50;1;54-61

    PUBMED: 29229984; PMC: 5742539; DOI: 10.1038/s41588-017-0005-8

  • Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis.

    Athanasiadis EI, Botthof JG, Andres H, Ferreira L, Lio P and Cvejic A

    Nature communications 2017;8;1;2045

    PUBMED: 29229905; PMC: 5725498; DOI: 10.1038/s41467-017-02305-6

  • Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.

    Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I et al.

    Cancer research 2017;78;3;769-780

    PUBMED: 29229604; PMC: 6522379; DOI: 10.1158/0008-5472.CAN-17-1679

  • The great escape.

    Heinz E

    Nature reviews. Microbiology 2017;16;1;4

    PUBMED: 29217841; DOI: 10.1038/nrmicro.2017.156

  • Myeloproliferative neoplasms: from origins to outcomes.

    Nangalia J and Green AR

    Hematology. American Society of Hematology. Education Program 2017;2017;1;470-479

    PUBMED: 29222295; PMC: 6142568; DOI: 10.1182/asheducation-2017.1.470

  • The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan.

    Laso-Jadart R, Harmant C, Quach H, Zidane N, Tyler-Smith C, Mehdi Q, Ayub Q, Quintana-Murci L and Patin E

    American journal of human genetics 2017;101;6;977-984

    PUBMED: 29129317; PMC: 5812914; DOI: 10.1016/j.ajhg.2017.09.025

  • ACTB Loss-of-Function Mutations Result in a Pleiotropic Developmental Disorder.

    Cuvertino S, Stuart HM, Chandler KE, Roberts NA, Armstrong R, Bernardini L, Bhaskar S, Callewaert B, Clayton-Smith J, Davalillo CH et al.

    American journal of human genetics 2017;101;6;1021-1033

    PUBMED: 29220674; PMC: 5812896; DOI: 10.1016/j.ajhg.2017.11.006

  • Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming.

    Ruetz T, Pfisterer U, Di Stefano B, Ashmore J, Beniazza M, Tian TV, Kaemena DF, Tosti L, Tan W, Manning JR et al.

    Cell stem cell 2017;21;6;791-805.e9

    PUBMED: 29174331; PMC: 5732323; DOI: 10.1016/j.stem.2017.10.013

  • Myeloproliferative neoplasms: from origins to outcomes.

    Nangalia J and Green AR

    Blood 2017;130;23;2475-2483

    PUBMED: 29212804; DOI: 10.1182/blood-2017-06-782037

  • Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach.

    Kumar K, Srinivasan P, Nold MJ, Moch JK, Reiter K, Sturdevant D, Otto TD, Squires RB, Herrera R, Nagarajan V et al.

    Scientific reports 2017;7;1;17146

    PUBMED: 29215067; PMC: 5719419; DOI: 10.1038/s41598-017-17505-9

  • Analysis of the genomic landscape of multiple myeloma highlights novel prognostic markers and disease subgroups.

    Bolli N, Biancon G, Moarii M, Gimondi S, Li Y, de Philippis C, Maura F, Sathiaseelan V, Tai YT, Mudie L et al.

    Leukemia 2017

    PUBMED: 29209042; PMC: 6092251; DOI: 10.1038/leu.2017.344

  • Biological and prognostic impact of APOBEC-induced mutations in the spectrum of plasma cell dyscrasias and multiple myeloma cell lines.

    Maura F, Petljak M, Lionetti M, Cifola I, Liang W, Pinatel E, Alexandrov LB, Fullam A, Martincorena I, Dawson KJ et al.

    Leukemia 2017;32;4;1044-1048

    PUBMED: 29209044; PMC: 5886048; DOI: 10.1038/leu.2017.345

  • Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans.

    Jagoda E, Lawson DJ, Wall JD, Lambert D, Muller C, Westaway M, Leavesley M, Capellini TD, Mirazón Lahr M, Gerbault P et al.

    Molecular biology and evolution 2017

    PUBMED: 29220488; PMC: 5850494; DOI: 10.1093/molbev/msx314

  • Immuno-oncology from the perspective of somatic evolution.

    González S, Volkova N, Beer P and Gerstung M

    Seminars in cancer biology 2017

    PUBMED: 29223477; DOI: 10.1016/j.semcancer.2017.12.001

  • The Human Cell Atlas.

    Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M et al.

    eLife 2017;6

    PUBMED: 29206104; PMC: 5762154; DOI: 10.7554/eLife.27041

  • Defined, serum/feeder-free conditions for expansion and drug screening of primary B-acute lymphoblastic leukemia.

    Jiang Z, Wu D, Ye W, Weng J, Lai P, Shi P, Guo X, Huang G, Deng Q, Tang Y et al.

    Oncotarget 2017;8;63;106382-106392

    PUBMED: 29290956; PMC: 5739741; DOI: 10.18632/oncotarget.22466

  • MiR-211 is essential for adult cone photoreceptor maintenance and visual function.

    Barbato S, Marrocco E, Intartaglia D, Pizzo M, Asteriti S, Naso F, Falanga D, Bhat RS, Meola N, Carissimo A et al.

    Scientific reports 2017;7;1;17004

    PUBMED: 29209045; PMC: 5717140; DOI: 10.1038/s41598-017-17331-z

  • Beyond the lysosome: Cholesterol role on endoplasmic reticulum and lipid droplets in Parkinson's disease.

    Fernandes HJR

    Movement disorders : official journal of the Movement Disorder Society 2017;33;2;342

    PUBMED: 29205489; DOI: 10.1002/mds.27249

  • An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers.

    Fisher CL, Marks H, Cho LT, Andrews R, Wormald S, Carroll T, Iyer V, Tate P, Rosen B, Stunnenberg HG et al.

    Nucleic acids research 2017;45;21;e174

    PUBMED: 28981838; PMC: 5716182; DOI: 10.1093/nar/gkx811

  • Antimicrobial resistance determinants and susceptibility profiles of pneumococcal isolates recovered in Trinidad and Tobago.

    Hawkins PA, Akpaka PE, Nurse-Lucas M, Gladstone R, Bentley SD, Breiman RF, McGee L and Swanston WH

    Journal of global antimicrobial resistance 2017;11;148-151

    PUBMED: 28818574; PMC: 5711790; DOI: 10.1016/j.jgar.2017.08.004

  • Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing.

    Wang K, Jin Q, Ruan D, Yang Y, Liu Q, Wu H, Zhou Z, Ouyang Z, Liu Z, Zhao Y et al.

    Genome research 2017;27;12;2061-2071

    PUBMED: 29146772; PMC: 5741047; DOI: 10.1101/gr.222521.117

  • Exome-wide association study of plasma lipids in >300,000 individuals.

    Liu DJ, Peloso GM, Yu H, Butterworth AS, Wang X, Mahajan A, Saleheen D, Emdin C, Alam D, Alves AC et al.

    Nature genetics 2017;49;12;1758-1766

    PUBMED: 29083408; PMC: 5709146; DOI: 10.1038/ng.3977

  • Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

    Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S et al.

    Nature genetics 2017;49;12;1714-1721

    PUBMED: 29083405; PMC: 5714271; DOI: 10.1038/ng.3959

  • Genome watch: Microbiota shuns the modern world.

    Kumar N and Forster SC

    Nature reviews. Microbiology 2017;15;12;710

    PUBMED: 29081498; DOI: 10.1038/nrmicro.2017.136

  • Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

    Ba Abdullah MM, Palermo RD, Palser AL, Grayson NE, Kellam P, Correia S, Szymula A and White RE

    Journal of virology 2017;91;23

    PUBMED: 28904201; PMC: 5686732; DOI: 10.1128/JVI.00920-17

  • High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

    Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R and Johnson R

    Nature genetics 2017;49;12;1731-1740

    PUBMED: 29106417; PMC: 5709232; DOI: 10.1038/ng.3988

  • Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer.

    Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindström S, Hui S, Lemaçon A, Soucy P, Dennis J et al.

    Nature genetics 2017;49;12;1767-1778

    PUBMED: 29058716; PMC: 5808456; DOI: 10.1038/ng.3785

  • Rare Variant, Gene-Based Association Study of Hereditary Melanoma Using Whole-Exome Sequencing.

    Artomov M, Stratigos AJ, Kim I, Kumar R, Lauss M, Reddy BY, Miao B, Daniela Robles-Espinoza C, Sankar A, Njauw CN et al.

    Journal of the National Cancer Institute 2017;109;12

    PUBMED: 29522175; PMC: 5939858; DOI: 10.1093/jnci/djx083

  • Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance.

    Nakatani Y, Opel-Reading HK, Merker M, Machado D, Andres S, Kumar SS, Moradigaravand D, Coll F, Perdigão J, Portugal I et al.

    Antimicrobial agents and chemotherapy 2017;61;12

    PUBMED: 28971867; PMC: 5700341; DOI: 10.1128/AAC.01575-17

  • A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations.

    Palmer EE, Kumar R, Gordon CT, Shaw M, Hubert L, Carroll R, Rio M, Murray L, Leffler M, Dudding-Byth T et al.

    American journal of human genetics 2017;101;6;995-1005

    PUBMED: 29198722; PMC: 5812890; DOI: 10.1016/j.ajhg.2017.10.009

  • An Unexpectedly Complex Architecture for Skin Pigmentation in Africans.

    Martin AR, Lin M, Granka JM, Myrick JW, Liu X, Sockell A, Atkinson EG, Werely CJ, Möller M, Sandhu MS et al.

    Cell 2017;171;6;1340-1353.e14

    PUBMED: 29195075; PMC: 5884124; DOI: 10.1016/j.cell.2017.11.015

  • Evolutionary insights from wild vervet genomes.

    Leffler EM

    Nature genetics 2017;49;12;1671-1672

    PUBMED: 29186128; PMC: 6548552; DOI: 10.1038/ng.3992

  • Genetic diversity of the African malaria vector Anopheles gambiae.

    Anopheles gambiae 1000 Genomes Consortium, Data analysis group, Partner working group, Sample collections&#x2014;Angola:, Burkina Faso:, Cameroon:, Gabon:, Guinea:, Guinea-Bissau:, Kenya: et al.

    Nature 2017;552;7683;96-100

    PUBMED: 29186111; PMC: 6026373; DOI: 10.1038/nature24995

  • Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting.

    Toleman MS, Watkins ER, Williams T, Blane B, Sadler B, Harrison EM, Coll F, Parkhill J, Nazareth B, Brown NM and Peacock SJ

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;65;12;2069-2077

    PUBMED: 29077854; PMC: 5850418; DOI: 10.1093/cid/cix539

  • Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

    Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC et al.

    Nature 2017;552;7684;239-243

    PUBMED: 29186120; PMC: 5768241; DOI: 10.1038/nature24675

  • Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets.

    Lam M, Trampush JW, Yu J, Knowles E, Davies G, Liewald DC, Starr JM, Djurovic S, Melle I, Sundet K et al.

    Cell reports 2017;21;9;2597-2613

    PUBMED: 29186694; PMC: 5789458; DOI: 10.1016/j.celrep.2017.11.028

  • Stem cell senescence drives age-attenuated induction of pituitary tumours in mouse models of paediatric craniopharyngioma.

    Gonzalez-Meljem JM, Haston S, Carreno G, Apps JR, Pozzi S, Stache C, Kaushal G, Virasami A, Panousopoulos L, Mousavy-Gharavy SN et al.

    Nature communications 2017;8;1;1819

    PUBMED: 29180744; PMC: 5703905; DOI: 10.1038/s41467-017-01992-5

  • Evaluating the Impact of Functional Genetic Variation on HIV-1 Control.

    McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N et al.

    The Journal of infectious diseases 2017;216;9;1063-1069

    PUBMED: 28968755; PMC: 5853944; DOI: 10.1093/infdis/jix470

  • HUWE1 variants cause dominant X-linked intellectual disability: a clinical study of 21 patients.

    Moortgat S, Berland S, Aukrust I, Maystadt I, Baker L, Benoit V, Caro-Llopis A, Cooper NS, Debray FG, Faivre L et al.

    European journal of human genetics : EJHG 2017;26;1;64-74

    PUBMED: 29180823; PMC: 5788272; DOI: 10.1038/s41431-017-0038-6

  • Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control.

    Barbieri I, Tzelepis K, Pandolfini L, Shi J, Millán-Zambrano G, Robson SC, Aspris D, Migliori V, Bannister AJ, Han N et al.

    Nature 2017;552;7683;126-131

    PUBMED: 29186125; PMC: 6217924; DOI: 10.1038/nature24678

  • Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

    Griffiths JA, Scialdone A and Marioni JC

    BMC genomics 2017;18;1;904

    PUBMED: 29178830; PMC: 5702132; DOI: 10.1186/s12864-017-4253-x

  • Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome.

    Abdi A, Yu L, Goulding D, Rono MK, Bejon P, Choudhary J and Rayner J

    Wellcome open research 2017;2;50

    PUBMED: 28944300; PMC: 5583745; DOI: 10.12688/wellcomeopenres.11910.2

  • From the Data on Many, Precision Medicine for "One": The Case for Widespread Genomic Data Sharing.

    Scollen S, Page A and Wilson J

    Biomedicine hub 2017;2;Suppl 1;104-110

    PUBMED: 31988941; PMC: 6945905; DOI: 10.1159/000481682

  • Relative Suffix Trees.

    Farruggia A, Gagie T, Navarro G, Puglisi SJ and Sirén J

    The computer journal 2017;61;5;773-788

    PUBMED: 29795706; PMC: 5956352; DOI: 10.1093/comjnl/bxx108

  • A high-resolution mRNA expression time course of embryonic development in zebrafish.

    White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T et al.

    eLife 2017;6

    PUBMED: 29144233; PMC: 5690287; DOI: 10.7554/eLife.30860

  • The Non-Homologous End Joining Protein PAXX Acts to Restrict HSV-1 Infection.

    Trigg BJ, Lauer KB, Fernandes Dos Santos P, Coleman H, Balmus G, Mansur DS and Ferguson BJ

    Viruses 2017;9;11

    PUBMED: 29144403; PMC: 5707549; DOI: 10.3390/v9110342

  • cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

    Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W and Stubbs TM

    Nucleic acids research 2017;45;20;11559-11569

    PUBMED: 29036576; PMC: 5714207; DOI: 10.1093/nar/gkx814

  • Molecular definition of multiple sites of antibody inhibition of malaria transmission-blocking vaccine antigen Pfs25.

    Scally SW, McLeod B, Bosch A, Miura K, Liang Q, Carroll S, Reponen S, Nguyen N, Giladi E, Rämisch S et al.

    Nature communications 2017;8;1;1568

    PUBMED: 29146922; PMC: 5691035; DOI: 10.1038/s41467-017-01924-3

  • Activation of the Aryl Hydrocarbon Receptor Interferes with Early Embryonic Development.

    Gialitakis M, Tolaini M, Li Y, Pardo M, Yu L, Toribio A, Choudhary JS, Niakan K, Papayannopoulos V and Stockinger B

    Stem cell reports 2017;9;5;1377-1386

    PUBMED: 29107595; PMC: 5831049; DOI: 10.1016/j.stemcr.2017.09.025

  • Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts.

    Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE, Lindgreen S, Gardner PP and MacKichan JK

    mSystems 2017;2;6

    PUBMED: 29152586; PMC: 5686521; DOI: 10.1128/mSystems.00127-17

  • On the effective depth of viral sequence data.

    Illingworth CJR, Roy S, Beale MA, Tutill H, Williams R and Breuer J

    Virus evolution 2017;3;2;vex030

    PUBMED: 29250429; PMC: 5724399; DOI: 10.1093/ve/vex030

  • Sub-minute Phosphoregulation of Cell Cycle Systems during Plasmodium Gamete Formation.

    Invergo BM, Brochet M, Yu L, Choudhary J, Beltrao P and Billker O

    Cell reports 2017;21;7;2017-2029

    PUBMED: 29141230; PMC: 5700370; DOI: 10.1016/j.celrep.2017.10.071

  • Human primary liver cancer-derived organoid cultures for disease modeling and drug screening.

    Broutier L, Mastrogiovanni G, Verstegen MM, Francies HE, Gavarró LM, Bradshaw CR, Allen GE, Arnes-Benito R, Sidorova O, Gaspersz MP et al.

    Nature medicine 2017;23;12;1424-1435

    PUBMED: 29131160; PMC: 5722201; DOI: 10.1038/nm.4438

  • Evaluating the glucose raising effect of established loci via a genetic risk score.

    Marouli E, Kanoni S, Mamakou V, Hackinger S, Southam L, Prins B, Rentari A, Dimitriou M, Zengini E, Gonidakis F et al.

    PloS one 2017;12;11;e0186669

    PUBMED: 29125842; PMC: 5681259; DOI: 10.1371/journal.pone.0186669

  • Genomic history of the seventh pandemic of cholera in Africa.

    Weill FX, Domman D, Njamkepo E, Tarr C, Rauzier J, Fawal N, Keddy KH, Salje H, Moore S, Mukhopadhyay AK et al.

    Science (New York, N.Y.) 2017;358;6364;785-789

    PUBMED: 29123067; DOI: 10.1126/science.aad5901

  • Integrated view of Vibrio cholerae in the Americas.

    Domman D, Quilici ML, Dorman MJ, Njamkepo E, Mutreja A, Mather AE, Delgado G, Morales-Espinosa R, Grimont PAD, Lizárraga-Partida ML et al.

    Science (New York, N.Y.) 2017;358;6364;789-793

    PUBMED: 29123068; DOI: 10.1126/science.aao2136

  • Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota.

    Iraola G, Forster SC, Kumar N, Lehours P, Bekal S, García-Peña FJ, Paolicchi F, Morsella C, Hotzel H, Hsueh PR et al.

    Nature communications 2017;8;1;1367

    PUBMED: 29118316; PMC: 5678084; DOI: 10.1038/s41467-017-01449-9

  • Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo.

    Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D, Pevsner-Fischer M, Furniss RCD, Dougan G, Dori-Bachash M, Yu L et al.

    Cell metabolism 2017;26;5;738-752.e6

    PUBMED: 28988824; PMC: 5695859; DOI: 10.1016/j.cmet.2017.09.003

  • f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

    Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC and Stegle O

    Genome biology 2017;18;1;212

    PUBMED: 29115968; PMC: 5674756; DOI: 10.1186/s13059-017-1334-8

  • Reply to Gatesy and Springer: Claims of homology errors and zombie lineages do not compromise the dating of placental diversification.

    Liu L, Zhang J, Rheindt FE, Lei F, Qu Y, Wang Y, Zhang Y, Sullivan C, Nie W, Wang J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;45;E9433-E9434

    PUBMED: 29078408; PMC: 5692603; DOI: 10.1073/pnas.1715371114

  • Molecular markers for artemisinin and partner drug resistance in natural Plasmodium falciparum populations following increased insecticide treated net coverage along the slope of mount Cameroon: cross-sectional study.

    Apinjoh TO, Mugri RN, Miotto O, Chi HF, Tata RB, Anchang-Kimbi JK, Fon EM, Tangoh DA, Nyingchu RV, Jacob C et al.

    Infectious diseases of poverty 2017;6;1;136

    PUBMED: 29110722; PMC: 5674235; DOI: 10.1186/s40249-017-0350-y

  • Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers.

    Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD et al.

    Science (New York, N.Y.) 2017;358;6363;659-662

    PUBMED: 28982795; DOI: 10.1126/science.aao1807

  • Paleolithic networking.

    Bergström A and Tyler-Smith C

    Science (New York, N.Y.) 2017;358;6363;586-587

    PUBMED: 29097532; DOI: 10.1126/science.aaq0771

  • An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells.

    Berrens RV, Andrews S, Spensberger D, Santos F, Dean W, Gould P, Sharif J, Olova N, Chandra T, Koseki H et al.

    Cell stem cell 2017;21;5;694-703.e7

    PUBMED: 29100015; PMC: 5678422; DOI: 10.1016/j.stem.2017.10.004

  • A high-throughput in vivo screening method in the mouse for identifying regulators of metastatic colonization.

    Speak AO, Swiatkowska A, Karp NA, Arends MJ, Adams DJ and van der Weyden L

    Nature protocols 2017;12;12;2465-2477

    PUBMED: 29095442; DOI: 10.1038/nprot.2017.118

  • Crosstalk between PKA and PKG controls pH-dependent host cell egress of Toxoplasma gondii.

    Jia Y, Marq JB, Bisio H, Jacot D, Mueller C, Yu L, Choudhary J, Brochet M and Soldati-Favre D

    The EMBO journal 2017;36;21;3250-3267

    PUBMED: 29030485; PMC: 5666616; DOI: 10.15252/embj.201796794

  • De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability.

    Küry S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S et al.

    American journal of human genetics 2017;101;5;768-788

    PUBMED: 29100089; PMC: 5673671; DOI: 10.1016/j.ajhg.2017.10.003

  • High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.

    Hamdan FF, Myers CT, Cossette P, Lemay P, Spiegelman D, Laporte AD, Nassif C, Diallo O, Monlong J, Cadieux-Dion M et al.

    American journal of human genetics 2017;101;5;664-685

    PUBMED: 29100083; PMC: 5673604; DOI: 10.1016/j.ajhg.2017.09.008

  • Human vaccination against RH5 induces neutralizing antimalarial antibodies that inhibit RH5 invasion complex interactions.

    Payne RO, Silk SE, Elias SC, Miura K, Diouf A, Galaway F, de Graaf H, Brendish NJ, Poulton ID, Griffiths OJ et al.

    JCI insight 2017;2;21

    PUBMED: 29093263; PMC: 5752323; DOI: 10.1172/jci.insight.96381

  • PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature.

    Reijnders MRF, Janowski R, Alvi M, Self JE, van Essen TJ, Vreeburg M, Rouhl RPW, Stevens SJC, Stegmann APA, Schieving J et al.

    Journal of medical genetics 2017;55;2;104-113

    PUBMED: 29097605; PMC: 5800346; DOI: 10.1136/jmedgenet-2017-104946

  • Short inverted repeats contribute to localized mutability in human somatic cells.

    Zou X, Morganella S, Glodzik D, Davies H, Li Y, Stratton MR and Nik-Zainal S

    Nucleic acids research 2017;45;19;11213-11221

    PUBMED: 28977645; PMC: 5737083; DOI: 10.1093/nar/gkx731

  • An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans.

    Scott RA, Scott LJ, Mägi R, Marullo L, Gaulton KJ, Kaakinen M, Pervjakova N, Pers TH, Johnson AD, Eicher JD et al.

    Diabetes 2017;66;11;2888-2902

    PUBMED: 28566273; PMC: 5652602; DOI: 10.2337/db16-1253

  • The Experimental Design Assistant.

    du Sert NP, Bamsey I, Bate ST, Berdoy M, Clark RA, Cuthill IC, Fry D, Karp NA, Macleod M, Moon L et al.

    Nature methods 2017;14;11;1024-1025

    PUBMED: 28960183; DOI: 10.1038/nmeth.4462

  • Accurate and comprehensive analysis of single nucleotide variants and large deletions of the human mitochondrial genome in DNA and single cells.

    Zambelli F, Vancampenhout K, Daneels D, Brown D, Mertens J, Van Dooren S, Caljon B, Gianaroli L, Sermon K, Voet T et al.

    European journal of human genetics : EJHG 2017;25;11;1229-1236

    PUBMED: 28832570; PMC: 5643964; DOI: 10.1038/ejhg.2017.129

  • Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.

    Lun ATL, Calero-Nieto FJ, Haim-Vilmovsky L, Göttgens B and Marioni JC

    Genome research 2017;27;11;1795-1806

    PUBMED: 29030468; PMC: 5668938; DOI: 10.1101/gr.222877.117

  • Carpe diet.

    Viciani E

    Nature reviews. Microbiology 2017;15;11;644

    PUBMED: 29021595; DOI: 10.1038/nrmicro.2017.123

  • Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.

    Hegazy AN, West NR, Stubbington MJT, Wendt E, Suijker KIM, Datsi A, This S, Danne C, Campion S, Duncan SH et al.

    Gastroenterology 2017;153;5;1320-1337.e16

    PUBMED: 28782508; PMC: 5687320; DOI: 10.1053/j.gastro.2017.07.047

  • Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

    Stubenrauch CJ, Dougan G, Lithgow T and Heinz E

    Open biology 2017;7;11

    PUBMED: 29142104; PMC: 5717340; DOI: 10.1098/rsob.170144

  • Disruption of the homeodomain transcription factor orthopedia homeobox (Otp) is associated with obesity and anxiety.

    Moir L, Bochukova EG, Dumbell R, Banks G, Bains RS, Nolan PM, Scudamore C, Simon M, Watson KA, Keogh J et al.

    Molecular metabolism 2017;6;11;1419-1428

    PUBMED: 29107289; PMC: 5681237; DOI: 10.1016/j.molmet.2017.08.006

  • Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability.

    Riazuddin S, Hussain M, Razzaq A, Iqbal Z, Shahzad M, Polla DL, Song Y, van Beusekom E, Khan AA, Tomas-Roca L et al.

    Molecular psychiatry 2017;22;11;1604-1614

    PUBMED: 27457812; PMC: 5658665; DOI: 10.1038/mp.2016.109

  • Genome stability of bovine in vivo-conceived cleavage-stage embryos is higher compared to in vitro-produced embryos.

    Tšuiko O, Catteeuw M, Zamani Esteki M, Destouni A, Bogado Pascottini O, Besenfelder U, Havlicek V, Smits K, Kurg A, Salumets A et al.

    Human reproduction (Oxford, England) 2017;32;11;2348-2357

    PUBMED: 29040498; DOI: 10.1093/humrep/dex286

  • Identification of novel risk loci for restless legs syndrome in genome-wide association studies in individuals of European ancestry: a meta-analysis.

    Schormair B, Zhao C, Bell S, Tilch E, Salminen AV, Pütz B, Dauvilliers Y, Stefani A, Högl B, Poewe W et al.

    The Lancet. Neurology 2017;16;11;898-907

    PUBMED: 29029846; PMC: 5755468; DOI: 10.1016/S1474-4422(17)30327-7

  • malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication.

    malERA Refresh Consultative Panel on Basic Science and Enabling Technologies

    PLoS medicine 2017;14;11;e1002451

    PUBMED: 29190277; PMC: 5708601; DOI: 10.1371/journal.pmed.1002451

  • mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay.

    Anderson JL, Mulligan TS, Shen MC, Wang H, Scahill CM, Tan FJ, Du SJ, Busch-Nentwich EM and Farber SA

    PLoS genetics 2017;13;11;e1007105

    PUBMED: 29161261; PMC: 5716581; DOI: 10.1371/journal.pgen.1007105

  • NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.

    Schwerd T, Bryant RV, Pandey S, Capitani M, Meran L, Cazier JB, Jung J, Mondal K, Parkes M, Mathew CG et al.

    Mucosal immunology 2017;11;2;562-574

    PUBMED: 29091079; PMC: 5924597; DOI: 10.1038/mi.2017.74

  • Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia.

    Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R et al.

    Nature communications 2017;8;1;1238

    PUBMED: 29089570; PMC: 5663702; DOI: 10.1038/s41467-017-01439-x

  • Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

    Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H, Gujaran S, Keane JA, Lithgow T, Ul-Haq I, Dougan G et al.

    Emerging infectious diseases 2017;23;11;1872-1875

    PUBMED: 29048298; PMC: 5652443; DOI: 10.3201/eid2311.170833

  • Statistical methods to detect pleiotropy in human complex traits.

    Hackinger S and Zeggini E

    Open biology 2017;7;11

    PUBMED: 29093210; PMC: 5717338; DOI: 10.1098/rsob.170125

  • Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

    Baker KS, Campos J, Pichel M, Della Gaspera A, Duarte-Martínez F, Campos-Chacón E, Bolaños-Acuña HM, Guzmán-Verri C, Mather AE, Diaz Velasco S et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017;23;11;845-853

    PUBMED: 28389276; PMC: 5667938; DOI: 10.1016/j.cmi.2017.03.021

  • Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors.

    Cheng J, Demeulemeester J, Wedge DC, Vollan HKM, Pitt JJ, Russnes HG, Pandey BP, Nilsen G, Nord S, Bignell GR et al.

    Nature communications 2017;8;1;1221

    PUBMED: 29089486; PMC: 5663922; DOI: 10.1038/s41467-017-01355-0

  • WD40-repeat 47, a microtubule-associated protein, is essential for brain development and autophagy.

    Kannan M, Bayam E, Wagner C, Rinaldi B, Kretz PF, Tilly P, Roos M, McGillewie L, Bär S, Minocha S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;44;E9308-E9317

    PUBMED: 29078390; PMC: 5676932; DOI: 10.1073/pnas.1713625114

  • The evolution of seasonal influenza viruses.

    Petrova VN and Russell CA

    Nature reviews. Microbiology 2017;16;1;47-60

    PUBMED: 29081496; DOI: 10.1038/nrmicro.2017.118

  • 'Basic and Applied Thermogenesis Research' Bridging the Gap.

    Carobbio S, Guénantin AC and Vidal-Puig A

    Trends in endocrinology and metabolism: TEM 2017;29;1;5-7

    PUBMED: 29110964; DOI: 10.1016/j.tem.2017.10.002

  • Enhancers looping to target genes.

    Trynka G

    Nature genetics 2017;49;11;1564-1565

    PUBMED: 29074944; DOI: 10.1038/ng.3982

  • The Hidden Genomics of Chlamydia trachomatis.

    Hadfield J, Bénard A, Domman D and Thomson N

    Current topics in microbiology and immunology 2017

    PUBMED: 29071471; DOI: 10.1007/82_2017_39

  • Environmental DNA metabarcoding: Transforming how we survey animal and plant communities.

    Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, de Vere N et al.

    Molecular ecology 2017;26;21;5872-5895

    PUBMED: 28921802; DOI: 10.1111/mec.14350

  • Expanding the clinical spectrum of recessive truncating mutations of KLHL7 to a Bohring-Opitz-like phenotype.

    Bruel AL, Bigoni S, Kennedy J, Whiteford M, Buxton C, Parmeggiani G, Wherlock M, Woodward G, Greenslade M, Williams M et al.

    Journal of medical genetics 2017;54;12;830-835

    PUBMED: 29074562; DOI: 10.1136/jmedgenet-2017-104748

  • Recurrent De Novo Mutations Disturbing the GTP/GDP Binding Pocket of RAB11B Cause Intellectual Disability and a Distinctive Brain Phenotype.

    Lamers IJC, Reijnders MRF, Venselaar H, Kraus A, DDD Study, Jansen S, de Vries BBA, Houge G, Gradek GA, Seo J et al.

    American journal of human genetics 2017;101;5;824-832

    PUBMED: 29106825; PMC: 5673605; DOI: 10.1016/j.ajhg.2017.09.015

  • Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.

    Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME et al.

    Science translational medicine 2017;9;413

    PUBMED: 29070701; PMC: 5683347; DOI: 10.1126/scitranslmed.aak9745

  • Wheeler graphs: A framework for BWT-based data structures.

    Gagie T, Manzini G and Sirén J

    Theoretical computer science 2017;698;67-78

    PUBMED: 29276331; PMC: 5727778; DOI: 10.1016/j.tcs.2017.06.016

  • Comprehensive Pharmacogenomic Profiling of Malignant Pleural Mesothelioma Identifies a Subgroup Sensitive to FGFR Inhibition.

    Quispel-Janssen JM, Badhai J, Schunselaar L, Price S, Brammeld J, Iorio F, Kolluri K, Garnett M, Berns A, Baas P et al.

    Clinical cancer research : an official journal of the American Association for Cancer Research 2017;24;1;84-94

    PUBMED: 29061644; DOI: 10.1158/1078-0432.CCR-17-1172

  • Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

    Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC et al.

    Nature communications 2017;8;1;1092

    PUBMED: 29061983; PMC: 5653656; DOI: 10.1038/s41467-017-01037-x

  • Synergistic malaria vaccine combinations identified by systematic antigen screening.

    Bustamante LY, Powell GT, Lin YC, Macklin MD, Cross N, Kemp A, Cawkill P, Sanderson T, Crosnier C, Muller-Sienerth N et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;45;12045-12050

    PUBMED: 29078270; PMC: 5692528; DOI: 10.1073/pnas.1702944114

  • GZD824 suppresses the growth of human B cell precursor acute lymphoblastic leukemia cells by inhibiting the SRC kinase and PI3K/AKT pathways.

    Ye W, Jiang Z, Lu X, Ren X, Deng M, Lin S, Xiao Y, Lin S, Wang S, Li B et al.

    Oncotarget 2017;8;50;87002-87015

    PUBMED: 29152059; PMC: 5675611; DOI: 10.18632/oncotarget.10881

  • Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos.

    Jennings RE, Berry AA, Gerrard DT, Wearne SJ, Strutt J, Withey S, Chhatriwala M, Piper Hanley K, Vallier L, Bobola N and Hanley NA

    Stem cell reports 2017;9;5;1387-1394

    PUBMED: 29056335; PMC: 5830993; DOI: 10.1016/j.stemcr.2017.09.018

  • Universal Patterns of Selection in Cancer and Somatic Tissues.

    Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR and Campbell PJ

    Cell 2017;171;5;1029-1041.e21

    PUBMED: 29056346; PMC: 5720395; DOI: 10.1016/j.cell.2017.09.042

  • The Human Cell Atlas: from vision to reality.

    Rozenblatt-Rosen O, Stubbington MJT, Regev A and Teichmann SA

    Nature 2017;550;7677;451-453

    PUBMED: 29072289; DOI: 10.1038/550451a

  • Matchmaker Exchange.

    Sobreira NLM, Arachchi H, Buske OJ, Chong JX, Hutton B, Foreman J, Schiettecatte F, Groza T, Jacobsen JOB, Haendel MA et al.

    Current protocols in human genetics 2017;95;9.31.1-9.31.15

    PUBMED: 29044468; PMC: 6016856; DOI: 10.1002/cphg.50

  • Arc Requires PSD95 for Assembly into Postsynaptic Complexes Involved with Neural Dysfunction and Intelligence.

    Fernández E, Collins MO, Frank RAW, Zhu F, Kopanitsa MV, Nithianantharajah J, Lemprière SA, Fricker D, Elsegood KA, McLaughlin CL et al.

    Cell reports 2017;21;3;679-691

    PUBMED: 29045836; PMC: 5656750; DOI: 10.1016/j.celrep.2017.09.045

  • Clonal Heterogeneity Influences the Fate of New Adaptive Mutations.

    Vázquez-García I, Salinas F, Li J, Fischer A, Barré B, Hallin J, Bergström A, Alonso-Perez E, Warringer J, Mustonen V and Liti G

    Cell reports 2017;21;3;732-744

    PUBMED: 29045840; PMC: 5656752; DOI: 10.1016/j.celrep.2017.09.046

  • Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

    Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M and Croucher NJ

    Nature ecology & evolution 2017;1;12;1950-1960

    PUBMED: 29038424; PMC: 5708525; DOI: 10.1038/s41559-017-0337-x

  • Transcriptional repression of Plxnc1 by Lmx1a and Lmx1b directs topographic dopaminergic circuit formation.

    Chabrat A, Brisson G, Doucet-Beaupré H, Salesse C, Schaan Profes M, Dovonou A, Akitegetse C, Charest J, Lemstra S, Côté D et al.

    Nature communications 2017;8;1;933

    PUBMED: 29038581; PMC: 5643336; DOI: 10.1038/s41467-017-01042-0

  • A point mutation in the ion conduction pore of AMPA receptor GRIA3 causes dramatically perturbed sleep patterns as well as intellectual disability.

    Davies B, Brown LA, Cais O, Watson J, Clayton AJ, Chang VT, Biggs D, Preece C, Hernandez-Pliego P, Krohn J et al.

    Human molecular genetics 2017;26;20;3869-3882

    PUBMED: 29016847; PMC: 5639461; DOI: 10.1093/hmg/ddx270

  • Panoptes: web-based exploration of large scale genome variation data.

    Vauterin P, Jeffery B, Miles A, Amato R, Hart L, Wright I and Kwiatkowski D

    Bioinformatics (Oxford, England) 2017;33;20;3243-3249

    PUBMED: 29028261; PMC: 5860036; DOI: 10.1093/bioinformatics/btx410

  • Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer.

    Drost J, van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, de Ligt J, Behjati S, Grolleman JE, van Wezel T et al.

    Science (New York, N.Y.) 2017;358;6360;234-238

    PUBMED: 28912133; PMC: 6038908; DOI: 10.1126/science.aao3130

  • The driver landscape of sporadic chordoma.

    Tarpey PS, Behjati S, Young MD, Martincorena I, Alexandrov LB, Farndon SJ, Guzzo C, Hardy C, Latimer C, Butler AP et al.

    Nature communications 2017;8;1;890

    PUBMED: 29026114; PMC: 5638846; DOI: 10.1038/s41467-017-01026-0

  • A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.

    Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S et al.

    Nature communications 2017;8;1;886

    PUBMED: 29026089; PMC: 5638796; DOI: 10.1038/s41467-017-00595-4

  • Establishment of mouse expanded potential stem cells.

    Yang J, Ryan DJ, Wang W, Tsang JC, Lan G, Masaki H, Gao X, Antunes L, Yu Y, Zhu Z et al.

    Nature 2017;550;7676;393-397

    PUBMED: 29019987; PMC: 5890884; DOI: 10.1038/nature24052

  • Heterozygous mutations affecting the protein kinase domain of CDK13 cause a syndromic form of developmental delay and intellectual disability.

    Hamilton MJ, Caswell RC, Canham N, Cole T, Firth HV, Foulds N, Heimdal K, Hobson E, Houge G, Joss S et al.

    Journal of medical genetics 2017;55;1;28-38

    PUBMED: 29021403; PMC: 5749303; DOI: 10.1136/jmedgenet-2017-104620

  • Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution.

    Mathys H, Adaikkan C, Gao F, Young JZ, Manet E, Hemberg M, De Jager PL, Ransohoff RM, Regev A and Tsai LH

    Cell reports 2017;21;2;366-380

    PUBMED: 29020624; PMC: 5642107; DOI: 10.1016/j.celrep.2017.09.039

  • Revealing hidden complexities of genomic rearrangements generated with Cas9.

    Boroviak K, Fu B, Yang F, Doe B and Bradley A

    Scientific reports 2017;7;1;12867

    PUBMED: 28993641; PMC: 5634419; DOI: 10.1038/s41598-017-12740-6

  • How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

    Marioni JC and Arendt D

    Annual review of cell and developmental biology 2017;33;537-553

    PUBMED: 28813177; DOI: 10.1146/annurev-cellbio-100616-060818

  • Single-cell epigenomics: Recording the past and predicting the future.

    Kelsey G, Stegle O and Reik W

    Science (New York, N.Y.) 2017;358;6359;69-75

    PUBMED: 28983045; DOI: 10.1126/science.aan6826

  • Single-cell transcriptomics to explore the immune system in health and disease.

    Stubbington MJT, Rozenblatt-Rosen O, Regev A and Teichmann SA

    Science (New York, N.Y.) 2017;358;6359;58-63

    PUBMED: 28983043; PMC: 5654495; DOI: 10.1126/science.aan6828

  • A reversible haploid mouse embryonic stem cell biobank resource for functional genomics.

    Elling U, Wimmer RA, Leibbrandt A, Burkard T, Michlits G, Leopoldi A, Micheler T, Abdeen D, Zhuk S, Aspalter IM et al.

    Nature 2017;550;7674;114-118

    PUBMED: 28953874; PMC: 6235111; DOI: 10.1038/nature24027

  • Emergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London.

    Otter JA, Doumith M, Davies F, Mookerjee S, Dyakova E, Gilchrist M, Brannigan ET, Bamford K, Galletly T, Donaldson H et al.

    Scientific reports 2017;7;1;12711

    PUBMED: 28983088; PMC: 5629223; DOI: 10.1038/s41598-017-12637-4

  • Fine-Scale Genetic Structure in Finland.

    Kerminen S, Havulinna AS, Hellenthal G, Martin AR, Sarin AP, Perola M, Palotie A, Salomaa V, Daly MJ, Ripatti S and Pirinen M

    G3 (Bethesda, Md.) 2017;7;10;3459-3468

    PUBMED: 28983069; PMC: 5633394; DOI: 10.1534/g3.117.300217

  • Optimisation of ex vivo memory B cell expansion/differentiation for interrogation of rare peripheral memory B cell subset responses.

    Muir L, McKay PF, Petrova VN, Klymenko OV, Kratochvil S, Pinder CL, Kellam P and Shattock RJ

    Wellcome open research 2017;2;97

    PUBMED: 29588920; PMC: 5843844; DOI: 10.12688/wellcomeopenres.11386.2

  • Prospects of Fine-Mapping Trait-Associated Genomic Regions by Using Summary Statistics from Genome-wide Association Studies.

    Benner C, Havulinna AS, Järvelin MR, Salomaa V, Ripatti S and Pirinen M

    American journal of human genetics 2017;101;4;539-551

    PUBMED: 28942963; PMC: 5630179; DOI: 10.1016/j.ajhg.2017.08.012

  • Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape.

    Leitman EM, Thobakgale CF, Adland E, Ansari MA, Raghwani J, Prendergast AJ, Tudor-Williams G, Kiepiela P, Hemelaar J, Brener J et al.

    The Journal of experimental medicine 2017;214;11;3239-3261

    PUBMED: 28983013; PMC: 5679167; DOI: 10.1084/jem.20162123

  • Deriving an optimal threshold of waist circumference for detecting cardiometabolic risk in sub-Saharan Africa.

    Ekoru K, Murphy GAV, Young EH, Delisle H, Jerome CS, Assah F, Longo-Mbenza B, Nzambi JPD, On'Kin JBK, Buntix F et al.

    International journal of obesity (2005) 2017;42;3;487-94

    PUBMED: 29087388; PMC: 5880575; DOI: 10.1038/ijo.2017.240

  • Enhanced nasopharyngeal infection and shedding associated with an epidemic lineage of emm3 group A Streptococcus.

    Afshar B, Turner CE, Lamagni TL, Smith KC, Al-Shahib A, Underwood A, Holden MTG, Efstratiou A and Sriskandan S

    Virulence 2017;8;7;1390-1400

    PUBMED: 28459299; PMC: 5711448; DOI: 10.1080/21505594.2017.1325070

  • High-throughput RNAi screen for essential genes and drug synergistic combinations in colorectal cancer.

    Williams SP, Barthorpe AS, Lightfoot H, Garnett MJ and McDermott U

    Scientific data 2017;4;170139

    PUBMED: 28972570; PMC: 5625556; DOI: 10.1038/sdata.2017.139

  • Sources of error in measurement of minimal residual disease in childhood acute lymphoblastic leukemia.

    Latham S, Hughes E, Budgen B, Mechinaud F, Crock C, Ekert H, Campbell P and Morley A

    PloS one 2017;12;10;e0185556

    PUBMED: 28973007; PMC: 5626434; DOI: 10.1371/journal.pone.0185556

  • A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children.

    Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J, Parkhill J, Bentley SD, Goldblatt D, Nosten F and Turner P

    PLoS neglected tropical diseases 2017;11;10;e0005975

    PUBMED: 28968382; PMC: 5638608; DOI: 10.1371/journal.pntd.0005975

  • Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).

    von Mentzer A, Tobias J, Wiklund G, Nordqvist S, Aslett M, Dougan G, Sjöling Å and Svennerholm AM

    Scientific reports 2017;7;1;12514

    PUBMED: 28970563; PMC: 5624918; DOI: 10.1038/s41598-017-12743-3

  • The evolving craniofacial phenotype of a patient with Sensenbrenner syndrome caused by IFT140 compound heterozygous mutations.

    Bayat A, Kerr B, Douzgou S and DDD Study

    Clinical dysmorphology 2017;26;4;247-251

    PUBMED: 28288023; DOI: 10.1097/MCD.0000000000000169

  • Anthropometric and cardiometabolic risk factors in parents and child obesity in Segamat, Malaysia.

    Partap U, Young EH, Allotey P, Sandhu MS and Reidpath DD

    International journal of epidemiology 2017;46;5;1523-1532

    PUBMED: 29106558; PMC: 5837730; DOI: 10.1093/ije/dyx114

  • ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.

    Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA and Harris SR

    Microbial genomics 2017;3;10;e000131

    PUBMED: 29177089; PMC: 5695208; DOI: 10.1099/mgen.0.000131

  • Characterization of the single-cell derived bovine induced pluripotent stem cells.

    Zhao L, Wang Z, Zhang J, Yang J, Gao X, Wu B, Zhao G, Bao S, Hu S, Liu P and Li X

    Tissue & cell 2017;49;5;521-527

    PUBMED: 28720304; DOI: 10.1016/j.tice.2017.05.005

  • Cross-Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex.

    Bernardini F, Galizi R, Wunderlich M, Taxiarchi C, Kranjc N, Kyrou K, Hammond A, Nolan T, Lawniczak MNK, Papathanos PA et al.

    Genetics 2017;207;2;729-740

    PUBMED: 28860320; PMC: 5629335; DOI: 10.1534/genetics.117.300221

  • Effects of chronic cobalt and chromium exposure after metal-on-metal hip resurfacing: An epigenome-wide association pilot study.

    Steinberg J, Shah KM, Gartland A, Zeggini E and Wilkinson JM

    Journal of orthopaedic research : official publication of the Orthopaedic Research Society 2017;35;10;2323-2328

    PUBMED: 28098396; PMC: 5655715; DOI: 10.1002/jor.23525

  • Evaluation of shared genetic aetiology between osteoarthritis and bone mineral density identifies SMAD3 as a novel osteoarthritis risk locus.

    Hackinger S, Trajanoska K, Styrkarsdottir U, Zengini E, Steinberg J, Ritchie GRS, Hatzikotoulas K, Gilly A, Evangelou E, Kemp JP et al.

    Human molecular genetics 2017;26;19;3850-3858

    PUBMED: 28934396; PMC: 5886098; DOI: 10.1093/hmg/ddx285

  • Genetic aetiology of glycaemic traits: approaches and insights.

    Wheeler E, Marenne G and Barroso I

    Human molecular genetics 2017;26;R2;R172-R184

    PUBMED: 28977447; PMC: 5886471; DOI: 10.1093/hmg/ddx293

  • Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form.

    Henke K, Daane JM, Hawkins MB, Dooley CM, Busch-Nentwich EM, Stemple DL and Harris MP

    Genetics 2017;207;2;609-623

    PUBMED: 28835471; PMC: 5629327; DOI: 10.1534/genetics.117.300187

  • HDSS Profile: The South East Asia Community Observatory Health and Demographic Surveillance System (SEACO HDSS).

    Partap U, Young EH, Allotey P, Soyiri IN, Jahan N, Komahan K, Devarajan N, Sandhu MS and Reidpath DD

    International journal of epidemiology 2017;46;5;1370-1371g

    PUBMED: 29024948; PMC: 5837190; DOI: 10.1093/ije/dyx113

  • How to use… lymph node biopsy in paediatrics.

    Farndon S, Behjati S, Jonas N and Messahel B

    Archives of disease in childhood. Education and practice edition 2017;102;5;244-248

    PUBMED: 28468821; DOI: 10.1136/archdischild-2015-309634

  • Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis.

    Kemp JP, Morris JA, Medina-Gomez C, Forgetta V, Warrington NM, Youlten SE, Zheng J, Gregson CL, Grundberg E, Trajanoska K et al.

    Nature genetics 2017;49;10;1468-1475

    PUBMED: 28869591; PMC: 5621629; DOI: 10.1038/ng.3949

  • Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease.

    Zhao W, Rasheed A, Tikkanen E, Lee JJ, Butterworth AS, Howson JMM, Assimes TL, Chowdhury R, Orho-Melander M, Damrauer S et al.

    Nature genetics 2017;49;10;1450-1457

    PUBMED: 28869590; PMC: 5844224; DOI: 10.1038/ng.3943

  • Key features of invasive pneumococcal isolates recovered in Lima, Peru determined through whole genome sequencing.

    Hawkins P, Mercado E, Chochua S, Castillo ME, Reyes I, Chaparro E, Gladstone R, Bentley SD, Breiman RF, Metcalf BJ et al.

    International journal of medical microbiology : IJMM 2017;307;7;415-421

    PUBMED: 28756964; PMC: 5615106; DOI: 10.1016/j.ijmm.2017.07.008

  • Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations.

    Silva Martins WF, Wilding CS, Steen K, Mawejje H, Antão TR and Donnelly MJ

    PLoS neglected tropical diseases 2017;11;10;e0005917

    PUBMED: 28972985; PMC: 5640252; DOI: 10.1371/journal.pntd.0005917

  • New Blood Pressure-Associated Loci Identified in Meta-Analyses of 475 000 Individuals.

    Kraja AT, Cook JP, Warren HR, Surendran P, Liu C, Evangelou E, Manning AK, Grarup N, Drenos F, Sim X et al.

    Circulation. Cardiovascular genetics 2017;10;5

    PUBMED: 29030403; PMC: 5776077; DOI: 10.1161/CIRCGENETICS.117.001778

  • Pathways to understanding the genomic aetiology of osteoarthritis.

    Cibrián Uhalte E, Wilkinson JM, Southam L and Zeggini E

    Human molecular genetics 2017;26;R2;R193-R201

    PUBMED: 28977450; PMC: 5886472; DOI: 10.1093/hmg/ddx302

  • Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights.

    Kiu R, Caim S, Alcon-Giner C, Belteki G, Clarke P, Pickard D, Dougan G and Hall LJ

    Genome biology and evolution 2017;9;10;2707-2714

    PUBMED: 29044436; PMC: 5647805; DOI: 10.1093/gbe/evx210

  • Pro-inflammatory fatty acid profile and colorectal cancer risk: A Mendelian randomisation analysis.

    May-Wilson S, Sud A, Law PJ, Palin K, Tuupanen S, Gylfe A, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J et al.

    European journal of cancer (Oxford, England : 1990) 2017;84;228-238

    PUBMED: 28829991; PMC: 5630201; DOI: 10.1016/j.ejca.2017.07.034

  • "Matching" consent to purpose: The example of the Matchmaker Exchange.

    Dyke SOM, Knoppers BM, Hamosh A, Firth HV, Hurles M, Brudno M, Boycott KM, Philippakis AA and Rehm HL

    Human mutation 2017;38;10;1281-1285

    PUBMED: 28699299; PMC: 5669800; DOI: 10.1002/humu.23278

  • Salmonella enterica serovar Typhi Producing CTX-M-15 Extended Spectrum β-Lactamase in the Democratic Republic of the Congo.

    Phoba MF, Barbé B, Lunguya O, Masendu L, Lulengwa D, Dougan G, Wong VK, Bertrand S, Ceyssens PJ, Jacobs J et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;65;7;1229-1231

    PUBMED: 29136410; PMC: 5849100; DOI: 10.1093/cid/cix342

  • Sanger Institute series: uncovering the genetics of cancer: an interview with David Adams.

    Adams DJ

    Future oncology (London, England) 2017;13;24;2133-2135

    PUBMED: 28984472; DOI: 10.2217/fon-2017-0312

  • Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation.

    Natarajan KN, Teichmann SA and Kolodziejczyk AA

    Current opinion in genetics & development 2017;46;66-76

    PUBMED: 28675884; DOI: 10.1016/j.gde.2017.06.003

  • Societal challenges of precision medicine: Bringing order to chaos.

    Salgado R, Moore H, Martens JWM, Lively T, Malik S, McDermott U, Michiels S, Moscow JA, Tejpar S, McKee T et al.

    European journal of cancer (Oxford, England : 1990) 2017;84;325-334

    PUBMED: 28865260; DOI: 10.1016/j.ejca.2017.07.028

  • Variability of human pluripotent stem cell lines.

    Ortmann D and Vallier L

    Current opinion in genetics & development 2017;46;179-185

    PUBMED: 28843810; DOI: 10.1016/j.gde.2017.07.004

  • AMR Surveillance in low and middle-income settings - A roadmap for participation in the Global Antimicrobial Surveillance System (GLASS).

    Seale AC, Gordon NC, Islam J, Peacock SJ and Scott JAG

    Wellcome open research 2017;2;92

    PUBMED: 29062918; PMC: 5645727; DOI: 10.12688/wellcomeopenres.12527.1

  • Identification of highly-protective combinations of Plasmodium vivax recombinant proteins for vaccine development.

    França CT, White MT, He WQ, Hostetler JB, Brewster J, Frato G, Malhotra I, Gruszczyk J, Huon C, Lin E et al.

    eLife 2017;6

    PUBMED: 28949293; PMC: 5655538; DOI: 10.7554/eLife.28673

  • De novo mutations in HNRNPU result in a neurodevelopmental syndrome.

    Yates TM, Vasudevan PC, Chandler KE, Donnelly DE, Stark Z, Sadedin S, Willoughby J, Broad Center for Mendelian Genomics, DDD study and Balasubramanian M

    American journal of medical genetics. Part A 2017;173;11;3003-3012

    PUBMED: 28944577; PMC: 6555908; DOI: 10.1002/ajmg.a.38492

  • The Pursuit of Therapeutic Biomarkers with High-Throughput Cancer Cell Drug Screens.

    Williams SP and McDermott U

    Cell chemical biology 2017;24;9;1066-1074

    PUBMED: 28736238; DOI: 10.1016/j.chembiol.2017.06.011

  • Genome editing reveals a role for OCT4 in human embryogenesis.

    Fogarty NME, McCarthy A, Snijders KE, Powell BE, Kubikova N, Blakeley P, Lea R, Elder K, Wamaitha SE, Kim D et al.

    Nature 2017;550;7674;67-73

    PUBMED: 28953884; PMC: 5815497; DOI: 10.1038/nature24033

  • A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

    Bergström A, Oppenheimer SJ, Mentzer AJ, Auckland K, Robson K, Attenborough R, Alpers MP, Koki G, Pomat W, Siba P et al.

    Science (New York, N.Y.) 2017;357;6356;1160-1163

    PUBMED: 28912245; PMC: 5802383; DOI: 10.1126/science.aan3842

  • Whole-Genome Sequencing Reveals Breast Cancers with Mismatch Repair Deficiency.

    Davies H, Morganella S, Purdie CA, Jang SJ, Borgen E, Russnes H, Glodzik D, Zou X, Viari A, Richardson AL et al.

    Cancer research 2017;77;18;4755-4762

    PUBMED: 28904067; DOI: 10.1158/0008-5472.CAN-17-1083

  • De novo SETD5 loss-of-function variant as a cause for intellectual disability in a 10-year old boy with an aberrant blind ending bronchus.

    Green C, Willoughby J, DDD Study and Balasubramanian M

    American journal of medical genetics. Part A 2017;173;12;3165-3171

    PUBMED: 28905509; DOI: 10.1002/ajmg.a.38461

  • The Typhoid Vaccine Acceleration Consortium (TyVAC): Vaccine effectiveness study designs: Accelerating the introduction of typhoid conjugate vaccines and reducing the global burden of enteric fever. Report from a meeting held on 26-27 October 2016, Oxford, UK.

    Meiring JE, Gibani M and TyVAC Consortium Meeting Group:

    Vaccine 2017;35;38;5081-5088

    PUBMED: 28802757; DOI: 10.1016/j.vaccine.2017.08.001

  • Association of Genetic Variants Related to CETP Inhibitors and Statins With Lipoprotein Levels and Cardiovascular Risk.

    Ference BA, Kastelein JJP, Ginsberg HN, Chapman MJ, Nicholls SJ, Ray KK, Packard CJ, Laufs U, Brook RD, Oliver-Williams C et al.

    JAMA 2017;318;10;947-956

    PUBMED: 28846118; PMC: 5710502; DOI: 10.1001/jama.2017.11467

  • Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage.

    Iantorno SA, Durrant C, Khan A, Sanders MJ, Beverley SM, Warren WC, Berriman M, Sacks DL, Cotton JA and Grigg ME

    mBio 2017;8;5

    PUBMED: 28900023; PMC: 5596349; DOI: 10.1128/mBio.01393-17

  • Genome wide in vivo mouse screen data from studies to assess host regulation of metastatic colonisation.

    van der Weyden L, Karp NA, Swiatkowska A, Adams DJ and Speak AO

    Scientific data 2017;4;170129

    PUBMED: 28895944; PMC: 5827107; DOI: 10.1038/sdata.2017.129

  • Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis.

    Wheeler E, Leong A, Liu CT, Hivert MF, Strawbridge RJ, Podmore C, Li M, Yao J, Sim X, Hong J et al.

    PLoS medicine 2017;14;9;e1002383

    PUBMED: 28898252; PMC: 5595282; DOI: 10.1371/journal.pmed.1002383

  • Conservation and diversification of small RNA pathways within flatworms.

    Fontenla S, Rinaldi G, Smircich P and Tort JF

    BMC evolutionary biology 2017;17;1;215

    PUBMED: 28893179; PMC: 5594548; DOI: 10.1186/s12862-017-1061-5

  • Galleria mellonella is low cost and suitable surrogate host for studying virulence of human pathogenic Vibrio cholerae.

    Bokhari H, Ali A, Noreen Z, Thomson N and Wren BW

    Gene 2017;628;1-7

    PUBMED: 28698162; DOI: 10.1016/j.gene.2017.07.019

  • Genome-wide analysis of health-related biomarkers in the UK Household Longitudinal Study reveals novel associations.

    Prins BP, Kuchenbaecker KB, Bao Y, Smart M, Zabaneh D, Fatemifar G, Luan J, Wareham NJ, Scott RA, Perry JRB et al.

    Scientific reports 2017;7;1;11008

    PUBMED: 28887542; PMC: 5591265; DOI: 10.1038/s41598-017-10812-1

  • Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa.

    Omedo I, Mogeni P, Bousema T, Rockett K, Amambua-Ngwa A, Oyier I, C Stevenson J, Y Baidjoe A, de Villiers EP, Fegan G et al.

    Wellcome open research 2017;2;10

    PUBMED: 28612053; PMC: 5445974; DOI: 10.12688/wellcomeopenres.10784.2

  • A Family Based Study of Carbon Monoxide and Nitric Oxide Signalling Genes and Preeclampsia.

    Bauer AE, Avery CL, Shi M, Weinberg CR, Olshan AF, Harmon QE, Luo J, Yang J, Manuck TA, Wu MC et al.

    Paediatric and perinatal epidemiology 2017;32;1;1-12

    PUBMED: 28881463; PMC: 5771849; DOI: 10.1111/ppe.12400

  • A Genome-wide Association Study of Dupuytren Disease Reveals 17 Additional Variants Implicated in Fibrosis.

    Ng M, Thakkar D, Southam L, Werker P, Ophoff R, Becker K, Nothnagel M, Franke A, Nürnberg P, Espirito-Santo AI et al.

    American journal of human genetics 2017;101;3;417-427

    PUBMED: 28886342; PMC: 5591021; DOI: 10.1016/j.ajhg.2017.08.006

  • Safety and effectiveness of mass drug administration to accelerate elimination of artemisinin-resistant falciparum malaria: A pilot trial in four villages of Eastern Myanmar.

    Landier J, Kajeechiwa L, Thwin MM, Parker DM, Chaumeau V, Wiladphaingern J, Imwong M, Miotto O, Patumrat K, Duanguppama J et al.

    Wellcome open research 2017;2;81

    PUBMED: 29062913; PMC: 5635445; DOI: 10.12688/wellcomeopenres.12240.1

  • Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.

    Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, Anun S, Blane B, Parkhill J, Peacock SJ and Chantratita N

    Genome medicine 2017;9;1;81

    PUBMED: 28877757; PMC: 5588602; DOI: 10.1186/s13073-017-0471-8

  • Geographic-genetic analysis of Plasmodium falciparum parasite populations from surveys of primary school children in Western Kenya.

    Omedo I, Mogeni P, Rockett K, Kamau A, Hubbart C, Jeffreys A, Ochola-Oyier LI, de Villiers EP, Gitonga CW, Noor AM et al.

    Wellcome open research 2017;2;29

    PUBMED: 28944299; PMC: 5527688; DOI: 10.12688/wellcomeopenres.11228.2

  • The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish.

    Scahill CM, Digby Z, Sealy IM, White RJ, Wali N, Collins JE, Stemple DL and Busch-Nentwich EM

    Wellcome open research 2017;2;77

    PUBMED: 29568807; PMC: 5840683; DOI: 10.12688/wellcomeopenres.12530.2

  • Chromosome contacts in activated T cells identify autoimmune disease candidate genes.

    Burren OS, Rubio García A, Javierre BM, Rainbow DB, Cairns J, Cooper NJ, Lambourne JJ, Schofield E, Castro Dopico X, Ferreira RC et al.

    Genome biology 2017;18;1;165

    PUBMED: 28870212; PMC: 5584004; DOI: 10.1186/s13059-017-1285-0

  • Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.

    Jamrozy D, Coll F, Mather AE, Harris SR, Harrison EM, MacGowan A, Karas A, Elston T, Estée Török M, Parkhill J and Peacock SJ

    BMC genomics 2017;18;1;684

    PUBMED: 28870171; PMC: 5584012; DOI: 10.1186/s12864-017-4065-z

  • The Experimental Design Assistant.

    Percie du Sert N, Bamsey I, Bate ST, Berdoy M, Clark RA, Cuthill I, Fry D, Karp NA, Macleod M, Moon L et al.

    PLoS biology 2017;15;9;e2003779

    PUBMED: 28957312; PMC: 5634641; DOI: 10.1371/journal.pbio.2003779

  • An untypeable enterotoxigenic Escherichia coli represents one of the dominant types causing human disease.

    Iguchi A, von Mentzer A, Kikuchi T and Thomson NR

    Microbial genomics 2017;3;9;e000121

    PUBMED: 29114400; PMC: 5643014; DOI: 10.1099/mgen.0.000121

  • Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

    Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B et al.

    PLoS genetics 2017;13;9;e1007001

    PUBMED: 28945760; PMC: 5628936; DOI: 10.1371/journal.pgen.1007001

  • Association analyses based on false discovery rate implicate new loci for coronary artery disease.

    Nelson CP, Goel A, Butterworth AS, Kanoni S, Webb TR, Marouli E, Zeng L, Ntalla I, Lai FY, Hopewell JC et al.

    Nature genetics 2017;49;9;1385-1391

    PUBMED: 28714975; DOI: 10.1038/ng.3913

  • Association of MicroRNA-618 Expression With Altered Frequency and Activation of Plasmacytoid Dendritic Cells in Patients With Systemic Sclerosis.

    Rossato M, Affandi AJ, Thordardottir S, Wichers CGK, Cossu M, Broen JCA, Moret FM, Bossini-Castillo L, Chouri E, van Bon L et al.

    Arthritis & rheumatology (Hoboken, N.J.) 2017;69;9;1891-1902

    PUBMED: 28556560; DOI: 10.1002/art.40163

  • Dietary (Poly)phenols, Brown Adipose Tissue Activation, and Energy Expenditure: A Narrative Review.

    Mele L, Bidault G, Mena P, Crozier A, Brighenti F, Vidal-Puig A and Del Rio D

    Advances in nutrition (Bethesda, Md.) 2017;8;5;694-704

    PUBMED: 28916570; PMC: 5593103; DOI: 10.3945/an.117.015792

  • Early loss of Crebbp confers malignant stem cell properties on lymphoid progenitors.

    Horton SJ, Giotopoulos G, Yun H, Vohra S, Sheppard O, Bashford-Rogers R, Rashid M, Clipson A, Chan WI, Sasca D et al.

    Nature cell biology 2017;19;9;1093-1104

    PUBMED: 28825697; PMC: 5633079; DOI: 10.1038/ncb3597

  • Epigenetic and Genetic Contributions to Adaptation in Chlamydomonas.

    Kronholm I, Bassett A, Baulcombe D and Collins S

    Molecular biology and evolution 2017;34;9;2285-2306

    PUBMED: 28535256; DOI: 10.1093/molbev/msx166

  • NBEAL2 is required for neutrophil and NK cell function and pathogen defense.

    Sowerby JM, Thomas DC, Clare S, Espéli M, Guerrero JA, Hoenderdos K, Harcourt K, Marsden M, Abdul-Karim J, Clement M et al.

    The Journal of clinical investigation 2017;127;9;3521-3526

    PUBMED: 28783043; DOI: 10.1172/JCI91684

  • Phenyl-γ-valerolactones, flavan-3-ol colonic metabolites, protect brown adipocytes from oxidative stress without affecting their differentiation or function.

    Mele L, Carobbio S, Brindani N, Curti C, Rodriguez-Cuenca S, Bidault G, Mena P, Zanotti I, Vacca M, Vidal-Puig A and Del Rio D

    Molecular nutrition & food research 2017;61;9

    PUBMED: 28276197; DOI: 10.1002/mnfr.201700074

  • Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes.

    Papa F, Windbichler N, Waterhouse RM, Cagnetti A, D'Amato R, Persampieri T, Lawniczak MKN, Nolan T and Papathanos PA

    Genome research 2017;27;9;1536-1548

    PUBMED: 28747381; PMC: 5580713; DOI: 10.1101/gr.217216.116

  • Regulation of bone mass through pineal-derived melatonin-MT2 receptor pathway.

    Sharan K, Lewis K, Furukawa T and Yadav VK

    Journal of pineal research 2017;63;2

    PUBMED: 28512916; PMC: 5575491; DOI: 10.1111/jpi.12423

  • Stronger together.

    Lees JA, Tonkin-Hill G and Bentley SD

    Nature reviews. Microbiology 2017;15;9;516

    PUBMED: 28781366; DOI: 10.1038/nrmicro.2017.95

  • Detection of structural mosaicism from targeted and whole-genome sequencing data.

    King DA, Sifrim A, Fitzgerald TW, Rahbari R, Hobson E, Homfray T, Mansour S, Mehta SG, Shehla M, Tomkins SE et al.

    Genome research 2017;27;10;1704-1714

    PUBMED: 28855261; PMC: 5630034; DOI: 10.1101/gr.212373.116

  • Illuminating microbial diversity.

    Forster SC

    Nature reviews. Microbiology 2017;15;10;578

    PUBMED: 28852214; DOI: 10.1038/nrmicro.2017.106

  • Genome-wide profiling of humoral immunity and pathogen genes under selection identifies immune evasion tactics of Chlamydia trachomatis during ocular infection.

    Pickering H, Teng A, Faal N, Joof H, Makalo P, Cassama E, Nabicassa M, Last AR, Burr SE, Rowland-Jones SL et al.

    Scientific reports 2017;7;1;9634

    PUBMED: 28851925; PMC: 5575166; DOI: 10.1038/s41598-017-09193-2

  • Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

    Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S et al.

    Cell reports 2017;20;9;2201-2214

    PUBMED: 28854368; PMC: 5583477; DOI: 10.1016/j.celrep.2017.08.010

  • Obesity-associated gene TMEM18 has a role in the central control of appetite and body weight regulation.

    Larder R, Sim MFM, Gulati P, Antrobus R, Tung YCL, Rimmington D, Ayuso E, Polex-Wolf J, Lam BYH, Dias C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;35;9421-9426

    PUBMED: 28811369; PMC: 5584443; DOI: 10.1073/pnas.1707310114

  • Skeletal Site-specific Changes in Bone Mass in a Genetic Mouse Model for Human 15q11-13 Duplication Seen in Autism.

    Lewis KE, Sharan K, Takumi T and Yadav VK

    Scientific reports 2017;7;1;9902

    PUBMED: 28851986; PMC: 5575059; DOI: 10.1038/s41598-017-09921-8

  • Expanded repertoire of RASGRP2 variants responsible for platelet dysfunction and severe bleeding.

    Westbury SK, Canault M, Greene D, Bermejo E, Hanlon K, Lambert MP, Millar CM, Nurden P, Obaji SG, Revel-Vilk S et al.

    Blood 2017;130;8;1026-1030

    PUBMED: 28637664; PMC: 5785798; DOI: 10.1182/blood-2017-03-776773

  • Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.

    Schlaffner CN, Pirklbauer GJ, Bender A and Choudhary JS

    Cell systems 2017;5;2;152-156.e4

    PUBMED: 28837811; PMC: 5571441; DOI: 10.1016/j.cels.2017.07.007

  • Molecular synergy underlies the co-occurrence patterns and phenotype of NPM1-mutant acute myeloid leukemia.

    Dovey OM, Cooper JL, Mupo A, Grove CS, Lynn C, Conte N, Andrews RM, Pacharne S, Tzelepis K, Vijayabaskar MS et al.

    Blood 2017;130;17;1911-1922

    PUBMED: 28835438; PMC: 5672315; DOI: 10.1182/blood-2017-01-760595

  • Phylogenetic characterisation of circulating, clinical influenza isolates from Bali, Indonesia: preliminary report from the BaliMEI project.

    Adisasmito W, Budayanti SN, Aisyah DN, Gallo Cassarino T, Rudge JW, Watson SJ, Kozlakidis Z, Smith GJD and Coker R

    BMC infectious diseases 2017;17;1;583

    PUBMED: 28830452; PMC: 5568394; DOI: 10.1186/s12879-017-2684-2

  • A gene expression atlas of adult Schistosoma mansoni and their gonads.

    Lu Z, Sessler F, Holroyd N, Hahnel S, Quack T, Berriman M and Grevelding CG

    Scientific data 2017;4;170118

    PUBMED: 28829433; PMC: 5566097; DOI: 10.1038/sdata.2017.118

  • Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes.

    Narasimhan VM, Rahbari R, Scally A, Wuster A, Mason D, Xue Y, Wright J, Trembath RC, Maher ER, van Heel DA et al.

    Nature communications 2017;8;1;303

    PUBMED: 28827725; PMC: 5566399; DOI: 10.1038/s41467-017-00323-y

  • Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis.

    Steinberg J, Ritchie GRS, Roumeliotis TI, Jayasuriya RL, Clark MJ, Brooks RA, Binch ALA, Shah KM, Coyle R, Pardo M et al.

    Scientific reports 2017;7;1;8935

    PUBMED: 28827734; PMC: 5566454; DOI: 10.1038/s41598-017-09335-6

  • A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation.

    Li MA, Amaral PP, Cheung P, Bergmann JH, Kinoshita M, Kalkan T, Ralser M, Robson S, von Meyenn F, Paramor M et al.

    eLife 2017;6

    PUBMED: 28820723; PMC: 5562443; DOI: 10.7554/eLife.23468

  • A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

    Haque A, Engel J, Teichmann SA and Lönnberg T

    Genome medicine 2017;9;1;75

    PUBMED: 28821273; PMC: 5561556; DOI: 10.1186/s13073-017-0467-4

  • Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium.

    Ondari EM, Heath JN, Klemm EJ, Langridge G, Barquist L, Goulding DA, Clare S, Dougan G, Kingsley RA and MacLennan CA

    Infection and immunity 2017;85;9

    PUBMED: 28674031; PMC: 5563563; DOI: 10.1128/IAI.00419-17

  • Community outbreaks of group A Streptococcus revealed by genome sequencing.

    Turner CE, Bedford L, Brown NM, Judge K, Török ME, Parkhill J and Peacock SJ

    Scientific reports 2017;7;1;8554

    PUBMED: 28819111; PMC: 5561225; DOI: 10.1038/s41598-017-08914-x

  • Draft Genome Sequences of Two Pseudomonas aeruginosa Bloodstream Infection Isolates Associated with Rapid Patient Death.

    McCarthy KL, Jennison AV, Wailan AM and Paterson DL

    Genome announcements 2017;5;33

    PUBMED: 28818886; PMC: 5604759; DOI: 10.1128/genomeA.00597-17

  • Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine.

    Rutledge GG, Marr I, Huang GKL, Auburn S, Marfurt J, Sanders M, White NJ, Berriman M, Newbold CI, Anstey NM et al.

    Emerging infectious diseases 2017;23;8;1300-1307

    PUBMED: 28430103; PMC: 5547787; DOI: 10.3201/eid2308.161582

  • Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells.

    Pardo M, Yu L, Shen S, Tate P, Bode D, Letney BL, Quelle DE, Skarnes W and Choudhary JS

    Scientific reports 2017;7;1;8157

    PUBMED: 28811661; PMC: 5557939; DOI: 10.1038/s41598-017-08456-2

  • Cliques and Schisms of Cancer Genes.

    Campbell PJ

    Cancer cell 2017;32;2;129-130

    PUBMED: 28810139; DOI: 10.1016/j.ccell.2017.07.009

  • Genomic Evolution of Breast Cancer Metastasis and Relapse.

    Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK et al.

    Cancer cell 2017;32;2;169-184.e7

    PUBMED: 28810143; PMC: 5559645; DOI: 10.1016/j.ccell.2017.07.005

  • CRISPR/Cas9-Mediated Deletion of Foxn1 in NOD/SCID/IL2rg-/- Mice Results in Severe Immunodeficiency.

    Wei X, Lai Y, Li B, Qin L, Xu Y, Lin S, Wang S, Wu Q, Liang Q, Huang G et al.

    Scientific reports 2017;7;1;7720

    PUBMED: 28798321; PMC: 5552779; DOI: 10.1038/s41598-017-08337-8

  • Immunogenomic approaches to understand the function of immune disease variants.

    Glinos DA, Soskic B and Trynka G

    Immunology 2017;152;4;527-535

    PUBMED: 28718505; PMC: 5680056; DOI: 10.1111/imm.12796

  • Not all SCN1A epileptic encephalopathies are Dravet syndrome: Early profound Thr226Met phenotype.

    Sadleir LG, Mountier EI, Gill D, Davis S, Joshi C, DeVile C, Kurian MA, DDD Study, Mandelstam S, Wirrell E et al.

    Neurology 2017;89;10;1035-1042

    PUBMED: 28794249; PMC: 5589790; DOI: 10.1212/WNL.0000000000004331

  • Preventing chemotherapy-induced myelosuppression by repurposing the FLT3 inhibitor quizartinib.

    Taylor SJ, Duyvestyn JM, Dagger SA, Dishington EJ, Rinaldi CA, Dovey OM, Vassiliou GS, Grove CS and Langdon WY

    Science translational medicine 2017;9;402

    PUBMED: 28794285; DOI: 10.1126/scitranslmed.aam8060

  • Therapeutics: Click and discover.

    Vassiliou GS and Balasubramanian S

    Nature 2017;548;7666;162-164

    PUBMED: 28796205; DOI: 10.1038/548162a

  • The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription.

    Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ et al.

    Developmental cell 2017;42;3;241-255.e6

    PUBMED: 28787591; PMC: 5554785; DOI: 10.1016/j.devcel.2017.07.002

  • Epigenetic germline inheritance in mammals: looking to the past to understand the future.

    Gapp K and Bohacek J

    Genes, brain, and behavior 2017

    PUBMED: 28782190; DOI: 10.1111/gbb.12407

  • Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England.

    Harrison EM, Coll F, Toleman MS, Blane B, Brown NM, Török ME, Parkhill J and Peacock SJ

    Scientific reports 2017;7;1;7406

    PUBMED: 28785112; PMC: 5547075; DOI: 10.1038/s41598-017-07662-2

  • Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries.

    Ong SH, Li Y, Koike-Yusa H and Yusa K

    Scientific reports 2017;7;1;7384

    PUBMED: 28785007; PMC: 5547152; DOI: 10.1038/s41598-017-07827-z

  • Genetic association analysis identifies variants associated with disease progression in primary sclerosing cholangitis.

    Alberts R, de Vries EMG, Goode EC, Jiang X, Sampaziotis F, Rombouts K, Böttcher K, Folseraas T, Weismüller TJ, Mason AL et al.

    Gut 2017;67;8;1517-1524

    PUBMED: 28779025; PMC: 5797498; DOI: 10.1136/gutjnl-2016-313598

  • Targeted Feature Detection for Data-Dependent Shotgun Proteomics.

    Weisser H and Choudhary JS

    Journal of proteome research 2017;16;8;2964-2974

    PUBMED: 28673088; PMC: 5547443; DOI: 10.1021/acs.jproteome.7b00248

  • Human Germline Genome Editing.

    Ormond KE, Mortlock DP, Scholes DT, Bombard Y, Brody LC, Faucett WA, Garrison NA, Hercher L, Isasi R, Middleton A et al.

    American journal of human genetics 2017;101;2;167-176

    PUBMED: 28777929; PMC: 5544380; DOI: 10.1016/j.ajhg.2017.06.012

  • Morphology, topology and dimensions of the heart and arteries of genetically normal and mutant mouse embryos at stages S21-S23.

    Geyer SH, Reissig LF, Hüsemann M, Höfle C, Wilson R, Prin F, Szumska D, Galli A, Adams DJ, White J et al.

    Journal of anatomy 2017

    PUBMED: 28776665; DOI: 10.1111/joa.12663

  • A recurrent de novo mutation in ACTG1 causes isolated ocular coloboma.

    Rainger J, Williamson KA, Soares DC, Truch J, Kurian D, Gillessen-Kaesbach G, Seawright A, Prendergast J, Halachev M, Wheeler A et al.

    Human mutation 2017;38;8;942-946

    PUBMED: 28493397; PMC: 5518294; DOI: 10.1002/humu.23246

  • Comparison of classical multi-locus sequence typing software for next-generation sequencing data.

    Page AJ, Alikhan NF, Carleton HA, Seemann T, Keane JA and Katz LS

    Microbial genomics 2017;3;8;e000124

    PUBMED: 29026660; PMC: 5610716; DOI: 10.1099/mgen.0.000124

  • Computational approaches for interpreting scRNA-seq data.

    Rostom R, Svensson V, Teichmann SA and Kar G

    FEBS letters 2017;591;15;2213-2225

    PUBMED: 28524227; PMC: 5575496; DOI: 10.1002/1873-3468.12684

  • Dataset of Sgo1 expression in cardiac, gastrointestinal, hepatic and neuronal tissue in mouse.

    Song AT, Galli A, Leclerc S, Nattel S, Mandato C and Andelfinger G

    Data in brief 2017;13;731-737

    PUBMED: 28748208; PMC: 5512188; DOI: 10.1016/j.dib.2017.06.046

  • Diversity of Streptococcus equi subsp. zooepidemicus strains isolated from the Spanish sheep and goat population and the identification, function and prevalence of a novel arbutin utilisation system.

    Steward KF, Robinson C, Holden MTG, Harris SR, Ros AF, Pérez GC, Baselga R and Waller AS

    Veterinary microbiology 2017;207;231-238

    PUBMED: 28757029; DOI: 10.1016/j.vetmic.2017.06.020

  • Epigenetic resetting of human pluripotency.

    Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W et al.

    Development (Cambridge, England) 2017;144;15;2748-2763

    PUBMED: 28765214; PMC: 5560041; DOI: 10.1242/dev.146811

  • Exploration of large, rare copy number variants associated with psychiatric and neurodevelopmental disorders in individuals with anorexia nervosa.

    Yilmaz Z, Szatkiewicz JP, Crowley JJ, Ancalade N, Brandys MK, van Elburg A, de Kovel CGF, Adan RAH, Hinney A, Hebebrand J et al.

    Psychiatric genetics 2017;27;4;152-158

    PUBMED: 28368970; PMC: 5493193; DOI: 10.1097/YPG.0000000000000172

  • Family aggregation of cardiovascular disease mortality: a register-based prospective study of pooled Nordic twin cohorts.

    Silventoinen K, Hjelmborg J, Möller S, Ripatti S, Skythe A, Tikkanen E, Pedersen NL, Magnusson PKE, Christensen K and Kaprio J

    International journal of epidemiology 2017;46;4;1223-1229

    PUBMED: 28338862; DOI: 10.1093/ije/dyx012

  • Genetic diversity of next generation antimalarial targets: A baseline for drug resistance surveillance programmes.

    Gomes AR, Ravenhall M, Benavente ED, Talman A, Sutherland C, Roper C, Clark TG and Campino S

    International journal for parasitology. Drugs and drug resistance 2017;7;2;174-180

    PUBMED: 28376349; PMC: 5379905; DOI: 10.1016/j.ijpddr.2017.03.001

  • Genetics: Taking single-cell transcriptomics to the bedside.

    Behjati S and Haniffa M

    Nature reviews. Clinical oncology 2017;14;10;590-592

    PUBMED: 28762386; DOI: 10.1038/nrclinonc.2017.117

  • Genomic Dissection of an Icelandic Epidemic of Respiratory Disease in Horses and Associated Zoonotic Cases.

    Björnsdóttir S, Harris SR, Svansson V, Gunnarsson E, Sigurðardóttir ÓG, Gammeljord K, Steward KF, Newton JR, Robinson C, Charbonneau ARL et al.

    mBio 2017;8;4

    PUBMED: 28765219; PMC: 5539424; DOI: 10.1128/mBio.00826-17

  • Human Y-chromosome variation in the genome-sequencing era.

    Jobling MA and Tyler-Smith C

    Nature reviews. Genetics 2017;18;8;485-497

    PUBMED: 28555659; DOI: 10.1038/nrg.2017.36

  • Hypoinsulinaemic, hypoketotic hypoglycaemia due to mosaic genetic activation of PI3-kinase.

    Leiter SM, Parker VER, Welters A, Knox R, Rocha N, Clark G, Payne F, Lotta L, Harris J, Guerrero-Fernández J et al.

    European journal of endocrinology 2017;177;2;175-186

    PUBMED: 28566443; PMC: 5488397; DOI: 10.1530/EJE-17-0132

  • Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome.

    Evrony GD, Cordero DR, Shen J, Partlow JN, Yu TW, Rodin RE, Hill RS, Coulter ME, Lam AN, Jayaraman D et al.

    Genome research 2017;27;8;1323-1335

    PUBMED: 28630177; PMC: 5538549; DOI: 10.1101/gr.219899.116

  • Intratumoral heterogeneity and subclonal diversification of early breast cancer.

    Yates LR

    Breast (Edinburgh, Scotland) 2017;34 Suppl 1;S36-S42

    PUBMED: 28666921; DOI: 10.1016/j.breast.2017.06.025

  • Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish.

    Scahill CM, Digby Z, Sealy IM, Wojciechowska S, White RJ, Collins JE, Stemple DL, Bartke T, Mathers ME, Patton EE and Busch-Nentwich EM

    PLoS genetics 2017;13;8;e1006959

    PUBMED: 28806732; PMC: 5570503; DOI: 10.1371/journal.pgen.1006959

  • No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions.

    Davey JW, Barker SL, Rastas PM, Pinharanda A, Martin SH, Durbin R, McMillan WO, Merrill RM and Jiggins CD

    Evolution letters 2017;1;3;138-154

    PUBMED: 30283645; PMC: 6122123; DOI: 10.1002/evl3.12

  • Novel genetic loci associated with long-term deterioration in blood lipid concentrations and coronary artery disease in European adults.

    Varga TV, Kurbasic A, Aine M, Eriksson P, Ali A, Hindy G, Gustafsson S, Luan J, Shungin D, Chen Y et al.

    International journal of epidemiology 2017;46;4;1211-1222

    PUBMED: 27864399; PMC: 5837581; DOI: 10.1093/ije/dyw245

  • Phase-variable methylation and epigenetic regulation by type I restriction-modification systems.

    De Ste Croix M, Vacca I, Kwun MJ, Ralph JD, Bentley SD, Haigh R, Croucher NJ and Oggioni MR

    FEMS microbiology reviews 2017;41;Supp_1;S3-S15

    PUBMED: 28830092; DOI: 10.1093/femsre/fux025

  • Principles of Reconstructing the Subclonal Architecture of Cancers.

    Dentro SC, Wedge DC and Van Loo P

    Cold Spring Harbor perspectives in medicine 2017;7;8

    PUBMED: 28270531; PMC: 5538405; DOI: 10.1101/cshperspect.a026625

  • Regulation of body weight and energy homeostasis by neuronal cell adhesion molecule 1.

    Rathjen T, Yan X, Kononenko NL, Ku MC, K, Ferrarese L, Tarallo V, Puchkov D, Kochlamazashvili G, Brachs S et al.

    Nature neuroscience 2017;20;8;1096-1103

    PUBMED: 28628102; PMC: 5533218; DOI: 10.1038/nn.4590

  • Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

    Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J et al.

    Cell reports 2017;20;5;1215-1228

    PUBMED: 28768204; PMC: 5554778; DOI: 10.1016/j.celrep.2017.07.009

  • Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

    Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ and Parkhill J

    Genome research 2017;27;8;1437-1449

    PUBMED: 28720578; PMC: 5538559; DOI: 10.1101/gr.216606.116

  • Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island.

    Sarovich DS, Chapple SNJ, Price EP, Mayo M, Holden MTG, Peacock SJ and Currie BJ

    Microbial genomics 2017;3;8;e000117

    PUBMED: 29026657; PMC: 5610713; DOI: 10.1099/mgen.0.000117

  • Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences.

    Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M et al.

    American journal of human genetics 2017;101;2;274-282

    PUBMED: 28757201; PMC: 5544389; DOI: 10.1016/j.ajhg.2017.06.013

  • Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration.

    Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J, Turner C, Turner P and Bentley SD

    eLife 2017;6

    PUBMED: 28742023; PMC: 5576492; DOI: 10.7554/eLife.26255

  • Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.

    Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B, Brown NM, Martin V, Török ME, Parkhill J and Peacock SJ

    Genome medicine 2017;9;1;70

    PUBMED: 28738847; DOI: 10.1186/s13073-017-0457-6

  • Control of virulence gene transcription by indirect readout in Vibrio cholerae and Salmonella enterica serovar Typhimurium.

    Dorman CJ and Dorman MJ

    Environmental microbiology 2017;19;10;3834-3845

    PUBMED: 28631437; PMC: 5655915; DOI: 10.1111/1462-2920.13838

  • Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney.

    Wain LV, Vaez A, Jansen R, Joehanes R, van der Most PJ, Erzurumluoglu AM, O'Reilly PF, Cabrera CP, Warren HR, Rose LM et al.

    Hypertension (Dallas, Tex. : 1979) 2017

    PUBMED: 28739976; PMC: 5783787; DOI: 10.1161/HYPERTENSIONAHA.117.09438

  • PhenoPlasm: a database of disruption phenotypes for malaria parasite genes.

    Sanderson T and Rayner JC

    Wellcome open research 2017;2;45

    PUBMED: 28748223; PMC: 5500895; DOI: 10.12688/wellcomeopenres.11896.2

  • Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya.

    Henson SP, Boinett CJ, Ellington MJ, Kagia N, Mwarumba S, Nyongesa S, Mturi N, Kariuki S, Scott JAG, Thomson NR and Morpeth SC

    International journal of medical microbiology : IJMM 2017;307;7;422-429

    PUBMED: 28789913; PMC: 5615107; DOI: 10.1016/j.ijmm.2017.07.006

  • Pro-death NMDA receptor signaling is promoted by the GluN2B C-terminus independently of Dapk1.

    McQueen J, Ryan TJ, McKay S, Marwick K, Baxter P, Carpanini SM, Wishart TM, Gillingwater TH, Manson JC, Wyllie DJA et al.

    eLife 2017;6

    PUBMED: 28731405; PMC: 5544426; DOI: 10.7554/eLife.17161

  • Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice.

    Harkins CP, Pichon B, Doumith M, Parkhill J, Westh H, Tomasz A, de Lencastre H, Bentley SD, Kearns AM and Holden MTG

    Genome biology 2017;18;1;130

    PUBMED: 28724393; PMC: 5517843; DOI: 10.1186/s13059-017-1252-9

  • Detection and quantitation of copy number variation in the voltage-gated sodium channel gene of the mosquito Culex quinquefasciatus.

    Martins WFS, Subramaniam K, Steen K, Mawejje H, Liloglou T, Donnelly MJ and Wilding CS

    Scientific reports 2017;7;1;5821

    PUBMED: 28725028; PMC: 5517494; DOI: 10.1038/s41598-017-06080-8

  • Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

    Zillikens MC, Demissie S, Hsu YH, Yerges-Armstrong LM, Chou WC, Stolk L, Livshits G, Broer L, Johnson T, Koller DL et al.

    Nature communications 2017;8;1;80

    PUBMED: 28724990; PMC: 5517526; DOI: 10.1038/s41467-017-00031-7

  • Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes.

    Unnikrishnan A, Papaemmanuil E, Beck D, Deshpande NP, Verma A, Kumari A, Woll PS, Richards LA, Knezevic K, Chandrakanthan V et al.

    Cell reports 2017;20;3;572-585

    PUBMED: 28723562; DOI: 10.1016/j.celrep.2017.06.067

  • The essential genomic landscape of the commensal Bifidobacterium breve UCC2003.

    Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD and van Sinderen D

    Scientific reports 2017;7;1;5648

    PUBMED: 28717159; PMC: 5514069; DOI: 10.1038/s41598-017-05795-y

  • Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients.

    Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Pilcher DV et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;65;2;208-215

    PUBMED: 28369261; PMC: 5850561; DOI: 10.1093/cid/cix270

  • The dental phenotype of hairless dogs with FOXI3 haploinsufficiency.

    Kupczik K, Cagan A, Brauer S and Fischer MS

    Scientific reports 2017;7;1;5459

    PUBMED: 28710361; PMC: 5511229; DOI: 10.1038/s41598-017-05764-5

  • Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease.

    Jaiswal S, Natarajan P, Silver AJ, Gibson CJ, Bick AG, Shvartz E, McConkey M, Gupta N, Gabriel S, Ardissino D et al.

    The New England journal of medicine 2017;377;2;111-121

    PUBMED: 28636844; PMC: 6717509; DOI: 10.1056/NEJMoa1701719

  • Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes.

    Bushell E, Gomes AR, Sanderson T, Anar B, Girling G, Herd C, Metcalf T, Modrzynska K, Schwach F, Martin RE et al.

    Cell 2017;170;2;260-272.e8

    PUBMED: 28708996; PMC: 5509546; DOI: 10.1016/j.cell.2017.06.030

  • Platelet function is modified by common sequence variation in megakaryocyte super enhancers.

    Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP et al.

    Nature communications 2017;8;16058

    PUBMED: 28703137; PMC: 5511350; DOI: 10.1038/ncomms16058

  • Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi.

    Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM et al.

    Vaccine 2017;35;35 Pt B;4594-4602

    PUBMED: 28711389; PMC: 5571440; DOI: 10.1016/j.vaccine.2017.07.009

  • HLA haplotypes in primary sclerosing cholangitis patients of admixed and non-European ancestry.

    Henriksen EKK, Viken MK, Wittig M, Holm K, Folseraas T, Mucha S, Melum E, Hov JR, Lazaridis KN, Juran BD et al.

    HLA 2017;90;4;228-233

    PUBMED: 28695657; PMC: 7359736; DOI: 10.1111/tan.13076

  • Nonenzymatic gluconeogenesis-like formation of fructose 1,6-bisphosphate in ice.

    Messner CB, Driscoll PC, Piedrafita G, De Volder MFL and Ralser M

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;28;7403-7407

    PUBMED: 28652321; DOI: 10.1073/pnas.1702274114

  • Adaptation... that's what you need?

    Chaguza C and Bentley SD

    Nature reviews. Microbiology 2017;15;8;452

    PUBMED: 28690321; DOI: 10.1038/nrmicro.2017.78

  • Prediction of Breast and Prostate Cancer Risks in Male BRCA1 and BRCA2 Mutation Carriers Using Polygenic Risk Scores.

    Lecarpentier J, Silvestri V, Kuchenbaecker KB, Barrowdale D, Dennis J, McGuffog L, Soucy P, Leslie G, Rizzolo P, Navazio AS et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2017;35;20;2240-2250

    PUBMED: 28448241; PMC: 5501359; DOI: 10.1200/JCO.2016.69.4935

  • Identifying transposon insertions and their effects from RNA-sequencing data.

    de Ruiter JR, Kas SM, Schut E, Adams DJ, Koudijs MJ, Wessels LFA and Jonkers J

    Nucleic acids research 2017;45;12;7064-7077

    PUBMED: 28575524; PMC: 5499543; DOI: 10.1093/nar/gkx461

  • Draft Genome Sequence of an IMP-7-Producing Pseudomonas aeruginosa Bloodstream Infection Isolate from Australia.

    McCarthy KL, Jennison A, Wailan AM and Paterson DL

    Genome announcements 2017;5;27

    PUBMED: 28684579; PMC: 5502860; DOI: 10.1128/genomeA.00596-17

  • WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features.

    Skraban CM, Wells CF, Markose P, Cho MT, Nesbitt AI, Au PYB, Begtrup A, Bernat JA, Bird LM, Cao K et al.

    American journal of human genetics 2017;101;1;139-148

    PUBMED: 28686853; PMC: 5501873; DOI: 10.1016/j.ajhg.2017.06.002

  • Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes.

    Moradigaravand D, Jamrozy D, Mostowy R, Anderson A, Nickerson EK, Thaipadungpanit J, Wuthiekanun V, Limmathurotsakul D, Tandhavanant S, Wikraiphat C et al.

    mBio 2017;8;4

    PUBMED: 28679748; PMC: 5573676; DOI: 10.1128/mBio.00802-17

  • Global, site-specific analysis of neuronal protein S-acylation.

    Collins MO, Woodley KT and Choudhary JS

    Scientific reports 2017;7;1;4683

    PUBMED: 28680068; PMC: 5498535; DOI: 10.1038/s41598-017-04580-1

  • Nutrient sensing modulates malaria parasite virulence.

    Mancio-Silva L, Slavic K, Grilo Ruivo MT, Grosso AR, Modrzynska KK, Vera IM, Sales-Dias J, Gomes AR, MacPherson CR, Crozet P et al.

    Nature 2017;547;7662;213-216

    PUBMED: 28678779; PMC: 5511512; DOI: 10.1038/nature23009

  • Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.

    Ludden C, Reuter S, Judge K, Gouliouris T, Blane B, Coll F, Naydenova P, Hunt M, Tracey A, Hopkins KL et al.

    Microbial genomics 2017;3;7;e000114

    PUBMED: 29026655; PMC: 5605956; DOI: 10.1099/mgen.0.000114

  • Reconstruction of the mouse extrahepatic biliary tree using primary human extrahepatic cholangiocyte organoids.

    Sampaziotis F, Justin AW, Tysoe OC, Sawiak S, Godfrey EM, Upponi SS, Gieseck RL, de Brito MC, Berntsen NL, Gómez-Vázquez MJ et al.

    Nature medicine 2017;23;8;954-963

    PUBMED: 28671689; DOI: 10.1038/nm.4360

  • TCTE1 is a conserved component of the dynein regulatory complex and is required for motility and metabolism in mouse spermatozoa.

    Castaneda JM, Hua R, Miyata H, Oji A, Guo Y, Cheng Y, Zhou T, Guo X, Cui Y, Shen B et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;27;E5370-E5378

    PUBMED: 28630322; PMC: 5502601; DOI: 10.1073/pnas.1621279114

  • The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys.

    Darton TC, Meiring JE, Tonks S, Khan MA, Khanam F, Shakya M, Thindwa D, Baker S, Basnyat B, Clemens JD et al.

    BMJ open 2017;7;6;e016283

    PUBMED: 28674145; PMC: 5726077; DOI: 10.1136/bmjopen-2017-016283

  • The Influence of HIV on the Evolution of Mycobacterium tuberculosis.

    Koch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V et al.

    Molecular biology and evolution 2017;34;7;1654-1668

    PUBMED: 28369607; PMC: 5455964; DOI: 10.1093/molbev/msx107

  • A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.

    Manning A, Highland HM, Gasser J, Sim X, Tukiainen T, Fontanillas P, Grarup N, Rivas MA, Mahajan A, Locke AE et al.

    Diabetes 2017;66;7;2019-2032

    PUBMED: 28341696; PMC: 5482074; DOI: 10.2337/db16-1329

  • Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.

    Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P et al.

    Journal of the American Medical Informatics Association : JAMIA 2017;24;4;799-805

    PUBMED: 28339683; PMC: 5881894; DOI: 10.1093/jamia/ocw167

  • Apolipoprotein(a) isoform size, lipoprotein(a) concentration, and coronary artery disease: a mendelian randomisation analysis.

    Saleheen D, Haycock PC, Zhao W, Rasheed A, Taleb A, Imran A, Abbas S, Majeed F, Akhtar S, Qamar N et al.

    The lancet. Diabetes & endocrinology 2017;5;7;524-533

    PUBMED: 28408323; PMC: 5483508; DOI: 10.1016/S2213-8587(17)30088-8

  • BCFtools/csq: haplotype-aware variant consequences.

    Danecek P and McCarthy SA

    Bioinformatics (Oxford, England) 2017;33;13;2037-2039

    PUBMED: 28205675; PMC: 5870570; DOI: 10.1093/bioinformatics/btx100

  • Brucella Genetic Variability in Wildlife Marine Mammals Populations Relates to Host Preference and Ocean Distribution.

    Suárez-Esquivel M, Baker KS, Ruiz-Villalobos N, Hernández-Mora G, Barquero-Calvo E, González-Barrientos R, Castillo-Zeledón A, Jiménez-Rojas C, Chacón-Díaz C, Cloeckaert A et al.

    Genome biology and evolution 2017;9;7;1901-1912

    PUBMED: 28854602; PMC: 5554395; DOI: 10.1093/gbe/evx137

  • Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam.

    Oude Munnink BB, Phan MVT, VIZIONS Consortium, Simmonds P, Koopmans MPG, Kellam P, van der Hoek L and Cotten M

    Virus evolution 2017;3;2;vex022

    PUBMED: 28948041; PMC: 5597861; DOI: 10.1093/ve/vex022

  • Combined immunodeficiency with severe inflammation and allergy caused by ARPC1B deficiency.

    Kuijpers TW, Tool ATJ, van der Bijl I, de Boer M, van Houdt M, de Cuyper IM, Roos D, van Alphen F, van Leeuwen K, Cambridge EL et al.

    The Journal of allergy and clinical immunology 2017;140;1;273-277.e10

    PUBMED: 27965109; DOI: 10.1016/j.jaci.2016.09.061

  • Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

    Hadfield J, Harris SR, Seth-Smith HMB, Parmar S, Andersson P, Giffard PM, Schachter J, Moncada J, Ellison L, Vaulet MLG et al.

    Genome research 2017;27;7;1220-1229

    PUBMED: 28588068; PMC: 5495073; DOI: 10.1101/gr.212647.116

  • Familial Hypercholesterolemia and Type 2 Diabetes in the Old Order Amish.

    Xu H, Ryan KA, Jaworek TJ, Southam L, Reid JG, Overton JD, Baras A, Puurunen MK, Zeggini E, Taylor SI et al.

    Diabetes 2017;66;7;2054-2058

    PUBMED: 28428224; PMC: 5482078; DOI: 10.2337/db17-0173

  • Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms.

    Howson JMM, Zhao W, Barnes DR, Ho WK, Young R, Paul DS, Waite LL, Freitag DF, Fauman EB, Salfati EL et al.

    Nature genetics 2017;49;7;1113-1119

    PUBMED: 28530674; PMC: 5555387; DOI: 10.1038/ng.3874

  • Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity.

    Doyle SR, Bourguinat C, Nana-Djeunga HC, Kengne-Ouafo JA, Pion SDS, Bopda J, Kamgno J, Wanji S, Che H, Kuesel AC et al.

    PLoS neglected tropical diseases 2017;11;7;e0005816

    PUBMED: 28746337; PMC: 5546710; DOI: 10.1371/journal.pntd.0005816

  • Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2.

    Tchasovnikarova IA, Timms RT, Douse CH, Roberts RC, Dougan G, Kingston RE, Modis Y and Lehner PJ

    Nature genetics 2017;49;7;1035-1044

    PUBMED: 28581500; PMC: 5493197; DOI: 10.1038/ng.3878

  • Malaria Host Candidate Genes Validated by Association With Current, Recent, and Historical Measures of Transmission Intensity.

    Sepúlveda N, Manjurano A, Campino SG, Lemnge M, Lusingu J, Olomi R, Rockett KA, Hubbart C, Jeffreys A, Rowlands K et al.

    The Journal of infectious diseases 2017;216;1;45-54

    PUBMED: 28541483; PMC: 5853769; DOI: 10.1093/infdis/jix250

  • Megakaryocytes in Myeloproliferative Neoplasms Have Unique Somatic Mutations.

    Guo BB, Allcock RJ, Mirzai B, Malherbe JA, Choudry FA, Frontini M, Chuah H, Liang J, Kavanagh SE, Howman R et al.

    The American journal of pathology 2017;187;7;1512-1522

    PUBMED: 28502479; PMC: 5500825; DOI: 10.1016/j.ajpath.2017.03.009

  • Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.

    Lun ATL and Marioni JC

    Biostatistics (Oxford, England) 2017;18;3;451-464

    PUBMED: 28334062; PMC: 5862359; DOI: 10.1093/biostatistics/kxw055

  • PGBD5 promotes site-specific oncogenic mutations in human tumors.

    Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S et al.

    Nature genetics 2017;49;7;1005-1014

    PUBMED: 28504702; PMC: 5489359; DOI: 10.1038/ng.3866

  • Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns.

    Donker T, Reuter S, Scriberras J, Reynolds R, Brown NM, Török ME, James R, Network EOEMR, Aanensen DM, Bentley SD et al.

    Microbial genomics 2017;3;7;e000113

    PUBMED: 29026654; PMC: 5605955; DOI: 10.1099/mgen.0.000113

  • Rapid identification of genes controlling virulence and immunity in malaria parasites.

    Abkallo HM, Martinelli A, Inoue M, Ramaprasad A, Xangsayarath P, Gitaka J, Tang J, Yahata K, Zoungrana A, Mitaka H et al.

    PLoS pathogens 2017;13;7;e1006447

    PUBMED: 28704525; PMC: 5507557; DOI: 10.1371/journal.ppat.1006447

  • Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex.

    Loveridge EJ, Jones C, Bull MJ, Moody SC, Kahl MW, Khan Z, Neilson L, Tomeva M, Adams SE, Wood AC et al.

    Journal of bacteriology 2017;199;13

    PUBMED: 28439036; PMC: 5472815; DOI: 10.1128/JB.00125-17

  • Reevaluation of SNP heritability in complex human traits.

    Speed D, Cai N, UCLEB Consortium, Johnson MR, Nejentsev S and Balding DJ

    Nature genetics 2017;49;7;986-992

    PUBMED: 28530675; PMC: 5493198; DOI: 10.1038/ng.3865

  • Testing for differential abundance in mass cytometry data.

    Lun ATL, Richard AC and Marioni JC

    Nature methods 2017;14;7;707-709

    PUBMED: 28504682; PMC: 6155493; DOI: 10.1038/nmeth.4295

  • TPL-2 restricts Ccl24-dependent immunity to Heligmosomoides polygyrus.

    Kannan Y, Entwistle LJ, Pelly VS, Perez-Lloret J, Walker AW, Ley SC and Wilson MS

    PLoS pathogens 2017;13;7;e1006536

    PUBMED: 28759611; PMC: 5560741; DOI: 10.1371/journal.ppat.1006536

  • Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK.

    Gladstone RA, Devine V, Jones J, Cleary D, Jefferies JM, Bentley SD, Faust SN and Clarke SC

    Microbial genomics 2017;3;6;e000119

    PUBMED: 29026652; PMC: 5628697; DOI: 10.1099/mgen.0.000119

  • Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity.

    Hendricks AE, Bochukova EG, Marenne G, Keogh JM, Atanassova N, Bounds R, Wheeler E, Mistry V, Henning E, Körner A et al.

    Scientific reports 2017;7;1;4394

    PUBMED: 28663568; PMC: 5491520; DOI: 10.1038/s41598-017-03054-8

  • Fine-mapping inflammatory bowel disease loci to single-variant resolution.

    Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F et al.

    Nature 2017;547;7662;173-178

    PUBMED: 28658209; PMC: 5511510; DOI: 10.1038/nature22969

  • In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors.

    Nelson AC, Cutty SJ, Gasiunas SN, Deplae I, Stemple DL and Wardle FC

    Cell reports 2017;19;13;2782-2795

    PUBMED: 28658625; PMC: 5494305; DOI: 10.1016/j.celrep.2017.06.011

  • The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability.

    Singh T, Walters JTR, Johnstone M, Curtis D, Suvisaari J, Torniainen M, Rees E, Iyegbe C, Blackwood D, McIntosh AM et al.

    Nature genetics 2017;49;8;1167-1173

    PUBMED: 28650482; PMC: 5533219; DOI: 10.1038/ng.3903

  • Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

    Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P et al.

    Nature genetics 2017;49;8;1231-1238

    PUBMED: 28650483; PMC: 5546242; DOI: 10.1038/ng.3901

  • Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.

    David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C, Buchrieser C, Harrison TG and Parkhill J

    PLoS genetics 2017;13;6;e1006855

    PUBMED: 28650958; PMC: 5507463; DOI: 10.1371/journal.pgen.1006855

  • Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

    Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A and Teichmann SA

    Nature communications 2017;8;1;36

    PUBMED: 28652613; PMC: 5484669; DOI: 10.1038/s41467-017-00052-2

  • Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma.

    Kas SM, de Ruiter JR, Schipper K, Annunziato S, Schut E, Klarenbeek S, Drenth AP, van der Burg E, Klijn C, Ten Hoeve JJ et al.

    Nature genetics 2017;49;8;1219-1230

    PUBMED: 28650484; DOI: 10.1038/ng.3905

  • Prevalence of sexual dimorphism in mammalian phenotypic traits.

    Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM et al.

    Nature communications 2017;8;15475

    PUBMED: 28650954; PMC: 5490203; DOI: 10.1038/ncomms15475

  • Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

    Xue Y, Mezzavilla M, Haber M, McCarthy S, Chen Y, Narasimhan V, Gilly A, Ayub Q, Colonna V, Southam L et al.

    Nature communications 2017;8;15927

    PUBMED: 28643794; PMC: 5490002; DOI: 10.1038/ncomms15927

  • Protein-Truncating Variants at the Cholesteryl Ester Transfer Protein Gene and Risk for Coronary Heart Disease.

    Nomura A, Won HH, Khera AV, Takeuchi F, Ito K, McCarthy S, Emdin CA, Klarin D, Natarajan P, Zekavat SM et al.

    Circulation research 2017;121;1;81-88

    PUBMED: 28506971; PMC: 5523940; DOI: 10.1161/CIRCRESAHA.117.311145

  • Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma.

    Behjati S, Tarpey PS, Haase K, Ye H, Young MD, Alexandrov LB, Farndon SJ, Collord G, Wedge DC, Martincorena I et al.

    Nature communications 2017;8;15936

    PUBMED: 28643781; PMC: 5490007; DOI: 10.1038/ncomms15936

  • Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy.

    Byars SG, Huang QQ, Gray LA, Bakshi A, Ripatti S, Abraham G, Stearns SC and Inouye M

    PLoS genetics 2017;13;6;e1006328

    PUBMED: 28640878; PMC: 5480811; DOI: 10.1371/journal.pgen.1006328

  • Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014.

    Schjørring S, Stegger M, Kjelsø C, Lilje B, Bangsborg JM, Petersen RF, David S, Uldum SA and ESCMID Study Group for Legionella Infections (ESGLI)

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017;22;25

    PUBMED: 28662761; PMC: 5490456; DOI: 10.2807/1560-7917.ES.2017.22.25.30558

  • SGBS cells as a model of human adipocyte browning: A comprehensive comparative study with primary human white subcutaneous adipocytes.

    Yeo CR, Agrawal M, Hoon S, Shabbir A, Shrivastava MK, Huang S, Khoo CM, Chhay V, Yassin MS, Tai ES et al.

    Scientific reports 2017;7;1;4031

    PUBMED: 28642596; DOI: 10.1038/s41598-017-04369-2

  • De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.

    Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK, Davies RM, Tischler G, Jackson DK, Keane TM, Li J et al.

    Scientific reports 2017;7;1;3935

    PUBMED: 28638050; PMC: 5479803; DOI: 10.1038/s41598-017-03996-z

  • Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt.

    Lamelas A, Hauser J, Dangy JP, Hamid AM, Röltgen K, Abdul Sater MR, Hodgson A, Sie A, Junghanss T, Harris SR et al.

    Microbial genomics 2017;3;8;e000120

    PUBMED: 29026659; PMC: 5610715; DOI: 10.1099/mgen.0.000120

  • Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1.

    Suri M, Evers JMG, Laskowski RA, O'Brien S, Baker K, Clayton-Smith J, Dabir T, Josifova D, Joss S, Kerr B et al.

    Molecular genetics & genomic medicine 2017;5;5;495-507

    PUBMED: 28944233; PMC: 5606886; DOI: 10.1002/mgg3.304

  • Risks of Breast, Ovarian, and Contralateral Breast Cancer for BRCA1 and BRCA2 Mutation Carriers.

    Kuchenbaecker KB, Hopper JL, Barnes DR, Phillips KA, Mooij TM, Roos-Blom MJ, Jervis S, van Leeuwen FE, Milne RL, Andrieu N et al.

    JAMA 2017;317;23;2402-2416

    PUBMED: 28632866; DOI: 10.1001/jama.2017.7112

  • Variants in the fetal genome near FLT1 are associated with risk of preeclampsia.

    McGinnis R, Steinthorsdottir V, Williams NO, Thorleifsson G, Shooter S, Hjartardottir S, Bumpstead S, Stefansdottir L, Hildyard L, Sigurdsson JK et al.

    Nature genetics 2017;49;8;1255-1260

    PUBMED: 28628106; DOI: 10.1038/ng.3895

  • An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion.

    Pasini EM, Böhme U, Rutledge GG, Voorberg-Van der Wel A, Sanders M, Berriman M, Kocken CH and Otto TD

    Wellcome open research 2017;2;42

    PUBMED: 28748222; PMC: 5500898; DOI: 10.12688/wellcomeopenres.11864.1

  • Discovery of novel heart rate-associated loci using the Exome Chip.

    van den Berg ME, Warren HR, Cabrera CP, Verweij N, Mifsud B, Haessler J, Bihlmeyer NA, Fu YP, Weiss S, Lin HJ et al.

    Human molecular genetics 2017;26;12;2346-2363

    PUBMED: 28379579; PMC: 5458336; DOI: 10.1093/hmg/ddx113

  • Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.

    Eduati F, Doldàn-Martelli V, Klinger B, Cokelaer T, Sieber A, Kogera F, Dorel M, Garnett MJ, Blüthgen N and Saez-Rodriguez J

    Cancer research 2017;77;12;3364-3375

    PUBMED: 28381545; PMC: 6433282; DOI: 10.1158/0008-5472.CAN-17-0078

  • Human vaccination against Plasmodium vivax Duffy-binding protein induces strain-transcending antibodies.

    Payne RO, Silk SE, Elias SC, Milne KH, Rawlinson TA, Llewellyn D, Shakri AR, Jin J, Labbé GM, Edwards NJ et al.

    JCI insight 2017;2;12

    PUBMED: 28614791; PMC: 5470884; DOI: 10.1172/jci.insight.93683

  • Mendelian randomisation implicates hyperlipidaemia as a risk factor for colorectal cancer.

    Rodriguez-Broadbent H, Law PJ, Sud A, Palin K, Tuupanen S, Gylfe A, Hänninen UA, Cajuso T, Tanskanen T, Kondelin J et al.

    International journal of cancer 2017;140;12;2701-2708

    PUBMED: 28340513; DOI: 10.1002/ijc.30709

  • Cracking Ali Baba's code.

    Billker O

    eLife 2017;6

    PUBMED: 28614050; PMC: 5470869; DOI: 10.7554/eLife.28600

  • "Like sugar in milk": reconstructing the genetic history of the Parsi population.

    Chaubey G, Ayub Q, Rai N, Prakash S, Mushrif-Tripathy V, Mezzavilla M, Pathak AK, Tamang R, Firasat S, Reidla M et al.

    Genome biology 2017;18;1;110

    PUBMED: 28615043; PMC: 5470188; DOI: 10.1186/s13059-017-1244-9

  • JAK2 V617F hematopoietic clones are present several years prior to MPN diagnosis and follow different expansion kinetics.

    McKerrell T, Park N, Chi J, Collord G, Moreno T, Ponstingl H, Dias J, Gerasimou P, Melanthiou K, Prokopiou C et al.

    Blood advances 2017;1;14;968-971

    PUBMED: 29296738; PMC: 5737599; DOI: 10.1182/bloodadvances.2017007047

  • Transmission of the gut microbiota: spreading of health.

    Browne HP, Neville BA, Forster SC and Lawley TD

    Nature reviews. Microbiology 2017;15;9;531-543

    PUBMED: 28603278; PMC: 5837012; DOI: 10.1038/nrmicro.2017.50

  • Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.

    Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J et al.

    PLoS biology 2017;15;6;e2001855

    PUBMED: 28604782; PMC: 5467800; DOI: 10.1371/journal.pbio.2001855

  • Permeability-driven selection in a semi-empirical protocell model: the roots of prebiotic systems evolution.

    Piedrafita G, Monnard PA, Mavelli F and Ruiz-Mirazo K

    Scientific reports 2017;7;1;3141

    PUBMED: 28600550; PMC: 5466667; DOI: 10.1038/s41598-017-02799-6

  • The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana.

    Zhabagin M, Balanovska E, Sabitov Z, Kuznetsova M, Agdzhoyan A, Balaganskaya O, Chukhryaeva M, Markina N, Romanov A, Skhalyakho R et al.

    Scientific reports 2017;7;1;3085

    PUBMED: 28596519; PMC: 5465200; DOI: 10.1038/s41598-017-03176-z

  • Pneumococcal capsule synthesis locus cps as evolutionary hotspot with potential to generate novel serotypes by recombination.

    Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X and Fraser C

    Molecular biology and evolution 2017

    PUBMED: 28595308; DOI: 10.1093/molbev/msx173

  • Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis.

    Song L, Jenner M, Masschelein J, Jones C, Bull MJ, Harris SR, Hartkoorn RC, Vocat A, Romero-Canelon I, Coupland P et al.

    Journal of the American Chemical Society 2017;139;23;7974-7981

    PUBMED: 28528545; DOI: 10.1021/jacs.7b03382

  • Genome watch: Klebsiella pneumoniae: when a colonizer turns bad.

    Dorman MJ and Short FL

    Nature reviews. Microbiology 2017;15;7;384

    PUBMED: 28579608; DOI: 10.1038/nrmicro.2017.64

  • The Profile and Dynamics of RNA Modifications in Animals.

    van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA and Balasubramanian S

    Chembiochem : a European journal of chemical biology 2017;18;11;979-984

    PUBMED: 28449301; PMC: 5784800; DOI: 10.1002/cbic.201700093

  • Adipocyte Accumulation in the Bone Marrow during Obesity and Aging Impairs Stem Cell-Based Hematopoietic and Bone Regeneration.

    Ambrosi TH, Scialdone A, Graja A, Gohlke S, Jank AM, Bocian C, Woelk L, Fan H, Logan DW, Schürmann A et al.

    Cell stem cell 2017;20;6;771-784.e6

    PUBMED: 28330582; PMC: 5459794; DOI: 10.1016/j.stem.2017.02.009

  • Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data.

    Epi4K Consortium, EuroEPINOMICS-RES Consortium and Epilepsy Phenome Genome Project

    European journal of human genetics : EJHG 2017;25;7;894-899

    PUBMED: 28513609; PMC: 5520073; DOI: 10.1038/ejhg.2017.61

  • Applications of CRISPR genome editing technology in drug target identification and validation.

    Lu Q, Livi GP, Modha S, Yusa K, Macarrón R and Dow DJ

    Expert opinion on drug discovery 2017;12;6;541-552

    PUBMED: 28388235; DOI: 10.1080/17460441.2017.1317244

  • Brucella neotomae Infection in Humans, Costa Rica.

    Suárez-Esquivel M, Ruiz-Villalobos N, Jiménez-Rojas C, Barquero-Calvo E, Chacón-Díaz C, Víquez-Ruiz E, Rojas-Campos N, Baker KS, Oviedo-Sánchez G, Amuy E et al.

    Emerging infectious diseases 2017;23;6;997-1000

    PUBMED: 28518028; PMC: 5443450; DOI: 10.3201/eid2306.162018

  • CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology.

    Cankorur-Cetinkaya A, Dias JML, Kludas J, Slater NKH, Rousu J, Oliver SG and Dikicioglu D

    Microbiology (Reading, England) 2017;163;6;829-839

    PUBMED: 28635591; PMC: 5817226; DOI: 10.1099/mic.0.000477

  • Chromatin determinants impart camptothecin sensitivity.

    Puddu F, Salguero I, Herzog M, Geisler NJ, Costanzo V and Jackson SP

    EMBO reports 2017;18;6;1000-1012

    PUBMED: 28389464; PMC: 5452016; DOI: 10.15252/embr.201643560

  • Detection of a microbial metabolite by STING regulates inflammasome activation in response to Chlamydia trachomatis infection.

    Webster SJ, Brode S, Ellis L, Fitzmaurice TJ, Elder MJ, Gekara NO, Tourlomousis P, Bryant C, Clare S, Chee R et al.

    PLoS pathogens 2017;13;6;e1006383

    PUBMED: 28570638; PMC: 5453623; DOI: 10.1371/journal.ppat.1006383

  • Evidence for large-scale gene-by-smoking interaction effects on pulmonary function.

    Aschard H, Tobin MD, Hancock DB, Skurnik D, Sood A, James A, Vernon Smith A, Manichaikul AW, Campbell A, Prins BP et al.

    International journal of epidemiology 2017;46;3;894-904

    PUBMED: 28082375; PMC: 5837518; DOI: 10.1093/ije/dyw318

  • Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

    Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H, Sulem P, Ruth KS, Whalen S, Sarkar AK, Albrecht E et al.

    Nature genetics 2017;49;6;834-841

    PUBMED: 28436984; PMC: 5841952; DOI: 10.1038/ng.3841

  • Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.

    Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE et al.

    The Journal of antimicrobial chemotherapy 2017;72;6;1602-1609

    PUBMED: 28333330; PMC: 5437524; DOI: 10.1093/jac/dkx058

  • Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing.

    Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S, Li S, Paulson JN, Almeida M, Domman D, Thomson NR et al.

    PLoS neglected tropical diseases 2017;11;6;e0005671

    PUBMED: 28622368; PMC: 5489214; DOI: 10.1371/journal.pntd.0005671

  • Most Alternative Isoforms Are Not Functionally Important.

    Tress ML, Abascal F and Valencia A

    Trends in biochemical sciences 2017;42;6;408-410

    PUBMED: 28483377; PMC: 6449685; DOI: 10.1016/j.tibs.2017.04.002

  • Mutational Signatures in Breast Cancer: The Problem at the DNA Level.

    Nik-Zainal S and Morganella S

    Clinical cancer research : an official journal of the American Association for Cancer Research 2017;23;11;2617-2629

    PUBMED: 28572256; PMC: 5458139; DOI: 10.1158/1078-0432.CCR-16-2810

  • No genetic association between attention-deficit/hyperactivity disorder (ADHD) and Parkinson's disease in nine ADHD candidate SNPs.

    Geissler JM, International Parkinson Disease Genomics Consortium members, Romanos M, Gerlach M, Berg D and Schulte C

    Attention deficit and hyperactivity disorders 2017;9;2;121-127

    PUBMED: 28176268; PMC: 6233883; DOI: 10.1007/s12402-017-0219-8

  • Normalizing single-cell RNA sequencing data: challenges and opportunities.

    Vallejos CA, Risso D, Scialdone A, Dudoit S and Marioni JC

    Nature methods 2017;14;6;565-571

    PUBMED: 28504683; PMC: 5549838; DOI: 10.1038/nmeth.4292

  • Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution.

    Duffy CW, Ba H, Assefa S, Ahouidi AD, Deh YB, Tandia A, Kirsebom FCM, Kwiatkowski DP and Conway DJ

    Molecular ecology 2017;26;11;2880-2894

    PUBMED: 28214367; PMC: 5485074; DOI: 10.1111/mec.14066

  • Tracking the Evolution of Non-Small-Cell Lung Cancer.

    Jamal-Hanjani M, Wilson GA, McGranahan N, Birkbak NJ, Watkins TBK, Veeriah S, Shafi S, Johnson DH, Mitter R, Rosenthal R et al.

    The New England journal of medicine 2017;376;22;2109-2121

    PUBMED: 28445112; DOI: 10.1056/NEJMoa1616288

  • Translational Genomics: Practical Applications of the Genomic Revolution in Breast Cancer.

    Yates LR and Desmedt C

    Clinical cancer research : an official journal of the American Association for Cancer Research 2017;23;11;2630-2639

    PUBMED: 28572257; DOI: 10.1158/1078-0432.CCR-16-2548

  • Wounding induces dedifferentiation of epidermal Gata6+ cells and acquisition of stem cell properties.

    Donati G, Rognoni E, Hiratsuka T, Liakath-Ali K, Hoste E, Kar G, Kayikci M, Russell R, Kretzschmar K, Mulder KW et al.

    Nature cell biology 2017;19;6;603-613

    PUBMED: 28504705; DOI: 10.1038/ncb3532

  • Defining the ABC of gene essentiality in streptococci.

    Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh JA, Maskell DJ and Waller AS

    BMC genomics 2017;18;1;426

    PUBMED: 28569133; PMC: 5452409; DOI: 10.1186/s12864-017-3794-3

  • Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes.

    Bassano I, Ong SH, Lawless N, Whitehead T, Fife M and Kellam P

    BMC genomics 2017;18;1;419

    PUBMED: 28558694; PMC: 5450142; DOI: 10.1186/s12864-017-3801-8

  • Genome annotation for clinical genomic diagnostics: strengths and weaknesses.

    Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A and Harrow J

    Genome medicine 2017;9;1;49

    PUBMED: 28558813; PMC: 5448149; DOI: 10.1186/s13073-017-0441-1

  • Loss of the homologous recombination gene rad51 leads to Fanconi anemia-like symptoms in zebrafish.

    Botthof JG, Bielczyk-Maczyńska E, Ferreira L and Cvejic A

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;22;E4452-E4461

    PUBMED: 28512217; PMC: 5465903; DOI: 10.1073/pnas.1620631114

  • Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits.

    Southam L, Gilly A, Süveges D, Farmaki AE, Schwartzentruber J, Tachmazidou I, Matchan A, Rayner NW, Tsafantakis E, Karaleftheri M et al.

    Nature communications 2017;8;15606

    PUBMED: 28548082; PMC: 5458552; DOI: 10.1038/ncomms15606

  • An evaluation of purified Salmonella Typhi protein antigens for the serological diagnosis of acute typhoid fever.

    Tran Vu Thieu N, Trinh Van T, Tran Tuan A, Klemm EJ, Nguyen Ngoc Minh C, Voong Vinh P, Pham Thanh D, Ho Ngoc Dan T, Pham Duc T, Langat P et al.

    The Journal of infection 2017;75;2;104-114

    PUBMED: 28551371; PMC: 5522525; DOI: 10.1016/j.jinf.2017.05.007

  • Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

    Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y et al.

    American journal of human genetics 2017;100;6;865-884

    PUBMED: 28552196; PMC: 5473732; DOI: 10.1016/j.ajhg.2017.04.014

  • Integration of Tmc1/2 into the mechanotransduction complex in zebrafish hair cells is regulated by Transmembrane O-methyltransferase (Tomt).

    Erickson T, Morgan CP, Olt J, Hardy K, Busch-Nentwich EM, Maeda R, Clemens-Grisham R, Krey JF, Nechiporuk AV, Barr-Gillespie PG et al.

    eLife 2017;6

    PUBMED: 28534737; DOI: 10.7554/eLife.28474

  • Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression.

    Dumetz F, Imamura H, Sanders M, Seblova V, Myskova J, Pescher P, Vanaerschot M, Meehan CJ, Cuypers B, De Muylder G et al.

    mBio 2017;8;3

    PUBMED: 28536289; PMC: 5442457; DOI: 10.1128/mBio.00599-17

  • Next-generation sequencing of a family with a high penetrance of monoclonal gammopathies for the identification of candidate risk alleles.

    Bolli N, Barcella M, Salvi E, D'Avila F, Vendramin A, De Philippis C, Munshi NC, Avet-Loiseau H, Campbell PJ, Mussetti A et al.

    Cancer 2017;123;19;3701-3708

    PUBMED: 28542843; DOI: 10.1002/cncr.30777

  • Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment.

    Kirschner K, Chandra T, Kiselev V, Flores-Santa Cruz D, Macaulay IC, Park HJ, Li J, Kent DG, Kumar R, Pask DC et al.

    Cell reports 2017;19;8;1503-1511

    PUBMED: 28538171; PMC: 5457484; DOI: 10.1016/j.celrep.2017.04.074

  • A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming.

    Vasiliauskaitė L, Vitsios D, Berrens RV, Carrieri C, Reik W, Enright AJ and O'Carroll D

    Nature structural & molecular biology 2017

    PUBMED: 28530707; DOI: 10.1038/nsmb.3413

  • Enhancing the genome editing toolbox: genome wide CRISPR arrayed libraries.

    Metzakopian E, Strong A, Iyer V, Hodgkins A, Tzelepis K, Antunes L, Friedrich MJ, Kang Q, Davidson T, Lamberth J et al.

    Scientific reports 2017;7;1;2244

    PUBMED: 28533524; PMC: 5440395; DOI: 10.1038/s41598-017-01766-5

  • Resistance to malaria through structural variation of red blood cell invasion receptors.

    Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F et al.

    Science (New York, N.Y.) 2017;356;6343

    PUBMED: 28522690; PMC: 5575826; DOI: 10.1126/science.aam6393

  • Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay.

    Weiss K, Wigby K, Fannemel M, Henderson LB, Beck N, Ghali N, Study DDD, Anderlid BM, Lundin J, Hamosh A et al.

    European journal of human genetics : EJHG 2017;25;8;946-951

    PUBMED: 28513610; PMC: 5567153; DOI: 10.1038/ejhg.2017.86

  • Natural variation of Epstein-Barr virus genes, proteins and pri-miRNA (revised).

    Correia S, Palser A, Elgueta Karstegl C, Middeldorp JM, Ramayanti O, Cohen JI, Hildesheim A, Fellner MD, Wiels J, White RE et al.

    Journal of virology 2017

    PUBMED: 28515295; DOI: 10.1128/JVI.00375-17

  • A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells.

    Ersing I, Nobre L, Wang LW, Soday L, Ma Y, Paulo JA, Narita Y, Ashbaugh CW, Jiang C, Grayson NE et al.

    Cell reports 2017;19;7;1479-1493

    PUBMED: 28514666; PMC: 5446956; DOI: 10.1016/j.celrep.2017.04.062

  • MRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore.

    Chow A, Lim VW, Khan A, Pettigrew K, Lye DCB, Kanagasabai K, Phua K, Krishnan P, Ang B, Marimuthu K et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;64;suppl_2;S76-S81

    PUBMED: 28475785; PMC: 5849126; DOI: 10.1093/cid/cix072

  • Artemisinin resistance without pfkelch13 mutations in Plasmodium falciparum isolates from Cambodia.

    Mukherjee A, Bopp S, Magistrado P, Wong W, Daniels R, Demas A, Schaffner S, Amaratunga C, Lim P, Dhorda M et al.

    Malaria journal 2017;16;1;195

    PUBMED: 28494763; PMC: 5427620; DOI: 10.1186/s12936-017-1845-5

  • Reshaping the tree of life.

    Heinz E and Domman D

    Nature reviews. Microbiology 2017;15;6;322

    PUBMED: 28496163; DOI: 10.1038/nrmicro.2017.51

  • Common genetic variation drives molecular heterogeneity in human iPSCs.

    Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ et al.

    Nature 2017;546;7658;370-375

    PUBMED: 28489815; PMC: 5524171; DOI: 10.1038/nature22403

  • Multiple short windows of calcium-dependent protein kinase 4 activity coordinate distinct cell cycle events during Plasmodium gametogenesis.

    Fang H, Klages N, Baechler B, Hillner E, Yu L, Pardo M, Choudhary J and Brochet M

    eLife 2017;6

    PUBMED: 28481199; PMC: 5457135; DOI: 10.7554/eLife.26524

  • Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

    Pärnamaa T and Parts L

    G3 (Bethesda, Md.) 2017;7;5;1385-1392

    PUBMED: 28391243; PMC: 5427497; DOI: 10.1534/g3.116.033654

  • European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

    Seth-Smith HMB, Busó LS, Livingstone M, Sait M, Harris SR, Aitchison KD, Vretou E, Siarkou VI, Laroucau K, Sachse K et al.

    BMC genomics 2017;18;1;344

    PUBMED: 28472926; PMC: 5415952; DOI: 10.1186/s12864-017-3657-y

  • International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases.

    Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT et al.

    American journal of human genetics 2017;100;5;695-705

    PUBMED: 28475856; PMC: 5420351; DOI: 10.1016/j.ajhg.2017.04.003

  • Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil.

    Everall I, Nogueira CL, Bryant JM, Sánchez-Busó L, Chimara E, Duarte RDS, Ramos JP, Lima KVB, Lopes ML, Palaci M et al.

    Microbial genomics 2017;3;5;e000111

    PUBMED: 28884021; PMC: 5562415; DOI: 10.1099/mgen.0.000111

  • The Expanding World of Human Leishmaniasis.

    Cotton JA

    Trends in parasitology 2017;33;5;341-344

    PUBMED: 28319012; DOI: 10.1016/j.pt.2017.02.002

  • A Road Map for Precision Cancer Medicine Using Personalized Models.

    Picco G and Garnett MJ

    Cancer discovery 2017;7;5;456-458

    PUBMED: 28461408; DOI: 10.1158/2159-8290.CD-17-0268

  • The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study.

    Imwong M, Suwannasin K, Kunasol C, Sutawong K, Mayxay M, Rekol H, Smithuis FM, Hlaing TM, Tun KM, van der Pluijm RW et al.

    The Lancet. Infectious diseases 2017;17;5;491-497

    PUBMED: 28161569; PMC: 5406483; DOI: 10.1016/S1473-3099(17)30048-8

  • A staging system for correct phenotype interpretation of mouse embryos harvested on embryonic day 14 (E14.5).

    Geyer SH, Reissig L, Rose J, Wilson R, Prin F, Szumska D, Ramirez-Solis R, Tudor C, White J, Mohun TJ and Weninger WJ

    Journal of anatomy 2017;230;5;710-719

    PUBMED: 28185240; PMC: 5382591; DOI: 10.1111/joa.12590

  • Annotation of plasmid genes.

    Thomas CM, Thomson NR, Cerdeño-Tárraga AM, Brown CJ, Top EM and Frost LS

    Plasmid 2017;91;61-67

    PUBMED: 28365184; DOI: 10.1016/j.plasmid.2017.03.006

  • Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases: A Mendelian Randomization Study.

    Telomeres Mendelian Randomization Collaboration, Haycock PC, Burgess S, Nounu A, Zheng J, Okoli GN, Bowden J, Wade KH, Timpson NJ, Evans DM et al.

    JAMA oncology 2017;3;5;636-651

    PUBMED: 28241208; PMC: 5638008; DOI: 10.1001/jamaoncol.2016.5945

  • Characterisation of the genomic landscape of CRLF2-rearranged acute lymphoblastic leukemia.

    Russell LJ, Jones L, Enshaei A, Tonin S, Ryan SL, Eswaran J, Nakjang S, Papaemmanuil E, Tubio JM, Fielding AK et al.

    Genes, chromosomes & cancer 2017;56;5;363-372

    PUBMED: 28033648; PMC: 5396319; DOI: 10.1002/gcc.22439

  • Chromosomal breaks at FRA18C: association with reduced DOK6 expression, altered oncogenic signaling and increased gastric cancer survival.

    Leong SH, Lwin KM, Lee SS, Ng WH, Ng KM, Tan SY, Ng BL, Carter NP, Tang C and Lian Kon O

    NPJ precision oncology 2017;1;1;9

    PUBMED: 29872697; PMC: 5859466; DOI: 10.1038/s41698-017-0012-3

  • Evolve and survive.

    Pance A

    Nature reviews. Microbiology 2017;15;5;258

    PUBMED: 28344347; DOI: 10.1038/nrmicro.2017.31

  • Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications.

    Ombrello MJ, Arthur VL, Remmers EF, Hinks A, Tachmazidou I, Grom AA, Foell D, Martini A, Gattorno M, Özen S et al.

    Annals of the rheumatic diseases 2017;76;5;906-913

    PUBMED: 27927641; PMC: 5530341; DOI: 10.1136/annrheumdis-2016-210324

  • Genome graphs and the evolution of genome inference.

    Paten B, Novak AM, Eizenga JM and Garrison E

    Genome research 2017;27;5;665-676

    PUBMED: 28360232; PMC: 5411762; DOI: 10.1101/gr.214155.116

  • Genomic analysis and clinical management of adolescent cutaneous melanoma.

    Rabbie R, Rashid M, Arance AM, Sánchez M, Tell-Marti G, Potrony M, Conill C, van Doorn R, Dentro S, Gruis NA et al.

    Pigment cell & melanoma research 2017;30;3;307-316

    PUBMED: 28097802; PMC: 5435926; DOI: 10.1111/pcmr.12574

  • Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing.

    Lam BYH, Cimino I, Polex-Wolf J, Nicole Kohnke S, Rimmington D, Iyemere V, Heeley N, Cossetti C, Schulte R, Saraiva LR et al.

    Molecular metabolism 2017;6;5;383-392

    PUBMED: 28462073; PMC: 5404100; DOI: 10.1016/j.molmet.2017.02.007

  • Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer.

    Phelan CM, Kuchenbaecker KB, Tyrer JP, Kar SP, Lawrenson K, Winham SJ, Dennis J, Pirie A, Riggan MJ, Chornokur G et al.

    Nature genetics 2017;49;5;680-691

    PUBMED: 28346442; PMC: 5612337; DOI: 10.1038/ng.3826

  • MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.

    Protasio AV, van Dongen S, Collins J, Quintais L, Ribeiro DM, Sessler F, Hunt M, Rinaldi G, Collins JJ, Enright AJ and Berriman M

    PLoS neglected tropical diseases 2017;11;5;e0005559

    PUBMED: 28542189; PMC: 5459504; DOI: 10.1371/journal.pntd.0005559

  • Molecular diagnoses of century-old childhood tumours.

    Virasami A, Farndon SJ, McDermott U, Sebire N and Behjati S

    The Lancet. Oncology 2017;18;5;e237

    PUBMED: 28495283; DOI: 10.1016/S1470-2045(17)30226-7

  • Past successes and future opportunities for the genetics of the human Y chromosome.

    Xue Y and Tyler-Smith C

    Human genetics 2017;136;5;481-483

    PUBMED: 28456835; PMC: 5418311; DOI: 10.1007/s00439-017-1806-7

  • Recurrent Rearrangements of Human Amylase Genes Create Multiple Independent CNV Series.

    Shwan NAA, Louzada S, Yang F and Armour JAL

    Human mutation 2017;38;5;532-539

    PUBMED: 28101908; DOI: 10.1002/humu.23182

  • Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease.

    David S, Afshar B, Mentasti M, Ginevra C, Podglajen I, Harris SR, Chalker VJ, Jarraud S, Harrison TG and Parkhill J

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;64;9;1251-1259

    PUBMED: 28203790; PMC: 5399934; DOI: 10.1093/cid/cix153

  • Sibling recurrence of total anomalous pulmonary venous drainage.

    McDermott JH, Study DD and Clayton-Smith J

    European journal of medical genetics 2017;60;5;265-267

    PUBMED: 28286254; DOI: 10.1016/j.ejmg.2017.03.003

  • Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese.

    Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C and Bertranpetit J

    Human genetics 2017;136;5;499-510

    PUBMED: 28444560; DOI: 10.1007/s00439-017-1800-0

  • Asymptomatic Plasmodium vivax infections induce robust IgG responses to multiple blood-stage proteins in a low-transmission region of western Thailand.

    Longley RJ, França CT, White MT, Kumpitak C, Sa-Angchai P, Gruszczyk J, Hostetler JB, Yadava A, King CL, Fairhurst RM et al.

    Malaria journal 2017;16;1;178

    PUBMED: 28454546; PMC: 5410030; DOI: 10.1186/s12936-017-1826-8

  • Melanoma: a global perspective.

    Ossio R, Roldán-Marín R, Martínez-Said H, Adams DJ and Robles-Espinoza CD

    Nature reviews. Cancer 2017;17;7;393-394

    PUBMED: 28450704; DOI: 10.1038/nrc.2017.43

  • The impact of rare and low-frequency genetic variants in common disease.

    Bomba L, Walter K and Soranzo N

    Genome biology 2017;18;1;77

    PUBMED: 28449691; PMC: 5408830; DOI: 10.1186/s13059-017-1212-4

  • Antimalarial efficacy of MMV390048, an inhibitor of Plasmodium phosphatidylinositol 4-kinase.

    Paquet T, Le Manach C, Cabrera DG, Younis Y, Henrich PP, Abraham TS, Lee MCS, Basak R, Ghidelli-Disse S, Lafuente-Monasterio MJ et al.

    Science translational medicine 2017;9;387

    PUBMED: 28446690; PMC: 5731459; DOI: 10.1126/scitranslmed.aad9735

  • Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits.

    Justice AE, Winkler TW, Feitosa MF, Graff M, Fisher VA, Young K, Barata L, Deng X, Czajkowski J, Hadley D et al.

    Nature communications 2017;8;14977

    PUBMED: 28443625; PMC: 5414044; DOI: 10.1038/ncomms14977

  • Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

    Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R et al.

    Nature 2017;545;7655;446-451

    PUBMED: 28445469; PMC: 5812436; DOI: 10.1038/nature22364

  • ANGPTL3 Deficiency and Protection Against Coronary Artery Disease.

    Stitziel NO, Khera AV, Wang X, Bierhals AJ, Vourakis AC, Sperry AE, Natarajan P, Klarin D, Emdin CA, Zekavat SM et al.

    Journal of the American College of Cardiology 2017;69;16;2054-2063

    PUBMED: 28385496; PMC: 5404817; DOI: 10.1016/j.jacc.2017.02.030

  • Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.

    Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W, Parry-Smith D, Goulding D, Pickard D, Roumeliotis T, Choudhary J et al.

    Nature communications 2017;8;15013

    PUBMED: 28440293; PMC: 5414054; DOI: 10.1038/ncomms15013

  • Insecticide-induced leg loss does not eliminate biting and reproduction in Anopheles gambiae mosquitoes.

    Isaacs AT, Lynd A and Donnelly MJ

    Scientific reports 2017;7;46674

    PUBMED: 28440300; PMC: 5404223; DOI: 10.1038/srep46674

  • Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated.

    Ibarra-Soria X, Nakahara TS, Lilue J, Jiang Y, Trimmer C, Souza MA, Netto PH, Ikegami K, Murphy NR, Kusma M et al.

    eLife 2017;6

    PUBMED: 28438259; PMC: 5404925; DOI: 10.7554/eLife.21476

  • Virus genomes reveal factors that spread and sustained the Ebola epidemic.

    Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D et al.

    Nature 2017;544;7650;309-315

    PUBMED: 28405027; PMC: 5712493; DOI: 10.1038/nature22040

  • Human biallelic MFN2 mutations induce mitochondrial dysfunction, upper body adipose hyperplasia, and suppression of leptin expression.

    Rocha N, Bulger DA, Frontini A, Titheradge H, Gribsholt SB, Knox R, Page M, Harris J, Payne F, Adams C et al.

    eLife 2017;6

    PUBMED: 28414270; PMC: 5422073; DOI: 10.7554/eLife.23813

  • Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity.

    Lindo J, Achilli A, Perego UA, Archer D, Valdiosera C, Petzelt B, Mitchell J, Worl R, Dixon EJ, Fifield TE et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;16;4093-4098

    PUBMED: 28377518; PMC: 5402414; DOI: 10.1073/pnas.1620410114

  • Massive introgression drives species radiation at the range limit of Anopheles gambiae.

    Vicente JL, Clarkson CS, Caputo B, Gomes B, Pombi M, Sousa CA, Antao T, Dinis J, Bottà G, Mancini E et al.

    Scientific reports 2017;7;46451

    PUBMED: 28417969; PMC: 5394460; DOI: 10.1038/srep46451

  • Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

    Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC et al.

    Nature genetics 2017;49;6;913-924

    PUBMED: 28416820; PMC: 5446901; DOI: 10.1038/ng.3847

  • Neutrophil-mediated IL-6 receptor trans-signaling and the risk of chronic obstructive pulmonary disease and asthma.

    Farahi N, Paige E, Balla J, Prudence E, Ferreira RC, Southwood M, Appleby SL, Bakke P, Gulsvik A, Litonjua AA et al.

    Human molecular genetics 2017;26;8;1584-1596

    PUBMED: 28334838; PMC: 5393150; DOI: 10.1093/hmg/ddx053

  • Concern regarding the alleged spread of hypervirulent lymphogranuloma venereum Chlamydia trachomatis strain in Europe.

    Seth-Smith HM, Galán JC, Goldenberger D, Lewis DA, Peuchant O, Bébéar C, de Barbeyrac B, Bénard A, Carter I, Kok J et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017;22;15

    PUBMED: 28449734; PMC: 5476980; DOI: 10.2807/1560-7917.ES.2017.22.15.30511

  • Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity.

    Saleheen D, Natarajan P, Armean IM, Zhao W, Rasheed A, Khetarpal SA, Won HH, Karczewski KJ, O'Donnell-Luria AH, Samocha KE et al.

    Nature 2017;544;7649;235-239

    PUBMED: 28406212; PMC: 5600291; DOI: 10.1038/nature22034

  • DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

    Angermueller C, Lee HJ, Reik W and Stegle O

    Genome biology 2017;18;1;67

    PUBMED: 28395661; PMC: 5387360; DOI: 10.1186/s13059-017-1189-z

  • Detection of Atherosclerotic Inflammation by 68Ga-DOTATATE PET Compared to [18F]FDG PET Imaging.

    Tarkin JM, Joshi FR, Evans NR, Chowdhury MM, Figg NL, Shah AV, Starks LT, Martin-Garrido A, Manavaki R, Yu E et al.

    Journal of the American College of Cardiology 2017;69;14;1774-1791

    PUBMED: 28385306; PMC: 5381358; DOI: 10.1016/j.jacc.2017.01.060

  • Multi-tissue DNA methylation age predictor in mouse.

    Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O and Reik W

    Genome biology 2017;18;1;68

    PUBMED: 28399939; PMC: 5389178; DOI: 10.1186/s13059-017-1203-5

  • The role of sex and body weight on the metabolic effects of high-fat diet in C57BL/6N mice.

    Ingvorsen C, Karp NA and Lelliott CJ

    Nutrition & diabetes 2017;7;4;e261

    PUBMED: 28394359; PMC: 5436097; DOI: 10.1038/nutd.2017.6

  • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

    Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D et al.

    Genome research 2017;27;5;849-864

    PUBMED: 28396521; PMC: 5411779; DOI: 10.1101/gr.213611.116

  • Challenges for achieving safe and effective radical cure of Plasmodium vivax: a round table discussion of the APMEN Vivax Working Group.

    Thriemer K, Ley B, Bobogare A, Dysoley L, Alam MS, Pasaribu AP, Sattabongkot J, Jambert E, Domingo GJ, Commons R et al.

    Malaria journal 2017;16;1;141

    PUBMED: 28381261; PMC: 5382417; DOI: 10.1186/s12936-017-1784-1

  • Evaluation of applicability of DNA microarray-based characterization of bovine Shiga toxin-producing Escherichia coli isolates using whole genome sequence analysis.

    Barth SA, Menge C, Eichhorn I, Semmler T, Pickard D and Geue L

    Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2017;29;5;721-724

    PUBMED: 28381114; DOI: 10.1177/1040638717700689

  • Human Y chromosome copy number variation in the next generation sequencing era and beyond.

    Massaia A and Xue Y

    Human genetics 2017

    PUBMED: 28378101; DOI: 10.1007/s00439-017-1788-5

  • The antiviral restriction factor IFN-induced transmembrane protein 3 prevents cytokine-driven CMV pathogenesis.

    Stacey MA, Clare S, Clement M, Marsden M, Abdul-Karim J, Kane L, Harcourt K, Brandt C, Fielding CA, Smith SE et al.

    The Journal of clinical investigation 2017;127;4;1463-1474

    PUBMED: 28240600; PMC: 5373880; DOI: 10.1172/JCI84889

  • Artificial and natural RNA interactions between bacteria and C. elegans.

    Braukmann F, Jordan D and Miska E

    RNA biology 2017;14;4;415-420

    PUBMED: 28332918; PMC: 5411122; DOI: 10.1080/15476286.2017.1297912

  • A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements.

    Ramírez-Vargas G, Quesada-Gómez C, Acuña-Amador L, López-Ureña D, Murillo T, Del Mar Gamboa-Coronado M, Chaves-Olarte E, Thomson N, Rodríguez-Cavallini E and Rodríguez C

    Antimicrobial agents and chemotherapy 2017;61;4

    PUBMED: 28137804; PMC: 5365686; DOI: 10.1128/AAC.02054-16

  • Benzalkonium tolerance genes and outcome in Listeria monocytogenes meningitis.

    Kremer PH, Lees JA, Koopmans MM, Ferwerda B, Arends AW, Feller MM, Schipper K, Valls Seron M, van der Ende A, Brouwer MC et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017;23;4;265.e1-265.e7

    PUBMED: 27998823; PMC: 5392494; DOI: 10.1016/j.cmi.2016.12.008

  • Complex chromosomal rearrangements by single catastrophic pathogenesis in NUT midline carcinoma.

    Lee JK, Louzada S, An Y, Kim SY, Kim S, Youk J, Park S, Koo SH, Keam B, Jeon YK et al.

    Annals of oncology : official journal of the European Society for Medical Oncology 2017;28;4;890-897

    PUBMED: 28203693; PMC: 5378225; DOI: 10.1093/annonc/mdw686

  • Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.

    Raven KE, Gouliouris T, Brodrick H, Coll F, Brown NM, Reynolds R, Reuter S, Török ME, Parkhill J and Peacock SJ

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;64;7;886-893

    PUBMED: 28362945; PMC: 5439346; DOI: 10.1093/cid/ciw872

  • Directed differentiation of human induced pluripotent stem cells into functional cholangiocyte-like cells.

    Sampaziotis F, de Brito MC, Geti I, Bertero A, Hannan NR and Vallier L

    Nature protocols 2017;12;4;814-827

    PUBMED: 28333915; PMC: 5467722; DOI: 10.1038/nprot.2017.011

  • DNA methylation homeostasis in human and mouse development.

    Iurlaro M, von Meyenn F and Reik W

    Current opinion in genetics & development 2017;43;101-109

    PUBMED: 28260631; DOI: 10.1016/j.gde.2017.02.003

  • Efficient gene targeting in mouse zygotes mediated by CRISPR/Cas9-protein.

    Jung CJ, Zhang J, Trenchard E, Lloyd KC, West DB, Rosen B and de Jong PJ

    Transgenic research 2017;26;2;263-277

    PUBMED: 27905063; PMC: 5350237; DOI: 10.1007/s11248-016-9998-5

  • Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia.

    Balanovsky O, Chukhryaeva M, Zaporozhchenko V, Urasin V, Zhabagin M, Hovhannisyan A, Agdzhoyan A, Dibirova K, Kuznetsova M, Koshel S et al.

    Human genetics 2017;136;4;437-450

    PUBMED: 28281087; DOI: 10.1007/s00439-017-1770-2

  • Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population.

    Carr DF, Bourgeois S, Chaponda M, Takeshita LY, Morris AP, Castro EM, Alfirevic A, Jones AR, Rigden DJ, Haldenby S et al.

    The Journal of antimicrobial chemotherapy 2017;72;4;1152-1162

    PUBMED: 28062682; PMC: 5400091; DOI: 10.1093/jac/dkw545

  • Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults.

    Graff M, Scott RA, Justice AE, Young KL, Feitosa MF, Barata L, Winkler TW, Chu AY, Mahajan A, Hadley D et al.

    PLoS genetics 2017;13;4;e1006528

    PUBMED: 28448500; PMC: 5407576; DOI: 10.1371/journal.pgen.1006528

  • K13 Propeller Mutations in Plasmodium falciparum Populations in Regions of Malaria Endemicity in Vietnam from 2009 to 2016.

    Thuy-Nhien N, Tuyen NK, Tong NT, Vy NT, Thanh NV, Van HT, Huong-Thu P, Quang HH, Boni MF, Dolecek C et al.

    Antimicrobial agents and chemotherapy 2017;61;4

    PUBMED: 28137815; PMC: 5365681; DOI: 10.1128/AAC.01578-16

  • Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling.

    Pardo M, Bode D, Yu L and Choudhary JS

    Journal of visualized experiments : JoVE 2017;122

    PUBMED: 28447986; PMC: 5564443; DOI: 10.3791/55498

  • Semantic prioritization of novel causative genomic variants.

    Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN and Hoehndorf R

    PLoS computational biology 2017;13;4;e1005500

    PUBMED: 28414800; PMC: 5411092; DOI: 10.1371/journal.pcbi.1005500

  • Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays.

    Ajileye A, Alvarez N, Merker M, Walker TM, Akter S, Brown K, Moradigaravand D, Schön T, Andres S, Schleusener V et al.

    Antimicrobial agents and chemotherapy 2017;61;4

    PUBMED: 28137812; PMC: 5365657; DOI: 10.1128/AAC.02169-16

  • Sphingolipids and glycerophospholipids - The "ying and yang" of lipotoxicity in metabolic diseases.

    Rodriguez-Cuenca S, Pellegrinelli V, Campbell M, Oresic M and Vidal-Puig A

    Progress in lipid research 2017;66;14-29

    PUBMED: 28104532; DOI: 10.1016/j.plipres.2017.01.002

  • Standardized experiments in mutant mice reveal behavioural similarity on 129S5 and C57BL/6J backgrounds.

    van de Lagemaat LN, Stanford LE, Pettit CM, Strathdee DJ, Strathdee KE, Elsegood KA, Fricker DG, Croning MD, Komiyama NH and Grant SG

    Genes, brain, and behavior 2017;16;4;409-418

    PUBMED: 27886459; DOI: 10.1111/gbb.12364

  • Tracking the embryonic stem cell transition from ground state pluripotency.

    Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS et al.

    Development (Cambridge, England) 2017;144;7;1221-1234

    PUBMED: 28174249; PMC: 5399622; DOI: 10.1242/dev.142711

  • Understanding the Genomic Structure of Copy-Number Variation of the Low-Affinity Fcγ Receptor Region Allows Confirmation of the Association of FCGR3B Deletion with Rheumatoid Arthritis.

    Rahbari R, Zuccherato LW, Tischler G, Chihota B, Ozturk H, Saleem S, Tarazona-Santos E, Machado LR and Hollox EJ

    Human mutation 2017;38;4;390-399

    PUBMED: 27995740; PMC: 5363352; DOI: 10.1002/humu.23159

  • Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore.

    Blackwell GA, Holt KE, Bentley SD, Hsu LY and Hall RM

    The Journal of antimicrobial chemotherapy 2017;72;4;1031-1039

    PUBMED: 28073968; PMC: 5400096; DOI: 10.1093/jac/dkw542

  • Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom.

    Chheda H, Palta P, Pirinen M, McCarthy S, Walter K, Koskinen S, Salomaa V, Daly M, Durbin R, Palotie A et al.

    European journal of human genetics : EJHG 2017;25;4;477-484

    PUBMED: 28145424; PMC: 5346294; DOI: 10.1038/ejhg.2016.205

  • Your DNA, Your Say.

    Middleton A

    The New bioethics : a multidisciplinary journal of biotechnology and the body 2017;23;1;74-80

    PUBMED: 28517993; PMC: 5448397; DOI: 10.1080/20502877.2017.1314890

  • Aging increases cell-to-cell transcriptional variability upon immune stimulation.

    Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA et al.

    Science (New York, N.Y.) 2017;355;6332;1433-1436

    PUBMED: 28360329; PMC: 5405862; DOI: 10.1126/science.aah4115

  • Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism.

    Hahn O, Grönke S, Stubbs TM, Ficz G, Hendrich O, Krueger F, Andrews S, Zhang Q, Wakelam MJ, Beyer A et al.

    Genome biology 2017;18;1;56

    PUBMED: 28351387; PMC: 5370449; DOI: 10.1186/s13059-017-1187-1

  • Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.

    Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M et al.

    The Journal of experimental medicine 2017;214;4;1111-1128

    PUBMED: 28351984; PMC: 5379978; DOI: 10.1084/jem.20161382

  • SC3: consensus clustering of single-cell RNA-seq data.

    Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR and Hemberg M

    Nature methods 2017;14;5;483-486

    PUBMED: 28346451; PMC: 5410170; DOI: 10.1038/nmeth.4236

  • Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments.

    Vieira Braga FA, Teichmann SA and Stubbington MJ

    Genome biology 2017;18;1;54

    PUBMED: 28340618; PMC: 5364640; DOI: 10.1186/s13059-017-1192-4

  • Inducible and Deterministic Forward Programming of Human Pluripotent Stem Cells into Neurons, Skeletal Myocytes, and Oligodendrocytes.

    Pawlowski M, Ortmann D, Bertero A, Tavares JM, Pedersen RA, Vallier L and Kotter MRN

    Stem cell reports 2017;8;4;803-812

    PUBMED: 28344001; PMC: 5390118; DOI: 10.1016/j.stemcr.2017.02.016

  • The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

    Chang D, Knapp M, Enk J, Lippold S, Kircher M, Lister A, MacPhee RD, Widga C, Czechowski P, Sommer R et al.

    Scientific reports 2017;7;44585

    PUBMED: 28327635; PMC: 5361112; DOI: 10.1038/srep44585

  • Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.

    Pagnamenta AT, Murakami Y, Taylor JM, Anzilotti C, Howard MF, Miller V, Johnson DS, Tadros S, Mansour S, Temple IK et al.

    European journal of human genetics : EJHG 2017;25;6;669-679

    PUBMED: 28327575; PMC: 5477361; DOI: 10.1038/ejhg.2017.32

  • PUF60 variants cause a syndrome of ID, short stature, microcephaly, coloboma, craniofacial, cardiac, renal and spinal features.

    Low KJ, Ansari M, Abou Jamra R, Clarke A, El Chehadeh S, FitzPatrick DR, Greenslade M, Henderson A, Hurst J, Keller K et al.

    European journal of human genetics : EJHG 2017;25;5;552-559

    PUBMED: 28327570; PMC: 5392357; DOI: 10.1038/ejhg.2017.27

  • Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.

    Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A et al.

    Nature 2017;543;7647;714-718

    PUBMED: 28329761; PMC: 6169740; DOI: 10.1038/nature21703

  • Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

    Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA and Surani MA

    eLife 2017;6

    PUBMED: 28323615; PMC: 5404928; DOI: 10.7554/eLife.22345

  • A single-copy Sleeping Beauty transposon mutagenesis screen identifies new PTEN-cooperating tumor suppressor genes.

    de la Rosa J, Weber J, Friedrich MJ, Li Y, Rad L, Ponstingl H, Liang Q, de Quirós SB, Noorani I, Metzakopian E et al.

    Nature genetics 2017;49;5;730-741

    PUBMED: 28319090; PMC: 5409503; DOI: 10.1038/ng.3817

  • Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma.

    Foijer F, Albacker LA, Bakker B, Spierings DC, Yue Y, Xie SZ, Davis S, Lutum-Jehle A, Takemoto D, Hare B et al.

    eLife 2017;6

    PUBMED: 28318489; PMC: 5400506; DOI: 10.7554/eLife.20873

  • Pacritinib versus best available therapy for the treatment of myelofibrosis irrespective of baseline cytopenias (PERSIST-1): an international, randomised, phase 3 trial.

    Mesa RA, Vannucchi AM, Mead A, Egyed M, Szoke A, Suvorov A, Jakucs J, Perkins A, Prasad R, Mayer J et al.

    The Lancet. Haematology 2017;4;5;e225-e236

    PUBMED: 28336242; PMC: 8209752; DOI: 10.1016/S2352-3026(17)30027-3

  • Editing the genome of hiPSC with CRISPR/Cas9: disease models.

    Bassett AR

    Mammalian genome : official journal of the International Mammalian Genome Society 2017;28;7-8;348-364

    PUBMED: 28303292; PMC: 5569153; DOI: 10.1007/s00335-017-9684-9

  • Angioimmunoblastic T cell lymphoma: novel molecular insights by mutation profiling.

    Wang M, Zhang S, Chuang SS, Ashton-Key M, Ochoa E, Bolli N, Vassiliou G, Gao Z and Du MQ

    Oncotarget 2017;8;11;17763-17770

    PUBMED: 28148900; PMC: 5392284; DOI: 10.18632/oncotarget.14846

  • Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification.

    Chen L, Jenjaroenpun P, Pillai AM, Ivshina AV, Ow GS, Efthimios M, Zhiqun T, Tan TZ, Lee SC, Rogers K et al.

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;11;E2215-E2224

    PUBMED: 28251929; PMC: 5358385; DOI: 10.1073/pnas.1701512114

  • Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity.

    Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K et al.

    Scientific reports 2017;7;43041

    PUBMED: 28287095; PMC: 5347126; DOI: 10.1038/srep43041

  • Bringing Treponema into the spotlight.

    Everall I and Sánchez-Busó L

    Nature reviews. Microbiology 2017;15;4;196

    PUBMED: 28286342; DOI: 10.1038/nrmicro.2017.23

  • HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

    Davies H, Glodzik D, Morganella S, Yates LR, Staaf J, Zou X, Ramakrishna M, Martin S, Boyault S, Sieuwerts AM et al.

    Nature medicine 2017;23;4;517-525

    PUBMED: 28288110; PMC: 5833945; DOI: 10.1038/nm.4292

  • Incorporation of a hinge domain improves the expansion of chimeric antigen receptor T cells.

    Qin L, Lai Y, Zhao R, Wei X, Weng J, Lai P, Li B, Lin S, Wang S, Wu Q et al.

    Journal of hematology & oncology 2017;10;1;68

    PUBMED: 28288656; PMC: 5347831; DOI: 10.1186/s13045-017-0437-8

  • Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

    Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F et al.

    Genome biology 2017;18;1;50

    PUBMED: 28283040; PMC: 5346261; DOI: 10.1186/s13059-017-1173-7

  • Association of Rare and Common Variation in the Lipoprotein Lipase Gene With Coronary Artery Disease.

    Khera AV, Won HH, Peloso GM, O'Dushlaine C, Liu D, Stitziel NO, Natarajan P, Nomura A, Emdin CA, Gupta N et al.

    JAMA 2017;317;9;937-946

    PUBMED: 28267856; PMC: 5664181; DOI: 10.1001/jama.2017.0972

  • Effects of long-term ethanol consumption and Aldh1b1 depletion on intestinal tumourigenesis in mice.

    Müller MF, Zhou Y, Adams DJ and Arends MJ

    The Journal of pathology 2017;241;5;649-660

    PUBMED: 28026023; DOI: 10.1002/path.4869

  • Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC) - the Hot Start experience.

    De Sousa PA, Steeg R, Wachter E, Bruce K, King J, Hoeve M, Khadun S, McConnachie G, Holder J, Kurtz A et al.

    Stem cell research 2017;20;105-114

    PUBMED: 28334554; DOI: 10.1016/j.scr.2017.03.002

  • The Y chromosomes of the great apes.

    Hallast P and Jobling MA

    Human genetics 2017

    PUBMED: 28265767; DOI: 10.1007/s00439-017-1769-8

  • Power analysis of single-cell RNA-sequencing experiments.

    Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A and Teichmann SA

    Nature methods 2017

    PUBMED: 28263961; DOI: 10.1038/nmeth.4220

  • The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania.

    Coughlan S, Mulhair P, Sanders M, Schonian G, Cotton JA and Downing T

    Scientific reports 2017;7;43747

    PUBMED: 28256610; PMC: 5335649; DOI: 10.1038/srep43747

  • Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

    Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U et al.

    Science immunology 2017;2;9

    PUBMED: 28345074; PMC: 5365145; DOI: 10.1126/sciimmunol.aal2192

  • Evolution of complexity in the zebrafish synapse proteome.

    Bayés À, Collins MO, Reig-Viader R, Gou G, Goulding D, Izquierdo A, Choudhary JS, Emes RD and Grant SG

    Nature communications 2017;8;14613

    PUBMED: 28252024; PMC: 5337974; DOI: 10.1038/ncomms14613

  • The rise and fall of pneumococcal serotypes carried in the PCV era.

    Devine VT, Cleary DW, Jefferies JM, Anderson R, Morris DE, Tuck AC, Gladstone RA, O'Doherty G, Kuruparan P, Bentley SD et al.

    Vaccine 2017;35;9;1293-1298

    PUBMED: 28161425; DOI: 10.1016/j.vaccine.2017.01.035

  • Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates.

    Azarian T, Grant LR, Georgieva M, Hammitt LL, Reid R, Bentley SD, Goldblatt D, Santosham M, Weatherholtz R, Burbidge P et al.

    The Journal of infectious diseases 2017;215;5;713-722

    PUBMED: 28035010; PMC: 6005115; DOI: 10.1093/infdis/jiw628

  • Bacterial microbiota of the upper respiratory tract and childhood asthma.

    Depner M, Ege MJ, Cox MJ, Dwyer S, Walker AW, Birzele LT, Genuneit J, Horak E, Braun-Fahrländer C, Danielewicz H et al.

    The Journal of allergy and clinical immunology 2017;139;3;826-834.e13

    PUBMED: 27576124; DOI: 10.1016/j.jaci.2016.05.050

  • Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages.

    Cairns MD, Preston MD, Hall CL, Gerding DN, Hawkey PM, Kato H, Kim H, Kuijper EJ, Lawley TD, Pituch H et al.

    Journal of clinical microbiology 2017;55;3;865-876

    PUBMED: 28031436; PMC: 5328454; DOI: 10.1128/JCM.01296-16

  • fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets.

    Madrigal P

    Bioinformatics (Oxford, England) 2017;33;5;746-748

    PUBMED: 27993776; PMC: 5408813; DOI: 10.1093/bioinformatics/btw724

  • Genetics of inflammatory bowel disease: beyond NOD2.

    Mirkov MU, Verstockt B and Cleynen I

    The lancet. Gastroenterology & hepatology 2017;2;3;224-234

    PUBMED: 28404137; DOI: 10.1016/S2468-1253(16)30111-X

  • Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets.

    Wain LV, Shrine N, Artigas MS, Erzurumluoglu AM, Noyvert B, Bossini-Castillo L, Obeidat M, Henry AP, Portelli MA, Hall RJ et al.

    Nature genetics 2017;49;3;416-425

    PUBMED: 28166213; PMC: 5326681; DOI: 10.1038/ng.3787

  • Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk.

    Warren HR, Evangelou E, Cabrera CP, Gao H, Ren M, Mifsud B, Ntalla I, Surendran P, Liu C, Cook JP et al.

    Nature genetics 2017;49;3;403-415

    PUBMED: 28135244; PMC: 5972004; DOI: 10.1038/ng.3768

  • Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq).

    Clark SJ, Smallwood SA, Lee HJ, Krueger F, Reik W and Kelsey G

    Nature protocols 2017;12;3;534-547

    PUBMED: 28182018; DOI: 10.1038/nprot.2016.187

  • GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium.

    Trampush JW, Yang ML, Yu J, Knowles E, Davies G, Liewald DC, Starr JM, Djurovic S, Melle I, Sundet K et al.

    Molecular psychiatry 2017;22;3;336-345

    PUBMED: 28093568; PMC: 5322272; DOI: 10.1038/mp.2016.244

  • Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape.

    Esson D, Gupta S, Bailey D, Wigley P, Wedley A, Mather AE, Méric G, Mastroeni P, Sheppard SK, Thomson NR et al.

    Microbial pathogenesis 2017;104;202-211

    PUBMED: 28131954; PMC: 5335918; DOI: 10.1016/j.micpath.2017.01.042

  • pfk13-Independent Treatment Failure in Four Imported Cases of Plasmodium falciparum Malaria Treated with Artemether-Lumefantrine in the United Kingdom.

    Sutherland CJ, Lansdell P, Sanders M, Muwanguzi J, van Schalkwyk DA, Kaur H, Nolder D, Tucker J, Bennett HM, Otto TD et al.

    Antimicrobial agents and chemotherapy 2017;61;3

    PUBMED: 28137810; PMC: 5328508; DOI: 10.1128/AAC.02382-16

  • Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania.

    Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, van Holst Pellekaan S et al.

    Journal of human genetics 2017;62;3;343-353

    PUBMED: 27904152; DOI: 10.1038/jhg.2016.147

  • Mutations in tropomyosin 4 underlie a rare form of human macrothrombocytopenia.

    Pleines I, Woods J, Chappaz S, Kew V, Foad N, Ballester-Beltrán J, Aurbach K, Lincetto C, Lane RM, Schevzov G et al.

    The Journal of clinical investigation 2017;127;3;814-829

    PUBMED: 28134622; PMC: 5330761; DOI: 10.1172/JCI86154

  • Principles guiding embryo selection following genome-wide haplotyping of preimplantation embryos.

    Dimitriadou E, Melotte C, Debrock S, Esteki MZ, Dierickx K, Voet T, Devriendt K, de Ravel T, Legius E, Peeraer K et al.

    Human reproduction (Oxford, England) 2017;32;3;687-697

    PUBMED: 28158716; DOI: 10.1093/humrep/dex011

  • Research benefits of storing genitourinary samples: 16S rRNA sequencing to evaluate vaginal bacterial communities.

    Wagner J, Kerry-Barnard S, Sadiq ST and Oakeshott P

    International journal of STD & AIDS 2017;28;3;315-317

    PUBMED: 28178906; PMC: 5305039; DOI: 10.1177/0956462416689441

  • Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.

    Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A and Gfeller D

    Genome research 2017;27;3;451-461

    PUBMED: 28087841; PMC: 5340972; DOI: 10.1101/gr.207704.116

  • Synthetic lethality: emerging targets and opportunities in melanoma.

    Thompson N, Adams DJ and Ranzani M

    Pigment cell & melanoma research 2017;30;2;183-193

    PUBMED: 28097822; PMC: 5396340; DOI: 10.1111/pcmr.12573

  • Typhoid in Africa and vaccine deployment.

    Dougan G

    The Lancet. Global health 2017;5;3;e236-e237

    PUBMED: 28193381; DOI: 10.1016/S2214-109X(17)30045-1

  • Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis.

    Lees JA, Brouwer M, van der Ende A, Parkhill J, van de Beek D and Bentley SD

    Infection and immunity 2017;85;3

    PUBMED: 28232521; PMC: 5328486; DOI: 10.1128/IAI.01061-16

  • Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase.

    Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A and Jurkowski TP

    Nucleic acids research 2017;45;4;1703-1713

    PUBMED: 27899645; PMC: 5389507; DOI: 10.1093/nar/gkw1112

  • Extreme mutation bias and high AT content in Plasmodium falciparum.

    Hamilton WL, Claessens A, Otto TD, Kekre M, Fairhurst RM, Rayner JC and Kwiatkowski D

    Nucleic acids research 2017;45;4;1889-1901

    PUBMED: 27994033; PMC: 5389722; DOI: 10.1093/nar/gkw1259

  • Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice.

    Wilson R, Geyer SH, Reissig L, Rose J, Szumska D, Hardman E, Prin F, McGuire C, Ramirez-Solis R, White J et al.

    Wellcome open research 2017;1;1

    PUBMED: 27996060; PMC: 5159622; DOI: 10.12688/wellcomeopenres.9899.2

  • Returning genome sequences to research participants: Policy and practice.

    Wright CF, Middleton A, Barrett JC, Firth HV, FitzPatrick DR, Hurles ME and Parker M

    Wellcome open research 2017;2;15

    PUBMED: 28317033; PMC: 5351846; DOI: 10.12688/wellcomeopenres.10942.1

  • An Organismal CNV Mutator Phenotype Restricted to Early Human Development.

    Liu P, Yuan B, Carvalho CMB, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z et al.

    Cell 2017;168;5;830-842.e7

    PUBMED: 28235197; PMC: 5407901; DOI: 10.1016/j.cell.2017.01.037

  • Mutational Processes Shaping the Genome in Early Human Embryos.

    Voet T and Vermeesch JR

    Cell 2017;168;5;751-753

    PUBMED: 28235191; DOI: 10.1016/j.cell.2017.02.008

  • Postdocs, What Would You Tell Your Younger Self?

    No authors listed

    Cell 2017;168;5;745-748

    PUBMED: 28235189; DOI: 10.1016/j.cell.2017.02.016

  • Summing up the parts of the hypothalamus.

    Hemberg M

    Nature neuroscience 2017;20;3;378-379

    PUBMED: 28230849; DOI: 10.1038/nn.4515

  • Evolution and Epidemiology of Multidrug-ResistantKlebsiella pneumoniaein the United Kingdom and Ireland.

    Moradigaravand D, Martin V, Peacock SJ and Parkhill J

    mBio 2017;8;1

    PUBMED: 28223459; PMC: 5358916; DOI: 10.1128/mBio.01976-16

  • Predicting evolution.

    Lässig M, Mustonen V and Walczak AM

    Nature ecology & evolution 2017;1;3;77

    PUBMED: 28812721; DOI: 10.1038/s41559-017-0077

  • Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease.

    Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NG, Jansen H, Kanoni S, Nelson CP, Ferrario PG, König IR et al.

    Journal of the American College of Cardiology 2017;69;7;823-836

    PUBMED: 28209224; PMC: 5314135; DOI: 10.1016/j.jacc.2016.11.056

  • Genetic Characterization of Vibrio cholerae O1 isolates from outbreaks between 2011 and 2015 in Tanzania.

    Kachwamba Y, Mohammed AA, Lukupulo H, Urio L, Majigo M, Mosha F, Matonya M, Kishimba R, Mghamba J, Lusekelo J et al.

    BMC infectious diseases 2017;17;1;157

    PUBMED: 28219321; PMC: 5319185; DOI: 10.1186/s12879-017-2252-9

  • The Ageing Brain: Effects on DNA Repair and DNA Methylation in Mice.

    Langie SA, Cameron KM, Ficz G, Oxley D, Tomaszewski B, Gorniak JP, Maas LM, Godschalk RW, van Schooten FJ, Reik W et al.

    Genes 2017;8;2

    PUBMED: 28218666; PMC: 5333064; DOI: 10.3390/genes8020075

  • KDM2A integrates DNA and histone modification signals through a CXXC/PHD module and direct interaction with HP1.

    Borgel J, Tyl M, Schiller K, Pusztai Z, Dooley CM, Deng W, Wooding C, White RJ, Warnecke T, Leonhardt H et al.

    Nucleic acids research 2017;45;3;1114-1129

    PUBMED: 28180290; PMC: 5388433; DOI: 10.1093/nar/gkw979

  • Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data.

    Mobegi FM, Cremers AJ, de Jonge MI, Bentley SD, van Hijum SA and Zomer A

    Scientific reports 2017;7;42808

    PUBMED: 28205635; PMC: 5311915; DOI: 10.1038/srep42808

  • Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand.

    Crispell J, Zadoks RN, Harris SR, Paterson B, Collins DM, de-Lisle GW, Livingstone P, Neill MA, Biek R, Lycett SJ et al.

    BMC genomics 2017;18;1;180

    PUBMED: 28209138; PMC: 5314462; DOI: 10.1186/s12864-017-3569-x

  • A population-based analysis of germline BAP1 mutations in melanoma.

    O'Shea SJ, Robles-Espinoza CD, McLellan L, Harrigan J, Jacq X, Hewinson J, Iyer V, Merchant W, Elliott F, Harland M et al.

    Human molecular genetics 2017;26;4;717-728

    PUBMED: 28062663; PMC: 5409081; DOI: 10.1093/hmg/ddw403

  • The secondary resistome of multidrug-resistant Klebsiella pneumoniae.

    Jana B, Cain AK, Doerrler WT, Boinett CJ, Fookes MC, Parkhill J and Guardabassi L

    Scientific reports 2017;7;42483

    PUBMED: 28198411; PMC: 5309761; DOI: 10.1038/srep42483

  • Efficient CRISPR/Cas9-assisted gene targeting enables rapid and precise genetic manipulation of mammalian neural stem cells.

    Bressan RB, Dewari PS, Kalantzaki M, Gangoso E, Matjusaitis M, Garcia-Diaz C, Blin C, Grant V, Bulstrode H, Gogolok S et al.

    Development (Cambridge, England) 2017;144;4;635-648

    PUBMED: 28096221; PMC: 5312033; DOI: 10.1242/dev.140855

  • gargammel: a sequence simulator for ancient DNA.

    Renaud G, Hanghøj K, Willerslev E and Orlando L

    Bioinformatics (Oxford, England) 2017;33;4;577-579

    PUBMED: 27794556; PMC: 5408798; DOI: 10.1093/bioinformatics/btw670

  • Jmjd2c facilitates the assembly of essential enhancer-protein complexes at the onset of embryonic stem cell differentiation.

    Tomaz RA, Harman JL, Karimlou D, Weavers L, Fritsch L, Bou-Kheir T, Bell E, Del Valle Torres I, Niakan KK, Fisher C et al.

    Development (Cambridge, England) 2017;144;4;567-579

    PUBMED: 28087629; PMC: 5312034; DOI: 10.1242/dev.142489

  • 11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project.

    Cai N, Bigdeli TB, Kretzschmar WW, Li Y, Liang J, Hu J, Peterson RE, Bacanu S, Webb BT, Riley B et al.

    Scientific data 2017;4;170011

    PUBMED: 28195579; PMC: 5308202; DOI: 10.1038/sdata.2017.11

  • Finding the needle in the haystack.

    Rutledge GG and Ariani CV

    Nature reviews. Microbiology 2017;15;3;136

    PUBMED: 28190880; DOI: 10.1038/nrmicro.2017.7

  • P113 is a merozoite surface protein that binds the N terminus of Plasmodium falciparum RH5.

    Galaway F, Drought LG, Fala M, Cross N, Kemp AC, Rayner JC and Wright GJ

    Nature communications 2017;8;14333

    PUBMED: 28186186; PMC: 5309799; DOI: 10.1038/ncomms14333

  • Revisiting olfactory receptors as putative drivers of cancer.

    Ranzani M, Iyer V, Ibarra-Soria X, Del Castillo Velasco-Herrera M, Garnett M, Logan D and Adams DJ

    Wellcome open research 2017;2;9

    PUBMED: 28492065; PMC: 5421569; DOI: 10.12688/wellcomeopenres.10646.1

  • Rare and low-frequency coding variants alter human adult height.

    Marouli E, Graff M, Medina-Gomez C, Lo KS, Wood AR, Kjaer TR, Fine RS, Lu Y, Schurmann C, Highland HM et al.

    Nature 2017;542;7640;186-190

    PUBMED: 28146470; PMC: 5302847; DOI: 10.1038/nature21039

  • Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.

    Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S et al.

    Genome research 2017;27;4;613-625

    PUBMED: 28179366; PMC: 5378179; DOI: 10.1101/gr.213546.116

  • Population structure of multidrug resistant Klebsiella oxytoca within hospitals across the UK and Ireland identifies sharing of virulence and resistance genes with K. pneumoniae.

    Moradigaravand D, Martin V, Peacock SJ and Parkhill J

    Genome biology and evolution 2017;9;3;574-587

    PUBMED: 28177070; PMC: 5381567; DOI: 10.1093/gbe/evx019

  • Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration.

    Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R, Al-Zahery N, Raveane A et al.

    BMC evolutionary biology 2017;17;Suppl 1;18

    PUBMED: 28251872; PMC: 5333174; DOI: 10.1186/s12862-016-0870-2

  • Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection.

    Brugat T, Reid AJ, Lin J, Cunningham D, Tumwine I, Kushinga G, McLaughlin S, Spence P, Böhme U, Sanders M et al.

    Nature microbiology 2017;2;16276

    PUBMED: 28165471; PMC: 5373435; DOI: 10.1038/nmicrobiol.2016.276

  • Heterozygous truncation mutations of the SMC1A gene cause a severe early onset epilepsy with cluster seizures in females: Detailed phenotyping of 10 new cases.

    Symonds JD, Joss S, Metcalfe KA, Somarathi S, Cruden J, Devlin AM, Donaldson A, DiDonato N, Fitzpatrick D, Kaiser FJ et al.

    Epilepsia 2017;58;4;565-575

    PUBMED: 28166369; DOI: 10.1111/epi.13669

  • Human evolution: a tale from ancient genomes.

    Llamas B, Willerslev E and Orlando L

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2017;372;1713

    PUBMED: 27994125; PMC: 5182416; DOI: 10.1098/rstb.2015.0484

  • The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.

    Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A and Feil EJ

    Frontiers in microbiology 2017;8;121

    PUBMED: 28217117; PMC: 5290457; DOI: 10.3389/fmicb.2017.00121

  • Clinical and molecular consequences of disease-associated de novo mutations in SATB2.

    Bengani H, Handley M, Alvi M, Ibitoye R, Lees M, Lynch SA, Lam W, Fannemel M, Nordgren A, Malmgren H et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2017;19;8;900-908

    PUBMED: 28151491; PMC: 5548934; DOI: 10.1038/gim.2016.211

  • The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.

    Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J and Kendler KS

    JAMA psychiatry 2017;74;2;162-168

    PUBMED: 28002544; PMC: 5319866; DOI: 10.1001/jamapsychiatry.2016.3578

  • The Genetic Landscape of Renal Complications in Type 1 Diabetes.

    Sandholm N, Van Zuydam N, Ahlqvist E, Juliusdottir T, Deshmukh HA, Rayner NW, Di Camillo B, Forsblom C, Fadista J, Ziemek D et al.

    Journal of the American Society of Nephrology : JASN 2017;28;2;557-574

    PUBMED: 27647854; PMC: 5280020; DOI: 10.1681/ASN.2016020231

  • A two-stage inter-rater approach for enrichment testing of variants associated with multiple traits.

    Asimit JL, Payne F, Morris AP, Cordell HJ and Barroso I

    European journal of human genetics : EJHG 2017;25;3;341-349

    PUBMED: 28000695; PMC: 5302181; DOI: 10.1038/ejhg.2016.171

  • Dynamic variation of CD5 surface expression levels within individual chronic lymphocytic leukemia clones.

    Bashford-Rogers RJ, Palser AL, Hodkinson C, Baxter J, Follows GA, Vassiliou GS and Kellam P

    Experimental hematology 2017;46;31-37.e10

    PUBMED: 27693386; PMC: 5261558; DOI: 10.1016/j.exphem.2016.09.010

  • Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index.

    Hinney A, Kesselmeier M, Jall S, Volckmar AL, Föcker M, Antel J, GCAN, WTCCC3, Heid IM, Winkler TW et al.

    Molecular psychiatry 2017;22;2;192-201

    PUBMED: 27184124; PMC: 5114162; DOI: 10.1038/mp.2016.71

  • Frontline Science: Coincidental null mutation of Csf2rα in a colony of PI3Kγ-/- mice causes alveolar macrophage deficiency and fatal respiratory viral infection.

    Schneider C, Nobs SP, Heer AK, Hirsch E, Penninger J, Siggs OM and Kopf M

    Journal of leukocyte biology 2017;101;2;367-376

    PUBMED: 27468760; PMC: 5610570; DOI: 10.1189/jlb.4HI0316-157R

  • Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease.

    Lee JC, Biasci D, Roberts R, Gearry RB, Mansfield JC, Ahmad T, Prescott NJ, Satsangi J, Wilson DC, Jostins L et al.

    Nature genetics 2017;49;2;262-268

    PUBMED: 28067912; PMC: 5730041; DOI: 10.1038/ng.3755

  • Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice.

    Friedrich MJ, Rad L, Bronner IF, Strong A, Wang W, Weber J, Mayho M, Ponstingl H, Engleitner T, Grove C et al.

    Nature protocols 2017;12;2;289-309

    PUBMED: 28079877; DOI: 10.1038/nprot.2016.164

  • Germline variants in ETV6 underlie reduced platelet formation, platelet dysfunction and increased levels of circulating CD34+ progenitors.

    Poggi M, Canault M, Favier M, Turro E, Saultier P, Ghalloussi D, Baccini V, Vidal L, Mezzapesa A, Chelghoum N et al.

    Haematologica 2017;102;2;282-294

    PUBMED: 27663637; PMC: 5286936; DOI: 10.3324/haematol.2016.147694

  • Guideline for the investigation and management of eosinophilia.

    Butt NM, Lambert J, Ali S, Beer PA, Cross NC, Duncombe A, Ewing J, Harrison CN, Knapper S, McLornan D et al.

    British journal of haematology 2017;176;4;553-572

    PUBMED: 28112388; DOI: 10.1111/bjh.14488

  • HUWE1 is a critical colonic tumour suppressor gene that prevents MYC signalling, DNA damage accumulation and tumour initiation.

    Myant KB, Cammareri P, Hodder MC, Wills J, Von Kriegsheim A, Győrffy B, Rashid M, Polo S, Maspero E, Vaughan L et al.

    EMBO molecular medicine 2017;9;2;181-197

    PUBMED: 28003334; PMC: 5286368; DOI: 10.15252/emmm.201606684

  • Improving the Identification of Phenotypic Abnormalities and Sexual Dimorphism in Mice When Studying Rare Event Categorical Characteristics.

    Karp NA, Heller R, Yaacoby S, White JK and Benjamini Y

    Genetics 2017;205;2;491-501

    PUBMED: 27932544; PMC: 5289831; DOI: 10.1534/genetics.116.195388

  • Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.

    Skwark MJ, Croucher NJ, Puranen S, Chewapreecha C, Pesonen M, Xu YY, Turner P, Harris SR, Beres SB, Musser JM et al.

    PLoS genetics 2017;13;2;e1006508

    PUBMED: 28207813; PMC: 5312804; DOI: 10.1371/journal.pgen.1006508

  • Plasmodium vivax vaccine research - we've only just begun.

    Tham WH, Beeson JG and Rayner JC

    International journal for parasitology 2017;47;2-3;111-118

    PUBMED: 27899329; DOI: 10.1016/j.ijpara.2016.09.006

  • Prognostic impact of p15 gene aberrations in acute leukemia.

    De Braekeleer M, Douet-Guilbert N and De Braekeleer E

    Leukemia & lymphoma 2017;58;2;257-265

    PUBMED: 27401303; DOI: 10.1080/10428194.2016.1201574

  • Regulation, evolution and consequences of cotranslational protein complex assembly.

    Natan E, Wells JN, Teichmann SA and Marsh JA

    Current opinion in structural biology 2017;42;90-97

    PUBMED: 27969102; DOI: 10.1016/j.sbi.2016.11.023

  • Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders.

    Evers JM, Laskowski RA, Bertolli M, Clayton-Smith J, Deshpande C, Eason J, Elmslie F, Flinter F, Gardiner C, Hurst JA et al.

    Human molecular genetics 2017;26;3;519-526

    PUBMED: 28053047; PMC: 5409128; DOI: 10.1093/hmg/ddw409

  • Visualization and Quantification of Browning Using a Ucp1-2A-Luciferase Knock-in Mouse Model.

    Mao L, Nie B, Nie T, Hui X, Gao X, Lin X, Liu X, Xu Y, Tang X, Yuan R et al.

    Diabetes 2017;66;2;407-417

    PUBMED: 28108609; DOI: 10.2337/db16-0343

  • Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas.

    Hu Y, Wu Q, Ma S, Ma T, Shan L, Wang X, Nie Y, Ning Z, Yan L, Xiu Y and Wei F

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;5;1081-1086

    PUBMED: 28096377; PMC: 5293045; DOI: 10.1073/pnas.1613870114

  • Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming.

    Milagre I, Stubbs TM, King MR, Spindel J, Santos F, Krueger F, Bachman M, Segonds-Pichon A, Balasubramanian S, Andrews SR et al.

    Cell reports 2017;18;5;1079-1089

    PUBMED: 28147265; PMC: 5300890; DOI: 10.1016/j.celrep.2017.01.008

  • SC83288 is a clinical development candidate for the treatment of severe malaria.

    Pegoraro S, Duffey M, Otto TD, Wang Y, Rösemann R, Baumgartner R, Fehler SK, Lucantoni L, Avery VM, Moreno-Sabater A et al.

    Nature communications 2017;8;14193

    PUBMED: 28139658; PMC: 5290327; DOI: 10.1038/ncomms14193

  • A quantitative proteomic screen of the Campylobacter jejuni flagellar-dependent secretome.

    Scanlan E, Yu L, Maskell D, Choudhary J and Grant A

    Journal of proteomics 2017;152;181-187

    PUBMED: 27865792; PMC: 5223770; DOI: 10.1016/j.jprot.2016.11.009

  • The Type III Secretion System Effector SptP of Salmonella enterica Serovar Typhi.

    Johnson R, Byrne A, Berger CN, Klemm E, Crepin VF, Dougan G and Frankel G

    Journal of bacteriology 2017;199;4

    PUBMED: 27920299; PMC: 5287405; DOI: 10.1128/JB.00647-16

  • Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

    Jansen IE, Ye H, Heetveld S, Lechler MC, Michels H, Seinstra RI, Lubbe SJ, Drouet V, Lesage S, Majounie E et al.

    Genome biology 2017;18;1;22

    PUBMED: 28137300; PMC: 5282828; DOI: 10.1186/s13059-017-1147-9

  • One-step generation of conditional and reversible gene knockouts.

    Andersson-Rolf A, Mustata RC, Merenda A, Kim J, Perera S, Grego T, Andrews K, Tremble K, Silva JC, Fink J et al.

    Nature methods 2017;14;3;287-289

    PUBMED: 28135257; PMC: 5777571; DOI: 10.1038/nmeth.4156

  • Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

    Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP et al.

    Genome biology 2017;18;1;18

    PUBMED: 28126036; PMC: 5270224; DOI: 10.1186/s13059-017-1156-8

  • Rare variants in GP1BB are responsible for autosomal dominant macrothrombocytopenia.

    Sivapalaratnam S, Westbury SK, Stephens JC, Greene D, Downes K, Kelly AM, Lentaigne C, Astle WJ, Huizinga EG, Nurden P et al.

    Blood 2017;129;4;520-524

    PUBMED: 28064200; PMC: 6037295; DOI: 10.1182/blood-2016-08-732248

  • Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution.

    Rutledge GG, Böhme U, Sanders M, Reid AJ, Cotton JA, Maiga-Ascofare O, Djimdé AA, Apinjoh TO, Amenga-Etego L, Manske M et al.

    Nature 2017;542;7639;101-104

    PUBMED: 28117441; PMC: 5326575; DOI: 10.1038/nature21038

  • Prevalence and architecture of de novo mutations in developmental disorders.

    Deciphering Developmental Disorders Study

    Nature 2017;542;7642;433-438

    PUBMED: 28135719; PMC: 6016744; DOI: 10.1038/nature21062

  • Culture adaptation of malaria parasites selects for convergent loss-of-function mutants.

    Claessens A, Affara M, Assefa SA, Kwiatkowski DP and Conway DJ

    Scientific reports 2017;7;41303

    PUBMED: 28117431; DOI: 10.1038/srep41303

  • Whole-exome sequencing of 228 patients with sporadic Parkinson's disease.

    Sandor C, Honti F, Haerty W, Szewczyk-Krolikowski K, Tomlinson P, Evetts S, Millin S, Keane T, McCarthy SA, Durbin R et al.

    Scientific reports 2017;7;41188

    PUBMED: 28117402; DOI: 10.1038/srep41188

  • Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae.

    Runcharoen C, Moradigaravand D, Blane B, Paksanont S, Thammachote J, Anun S, Parkhill J, Chantratita N and Peacock SJ

    Genome medicine 2017;9;1;6

    PUBMED: 28118859; PMC: 5264300; DOI: 10.1186/s13073-017-0397-1

  • A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers.

    Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M et al.

    Nature genetics 2017;49;3;341-348

    PUBMED: 28112740; PMC: 5988034; DOI: 10.1038/ng.3771

  • Global and regional dissemination and evolution of Burkholderia pseudomallei.

    Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z, Harris SR, Mather AE, Tuanyok A, De Smet B, Le Hello S et al.

    Nature microbiology 2017;2;16263

    PUBMED: 28112723; PMC: 5300093; DOI: 10.1038/nmicrobiol.2016.263

  • Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.

    Jones GT, Tromp G, Kuivaniemi H, Gretarsdottir S, Baas AF, Giusti B, Strauss E, Van't Hof FN, Webb TR, Erdman R et al.

    Circulation research 2017;120;2;341-353

    PUBMED: 27899403; PMC: 5253231; DOI: 10.1161/CIRCRESAHA.116.308765

  • Delineating the phenotypic spectrum of Bainbridge-Ropers syndrome: 12 new patients with de novo, heterozygous, loss-of-function mutations in ASXL3 and review of published literature.

    Balasubramanian M, Willoughby J, Fry AE, Weber A, Firth HV, Deshpande C, Berg JN, Chandler K, Metcalfe KA, Lam W et al.

    Journal of medical genetics 2017;54;8;537-543

    PUBMED: 28100473; DOI: 10.1136/jmedgenet-2016-104360

  • Tracing the peopling of the world through genomics.

    Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S and Willerslev E

    Nature 2017;541;7637;302-310

    PUBMED: 28102248; PMC: 5772775; DOI: 10.1038/nature21347

  • Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening.

    Croucher NJ, Campo JJ, Le TQ, Liang X, Bentley SD, Hanage WP and Lipsitch M

    Proceedings of the National Academy of Sciences of the United States of America 2017;114;3;E357-E366

    PUBMED: 28053228; PMC: 5255586; DOI: 10.1073/pnas.1613937114

  • Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease.

    Tunjungputri RN, Mobegi FM, Cremers AJ, van der Gaast-de Jongh CE, Ferwerda G, Meis JF, Roeleveld N, Bentley SD, Pastura AS, van Hijum SA et al.

    mBio 2017;8;1

    PUBMED: 28096486; PMC: 5241397; DOI: 10.1128/mBio.01984-16

  • Clinical and biological insights from viral genome sequencing.

    Houldcroft CJ, Beale MA and Breuer J

    Nature reviews. Microbiology 2017;15;3;183-192

    PUBMED: 28090077; PMC: 7097211; DOI: 10.1038/nrmicro.2016.182

  • Comparative genomics of canine-isolated Leishmania (Leishmania) amazonensis from an endemic focus of visceral leishmaniasis in Governador Valadares, southeastern Brazil.

    Valdivia HO, Almeida LV, Roatt BM, Reis-Cunha JL, Pereira AA, Gontijo C, Fujiwara RT, Reis AB, Sanders MJ, Cotton JA and Bartholomeu DC

    Scientific reports 2017;7;40804

    PUBMED: 28091623; PMC: 5238499; DOI: 10.1038/srep40804

  • Precision oncology for acute myeloid leukemia using a knowledge bank approach.

    Gerstung M, Papaemmanuil E, Martincorena I, Bullinger L, Gaidzik VI, Paschka P, Heuser M, Thol F, Bolli N, Ganly P et al.

    Nature genetics 2017;49;3;332-340

    PUBMED: 28092685; PMC: 5764082; DOI: 10.1038/ng.3756

  • You are where you live.

    Kidman SE and Bryant JM

    Nature reviews. Microbiology 2017;15;2;68

    PUBMED: 28090080; DOI: 10.1038/nrmicro.2016.203

  • Single-Cell Multiomics: Multiple Measurements from Single Cells.

    Macaulay IC, Ponting CP and Voet T

    Trends in genetics : TIG 2017;33;2;155-168

    PUBMED: 28089370; PMC: 5303816; DOI: 10.1016/j.tig.2016.12.003

  • A Knockout Screen of ApiAP2 Genes Reveals Networks of Interacting Transcriptional Regulators Controlling the Plasmodium Life Cycle.

    Modrzynska K, Pfander C, Chappell L, Yu L, Suarez C, Dundas K, Gomes AR, Goulding D, Rayner JC, Choudhary J and Billker O

    Cell host & microbe 2017;21;1;11-22

    PUBMED: 28081440; PMC: 5241200; DOI: 10.1016/j.chom.2016.12.003

  • Role of Anopheles (Cellia) rufipes (Gough, 1910) and other local anophelines in human malaria transmission in the northern savannah of Cameroon: a cross-sectional survey.

    Tabue RN, Awono-Ambene P, Etang J, Atangana J, C AN, Toto JC, Patchoke S, Leke RG, Fondjo E, Mnzava AP et al.

    Parasites & vectors 2017;10;1;22

    PUBMED: 28077167; PMC: 5225577; DOI: 10.1186/s13071-016-1933-3

  • The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1.

    Cornick JE, Tastan Bishop Ö, Yalcin F, Kiran AM, Kumwenda B, Chaguza C, Govindpershad S, Ousmane S, Senghore M, du Plessis M et al.

    Vaccine 2017;35;6;972-980

    PUBMED: 28081968; PMC: 5287219; DOI: 10.1016/j.vaccine.2016.12.037

  • Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia.

    Clarke GM, Rockett K, Kivinen K, Hubbart C, Jeffreys AE, Rowlands K, Jallow M, Conway DJ, Bojang KA, Pinder M et al.

    eLife 2017;6

    PUBMED: 28067620; PMC: 5222559; DOI: 10.7554/eLife.15085

  • Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7.

    Luo Y, de Lange KM, Jostins L, Moutsianas L, Randall J, Kennedy NA, Lamb CA, McCarthy S, Ahmad T, Edwards C et al.

    Nature genetics 2017;49;2;186-192

    PUBMED: 28067910; PMC: 5289625; DOI: 10.1038/ng.3761

  • Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease.

    de Lange KM, Moutsianas L, Lee JC, Lamb CA, Luo Y, Kennedy NA, Jostins L, Rice DL, Gutierrez-Achury J, Ji SG et al.

    Nature genetics 2017;49;2;256-261

    PUBMED: 28067908; PMC: 5289481; DOI: 10.1038/ng.3760

  • Mapping Post-Glacial expansions: The Peopling of Southwest Asia.

    Platt DE, Haber M, Dagher-Kharrat MB, Douaihy B, Khazen G, Ashrafian Bonab M, Salloum A, Mouzaya F, Luiselli D, Tyler-Smith C et al.

    Scientific reports 2017;7;40338

    PUBMED: 28059138; PMC: 5216412; DOI: 10.1038/srep40338

  • A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.

    Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F et al.

    G3 (Bethesda, Md.) 2017;7;1;109-117

    PUBMED: 27852011; PMC: 5217101; DOI: 10.1534/g3.116.035923

  • Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.

    Wahl S, Drong A, Lehne B, Loh M, Scott WR, Kunze S, Tsai PC, Ried JS, Zhang W, Yang Y et al.

    Nature 2017;541;7635;81-86

    PUBMED: 28002404; PMC: 5570525; DOI: 10.1038/nature20784

  • The Human Phenotype Ontology in 2017.

    Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM et al.

    Nucleic acids research 2017;45;D1;D865-D876

    PUBMED: 27899602; PMC: 5210535; DOI: 10.1093/nar/gkw1039

  • EuPathDB: the eukaryotic pathogen genomics database resource.

    Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S et al.

    Nucleic acids research 2017;45;D1;D581-D591

    PUBMED: 27903906; PMC: 5210576; DOI: 10.1093/nar/gkw1105

  • Genome-wide in vivo screen identifies novel host regulators of metastatic colonization.

    van der Weyden L, Arends MJ, Campbell AD, Bald T, Wardle-Jones H, Griggs N, Velasco-Herrera MD, Tüting T, Sansom OJ, Karp NA et al.

    Nature 2017;541;7636;233-236

    PUBMED: 28052056; PMC: 5603286; DOI: 10.1038/nature20792

  • The H3K9 dimethyltransferases EHMT1/2 protect against pathological cardiac hypertrophy.

    Thienpont B, Aronsen JM, Robinson EL, Okkenhaug H, Loche E, Ferrini A, Brien P, Alkass K, Tomasso A, Agrawal A et al.

    The Journal of clinical investigation 2017;127;1;335-348

    PUBMED: 27893464; PMC: 5199699; DOI: 10.1172/JCI88353

  • The AURORA pilot study for molecular screening of patients with advanced breast cancer-a study of the breast international group.

    Maetens M, Brown D, Irrthum A, Aftimos P, Viale G, Loibl S, Laes JF, Campbell PJ, Thompson A, Cortes J et al.

    NPJ breast cancer 2017;3;23

    PUBMED: 28685159; PMC: 5491498; DOI: 10.1038/s41523-017-0026-6

  • An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan.

    Pagani L, Colonna V, Tyler-Smith C and Ayub Q

    Man in India 2017;97;1;267-278

    PUBMED: 28381901; PMC: 5378296

  • The exported chaperone Hsp70-x supports virulence functions for Plasmodium falciparum blood stage parasites.

    Charnaud SC, Dixon MWA, Nie CQ, Chappell L, Sanders PR, Nebl T, Hanssen E, Berriman M, Chan JA, Blanch AJ et al.

    PloS one 2017;12;7;e0181656

    PUBMED: 28732045; DOI: 10.1371/journal.pone.0181656

  • A graph extension of the positional Burrows-Wheeler transform and its applications.

    Novak AM, Garrison E and Paten B

    Algorithms for molecular biology : AMB 2017;12;18

    PUBMED: 28702075; PMC: 5505026; DOI: 10.1186/s13015-017-0109-9

  • THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.

    Chang HH, Worby CJ, Yeka A, Nankabirwa J, Kamya MR, Staedke SG, Dorsey G, Murphy M, Neafsey DE, Jeffreys AE et al.

    PLoS computational biology 2017;13;1;e1005348

    PUBMED: 28125584; PMC: 5300274; DOI: 10.1371/journal.pcbi.1005348

  • Accurate and fast feature selection workflow for high-dimensional omics data.

    Perez-Riverol Y, Kuhn M, Vizcaíno JA, Hitz MP and Audain E

    PloS one 2017;12;12;e0189875

    PUBMED: 29261781; PMC: 5738110; DOI: 10.1371/journal.pone.0189875

  • Adipose Tissue Function and Expandability as Determinants of Lipotoxicity and the Metabolic Syndrome.

    Carobbio S, Pellegrinelli V and Vidal-Puig A

    Advances in experimental medicine and biology 2017;960;161-196

    PUBMED: 28585199; DOI: 10.1007/978-3-319-48382-5_7

  • Adults with suspected central nervous system infection: A prospective study of diagnostic accuracy.

    Khatib U, van de Beek D, Lees JA and Brouwer MC

    The Journal of infection 2017;74;1;1-9

    PUBMED: 27746160; DOI: 10.1016/j.jinf.2016.09.007

  • Antimicrobial resistance in human populations: challenges and opportunities.

    Allcock S, Young EH, Holmes M, Gurdasani D, Dougan G, Sandhu MS, Solomon L and Török ME

    Global health, epidemiology and genomics 2017;2;e4

    PUBMED: 29276617; PMC: 5732576; DOI: 10.1017/gheg.2017.4

  • Cancer stem cell-related gene expression as a potential biomarker of response for first-in-class imipridone ONC201 in solid tumors.

    Prabhu VV, Lulla AR, Madhukar NS, Ralff MD, Zhao D, Kline CLB, Van den Heuvel APJ, Lev A, Garnett MJ, McDermott U et al.

    PloS one 2017;12;8;e0180541

    PUBMED: 28767654; PMC: 5540272; DOI: 10.1371/journal.pone.0180541

  • CD215+ Myeloid Cells Respond to Interleukin 15 Stimulation and Promote Tumor Progression.

    Lin S, Huang G, Xiao Y, Sun W, Jiang Y, Deng Q, Peng M, Wei X, Ye W, Li B et al.

    Frontiers in immunology 2017;8;1713

    PUBMED: 29255466; PMC: 5722806; DOI: 10.3389/fimmu.2017.01713

  • Cell lineage specification at single cell resolution.

    Yang J and Liu P

    Stem cell investigation 2017;4;76

    PUBMED: 29057248; PMC: 5639035; DOI: 10.21037/sci.2017.09.03

  • Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.

    Hansen HB, Damgaard PB, Margaryan A, Stenderup J, Lynnerup N, Willerslev E and Allentoft ME

    PloS one 2017;12;1;e0170940

    PUBMED: 28129388; PMC: 5271384; DOI: 10.1371/journal.pone.0170940

  • Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.

    de Vries PS, Sabater-Lleal M, Chasman DI, Trompet S, Ahluwalia TS, Teumer A, Kleber ME, Chen MH, Wang JJ, Attia JR et al.

    PloS one 2017;12;1;e0167742

    PUBMED: 28107422; PMC: 5249120; DOI: 10.1371/journal.pone.0167742

  • Consumer Health Informatics Aspects of Direct-to-Consumer Personal Genomic Testing.

    Gray K, Stephen R, Terrill B, Wilson B, Middleton A, Tytherleigh R, Turbitt E, Gaff C, Savard J, Hickerton C et al.

    Studies in health technology and informatics 2017;245;89-93

    PUBMED: 29295058

  • Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

    Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C et al.

    PloS one 2017;12;12;e0189838

    PUBMED: 29281674; PMC: 5744980; DOI: 10.1371/journal.pone.0189838

  • Cytogenetic Resources and Information.

    De Braekeleer E, Huret JL, Mossafa H and Dessen P

    Methods in molecular biology (Clifton, N.J.) 2017;1541;311-331

    PUBMED: 27910033; DOI: 10.1007/978-1-4939-6703-2_25

  • Design and Application of Multiplex PCR Seq for the Detection of Somatic Mutations Associated with Myeloid Malignancies.

    Park N and Vassiliou G

    Methods in molecular biology (Clifton, N.J.) 2017;1633;87-99

    PUBMED: 28735482; DOI: 10.1007/978-1-4939-7142-8_6

  • Disentangling PTEN-cooperating tumor suppressor gene networks in cancer.

    de la Rosa J, Weber J, Rad R, Bradley A and Cadiñanos J

    Molecular & cellular oncology 2017;4;4;e1325550

    PUBMED: 28868343; PMC: 5540202; DOI: 10.1080/23723556.2017.1325550

  • Document retrieval on repetitive string collections.

    Gagie T, Hartikainen A, Karhu K, Kärkkäinen J, Navarro G, Puglisi SJ and Sirén J

    Information retrieval 2017;20;3;253-291

    PUBMED: 28596702; PMC: 5445192; DOI: 10.1007/s10791-017-9297-7

  • Dynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods.

    Kosicki M, Rajan SS, Lorenzetti FC, Wandall HH, Narimatsu Y, Metzakopian E and Bennett EP

    Progress in molecular biology and translational science 2017;152;49-67

    PUBMED: 29150004; DOI: 10.1016/bs.pmbts.2017.09.003

  • Effect of Genetic Variability in the CYP4F2, CYP4F11, and CYP4F12 Genes on Liver mRNA Levels and Warfarin Response.

    Zhang JE, Klein K, Jorgensen AL, Francis B, Alfirevic A, Bourgeois S, Deloukas P, Zanger UM and Pirmohamed M

    Frontiers in pharmacology 2017;8;323

    PUBMED: 28620303; PMC: 5449482; DOI: 10.3389/fphar.2017.00323

  • Embedding gender equality into institutional strategy.

    Ahmed S

    Global health, epidemiology and genomics 2017;2;e5

    PUBMED: 29868216; PMC: 5870430; DOI: 10.1017/gheg.2017.5

  • Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

    Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K et al.

    Database : the journal of biological databases and curation 2017;2017;1

    PUBMED: 28365736; PMC: 5467575; DOI: 10.1093/database/bax020

  • Evidence for Contemporary Switching of the O-Antigen Gene Cluster between Shiga Toxin-Producing Escherichia coli Strains Colonizing Cattle.

    Geue L, Menge C, Eichhorn I, Semmler T, Wieler LH, Pickard D, Berens C and Barth SA

    Frontiers in microbiology 2017;8;424

    PUBMED: 28377748; PMC: 5359238; DOI: 10.3389/fmicb.2017.00424

  • Faster Average Case Low Memory Semi-external Construction of the Burrows–Wheeler Transform

    Tischlerm G,

    Mathematics in Computer Science 2017;11;2;159-76

    DOI: 10.1007/s11786-017-0296-2

  • First Draft Genome Sequence of the Dourine Causative Agent: Trypanosoma Equiperdum Strain OVI.

    Hébert L, Moumen B, Madeline A, Steinbiss S, Lakhdar L, Van Reet N, Büscher P, Laugier C, Cauchard J and Petry S

    Journal of genomics 2017;5;1-3

    PUBMED: 28138343; PMC: 5278650; DOI: 10.7150/jgen.17904

  • Genetics in the 21st Century: Implications for patients, consumers and citizens.

    Roberts J and Middleton A

    F1000Research 2017;6;2020

    PUBMED: 29259772; PMC: 5721930.2; DOI: 10.12688/f1000research.12850.2

  • Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

    Yahara K, Méric G, Taylor AJ, de Vries SP, Murray S, Pascoe B, Mageiros L, Torralbo A, Vidal A, Ridley A et al.

    Environmental microbiology 2017;19;1;361-380

    PUBMED: 27883255; DOI: 10.1111/1462-2920.13628

  • Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells.

    Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM and Jackson SP

    Nature chemical biology 2017;13;1;12-14

    PUBMED: 27820796; PMC: 5164930; DOI: 10.1038/nchembio.2226

  • Increased Expression of a MicroRNA Correlates with Anthelmintic Resistance in Parasitic Nematodes.

    Gillan V, Maitland K, Laing R, Gu H, Marks ND, Winter AD, Bartley D, Morrison A, Skuce PJ, Rezansoff AM et al.

    Frontiers in cellular and infection microbiology 2017;7;452

    PUBMED: 29209592; PMC: 5701612; DOI: 10.3389/fcimb.2017.00452

  • Indexing variation graphs

    Sirén,J

    Proceedings of the Workshop on Algorithm Engineering and Experiments 2017;13

    DOI: 10.1137/1.9781611974768.2

  • Induction of Cell Cycle and NK Cell Responses by Live-Attenuated Oral Vaccines against Typhoid Fever.

    Blohmke CJ, Hill J, Darton TC, Carvalho-Burger M, Eustace A, Jones C, Schreiber F, Goodier MR, Dougan G, Nakaya HI and Pollard AJ

    Frontiers in immunology 2017;8;1276

    PUBMED: 29075261; PMC: 5643418; DOI: 10.3389/fimmu.2017.01276

  • Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance.

    Lotta LA, Gulati P, Day FR, Payne F, Ongen H, van de Bunt M, Gaulton KJ, Eicher JD, Sharp SJ, Luan J et al.

    Nature genetics 2017;49;1;17-26

    PUBMED: 27841877; PMC: 5774584; DOI: 10.1038/ng.3714

  • Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE.

    Wu YL, Stubbington MJ, Daly M, Teichmann SA and Rada C

    The Journal of experimental medicine 2017;214;1;183-196

    PUBMED: 27994069; PMC: 5206502; DOI: 10.1084/jem.20161056

  • Karyotype Evolution and Phylogenetic Relationships of Cricetulus sokolovi Orlov et Malygin 1988 (Cricetidae, Rodentia) Inferred from Chromosomal Painting and Molecular Data.

    Poplavskaya NS, Romanenko SA, Serdyukova NA, Trifonov VA, Yang F, Nie W, Wang J, Bannikova AA, Surov AV and Lebedev VS

    Cytogenetic and genome research 2017;152;2;65-72

    PUBMED: 28719894; DOI: 10.1159/000477521

  • Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis.

    Lees JA, Kremer PHC, Manso AS, Croucher NJ, Ferwerda B, Serón MV, Oggioni MR, Parkhill J, Brouwer MC, van der Ende A et al.

    Microbial genomics 2017;3;1;e000103

    PUBMED: 28348877; PMC: 5361624; DOI: 10.1099/mgen.0.000103

  • Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.

    Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium

    Molecular autism 2017;8;21

    PUBMED: 28540026; PMC: 5441062; DOI: 10.1186/s13229-017-0137-9

  • Microbial genome-wide association studies: lessons from human GWAS.

    Power RA, Parkhill J and de Oliveira T

    Nature reviews. Genetics 2017;18;1;41-50

    PUBMED: 27840430; DOI: 10.1038/nrg.2016.132

  • MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.

    Georgakopoulos-Soares I, Jain N, Gray JM and Hemberg M

    Bioinformatics (Oxford, England) 2017;33;1;137-138

    PUBMED: 27605100; PMC: 5198521; DOI: 10.1093/bioinformatics/btw584

  • No Functional Role for microRNA-342 in a Mouse Model of Pancreatic Acinar Carcinoma.

    Dooley J, Lagou V, Pasciuto E, Linterman MA, Prosser HM, Himmelreich U and Liston A

    Frontiers in oncology 2017;7;101

    PUBMED: 28573106; PMC: 5435746; DOI: 10.3389/fonc.2017.00101

  • Physical enrichment of transposon mutants from saturation mutant libraries using the TraDISort approach.

    Paulsen IT, Cain AK and Hassan KA

    Mobile genetic elements 2017;7;3;1-7

    PUBMED: 28580195; PMC: 5443658; DOI: 10.1080/2159256X.2017.1313805

  • Platelet responses to agonists in a cohort of highly characterised platelet donors are consistent over time.

    Garner SF, Furnell A, Kahan BC, Jones CI, Attwood A, Harrison P, Kelly AM, Goodall AH, Cardigan R and Ouwehand WH

    Vox sanguinis 2017;112;1;18-24

    PUBMED: 28001309; PMC: 5299478; DOI: 10.1111/vox.12468

  • Pooling strategy and chromosome painting characterize a living zebroid for the first time.

    Iannuzzi A, Pereira J, Iannuzzi C, Fu B and Ferguson-Smith M

    PloS one 2017;12;7;e0180158

    PUBMED: 28700625; PMC: 5507506; DOI: 10.1371/journal.pone.0180158

  • Prevalence of M75 Streptococcus pyogenes Strains Harboring slaA Gene in Patients Affected by Pediatric Obstructive Sleep Apnea Syndrome in Central Italy.

    Viciani E, Montagnani F, Tordini G, Romano A, Salerni L, De Luca A, Ruggiero P and Manetti AG

    Frontiers in microbiology 2017;8;294

    PUBMED: 28293224; PMC: 5329643; DOI: 10.3389/fmicb.2017.00294

  • PSCA and MUC1 in non-small-cell lung cancer as targets of chimeric antigen receptor T cells.

    Wei X, Lai Y, Li J, Qin L, Xu Y, Zhao R, Li B, Lin S, Wang S, Wu Q et al.

    Oncoimmunology 2017;6;3;e1284722

    PUBMED: 28405515; PMC: 5384358; DOI: 10.1080/2162402X.2017.1284722

  • PSM Scoring and Validation

    Wright, J.C and Choudhary, J.S

    New Developments in Mass Spectrometry 2017;Chapter 4;69-92

    DOI: 10.1039/9781782626732-00069

  • Recent advances in congenital heart disease genomics.

    Wilsdon A, Sifrim A, Hitz MP, Hurles M and Brook JD

    F1000Research 2017;6;869

    PUBMED: 28663792; PMC: 5473412; DOI: 10.12688/f1000research.10113.1

  • Targeting DNA Repair in Cancer: Beyond PARP Inhibitors.

    Brown JS, O'Carrigan B, Jackson SP and Yap TA

    Cancer discovery 2017;7;1;20-37

    PUBMED: 28003236; PMC: 5300099; DOI: 10.1158/2159-8290.CD-16-0860

  • Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

    Oshota O, Conway M, Fookes M, Schreiber F, Chaudhuri RR, Yu L, Morgan FJE, Clare S, Choudhary J, Thomson NR et al.

    PloS one 2017;12;8;e0181365

    PUBMED: 28796780; PMC: 5552096; DOI: 10.1371/journal.pone.0181365

  • Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.

    Agoti CN, Munywoki PK, Phan MVT, Otieno JR, Kamau E, Bett A, Kombe I, Githinji G, Medley GF, Cane PA et al.

    Virus evolution 2017;3;1;vex006

    PUBMED: 28458916; PMC: 5399923; DOI: 10.1093/ve/vex006

  • Whole-genome association study of antibody response to Epstein-Barr virus in an African population: a pilot.

    Sallah N, Carstensen T, Wakeham K, Bagni R, Labo N, Pollard MO, Gurdasani D, Ekoru K, Pomilla C, Young EH et al.

    Global health, epidemiology and genomics 2017;2;e18

    PUBMED: 29868224; PMC: 5870407; DOI: 10.1017/gheg.2017.16

  • Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae.

    Bossé JT, Li Y, Rogers J, Fernandez Crespo R, Li Y, Chaudhuri RR, Holden MT, Maskell DJ, Tucker AW, Wren BW et al.

    Frontiers in microbiology 2017;8;311

    PUBMED: 28321207; PMC: 5337627; DOI: 10.3389/fmicb.2017.00311

  • You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey.

    Roura Á, Doyle SR, Nande M and Strugnell JM

    Frontiers in physiology 2017;8;362

    PUBMED: 28620315; PMC: 5450036; DOI: 10.3389/fphys.2017.00362

2016

  • Phenotypic Characterization of Genetically Lowered Human Lipoprotein(a) Levels.

    Emdin CA, Khera AV, Natarajan P, Klarin D, Won HH, Peloso GM, Stitziel NO, Nomura A, Zekavat SM, Bick AG et al.

    Journal of the American College of Cardiology 2016;68;25;2761-2772

    PUBMED: 28007139; PMC: 5328146; DOI: 10.1016/j.jacc.2016.10.033

  • De Novo Mutations in EBF3 Cause a Neurodevelopmental Syndrome.

    Sleven H, Welsh SJ, Yu J, Churchill MEA, Wright CF, Henderson A, Horvath R, Rankin J, Vogt J, Magee A et al.

    American journal of human genetics 2016;100;1;138-150

    PUBMED: 28017370; PMC: 5223060; DOI: 10.1016/j.ajhg.2016.11.020

  • Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.

    Yebra G, Hodcroft EB, Ragonnet-Cronin ML, Pillay D, Brown AJ, PANGEA_HIV Consortium and ICONIC Project

    Scientific reports 2016;6;39489

    PUBMED: 28008945; PMC: 5180198; DOI: 10.1038/srep39489

  • An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus.

    Cotton JA, Steinbiss S, Yokoi T, Tsai IJ and Kikuchi T

    Scientific reports 2016;6;39749

    PUBMED: 28004836; PMC: 5177903; DOI: 10.1038/srep39749

  • Frequency doubling in the cyanobacterial circadian clock.

    Martins BM, Das AK, Antunes L and Locke JC

    Molecular systems biology 2016;12;12;896

    PUBMED: 28007935; PMC: 5199125; DOI: 10.15252/msb.20167087

  • Genome Sequences of a Novel Vietnamese Bat Bunyavirus.

    Oude Munnink BB, Phan MV, van der Hoek L, Kellam P, Cotten M and VIZIONS Consortium

    Genome announcements 2016;4;6

    PUBMED: 28007850; PMC: 5180378; DOI: 10.1128/genomeA.01366-16

  • Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification.

    Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, Rutledge GG, Redmond S, Manske M, Jyothi D et al.

    Malaria journal 2016;15;1;597

    PUBMED: 27998271; PMC: 5175302; DOI: 10.1186/s12936-016-1641-7

  • The mountainous Cretan dietary patterns and their relationship with cardiovascular risk factors: the Hellenic Isolated Cohorts MANOLIS study.

    Farmaki AE, Rayner NW, Matchan A, Spiliopoulou P, Gilly A, Kariakli V, Kiagiadaki C, Tsafantakis E, Zeggini E and Dedoussis G

    Public health nutrition 2016;20;6;1063-1074

    PUBMED: 27989266; DOI: 10.1017/S1368980016003207

  • Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease.

    Ji SG, Juran BD, Mucha S, Folseraas T, Jostins L, Melum E, Kumasaka N, Atkinson EJ, Schlicht EM, Liu JZ et al.

    Nature genetics 2016;49;2;269-273

    PUBMED: 27992413; PMC: 5540332; DOI: 10.1038/ng.3745

  • Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

    Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C et al.

    Oncogene 2016;36;19;2737-2749

    PUBMED: 27991928; PMC: 5442428; DOI: 10.1038/onc.2016.427

  • Dawning of the age of genomics for platelet granule disorders: improving insight, diagnosis and management.

    Bariana TK, Ouwehand WH, Guerrero JA, Gomez K and BRIDGE Bleeding, Thrombotic and Platelet Disorders and ThromboGenomics Consortia

    British journal of haematology 2016

    PUBMED: 27984638; DOI: 10.1111/bjh.14471

  • Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.

    Dolle DD, Liu Z, Cotten M, Simpson JT, Iqbal Z, Durbin R, McCarthy SA and Keane TM

    Genome research 2016;27;2;300-309

    PUBMED: 27986821; PMC: 5287235; DOI: 10.1101/gr.211748.116

  • Decreased Rate of Plasma Arginine Appearance in Murine Malaria May Explain Hypoargininemia in Children With Cerebral Malaria.

    Alkaitis MS, Wang H, Ikeda AK, Rowley CA, MacCormick IJ, Chertow JH, Billker O, Suffredini AF, Roberts DJ, Taylor TE et al.

    The Journal of infectious diseases 2016;214;12;1840-1849

    PUBMED: 27923948; PMC: 5142086; DOI: 10.1093/infdis/jiw452

  • PRMT5 is essential for the maintenance of chondrogenic progenitor cells in the limb bud.

    Norrie JL, Li Q, Co S, Huang BL, Ding D, Uy JC, Ji Z, Mackem S, Bedford MT, Galli A et al.

    Development (Cambridge, England) 2016;143;24;4608-4619

    PUBMED: 27827819; DOI: 10.1242/dev.140715

  • Radiographic endophenotyping in hip osteoarthritis improves the precision of genetic association analysis.

    Panoutsopoulou K, Thiagarajah S, Zengini E, Day-Williams AG, Ramos YF, Meessen JM, Huetink K, Nelissen RG, Southam L, Rayner NW et al.

    Annals of the rheumatic diseases 2016;76;7;1199-1206

    PUBMED: 27974301; PMC: 5530347; DOI: 10.1136/annrheumdis-2016-210373

  • Extensive Proliferation of a Subset of Differentiated, yet Plastic, Medial Vascular Smooth Muscle Cells Contributes to Neointimal Formation in Mouse Injury and Atherosclerosis Models.

    Chappell J, Harman JL, Narasimhan VM, Yu H, Foote K, Simons BD, Bennett MR and Jørgensen HF

    Circulation research 2016;119;12;1313-1323

    PUBMED: 27682618; PMC: 5149073; DOI: 10.1161/CIRCRESAHA.116.309799

  • Last parasite standing.

    Rutledge GG and Otto TD

    Nature reviews. Microbiology 2016;15;1;4

    PUBMED: 27932794; DOI: 10.1038/nrmicro.2016.181

  • Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing.

    Demeulemeester J, Kumar P, Møller EK, Nord S, Wedge DC, Peterson A, Mathiesen RR, Fjelldal R, Zamani Esteki M, Theunis K et al.

    Genome biology 2016;17;1;250

    PUBMED: 27931250; PMC: 5146893; DOI: 10.1186/s13059-016-1109-7

  • ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.

    Raine KM, Van Loo P, Wedge DC, Jones D, Menzies A, Butler AP, Teague JW, Tarpey P, Nik-Zainal S and Campbell PJ

    Current protocols in bioinformatics 2016;56;15.9.1-15.9.17

    PUBMED: 27930809; PMC: 6097604; DOI: 10.1002/cpbi.17

  • cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.

    Jones D, Raine KM, Davies H, Tarpey PS, Butler AP, Teague JW, Nik-Zainal S and Campbell PJ

    Current protocols in bioinformatics 2016;56;15.10.1-15.10.18

    PUBMED: 27930805; PMC: 6097605; DOI: 10.1002/cpbi.20

  • Genetic invalidation of Lp-PLA2 as a therapeutic target: Large-scale study of five functional Lp-PLA2-lowering alleles.

    Gregson JM, Freitag DF, Surendran P, Stitziel NO, Chowdhury R, Burgess S, Kaptoge S, Gao P, Staley JR, Willeit P et al.

    European journal of preventive cardiology 2016;24;5;492-504

    PUBMED: 27940953; PMC: 5460752; DOI: 10.1177/2047487316682186

  • Mutations in the Chromatin Regulator Gene BRPF1 Cause Syndromic Intellectual Disability and Deficient Histone Acetylation.

    Yan K, Rousseau J, Littlejohn RO, Kiss C, Lehman A, Rosenfeld JA, Stumpel CTR, Stegmann APA, Robak L, Scaglia F et al.

    American journal of human genetics 2016;100;1;91-104

    PUBMED: 27939640; PMC: 5223032; DOI: 10.1016/j.ajhg.2016.11.011

  • Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.

    Morgan AP, Didion JP, Doran AG, Holt JM, McMillan L, Keane TM and de Villena FP

    G3 (Bethesda, Md.) 2016;6;12;4211-4216

    PUBMED: 27765810; PMC: 5144988; DOI: 10.1534/g3.116.034751

  • Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster.

    Arora N, Schuenemann VJ, Jäger G, Peltzer A, Seitz A, Herbig A, Strouhal M, Grillová L, Sánchez-Busó L, Kühnert D et al.

    Nature microbiology 2016;2;16245

    PUBMED: 27918528; DOI: 10.1038/nmicrobiol.2016.245

  • Genomic variations leading to alterations in cell morphology of Campylobacter spp.

    Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK et al.

    Scientific reports 2016;6;38303

    PUBMED: 27910897; DOI: 10.1038/srep38303

  • Retracing embryological fate.

    Behjati S

    Science (New York, N.Y.) 2016;354;6316;1109

    PUBMED: 27934728; DOI: 10.1126/science.aal2189

  • Comprehensive Screening of Eight Known Causative Genes in Congenital Hypothyroidism With Gland-in-Situ.

    Nicholas AK, Serra EG, Cangul H, Alyaarubi S, Ullah I, Schoenmakers E, Deeb A, Habeb AM, Almaghamsi M, Peters C et al.

    The Journal of clinical endocrinology and metabolism 2016;101;12;4521-4531

    PUBMED: 27525530; PMC: 5155683; DOI: 10.1210/jc.2016-1879

  • Cytomegalovirus-Specific IL-10-Producing CD4+ T Cells Are Governed by Type-I IFN-Induced IL-27 and Promote Virus Persistence.

    Clement M, Marsden M, Stacey MA, Abdul-Karim J, Gimeno Brias S, Costa Bento D, Scurr MJ, Ghazal P, Weaver CT, Carlesso G et al.

    PLoS pathogens 2016;12;12;e1006050

    PUBMED: 27926930; DOI: 10.1371/journal.ppat.1006050

  • Dataset for a Dugesia japonica de novo transcriptome assembly, utilized for defining the voltage-gated like ion channel superfamily.

    Chan JD, Zhang D, Liu X, Zarowiecki MZ, Berriman M and Marchant JS

    Data in brief 2016;9;1044-1047

    PUBMED: 27909700; PMC: 5124351; DOI: 10.1016/j.dib.2016.11.022

  • DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.

    Farlik M, Halbritter F, Müller F, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A et al.

    Cell stem cell 2016;19;6;808-822

    PUBMED: 27867036; PMC: 5145815; DOI: 10.1016/j.stem.2016.10.019

  • Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.

    Seni J, Mshana SE, Msigwa F, Matee M, Mazigo H, Parkhill J, Holmes MA and Paterson GK

    Genome announcements 2016;4;6

    PUBMED: 27908999; PMC: 5137413; DOI: 10.1128/genomeA.01345-16

  • Eye on the B-ALL: B-cell receptor repertoires reveal persistence of numerous B-lymphoblastic leukemia subclones from diagnosis to relapse.

    Bashford-Rogers RJ, Nicolaou KA, Bartram J, Goulden NJ, Loizou L, Koumas L, Chi J, Hubank M, Kellam P, Costeas PA and Vassiliou GS

    Leukemia 2016;30;12;2312-2321

    PUBMED: 27211266; PMC: 5155029; DOI: 10.1038/leu.2016.142

  • Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.

    Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E and Orlando L

    Molecular biology and evolution 2016;33;12;3284-3298

    PUBMED: 27624717; PMC: 5100044; DOI: 10.1093/molbev/msw184

  • Optimized inducible shRNA and CRISPR/Cas9 platforms for in vitro studies of human development using hPSCs.

    Bertero A, Pawlowski M, Ortmann D, Snijders K, Yiangou L, Cardoso de Brito M, Brown S, Bernard WG, Cooper JD, Giacomelli E et al.

    Development (Cambridge, England) 2016;143;23;4405-4418

    PUBMED: 27899508; PMC: 5201041; DOI: 10.1242/dev.138081

  • Report of a Meeting on Contemporary Topics in Zebrafish Husbandry and Care.

    Osborne N, Paull G, Grierson A, Dunford K, Busch-Nentwich EM, Sneddon LU, Wren N, Higgins J and Hawkins P

    Zebrafish 2016;13;6;584-589

    PUBMED: 27537782; PMC: 5124746; DOI: 10.1089/zeb.2016.1324

  • Validation of self-administered nasal swabs and postage for the isolation of Staphylococcus aureus.

    Harrison EM, Gleadall NS, Ba X, Danesh J, Peacock SJ and Holmes M

    Journal of medical microbiology 2016;65;12;1434-1437

    PUBMED: 27902394; PMC: 5203668; DOI: 10.1099/jmm.0.000381

  • Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant Staphylococcus aureus ST93 clone in a remote Indigenous community.

    Meumann EM, Andersson P, Yeaman F, Oldfield S, Lilliebridge R, Bentley SD, Krause V, Beaman M, Currie BJ, Holt DC et al.

    Microbial genomics 2016;2;12;e000098

    PUBMED: 28348837; PMC: 5359412; DOI: 10.1099/mgen.0.000098

  • Clinical features associated with CTNNB1 de novo loss of function mutations in ten individuals.

    Kharbanda M, Pilz DT, Tomkins S, Chandler K, Saggar A, Fryer A, McKay V, Louro P, Smith JC, Burn J et al.

    European journal of medical genetics 2016;60;2;130-135

    PUBMED: 27915094; PMC: 6070129; DOI: 10.1016/j.ejmg.2016.11.008

  • Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

    Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H et al.

    Microbial genomics 2016;2;11;e000093

    PUBMED: 28348833; PMC: 5320705; DOI: 10.1099/mgen.0.000093

  • Rapid detection and evolutionary analysis of Legionella pneumophila serogroup 1 sequence type 47.

    Mentasti M, Cassier P, David S, Ginevra C, Gomez-Valero L, Underwood A, Afshar B, Etienne J, Parkhill J, Chalker V et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016;23;4;264.e1-264.e9

    PUBMED: 27915212; DOI: 10.1016/j.cmi.2016.11.019

  • The need for an integrated approach for chronic disease research and care in Africa

    BARR, A.L., YOUNG, E.H., Smeeth, L., Newton, R., Seeley, J. et al.

    Global Health, Epidemiology and Genomics 2016;1;e19

    DOI: 10.1017/gheg.2016.16; URL: https://www.cambridge.org/core/jo...urnals/global-health-epidemiology-and-genomics/article/need-for-an-integrated-approach-for-chronic-disease-research-and-care-in-africa/8577B62385A0DF911C1AB375C1F37EB9

  • Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi.

    Ravenhall M, Benavente ED, Mipando M, Jensen AT, Sutherland CJ, Roper C, Sepúlveda N, Kwiatkowski DP, Montgomery J, Phiri KS et al.

    Malaria journal 2016;15;1;575

    PUBMED: 27899115; PMC: 5129638; DOI: 10.1186/s12936-016-1634-6

  • Expansion of the Gene Ontology knowledgebase and resources.

    The Gene Ontology Consortium

    Nucleic acids research 2016;45;D1;D331-D338

    PUBMED: 27899567; PMC: 5210579; DOI: 10.1093/nar/gkw1108

  • Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.

    Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A et al.

    Nature communications 2016;7;13555

    PUBMED: 27898055; PMC: 5141286; DOI: 10.1038/ncomms13555

  • Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health.

    Jubb HC, Pandurangan AP, Turner MA, Ochoa-Montaño B, Blundell TL and Ascher DB

    Progress in biophysics and molecular biology 2016

    PUBMED: 27913149; DOI: 10.1016/j.pbiomolbio.2016.10.002

  • Open Targets: a platform for therapeutic target identification and validation.

    Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E et al.

    Nucleic acids research 2016;45;D1;D985-D994

    PUBMED: 27899665; PMC: 5210543; DOI: 10.1093/nar/gkw1055

  • Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression.

    Rangel R, Lee SC, Hon-Kim Ban K, Guzman-Rojas L, Mann MB, Newberg JY, Kodama T, McNoe LA, Selvanesan L, Ward JM et al.

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;48;E7749-E7758

    PUBMED: 27849608; PMC: 5137755; DOI: 10.1073/pnas.1613859113

  • COSMIC: somatic cancer genetics at high-resolution.

    Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, Cole CG, Ward S, Dawson E, Ponting L et al.

    Nucleic acids research 2016;45;D1;D777-D783

    PUBMED: 27899578; PMC: 5210583; DOI: 10.1093/nar/gkw1121

  • Ensembl 2017.

    Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P et al.

    Nucleic acids research 2016

    PUBMED: 27899575; DOI: 10.1093/nar/gkw1104

  • WormBase ParaSite - a comprehensive resource for helminth genomics.

    Howe KL, Bolt BJ, Shafie M, Kersey P and Berriman M

    Molecular and biochemical parasitology 2016;215;2-10

    PUBMED: 27899279; PMC: 5486357; DOI: 10.1016/j.molbiopara.2016.11.005

  • A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape.

    Ried JS, Jeff M J, Chu AY, Bragg-Gresham JL, van Dongen J, Huffman JE, Ahluwalia TS, Cadby G, Eklund N, Eriksson J et al.

    Nature communications 2016;7;13357

    PUBMED: 27876822; PMC: 5114527; DOI: 10.1038/ncomms13357

  • Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.

    Haber M, Mezzavilla M, Bergström A, Prado-Martinez J, Hallast P, Saif-Ali R, Al-Habori M, Dedoussis G, Zeggini E, Blue-Smith J et al.

    American journal of human genetics 2016;99;6;1316-1324

    PUBMED: 27889059; PMC: 5142112; DOI: 10.1016/j.ajhg.2016.10.012

  • Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

    Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I and Wessels LF

    Scientific reports 2016;6;36812

    PUBMED: 27876821; PMC: 5120272; DOI: 10.1038/srep36812

  • Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont.

    Bennuru S, Cotton JA, Ribeiro JM, Grote A, Harsha B, Holroyd N, Mhashilkar A, Molina DM, Randall AZ, Shandling AD et al.

    mBio 2016;7;6

    PUBMED: 27881553; PMC: 5137501; DOI: 10.1128/mBio.02028-16

  • The genome of Onchocerca volvulus, agent of river blindness.

    Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N et al.

    Nature microbiology 2016;2;16216

    PUBMED: 27869790; PMC: 5310847; DOI: 10.1038/nmicrobiol.2016.216

  • Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA.

    Sigsgaard EE, Nielsen IB, Bach SS, Lorenzen ED, Robinson DP, Knudsen SW, Pedersen MW, Jaidah MA, Orlando L, Willerslev E et al.

    Nature ecology & evolution 2016;1;1;4

    PUBMED: 28812572; DOI: 10.1038/s41559-016-0004

  • The Role of Folate Transport in Antifolate Drug Action in Trypanosoma brucei.

    Dewar S, Sienkiewicz N, Ong HB, Wall RJ, Horn D and Fairlamb AH

    The Journal of biological chemistry 2016;291;47;24768-24778

    PUBMED: 27703008; PMC: 5114424; DOI: 10.1074/jbc.M116.750422

  • Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study.

    Grundmann H, Glasner C, Albiger B, Aanensen DM, Tomlinson CT, Andrasević AT, Cantón R, Carmeli Y, Friedrich AW, Giske CG et al.

    The Lancet. Infectious diseases 2016;17;2;153-163

    PUBMED: 27866944; DOI: 10.1016/S1473-3099(16)30257-2

  • The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

    Astle WJ, Elding H, Jiang T, Allen D, Ruklisa D, Mann AL, Mead D, Bouman H, Riveros-Mckay F, Kostadima MA et al.

    Cell 2016;167;5;1415-1429.e19

    PUBMED: 27863252; PMC: 5300907; DOI: 10.1016/j.cell.2016.10.042

  • Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

    Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S et al.

    Cell 2016;167;5;1398-1414.e24

    PUBMED: 27863251; PMC: 5119954; DOI: 10.1016/j.cell.2016.10.026

  • Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

    Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ et al.

    Cell 2016;167;5;1369-1384.e19

    PUBMED: 27863249; DOI: 10.1016/j.cell.2016.09.037

  • A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules.

    Labbate M, Orata FD, Petty NK, Jayatilleke ND, King WL, Kirchberger PC, Allen C, Mann G, Mutreja A, Thomson NR et al.

    Scientific reports 2016;6;36891

    PUBMED: 27845364; PMC: 5109276; DOI: 10.1038/srep36891

  • A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes.

    Auburn S, Böhme U, Steinbiss S, Trimarsanto H, Hostetler J, Sanders M, Gao Q, Nosten F, Newbold CI, Berriman M et al.

    Wellcome open research 2016;1;4

    PUBMED: 28008421; PMC: 5172418; DOI: 10.12688/wellcomeopenres.9876.1

  • A time transect of exomes from a Native American population before and after European contact.

    Lindo J, Huerta-Sánchez E, Nakagome S, Rasmussen M, Petzelt B, Mitchell J, Cybulski JS, Willerslev E, DeGiorgio M and Malhi RS

    Nature communications 2016;7;13175

    PUBMED: 27845766; PMC: 5116069; DOI: 10.1038/ncomms13175

  • Circulation of multiple genotypes of H1N2 viruses in a swine farm in Italy over a two-month period.

    Beato MS, Tassoni L, Milani A, Salviato A, Di Martino G, Mion M, Bonfanti L, Monne I, Watson SJ and Fusaro A

    Veterinary microbiology 2016;195;25-29

    PUBMED: 27771067; DOI: 10.1016/j.vetmic.2016.08.015

  • Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.

    Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JHA, Pourfarzad F, Kuijpers TW, Burden F, Farrow S et al.

    Cell reports 2016;17;8;2101-2111

    PUBMED: 27851971; PMC: 5889099; DOI: 10.1016/j.celrep.2016.10.054

  • eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.

    Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M et al.

    Cell reports 2016;17;8;2137-2150

    PUBMED: 27851974; PMC: 5120369; DOI: 10.1016/j.celrep.2016.10.059

  • Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013.

    Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D and Lipsitch M

    The Journal of infectious diseases 2016;214;10;1579-1587

    PUBMED: 27638945; PMC: 5091375; DOI: 10.1093/infdis/jiw420

  • Quantifying side-chain conformational variations in protein structure.

    Miao Z and Cao Y

    Scientific reports 2016;6;37024

    PUBMED: 27845406; PMC: 5109468; DOI: 10.1038/srep37024

  • Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification.

    Wagner J, Coupland P, Browne HP, Lawley TD, Francis SC and Parkhill J

    BMC microbiology 2016;16;1;274

    PUBMED: 27842515; PMC: 5109829; DOI: 10.1186/s12866-016-0891-4

  • Genomic prediction of coronary heart disease.

    Abraham G, Havulinna AS, Bhalala OG, Byars SG, De Livera AM, Yetukuri L, Tikkanen E, Perola M, Schunkert H, Sijbrands EJ et al.

    European heart journal 2016;37;43;3267-3278

    PUBMED: 27655226; PMC: 5146693; DOI: 10.1093/eurheartj/ehw450

  • A non-endoscopic device to sample the oesophageal microbiota: a case-control study.

    Elliott DRF, Walker AW, O'Donovan M, Parkhill J and Fitzgerald RC

    The lancet. Gastroenterology & hepatology 2016;2;1;32-42

    PUBMED: 28404012; PMC: 5656094; DOI: 10.1016/S2468-1253(16)30086-3

  • Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.

    Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P et al.

    Science (New York, N.Y.) 2016;354;6313;751-757

    PUBMED: 27846606; PMC: 5142603; DOI: 10.1126/science.aaf8156

  • Ideal cardiovascular health influences cardiovascular disease risk associated with high lipoprotein(a) levels and genotype: The EPIC-Norfolk prospective population study.

    Perrot N, Verbeek R, Sandhu M, Boekholdt SM, Hovingh GK, Wareham NJ, Khaw KT and Arsenault BJ

    Atherosclerosis 2016;256;47-52

    PUBMED: 27998826; DOI: 10.1016/j.atherosclerosis.2016.11.010

  • Species Mash-up.

    Argimón S and Aanensen DM

    Nature reviews. Microbiology 2016;14;12;730

    PUBMED: 27833107; DOI: 10.1038/nrmicro.2016.175

  • Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.

    Weisser H, Wright JC, Mudge JM, Gutenbrunner P and Choudhary JS

    Journal of proteome research 2016;15;12;4686-4695

    PUBMED: 27786492; PMC: 5703597; DOI: 10.1021/acs.jproteome.6b00765

  • Analysis of anti-malarial resistance markers in pfmdr1 and pfcrt across Southeast Asia in the Tracking Resistance to Artemisinin Collaboration.

    Srimuang K, Miotto O, Lim P, Fairhurst RM, Kwiatkowski DP, Woodrow CJ, Imwong M and Tracking Resistance to Artemisinin Collaboration

    Malaria journal 2016;15;1;541

    PUBMED: 27825353; PMC: 5101715; DOI: 10.1186/s12936-016-1598-6

  • Mitochondrial Protein Lipoylation and the 2-Oxoglutarate Dehydrogenase Complex Controls HIF1α Stability in Aerobic Conditions.

    Burr SP, Costa AS, Grice GL, Timms RT, Lobb IT, Freisinger P, Dodd RB, Dougan G, Lehner PJ, Frezza C and Nathan JA

    Cell metabolism 2016;24;5;740-752

    PUBMED: 27923773; PMC: 5106373; DOI: 10.1016/j.cmet.2016.09.015

  • Perturbed hematopoietic stem and progenitor cell hierarchy in myelodysplastic syndromes patients with monosomy 7 as the sole cytogenetic abnormality.

    Dimitriou M, Woll PS, Mortera-Blanco T, Karimi M, Wedge DC, Doolittle H, Douagi I, Papaemmanuil E, Jacobsen SE and Hellström-Lindberg E

    Oncotarget 2016;7;45;72685-72698

    PUBMED: 27683035; PMC: 5341937; DOI: 10.18632/oncotarget.12234

  • Single-cell analysis at the threshold.

    Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV and Teichmann SA

    Nature biotechnology 2016;34;11;1111-1118

    PUBMED: 27824834; DOI: 10.1038/nbt.3721

  • Understanding pneumococcal serotype 1 biology through population genomic analysis.

    Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M et al.

    BMC infectious diseases 2016;16;1;649

    PUBMED: 27821148; PMC: 5100261; DOI: 10.1186/s12879-016-1987-z

  • EphrinB1/EphB3b Coordinate Bidirectional Epithelial-Mesenchymal Interactions Controlling Liver Morphogenesis and Laterality.

    Cayuso J, Dzementsei A, Fischer JC, Karemore G, Caviglia S, Bartholdson J, Wright GJ and Ober EA

    Developmental cell 2016;39;3;316-328

    PUBMED: 27825440; PMC: 5107609; DOI: 10.1016/j.devcel.2016.10.009

  • Genome-wide association studies of quantitative glycaemic traits

    Barroso,I. and Scott,R.

    The Genetics of Type 2 Diabetes and Related Traits: Biology, Physiology and Translation 2016;63-89

    DOI: 10.1007/978-3-319-01574-3_3; URL: https://dx.doi.org/10.1007/97...8-3-319-01574-3_3

  • Microbial Genomics: Diagnosis, Prevention, and Treatment

    Mutreja,A.

    Medical and Health Genomics 2016;101-6

    DOI: 10.1016/B978-0-12-420196-5.00008-3; URL: https://dx.doi.org/10.1016/B9...78-0-12-420196-5.00008-3

  • Mutational signatures associated with tobacco smoking in human cancer.

    Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T et al.

    Science (New York, N.Y.) 2016;354;6312;618-622

    PUBMED: 27811275; PMC: 6141049; DOI: 10.1126/science.aag0299

  • New Approaches for Needed Vaccines: Bacteria

    MacLennan,C.A., Mutreja,A. and Dougan,G.

    The Vaccine Book: Second Edition 2016;311-29

    DOI: 10.1016/B978-0-12-802174-3.00016-3; URL: https://dx.doi.org/10.1016/B9...78-0-12-802174-3.00016-3

  • Notes on the implementation of FAM

    Angelopoulos,N

    CEUR Workshop Proceedings 2016;1661;46-58

    URL: https://ceur-ws.org/Vol-1661/p...aper-05.pdf

  • RLZAP: Relative lempel-Ziv with adaptive pointers

    Cox,A.J., Farruggia,A., Gagie,T., Puglisi,S.J. and Siren,J.

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2016;9954 LNCS;1-14

    DOI: 10.1007/978-3-319-46049-9_1; URL: https://dx.doi.org/10.1007/97...8-3-319-46049-9_1

  • Comparative Antibody Responses Against three Antimalarial Vaccine Candidate Antigens from Urban and Rural Exposed Individuals in Gabon.

    Imboumy-Limoukou RK, Oyegue-Liabagui SL, Ndidi S, Pegha-Moukandja I, Kouna CL, Galaway F, Florent I and Lekana-Douki JB

    European journal of microbiology & immunology 2016;6;4;287-297

    PUBMED: 27980857; PMC: 5146647; DOI: 10.1556/1886.2016.00027

  • Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

    Fazal MA, Alexander S, Burnett E, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J and Russell JE

    Genome announcements 2016;4;6

    PUBMED: 27811100; PMC: 5095470; DOI: 10.1128/genomeA.01219-16

  • Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.

    Amato R, Lim P, Miotto O, Amaratunga C, Dek D, Pearson RD, Almagro-Garcia J, Neal AT, Sreng S, Suon S et al.

    The Lancet. Infectious diseases 2016;17;2;164-173

    PUBMED: 27818095; PMC: 5564489; DOI: 10.1016/S1473-3099(16)30409-1

  • Harmine Induces Adipocyte Thermogenesis through RAC1-MEK-ERK-CHD4 Axis.

    Nie T, Hui X, Mao L, Nie B, Li K, Sun W, Gao X, Tang X, Xu Y, Jiang B et al.

    Scientific reports 2016;6;36382

    PUBMED: 27805061; PMC: 5090989; DOI: 10.1038/srep36382

  • Powerful decomposition of complex traits in a diploid model.

    Hallin J, Märtens K, Young AI, Zackrisson M, Salinas F, Parts L, Warringer J and Liti G

    Nature communications 2016;7;13311

    PUBMED: 27804950; PMC: 5097135; DOI: 10.1038/ncomms13311

  • Activation of Bicyclic Nitro-drugs by a Novel Nitroreductase (NTR2) in Leishmania.

    Wyllie S, Roberts AJ, Norval S, Patterson S, Foth BJ, Berriman M, Read KD and Fairlamb AH

    PLoS pathogens 2016;12;11;e1005971

    PUBMED: 27812217; PMC: 5094698; DOI: 10.1371/journal.ppat.1005971

  • Genetic Predisposition to an Impaired Metabolism of the Branched-Chain Amino Acids and Risk of Type 2 Diabetes: A Mendelian Randomisation Analysis.

    Lotta LA, Scott RA, Sharp SJ, Burgess S, Luan J, Tillin T, Schmidt AF, Imamura F, Stewart ID, Perry JR et al.

    PLoS medicine 2016;13;11;e1002179

    PUBMED: 27898682; PMC: 5127513; DOI: 10.1371/journal.pmed.1002179

  • Genetic support for the causal role of insulin in coronary heart disease.

    Tikkanen E, Pirinen M, Sarin AP, Havulinna AS, Männistö S, Saltevo J, Lokki ML, Sinisalo J, Lundqvist A, Jula A et al.

    Diabetologia 2016;59;11;2369-2377

    PUBMED: 27561896; DOI: 10.1007/s00125-016-4081-6

  • Identification of new heat-stable (STa) enterotoxin allele variants produced by human enterotoxigenic Escherichia coli (ETEC).

    Joffré E, von Mentzer A, Svennerholm AM and Sjöling Å

    International journal of medical microbiology : IJMM 2016;306;7;586-594

    PUBMED: 27350142; DOI: 10.1016/j.ijmm.2016.05.016

  • New texts in science communication.

    Roberts J

    Public understanding of science (Bristol, England) 2016;25;8;1014-1016

    PUBMED: 27856830; DOI: 10.1177/0963662515619545

  • Reduced Efficacy of Praziquantel Against Schistosoma mansoni Is Associated With Multiple Rounds of Mass Drug Administration.

    Crellen T, Walker M, Lamberton PH, Kabatereine NB, Tukahebwa EM, Cotton JA and Webster JP

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016;63;9;1151-1159

    PUBMED: 27470241; PMC: 5064161; DOI: 10.1093/cid/ciw506

  • Six-Year Incidence of Blindness and Visual Impairment in Kenya: The Nakuru Eye Disease Cohort Study.

    Bastawrous A, Mathenge W, Wing K, Rono H, Gichangi M, Weiss HA, Macleod D, Foster A, Burton MJ and Kuper H

    Investigative ophthalmology & visual science 2016;57;14;5974-5983

    PUBMED: 27820953; PMC: 5102568; DOI: 10.1167/iovs.16-19835

  • Tyrosine kinase 2 is not limiting human antiviral type III interferon responses.

    Fuchs S, Kaiser-Labusch P, Bank J, Ammann S, Kolb-Kokocinski A, Edelbusch C, Omran H and Ehl S

    European journal of immunology 2016;46;11;2639-2649

    PUBMED: 27615517; DOI: 10.1002/eji.201646519

  • Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole.

    Fougère A, Jackson AP, Bechtsi DP, Braks JA, Annoura T, Fonager J, Spaccapelo R, Ramesar J, Chevalley-Maurel S, Klop O et al.

    PLoS pathogens 2016;12;11;e1005917

    PUBMED: 27851824; PMC: 5113031; DOI: 10.1371/journal.ppat.1005917

  • WGS analysis and molecular resistance mechanisms of azithromycin-resistant (MIC >2 mg/L) Neisseria gonorrhoeae isolates in Europe from 2009 to 2014.

    Jacobsson S, Golparian D, Cole M, Spiteri G, Martin I, Bergheim T, Borrego MJ, Crowley B, Crucitti T, Van Dam AP et al.

    The Journal of antimicrobial chemotherapy 2016;71;11;3109-3116

    PUBMED: 27432597; DOI: 10.1093/jac/dkw279

  • Association of breast cancer risk in BRCA1 and BRCA2 mutation carriers with genetic variants showing differential allelic expression: identification of a modifier of breast cancer risk at locus 11q22.3.

    Hamdi Y, Soucy P, Kuchenbaeker KB, Pastinen T, Droit A, Lemaçon A, Adlard J, Aittomäki K, Andrulis IL, Arason A et al.

    Breast cancer research and treatment 2016

    PUBMED: 27796716; DOI: 10.1007/s10549-016-4018-2

  • FHF1 (FGF12) epileptic encephalopathy.

    Al-Mehmadi S, Splitt M, For DDD Study group*, Ramesh V, DeBrosse S, Dessoffy K, Xia F, Yang Y, Rosenfeld JA, Cossette P et al.

    Neurology. Genetics 2016;2;6;e115

    PUBMED: 27830185; PMC: 5087254; DOI: 10.1212/NXG.0000000000000115

  • Chimpanzee genomic diversity reveals ancient admixture with bonobos.

    de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P et al.

    Science (New York, N.Y.) 2016;354;6311;477-481

    PUBMED: 27789843; PMC: 5546212; DOI: 10.1126/science.aag2602

  • Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms.

    Hore TA, von Meyenn F, Ravichandran M, Bachman M, Ficz G, Oxley D, Santos F, Balasubramanian S, Jurkowski TP and Reik W

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;43;12202-12207

    PUBMED: 27729528; PMC: 5086989; DOI: 10.1073/pnas.1608679113

  • The mitochondrial protein CHCHD2 primes the differentiation potential of human induced pluripotent stem cells to neuroectodermal lineages.

    Zhu L, Gomez-Duran A, Saretzki G, Jin S, Tilgner K, Melguizo-Sanchis D, Anyfantis G, Al-Aama J, Vallier L, Chinnery P et al.

    The Journal of cell biology 2016;215;2;187-202

    PUBMED: 27810911; PMC: 5084643; DOI: 10.1083/jcb.201601061

  • The state of play in higher eukaryote gene annotation.

    Mudge JM and Harrow J

    Nature reviews. Genetics 2016

    PUBMED: 27773922; DOI: 10.1038/nrg.2016.119

  • Comparison of high-throughput sequencing data compression tools.

    Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M and Sahinalp SC

    Nature methods 2016;13;12;1005-1008

    PUBMED: 27776113; DOI: 10.1038/nmeth.4037

  • Compound heterozygous variants in NBAS as a cause of atypical osteogenesis imperfecta.

    Balasubramanian M, Hurst J, Brown S, Bishop NJ, Arundel P, DeVile C, Pollitt RC, Crooks L, Longman D, Caceres JF et al.

    Bone 2016;94;65-74

    PUBMED: 27789416; PMC: 6067660; DOI: 10.1016/j.bone.2016.10.023

  • Genomic heterogeneity of multiple synchronous lung cancer.

    Liu Y, Zhang J, Li L, Yin G, Zhang J, Zheng S, Cheung H, Wu N, Lu N, Mao X et al.

    Nature communications 2016;7;13200

    PUBMED: 27767028; DOI: 10.1038/ncomms13200

  • HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni.

    Suttiprapa S, Rinaldi G, Tsai IJ, Mann VH, Dubrovsky L, Yan HB, Holroyd N, Huckvale T, Durrant C, Protasio AV et al.

    PLoS pathogens 2016;12;10;e1005931

    PUBMED: 27764257; PMC: 5072744; DOI: 10.1371/journal.ppat.1005931

  • Insulin resistance uncoupled from dyslipidemia due to C-terminal PIK3R1 mutations.

    Huang-Doran I, Tomlinson P, Payne F, Gast A, Sleigh A, Bottomley W, Harris J, Daly A, Rocha N, Rudge S et al.

    JCI insight 2016;1;17;e88766

    PUBMED: 27766312; PMC: 5070960; DOI: 10.1172/jci.insight.88766

  • Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca(2+) channel in neuromuscular function and regeneration.

    Chan JD, Zhang D, Liu X, Zarowiecki MZ, Berriman M and Marchant JS

    Biochimica et biophysica acta 2016

    PUBMED: 27771293; DOI: 10.1016/j.bbamcr.2016.10.010

  • A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia.

    Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M et al.

    Cell reports 2016;17;4;1193-1205

    PUBMED: 27760321; PMC: 5081405; DOI: 10.1016/j.celrep.2016.09.079

  • Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand.

    Auburn S, Serre D, Pearson RD, Amato R, Sriprawat K, To S, Handayuni I, Suwanarusk R, Russell B, Drury E et al.

    The Journal of infectious diseases 2016;214;8;1235-42

    PUBMED: 27456706; PMC: 5034950; DOI: 10.1093/infdis/jiw323

  • A novel signalling screen demonstrates that CALR mutations activate essential MAPK signalling and facilitate megakaryocyte differentiation.

    Kollmann K, Warsch W, Gonzalez-Arias C, Nice FL, Avezov E, Milburn J, Li J, Dimitropoulou D, Biddie S, Wang M et al.

    Leukemia 2016

    PUBMED: 27740635; DOI: 10.1038/leu.2016.280

  • Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene.

    Balasubramanian M, Lord H, Levesque S, Guturu H, Thuriot F, Sillon G, Wenger AM, Sureka DL, Lester T, Johnson DS et al.

    Journal of medical genetics 2016;54;3;157-165

    PUBMED: 27738187; DOI: 10.1136/jmedgenet-2016-104143

  • Genome-wide associations for birth weight and correlations with adult disease.

    Horikoshi M, Beaumont RN, Day FR, Warrington NM, Kooijman MN, Fernandez-Tajes J, Feenstra B, van Zuydam NR, Gaulton KJ, Grarup N et al.

    Nature 2016;538;7624;248-252

    PUBMED: 27680694; PMC: 5164934; DOI: 10.1038/nature19806

  • Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis.

    Martin CA, Murray JE, Carroll P, Leitch A, Mackenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A et al.

    Genes & development 2016;30;19;2158-2172

    PUBMED: 27737959; PMC: 5088565; DOI: 10.1101/gad.286351.116

  • A CRISPR outlook for apicomplexans.

    Carrasquilla M and Owusu CK

    Nature reviews. Microbiology 2016;14;11;668

    PUBMED: 27795546; DOI: 10.1038/nrmicro.2016.153

  • A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns.

    Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AM, Kim JC et al.

    Nature 2016;538;7625;378-382

    PUBMED: 27732578; PMC: 5446075; DOI: 10.1038/nature19823

  • No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.

    Loley C, Alver M, Assimes TL, Bjonnes A, Goel A, Gustafsson S, Hernesniemi J, Hopewell JC, Kanoni S, Kleber ME et al.

    Scientific reports 2016;6;35278

    PUBMED: 27731410; PMC: 5059659; DOI: 10.1038/srep35278

  • Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction.

    Foster TL, Wilson H, Iyer SS, Coss K, Doores K, Smith S, Kellam P, Finzi A, Borrow P, Hahn BH and Neil SJD

    Cell host & microbe 2016;20;4;429-442

    PUBMED: 27640936; PMC: 5075283; DOI: 10.1016/j.chom.2016.08.006

  • ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex.

    Timms RT, Tchasovnikarova IA, Antrobus R, Dougan G and Lehner PJ

    Cell reports 2016;17;3;653-659

    PUBMED: 27732843; DOI: 10.1016/j.celrep.2016.09.050

  • COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer.

    Forbes SA, Beare D, Bindal N, Bamford S, Ward S, Cole CG, Jia M, Kok C, Boutselakis H, De T et al.

    Current protocols in human genetics 2016;91;10.11.1-10.11.37

    PUBMED: 27727438; DOI: 10.1002/cphg.21

  • The type III secretion system effector SeoC of Salmonella enterica subspecies salamae and arizonae ADP-ribosylates Src and inhibits opsono-phagocytosis.

    Pollard DJ, Young JC, Covarelli V, Herrera-León S, Connor TR, Fookes M, Walker D, Echeita A, Thomson NR, Berger CN and Frankel G

    Infection and immunity 2016

    PUBMED: 27736780; DOI: 10.1128/IAI.00704-16

  • Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification.

    von Meyenn F, Berrens RV, Andrews S, Santos F, Collier AJ, Krueger F, Osorno R, Dean W, Rugg-Gunn PJ and Reik W

    Developmental cell 2016;39;1;104-115

    PUBMED: 27728778; PMC: 5064768; DOI: 10.1016/j.devcel.2016.09.015

  • Environmental context for understanding the iconic adaptive radiation of cichlid fishes in Lake Malawi.

    Malinsky M and Salzburger W

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;42;11654-11656

    PUBMED: 27791049; PMC: 5081610; DOI: 10.1073/pnas.1614272113

  • An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.

    Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M et al.

    Nature communications 2016;7;12827

    PUBMED: 27703135; DOI: 10.1038/ncomms12827

  • Association Between Low-Density Lipoprotein Cholesterol-Lowering Genetic Variants and Risk of Type 2 Diabetes: A Meta-analysis.

    Lotta LA, Sharp SJ, Burgess S, Perry JRB, Stewart ID, Willems SM, Luan J, Ardanaz E, Arriola L, Balkau B et al.

    JAMA 2016;316;13;1383-1391

    PUBMED: 27701660; PMC: 5386134; DOI: 10.1001/jama.2016.14568

  • The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.

    Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB et al.

    Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2016;26;1;126-135

    PUBMED: 27697780; PMC: 5224974; DOI: 10.1158/1055-9965.EPI-16-0106

  • Alternative Splicing May Not Be the Key to Proteome Complexity.

    Tress ML, Abascal F and Valencia A

    Trends in biochemical sciences 2016;42;2;98-110

    PUBMED: 27712956; PMC: 6526280; DOI: 10.1016/j.tibs.2016.08.008

  • Reference-based phasing using the Haplotype Reference Consortium panel.

    Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y, K Finucane H, Schoenherr S, Forer L, McCarthy S, Abecasis GR et al.

    Nature genetics 2016;48;11;1443-1448

    PUBMED: 27694958; PMC: 5096458; DOI: 10.1038/ng.3679

  • Tissue-specific mutation accumulation in human adult stem cells during life.

    Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P et al.

    Nature 2016;538;7624;260-264

    PUBMED: 27698416; PMC: 5536223; DOI: 10.1038/nature19768

  • Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks.

    Harrison EM, Ludden C, Brodrick HJ, Blane B, Brennan G, Morris D, Coll F, Reuter S, Brown NM, Holmes MA et al.

    Genome medicine 2016;8;1;102

    PUBMED: 27716432; PMC: 5048656; DOI: 10.1186/s13073-016-0353-5

  • A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland.

    Raven KE, Reuter S, Reynolds R, Brodrick HJ, Russell JE, Török ME, Parkhill J and Peacock SJ

    Genome research 2016;26;10;1388-1396

    PUBMED: 27527616; PMC: 5052055; DOI: 10.1101/gr.204024.116

  • The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals.

    Ehret GB, Ferreira T, Chasman DI, Jackson AU, Schmidt EM, Johnson T, Thorleifsson G, Luan J, Donnelly LA, Kanoni S et al.

    Nature genetics 2016;48;10;1171-1184

    PUBMED: 27618452; PMC: 5042863; DOI: 10.1038/ng.3667

  • Effect of Insulin Resistance on Monounsaturated Fatty Acid Levels: A Multi-cohort Non-targeted Metabolomics and Mendelian Randomization Study.

    Nowak C, Salihovic S, Ganna A, Brandmaier S, Tukiainen T, Broeckling CD, Magnusson PK, Prenni JE, Wang-Sattler R, Peters A et al.

    PLoS genetics 2016;12;10;e1006379

    PUBMED: 27768686; DOI: 10.1371/journal.pgen.1006379

  • Elevated Cytosolic Cl- Concentrations in Dendritic Knobs of Mouse Vomeronasal Sensory Neurons.

    Untiet V, Moeller LM, Ibarra-Soria X, Sánchez-Andrade G, Stricker M, Neuhaus EM, Logan DW, Gensch T and Spehr M

    Chemical senses 2016;41;8;669-76

    PUBMED: 27377750; PMC: 5030740; DOI: 10.1093/chemse/bjw077

  • Genetic Complexity of Crohn's Disease in Two Large Ashkenazi Jewish Families.

    Levine AP, Pontikos N, Schiff ER, Jostins L, Speed D, NIDDK Inflammatory Bowel Disease Genetics Consortium, Lovat LB, Barrett JC, Grasberger H, Plagnol V and Segal AW

    Gastroenterology 2016;151;4;698-709

    PUBMED: 27373512; PMC: 5643259; DOI: 10.1053/j.gastro.2016.06.040

  • Genetics and immunity in the era of single-cell genomics.

    Vieira Braga FA, Teichmann SA and Chen X

    Human molecular genetics 2016;25;R2;R141-R148

    PUBMED: 27412011; PMC: 5036872; DOI: 10.1093/hmg/ddw192

  • Genomes

    Harb OS, Boehme U, Crouch K, Ifeonu OO, Roos DS, Silva JC, Silva-Franco F, Svärd S, Tretina K and Weedall G

    Molecular Parasitology: Protozoan Parasites and their Molecules 2016;Springer

    PUBMED: 32348078

  • Independent Origin and Global Distribution of Distinct Plasmodium vivax Duffy Binding Protein Gene Duplications.

    Hostetler JB, Lo E, Kanjee U, Amaratunga C, Suon S, Sreng S, Mao S, Yewhalaw D, Mascarenhas A, Kwiatkowski DP et al.

    PLoS neglected tropical diseases 2016;10;10;e0005091

    PUBMED: 27798646; PMC: 5087946; DOI: 10.1371/journal.pntd.0005091

  • Invasion of hepatocytes by Plasmodium sporozoites requires cGMP-dependent protein kinase and calcium dependent protein kinase 4.

    Govindasamy K, Jebiwott S, Jaijyan DK, Davidow A, Ojo KK, Van Voorhis WC, Brochet M, Billker O and Bhanot P

    Molecular microbiology 2016;102;2;349-363

    PUBMED: 27425827; DOI: 10.1111/mmi.13466

  • Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis.

    Castaño-Betancourt MC, Evans DS, Ramos YF, Boer CG, Metrustry S, Liu Y, den Hollander W, van Rooij J, Kraus VB, Yau MS et al.

    PLoS genetics 2016;12;10;e1006260

    PUBMED: 27701424; PMC: 5049763; DOI: 10.1371/journal.pgen.1006260

  • Prenatal whole exome sequencing: the views of clinicians, scientists, genetic counsellors and patient representatives.

    Quinlan-Jones E, Kilby MD, Greenfield S, Parker M, McMullan D, Hurles ME and Hillman SC

    Prenatal diagnosis 2016;36;10;935-941

    PUBMED: 27550507; DOI: 10.1002/pd.4916

  • Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia.

    Picaud S, Leonards K, Lambert JP, Dovey O, Wells C, Fedorov O, Monteiro O, Fujisawa T, Wang CY, Lingard H et al.

    Science advances 2016;2;10;e1600760

    PUBMED: 27757418; PMC: 5061470; DOI: 10.1126/sciadv.1600760

  • Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes.

    van Tonder AJ, Bray JE, Quirk SJ, Haraldsson G, Jolley KA, Maiden MCJ, Hoffmann S, Bentley SD, Haraldsson Á, Erlendsdóttir H et al.

    Microbial genomics 2016;2;10;000090

    PUBMED: 28133541; PMC: 5266551; DOI: 10.1099/mgen.0.000090

  • Rapid phenotyping of knockout mice to identify genetic determinants of bone strength.

    Freudenthal B, Logan J, Sanger Institute Mouse Pipelines, Croucher PI, Williams GR and Bassett JH

    The Journal of endocrinology 2016;231;1;R31-46

    PUBMED: 27535945; PMC: 5064764; DOI: 10.1530/JOE-16-0258

  • Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process.

    Karlsson SL, Thomson N, Mutreja A, Connor T, Sur D, Ali M, Clemens J, Dougan G, Holmgren J and Lebens M

    PLoS neglected tropical diseases 2016;10;10;e0005044

    PUBMED: 27706170; DOI: 10.1371/journal.pntd.0005044

  • Rubinstein-Taybi syndrome type 2: report of nine new cases that extend the phenotypic and genotypic spectrum.

    Hamilton MJ, Newbury-Ecob R, Holder-Espinasse M, Yau S, Lillis S, Hurst JA, Clement E, Reardon W, Joss S, Hobson E et al.

    Clinical dysmorphology 2016;25;4;135-45

    PUBMED: 27465822; DOI: 10.1097/MCD.0000000000000143

  • Synthetic lethality between PAXX and XLF in mammalian development.

    Balmus G, Barros AC, Wijnhoven PW, Lescale C, Hasse HL, Boroviak K, le Sage C, Doe B, Speak AO, Galli A et al.

    Genes & development 2016;30;19;2152-2157

    PUBMED: 27798842; PMC: 5088564; DOI: 10.1101/gad.290510.116

  • Targeting Chromatin Regulators Inhibits Leukemogenic Gene Expression in NPM1 Mutant Leukemia.

    Kühn MW, Song E, Feng Z, Sinha A, Chen CW, Deshpande AJ, Cusan M, Farnoud N, Mupo A, Grove C et al.

    Cancer discovery 2016;6;10;1166-1181

    PUBMED: 27535106; PMC: 5584808; DOI: 10.1158/2159-8290.CD-16-0237

  • Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension.

    Surendran P, Drenos F, Young R, Warren H, Cook JP, Manning AK, Grarup N, Sim X, Barnes DR, Witkowska K et al.

    Nature genetics 2016;48;10;1151-61

    PUBMED: 27618447; DOI: 10.1038/ng.3654

  • Whole-exome sequencing in an isolated population from the Dalmatian island of Vis.

    Jeroncic A, Memari Y, Ritchie GR, Hendricks AE, Kolb-Kokocinski A, Matchan A, Vitart V, Hayward C, Kolcic I, Glodzik D et al.

    European journal of human genetics : EJHG 2016;24;10;1479-87

    PUBMED: 27049301; PMC: 4950961; DOI: 10.1038/ejhg.2016.23

  • Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study.

    Casali N, Broda A, Harris SR, Parkhill J, Brown T and Drobniewski F

    PLoS medicine 2016;13;10;e1002137

    PUBMED: 27701423; PMC: 5049847; DOI: 10.1371/journal.pmed.1002137

  • The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity.

    Torres CM, Biran A, Burney MJ, Patel H, Henser-Brownhill T, Cohen AS, Li Y, Ben-Hamo R, Nye E, Spencer-Dene B et al.

    Science (New York, N.Y.) 2016;353;6307

    PUBMED: 27708074; PMC: 5131846; DOI: 10.1126/science.aaf1644

  • Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species.

    Linz B, Ivanov YV, Preston A, Brinkac L, Parkhill J, Kim M, Harris SR, Goodfield LL, Fry NK, Gorringe AR et al.

    BMC genomics 2016;17;1;767

    PUBMED: 27716057; PMC: 5045587; DOI: 10.1186/s12864-016-3112-5

  • CD4-Transgenic Zebrafish Reveal Tissue-Resident Th2- and Regulatory T Cell-like Populations and Diverse Mononuclear Phagocytes.

    Dee CT, Nagaraju RT, Athanasiadis EI, Gray C, Fernandez Del Ama L, Johnston SA, Secombes CJ, Cvejic A and Hurlstone AF

    Journal of immunology (Baltimore, Md. : 1950) 2016;197;9;3520-3530

    PUBMED: 27694495; PMC: 5073357; DOI: 10.4049/jimmunol.1600959

  • Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

    Macaulay IC, Teng MJ, Haerty W, Kumar P, Ponting CP and Voet T

    Nature protocols 2016;11;11;2081-103

    PUBMED: 27685099; DOI: 10.1038/nprot.2016.138

  • Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway.

    Yu Y, Tsang JC, Wang C, Clare S, Wang J, Chen X, Brandt C, Kane L, Campos LS, Lu L et al.

    Nature 2016;539;7627;102-106

    PUBMED: 27749818; DOI: 10.1038/nature20105

  • A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.

    Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J and Overington JP

    Journal of biomedical semantics 2016;7;1;59

    PUBMED: 27678076; PMC: 5039825; DOI: 10.1186/s13326-016-0102-0

  • MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.

    Eckersley-Maslin MA, Svensson V, Krueger C, Stubbs TM, Giehr P, Krueger F, Miragaia RJ, Kyriakopoulos C, Berrens RV, Milagre I et al.

    Cell reports 2016;17;1;179-192

    PUBMED: 27681430; PMC: 5055476; DOI: 10.1016/j.celrep.2016.08.087

  • Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.

    Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, Kamng'ona AW, Parkhill J, French N, Heyderman RS et al.

    mBio 2016;7;5

    PUBMED: 27677790; PMC: 5040112; DOI: 10.1128/mBio.01053-16

  • The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland.

    Moradigaravand D, Reuter S, Martin V, Peacock SJ and Parkhill J

    Nature microbiology 2016;1;16173

    PUBMED: 27669519; PMC: 6103429; DOI: 10.1038/nmicrobiol.2016.173

  • Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.

    Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van der Smissen WJ, Vlugt-Daane MV, van Galen A, Nik-Zainal S, Staaf J, Brinkman AB et al.

    Nature communications 2016;7;12910

    PUBMED: 27666519; PMC: 5052682; DOI: 10.1038/ncomms12910

  • Clinical and genetic aspects of KBG syndrome.

    Low K, Ashraf T, Canham N, Clayton-Smith J, Deshpande C, Donaldson A, Fisher R, Flinter F, Foulds N, Fryer A et al.

    American journal of medical genetics. Part A 2016;170;11;2835-2846

    PUBMED: 27667800; PMC: 5435101; DOI: 10.1002/ajmg.a.37842

  • Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps.

    Iotchkova V, Huang J, Morris JA, Jain D, Barbieri C, Walter K, Min JL, Chen L, Astle W, Cocca M et al.

    Nature genetics 2016;48;11;1303-1312

    PUBMED: 27668658; PMC: 5279872; DOI: 10.1038/ng.3668

  • A robust activity marking system for exploring active neuronal ensembles.

    Sørensen AT, Cooper YA, Baratta MV, Weng FJ, Zhang Y, Ramamoorthi K, Fropf R, LaVerriere E, Xue J, Young A et al.

    eLife 2016;5

    PUBMED: 27661450; PMC: 5035142; DOI: 10.7554/eLife.13918

  • Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently.

    David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L et al.

    Genome research 2016;26;11;1555-1564

    PUBMED: 27662900; PMC: 5088597; DOI: 10.1101/gr.209536.116

  • The AMP-activated protein kinase beta 1 subunit modulates erythrocyte integrity.

    Cambridge EL, McIntyre Z, Clare S, Arends MJ, Goulding D, Isherwood C, Caetano SS, Reviriego CB, Swiatkowska A, Kane L et al.

    Experimental hematology 2016;45;64-68.e5

    PUBMED: 27666489; PMC: 5823972; DOI: 10.1016/j.exphem.2016.09.006

  • Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.

    Alexander S, Fazal MA, Burnett E, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J and Russell JE

    Genome announcements 2016;4;5

    PUBMED: 27660796; PMC: 5034147; DOI: 10.1128/genomeA.01031-16

  • Heterogeneity of CD34 and CD38 expression in acute B lymphoblastic leukemia cells is reversible and not hierarchically organized.

    Jiang Z, Deng M, Wei X, Ye W, Xiao Y, Lin S, Wang S, Li B, Liu X, Zhang G et al.

    Journal of hematology & oncology 2016;9;1;94

    PUBMED: 27660152; PMC: 5034590; DOI: 10.1186/s13045-016-0310-1

  • High-throughput discovery of novel developmental phenotypes.

    Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H et al.

    Nature 2016;537;7621;508-514

    PUBMED: 27626380; PMC: 5295821; DOI: 10.1038/nature19356

  • A computational lens for sexual-stage transmission, reproduction, fitness and kinetics in Plasmodium falciparum.

    Lawniczak MK and Eckhoff PA

    Malaria journal 2016;15;1;487

    PUBMED: 27653663; PMC: 5031309; DOI: 10.1186/s12936-016-1538-5

  • A genomic history of Aboriginal Australia.

    Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE et al.

    Nature 2016;538;7624;207-214

    PUBMED: 27654914; PMC: 7617037; DOI: 10.1038/nature18299

  • The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

    Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A et al.

    Nature 2016;538;7624;201-206

    PUBMED: 27654912; PMC: 5161557; DOI: 10.1038/nature18964

  • Genomic analyses inform on migration events during the peopling of Eurasia.

    Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L et al.

    Nature 2016;538;7624;238-242

    PUBMED: 27654910; PMC: 5164938; DOI: 10.1038/nature19792

  • Recruitment and representativeness of blood donors in the INTERVAL randomised trial assessing varying inter-donation intervals.

    Moore C, Bolton T, Walker M, Kaptoge S, Allen D, Daynes M, Mehenny S, Sambrook J, Watkins NA, Miflin G et al.

    Trials 2016;17;1;458

    PUBMED: 27645285; PMC: 5029021; DOI: 10.1186/s13063-016-1579-7

  • Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks.

    Chanut P, Britton S, Coates J, Jackson SP and Calsou P

    Nature communications 2016;7;12889

    PUBMED: 27641979; PMC: 5031800; DOI: 10.1038/ncomms12889

  • UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes.

    Lim MY, LaMonte G, Lee MCS, Reimer C, Tan BH, Corey V, Tjahjadi BF, Chua A, Nachon M, Wintjens R et al.

    Nature microbiology 2016;1;16166

    PUBMED: 27642791; PMC: 5575994; DOI: 10.1038/nmicrobiol.2016.166

  • Oxford Nanopore MinION Sequencing and Genome Assembly.

    Lu H, Giordano F and Ning Z

    Genomics, proteomics & bioinformatics 2016;14;5;265-279

    PUBMED: 27646134; PMC: 5093776; DOI: 10.1016/j.gpb.2016.05.004

  • Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.

    Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY et al.

    Nature communications 2016;7;12797

    PUBMED: 27633831; PMC: 5028413; DOI: 10.1038/ncomms12797

  • A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds.

    Bruna A, Rueda OM, Greenwood W, Batra AS, Callari M, Batra RN, Pogrebniak K, Sandoval J, Cassidy JW, Tufegdzic-Vidakovic A et al.

    Cell 2016;167;1;260-274.e22

    PUBMED: 27641504; PMC: 5037319; DOI: 10.1016/j.cell.2016.08.041

  • Analysis with the exome array identifies multiple new independent variants in lipid loci.

    Kanoni S, Masca NG, Stirrups KE, Varga TV, Warren HR, Scott RA, Southam L, Zhang W, Yaghootkar H, Müller-Nurasyid M et al.

    Human molecular genetics 2016;25;18;4094-4106

    PUBMED: 27466198; PMC: 5291227; DOI: 10.1093/hmg/ddw227

  • Targeting the RB-E2F pathway in breast cancer.

    Johnson J, Thijssen B, McDermott U, Garnett M, Wessels LF and Bernards R

    Oncogene 2016;35;37;4829-35

    PUBMED: 26923330; PMC: 4950965; DOI: 10.1038/onc.2016.32

  • Linking an unchained malady.

    Sánchez-Busó L and Harris SR

    Nature reviews. Microbiology 2016;14;10;608

    PUBMED: 27620944; DOI: 10.1038/nrmicro.2016.137

  • Specific Roles of XRCC4 Paralogs PAXX and XLF during V(D)J Recombination.

    Lescale C, Lenden Hasse H, Blackford AN, Balmus G, Bianchi JJ, Yu W, Bacoccina L, Jarade A, Clouin C, Sivapalan R et al.

    Cell reports 2016;16;11;2967-2979

    PUBMED: 27601299; PMC: 5033762; DOI: 10.1016/j.celrep.2016.08.069

  • Mutational signatures of ionizing radiation in second malignancies.

    Behjati S, Gundem G, Wedge DC, Roberts ND, Tarpey PS, Cooke SL, Van Loo P, Alexandrov LB, Ramakrishna M, Davies H et al.

    Nature communications 2016;7;12605

    PUBMED: 27615322; PMC: 5027243; DOI: 10.1038/ncomms12605

  • Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.

    Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, GEUVADIS Consortium, Rosenstiel P et al.

    Scientific reports 2016;6;32406

    PUBMED: 27617755; PMC: 5019111; DOI: 10.1038/srep32406

  • Genomic analysis of Salmonella enterica serovar Typhimurium from wild passerines in England and Wales.

    Mather AE, Lawson B, de Pinna E, Wigley P, Parkhill J, Thomson NR, Page AJ, Holmes MA and Paterson GK

    Applied and environmental microbiology 2016

    PUBMED: 27613688; DOI: 10.1128/AEM.01660-16

  • Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.

    Judge K, Hunt M, Reuter S, Tracey A, Quail MA, Parkhill J and Peacock SJ

    Microbial genomics 2016;2;9;e000085

    PUBMED: 28348876; PMC: 5320651; DOI: 10.1099/mgen.0.000085

  • Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts.

    Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K et al.

    Leukemia 2016;31;3;720-727

    PUBMED: 27604819; PMC: 5336192; DOI: 10.1038/leu.2016.251

  • Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice.

    Sok D, Briney B, Jardine JG, Kulp DW, Menis S, Pauthner M, Wood A, Lee EC, Le KM, Jones M et al.

    Science (New York, N.Y.) 2016

    PUBMED: 27608668; DOI: 10.1126/science.aah3945

  • Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii.

    Hassan KA, Cain AK, Huang T, Liu Q, Elbourne LD, Boinett CJ, Brzoska AJ, Li L, Ostrowski M, Nhu NT et al.

    mBio 2016;7;5

    PUBMED: 27601573; PMC: 5013296; DOI: 10.1128/mBio.01200-16

  • Genome-wide association study of antisocial personality disorder.

    Rautiainen MR, Paunio T, Repo-Tiihonen E, Virkkunen M, Ollila HM, Sulkava S, Jolanki O, Palotie A and Tiihonen J

    Translational psychiatry 2016;6;9;e883

    PUBMED: 27598967; PMC: 5048197; DOI: 10.1038/tp.2016.155

  • Intra-host dynamics of Ebola virus during 2014.

    Ni M, Chen C, Qian J, Xiao HX, Shi WF, Luo Y, Wang HY, Li Z, Wu J, Xu PS et al.

    Nature microbiology 2016;1;11;16151

    PUBMED: 27595345; DOI: 10.1038/nmicrobiol.2016.151

  • A DNA target-enrichment approach to detect mutations, copy number changes and immunoglobulin translocations in multiple myeloma.

    Bolli N, Li Y, Sathiaseelan V, Raine K, Jones D, Ganly P, Cocito F, Bignell G, Chapman MA, Sperling AS et al.

    Blood cancer journal 2016;6;9;e467

    PUBMED: 27588520; PMC: 5056967; DOI: 10.1038/bcj.2016.72

  • Sperm Meets Egg: The Genetics of Mammalian Fertilization.

    Bianchi E and Wright GJ

    Annual review of genetics 2016

    PUBMED: 27617973; DOI: 10.1146/annurev-genet-121415-121834

  • The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle.

    Barth SA, Menge C, Eichhorn I, Semmler T, Wieler LH, Pickard D, Belka A, Berens C and Geue L

    Applied and environmental microbiology 2016;82;17;5455-64

    PUBMED: 27371579; PMC: 4988194; DOI: 10.1128/AEM.00909-16

  • The Evolutionary Fates of a Large Segmental Duplication in Mouse.

    Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P et al.

    Genetics 2016;204;1;267-85

    PUBMED: 27371833; PMC: 5012392; DOI: 10.1534/genetics.116.191007

  • The role of hepatocyte nuclear factor 1β in disease and development.

    El-Khairi R and Vallier L

    Diabetes, obesity & metabolism 2016;18 Suppl 1;23-32

    PUBMED: 27615128; DOI: 10.1111/dom.12715

  • A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

    Smedley D, Schubach M, Jacobsen JO, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA et al.

    American journal of human genetics 2016;99;3;595-606

    PUBMED: 27569544; DOI: 10.1016/j.ajhg.2016.07.005

  • Alphavirus Restriction by IFITM Proteins.

    Weston S, Czieso S, White IJ, Smith SE, Wash RS, Diaz-Soria C, Kellam P and Marsh M

    Traffic (Copenhagen, Denmark) 2016;17;9;997-1013

    PUBMED: 27219333; PMC: 5025721; DOI: 10.1111/tra.12416

  • Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.

    Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, Kodama T, Ward JM, Rust AG, van der Weyden L et al.

    Nature biotechnology 2016;34;9;962-72

    PUBMED: 27479497; PMC: 6124494; DOI: 10.1038/nbt.3637

  • Bacterial pathogenesis: Getting all tangled up.

    Du Toit A

    Nature reviews. Microbiology 2016;14;9;545

    PUBMED: 27424941; DOI: 10.1038/nrmicro.2016.112

  • C13orf31 (FAMIN) is a central regulator of immunometabolic function.

    Cader MZ, Boroviak K, Zhang Q, Assadi G, Kempster SL, Sewell GW, Saveljeva S, Ashcroft JW, Clare S, Mukhopadhyay S et al.

    Nature immunology 2016;17;9;1046-56

    PUBMED: 27478939; PMC: 6581540; DOI: 10.1038/ni.3532

  • CRISPR-Cas9 enables conditional mutagenesis of challenging loci.

    Schick JA, Seisenberger C, Beig J, Bürger A, Iyer V, Maier V, Perera S, Rosen B, Skarnes WC and Wurst W

    Scientific reports 2016;6;32326

    PUBMED: 27580957; PMC: 5007477; DOI: 10.1038/srep32326

  • Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

    Sousa FL, Parente DJ, Hessman JA, Chazelle A, Teichmann SA and Swint-Kruse L

    Data in brief 2016;8;948-57

    PUBMED: 27508249; PMC: 4961497; DOI: 10.1016/j.dib.2016.07.006

  • Established BMI-associated genetic variants and their prospective associations with BMI and other cardiometabolic traits: the GLACIER Study.

    Ahmad S, Poveda A, Shungin D, Barroso I, Hallmans G, Renström F and Franks PW

    International journal of obesity (2005) 2016;40;9;1346-52

    PUBMED: 27121252; DOI: 10.1038/ijo.2016.72

  • Genomic Classification in Acute Myeloid Leukemia.

    Papaemmanuil E, Döhner H and Campbell PJ

    The New England journal of medicine 2016;375;9;900-1

    PUBMED: 27579651; DOI: 10.1056/NEJMc1608739

  • Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.

    Miles A, Iqbal Z, Vauterin P, Pearson R, Campino S, Theron M, Gould K, Mead D, Drury E, O'Brien J et al.

    Genome research 2016;26;9;1288-99

    PUBMED: 27531718; PMC: 5052046; DOI: 10.1101/gr.203711.115

  • Meningococcal Two-Partner Secretion Systems and Their Association with Outcome in Patients with Meningitis.

    Piet JR, van Ulsen P, Ur Rahman S, Bovenkerk S, Bentley SD, van de Beek D and van der Ende A

    Infection and immunity 2016;84;9;2534-40

    PUBMED: 27324486; PMC: 4995907; DOI: 10.1128/IAI.00160-16

  • Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.

    International Typhoid Consortium, Wong VK, Holt KE, Okoro C, Baker S, Pickard DJ, Marks F, Page AJ, Olanipekun G, Munir H et al.

    PLoS neglected tropical diseases 2016;10;9;e0004781

    PUBMED: 27657909; PMC: 5033494; DOI: 10.1371/journal.pntd.0004781

  • Postglacial viability and colonization in North America's ice-free corridor.

    Pedersen MW, Ruter A, Schweger C, Friebe H, Staff RA, Kjeldsen KK, Mendoza ML, Beaudoin AB, Zutter C, Larsen NK et al.

    Nature 2016;537;7618;45-49

    PUBMED: 27509852; DOI: 10.1038/nature19085

  • Sugar-sweetened beverage consumption and genetic predisposition to obesity in 2 Swedish cohorts.

    Brunkwall L, Chen Y, Hindy G, Rukh G, Ericson U, Barroso I, Johansson I, Franks PW, Orho-Melander M and Renström F

    The American journal of clinical nutrition 2016;104;3;809-15

    PUBMED: 27465381; PMC: 4997292; DOI: 10.3945/ajcn.115.126052

  • Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities.

    Baker KS, Dallman TJ, Behar A, Weill FX, Gouali M, Sobel J, Fookes M, Valinsky L, Gal-Mor O, Connor TR et al.

    Emerging infectious diseases 2016;22;9;1545-53

    PUBMED: 27532625; PMC: 4994374; DOI: 10.3201/eid2209.151953

  • Whole genome sequencing of emerging multidrug resistant Candida auris isolates in India demonstrates low genetic variation.

    Sharma C, Kumar N, Pandey R, Meis JF and Chowdhary A

    New microbes and new infections 2016;13;77-82

    PUBMED: 27617098; PMC: 5006800; DOI: 10.1016/j.nmni.2016.07.003

  • Whole-genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates from Myanmar.

    Aung HL, Tun T, Moradigaravand D, Köser CU, Nyunt WW, Aung ST, Lwin T, Thinn KK, Crump JA, Parkhill J et al.

    Journal of global antimicrobial resistance 2016;6;113-117

    PUBMED: 27530852; PMC: 5010037; DOI: 10.1016/j.jgar.2016.04.008

  • Wild-Type and Non-Wild-Type Mycobacterium tuberculosis MIC Distributions for the Novel Fluoroquinolone Antofloxacin Compared with Those for Ofloxacin, Levofloxacin, and Moxifloxacin.

    Yu X, Wang G, Chen S, Wei G, Shang Y, Dong L, Schön T, Moradigaravand D, Parkhill J, Peacock SJ et al.

    Antimicrobial agents and chemotherapy 2016;60;9;5232-7

    PUBMED: 27324769; PMC: 4997829; DOI: 10.1128/AAC.00393-16

  • OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

    Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E et al.

    Nature methods 2016;13;9;741-8

    PUBMED: 27575624; DOI: 10.1038/nmeth.3959

  • Phosphorylation of a constrained azacyclic FTY720 analog enhances anti-leukemic activity without inducing S1P receptor activation.

    McCracken AN, McMonigle RJ, Tessier J, Fransson R, Perryman MS, Chen B, Keebaugh A, Selwan E, Barr SA, Kim SM et al.

    Leukemia 2016

    PUBMED: 27573555; DOI: 10.1038/leu.2016.244

  • The essential mycobacterial amidotransferase GatCAB is a modulator of specific translational fidelity.

    Su HW, Zhu JH, Li H, Cai RJ, Ealand C, Wang X, Chen YX, Kayani MU, Zhu TF, Moradigaravand D et al.

    Nature microbiology 2016;1;11;16147

    PUBMED: 27564922; DOI: 10.1038/nmicrobiol.2016.147

  • The diversity of Klebsiella pneumoniae surface polysaccharides.

    Follador R, Heinz E, Wyres KL, Ellington MJ, Kowarik M, Holt KE and Thomson NR

    Microbial genomics 2016;2;8;e000073

    PUBMED: 28348868; PMC: 5320592; DOI: 10.1099/mgen.0.000073

  • Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.

    Alexander S, Fazal MA, Burnett E, Deheer-Graham A, Oliver K, Holroyd N, Parkhill J and Russell JE

    Genome announcements 2016;4;4

    PUBMED: 27563039; PMC: 5000823; DOI: 10.1128/genomeA.00815-16

  • JAK2 V617F clonal disorders: fate or chance?

    Vassiliou GS

    Blood 2016;128;8;1032-3

    PUBMED: 27563148; DOI: 10.1182/blood-2016-07-726448

  • Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

    Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, Otto TD and Keane JA

    Microbial genomics 2016;2;8;e000083

    PUBMED: 28348874; PMC: 5320598; DOI: 10.1099/mgen.0.000083

  • Aneuploid embryonic stem cells exhibit impaired differentiation and increased neoplastic potential.

    Zhang M, Cheng L, Jia Y, Liu G, Li C, Song S, Bradley A and Huang Y

    The EMBO journal 2016

    PUBMED: 27558554; DOI: 10.15252/embj.201593103

  • Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution.

    McConnell SC, Hernandez KM, Wcisel DJ, Kettleborough RN, Stemple DL, Yoder JA, Andrade J and de Jong JL

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;34;E5014-23

    PUBMED: 27493218; PMC: 5003237; DOI: 10.1073/pnas.1607602113

  • De novo and inherited mutations in the X-linked gene CLCN4 are associated with syndromic intellectual disability and behavior and seizure disorders in males and females.

    Palmer EE, Stuhlmann T, Weinert S, Haan E, Van Esch H, Holvoet M, Boyle J, Leffler M, Raynaud M, Moraine C et al.

    Molecular psychiatry 2016;23;2;222-230

    PUBMED: 27550844; PMC: 5794876; DOI: 10.1038/mp.2016.135

  • What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

    Connor TR, Owen SV, Langridge G, Connell S, Nair S, Reuter S, Dallman TJ, Corander J, Tabing KC, Le Hello S et al.

    mBio 2016;7;4

    PUBMED: 27555304; PMC: 4999539; DOI: 10.1128/mBio.00527-16

  • A reference panel of 64,976 haplotypes for genotype imputation.

    McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K et al.

    Nature genetics 2016;48;10;1279-83

    PUBMED: 27548312; PMC: 5388176; DOI: 10.1038/ng.3643

  • A single dividing cell population with imbalanced fate drives oesophageal tumour growth.

    Frede J, Greulich P, Nagy T, Simons BD and Jones PH

    Nature cell biology 2016;18;9;967-78

    PUBMED: 27548914; PMC: 5870829; DOI: 10.1038/ncb3400

  • Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

    Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T et al.

    Nature genetics 2016;48;10;1211-1217

    PUBMED: 27548315; PMC: 5047355; DOI: 10.1038/ng.3644

  • Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

    Long HK, King HW, Patient RK, Odom DT and Klose RJ

    Nucleic acids research 2016;44;14;6693-706

    PUBMED: 27084945; PMC: 5001583; DOI: 10.1093/nar/gkw258

  • Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy.

    Muona M, Ishimura R, Laari A, Ichimura Y, Linnankivi T, Keski-Filppula R, Herva R, Rantala H, Paetau A, Pöyhönen M et al.

    American journal of human genetics 2016;99;3;683-694

    PUBMED: 27545674; PMC: 5010641; DOI: 10.1016/j.ajhg.2016.06.020

  • De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome.

    Kim JH, Shinde DN, Reijnders MRF, Hauser NS, Belmonte RL, Wilson GR, Bosch DGM, Bubulya PA, Shashi V, Petrovski S et al.

    American journal of human genetics 2016;99;3;711-719

    PUBMED: 27545680; PMC: 5011044; DOI: 10.1016/j.ajhg.2016.06.029

  • Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

    Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C et al.

    Nature communications 2016;7;12339

    PUBMED: 27531712; PMC: 4992054; DOI: 10.1038/ncomms12339

  • An Isochore-Like Structure in the Genome of the Flatworm Schistosoma mansoni.

    Lamolle G, Protasio AV, Iriarte A, Jara E, Simón D and Musto H

    Genome biology and evolution 2016;8;8;2312-8

    PUBMED: 27435793; PMC: 5010904; DOI: 10.1093/gbe/evw170

  • A bit of a mouthful.

    Hadfield J and David S

    Nature reviews. Microbiology 2016;14;9;548

    PUBMED: 27510861; DOI: 10.1038/nrmicro.2016.124

  • Contrasting origin of B chromosomes in two cervids (Siberian roe deer and grey brocket deer) unravelled by chromosome-specific DNA sequencing.

    Makunin AI, Kichigin IG, Larkin DM, O'Brien PC, Ferguson-Smith MA, Yang F, Proskuryakova AA, Vorobieva NV, Chernyaeva EN, O'Brien SJ et al.

    BMC genomics 2016;17;1;618

    PUBMED: 27516089; PMC: 4982142; DOI: 10.1186/s12864-016-2933-6

  • Endothelial Cell Junctional Adhesion Molecules: Role and Regulation of Expression in Inflammation.

    Reglero-Real N, Colom B, Bodkin JV and Nourshargh S

    Arteriosclerosis, thrombosis, and vascular biology 2016;36;10;2048-2057

    PUBMED: 27515379; PMC: 5035539; DOI: 10.1161/ATVBAHA.116.307610

  • A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice.

    McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G et al.

    G3 (Bethesda, Md.) 2016;6;8;2343-54

    PUBMED: 27233670; PMC: 4978889; DOI: 10.1534/g3.116.030767

  • A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.

    Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F et al.

    Nature communications 2016;7;12342

    PUBMED: 27503255; PMC: 4980482; DOI: 10.1038/ncomms12342

  • A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

    Wheeler NE, Barquist L, Kingsley RA and Gardner PP

    Bioinformatics (Oxford, England) 2016;32;23;3566-3574

    PUBMED: 27503221; PMC: 5181535; DOI: 10.1093/bioinformatics/btw518

  • Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay.

    Lu Z, Sessler F, Holroyd N, Hahnel S, Quack T, Berriman M and Grevelding CG

    Scientific reports 2016;6;31150

    PUBMED: 27499125; PMC: 4976352; DOI: 10.1038/srep31150

  • Ebola virus disease cluster — Northern Sierra Leone, January 2016

    Alpren,C., Sloan,M., Boegler,K.A., Martin,D.W., Ervin,E., Washburn,F., Rickert,R., Singh,T., Redd,J.T., Bangalie,A. et al.

    Morbidity and Mortality Weekly Report 2016;65;26;681-3

    DOI: 10.15585/mmwr.mm6526a4; URL: https://dx.doi.org/10.15585/m...mwr.mm6526a4.

  • Estimating Geographical Variation in the Risk of Zoonotic Plasmodium knowlesi Infection in Countries Eliminating Malaria.

    Shearer FM, Huang Z, Weiss DJ, Wiebe A, Gibson HS, Battle KE, Pigott DM, Brady OJ, Putaporntip C, Jongwutiwes S et al.

    PLoS neglected tropical diseases 2016;10;8;e0004915

    PUBMED: 27494405; PMC: 4975412; DOI: 10.1371/journal.pntd.0004915

  • The genetic architecture of type 2 diabetes.

    Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ et al.

    Nature 2016;536;7614;41-47

    PUBMED: 27398621; PMC: 5034897; DOI: 10.1038/nature18642

  • Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer.

    Shlien A, Raine K, Fuligni F, Arnold R, Nik-Zainal S, Dronov S, Mamanova L, Rosic A, Ju YS, Cooke SL et al.

    Cell reports 2016;16;7;2032-46

    PUBMED: 27498871; PMC: 4987284; DOI: 10.1016/j.celrep.2016.07.028

  • From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.

    Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š, Edwards S, Jurriaans S, Bakker M, Ong SH, Gras L et al.

    Virus research 2016;239;10-16

    PUBMED: 27497916; DOI: 10.1016/j.virusres.2016.08.004

  • TTC25 Deficiency Results in Defects of the Outer Dynein Arm Docking Machinery and Primary Ciliary Dyskinesia with Left-Right Body Asymmetry Randomization.

    Wallmeier J, Shiratori H, Dougherty GW, Edelbusch C, Hjeij R, Loges NT, Menchen T, Olbrich H, Pennekamp P, Raidt J et al.

    American journal of human genetics 2016;99;2;460-9

    PUBMED: 27486780; PMC: 4974089; DOI: 10.1016/j.ajhg.2016.06.014

  • Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis.

    Polfus LM, Khajuria RK, Schick UM, Pankratz N, Pazoki R, Brody JA, Chen MH, Auer PL, Floyd JS, Huang J et al.

    American journal of human genetics 2016;99;2;481-8

    PUBMED: 27486782; PMC: 4974169; DOI: 10.1016/j.ajhg.2016.06.016

  • The Genomic Landscape of Pancreatic and Periampullary Adenocarcinoma.

    Sandhu V, Wedge DC, Bowitz Lothe IM, Labori KJ, Dentro SC, Buanes T, Skrede ML, Dalsgaard AM, Munthe E, Myklebost O et al.

    Cancer research 2016;76;17;5092-102

    PUBMED: 27488532; DOI: 10.1158/0008-5472.CAN-16-0658

  • Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum.

    Peel AJ, Baker KS, Hayman DT, Suu-Ire R, Breed AC, Gembu GC, Lembo T, Fernández-Loras A, Sargan DR, Fooks AR et al.

    Scientific data 2016;3;160049

    PUBMED: 27479120; PMC: 4968192; DOI: 10.1038/sdata.2016.49

  • Closing the gap in Genetic Data Analysis pipelines with ASPIREdb.

    Swaminathan J

    Human mutation 2016;37;8;717

    PUBMED: 27396953; DOI: 10.1002/humu.23029

  • Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations.

    Doran AG, Wong K, Flint J, Adams DJ, Hunter KW and Keane TM

    Genome biology 2016;17;1;167

    PUBMED: 27480531; PMC: 4968449; DOI: 10.1186/s13059-016-1024-y

  • Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing.

    Sifrim A, Hitz MP, Wilsdon A, Breckpot J, Turki SH, Thienpont B, McRae J, Fitzgerald TW, Singh T, Swaminathan GJ et al.

    Nature genetics 2016;48;9;1060-5

    PUBMED: 27479907; PMC: 5988037; DOI: 10.1038/ng.3627

  • DNAH11 Localization in the Proximal Region of Respiratory Cilia Defines Distinct Outer Dynein Arm Complexes.

    Dougherty GW, Loges NT, Klinkenbusch JA, Olbrich H, Pennekamp P, Menchen T, Raidt J, Wallmeier J, Werner C, Westermann C et al.

    American journal of respiratory cell and molecular biology 2016;55;2;213-24

    PUBMED: 26909801; PMC: 4979367; DOI: 10.1165/rcmb.2015-0353OC

  • Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.

    Nicod J, Davies RW, Cai N, Hassett C, Goodstadt L, Cosgrove C, Yee BK, Lionikaite V, McIntyre RE, Remme CA et al.

    Nature genetics 2016;48;8;912-8

    PUBMED: 27376238; PMC: 4966644; DOI: 10.1038/ng.3595

  • High-throughput functional comparison of promoter and enhancer activities.

    Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M and Gray JM

    Genome research 2016;26;8;1023-33

    PUBMED: 27311442; PMC: 4971761; DOI: 10.1101/gr.204834.116

  • Identification of a germline F692L drug resistance variant in cis with Flt3-internal tandem duplication in knock-in mice.

    Dovey OM, Chen B, Mupo A, Friedrich M, Grove CS, Cooper JL, Lee B, Varela I, Huang Y and Vassiliou GS

    Haematologica 2016;101;8;e328-31

    PUBMED: 27175030; PMC: 4967582; DOI: 10.3324/haematol.2016.146159

  • Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.

    Gormley P, Anttila V, Winsvold BS, Palta P, Esko T, Pers TH, Farh KH, Cuenca-Leon E, Muona M, Furlotte NA et al.

    Nature genetics 2016;48;8;856-66

    PUBMED: 27322543; PMC: 5331903; DOI: 10.1038/ng.3598

  • Navigating the Phenotype Frontier: The Monarch Initiative.

    McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M et al.

    Genetics 2016;203;4;1491-5

    PUBMED: 27516611; PMC: 4981258; DOI: 10.1534/genetics.116.188870

  • South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study.

    Chung The H, Rabaa MA, Pham Thanh D, De Lappe N, Cormican M, Valcanis M, Howden BP, Wangchuk S, Bodhidatta L, Mason CJ et al.

    PLoS medicine 2016;13;8;e1002055

    PUBMED: 27483136; PMC: 4970813; DOI: 10.1371/journal.pmed.1002055

  • Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England.

    Toleman MS, Reuter S, Coll F, Harrison EM, Blane B, Brown NM, Török ME, Parkhill J and Peacock SJ

    The Journal of infectious diseases 2016;214;3;447-53

    PUBMED: 27122590; PMC: 4936647; DOI: 10.1093/infdis/jiw166

  • Unravelling the Laverania.

    Proto WR

    Nature reviews. Microbiology 2016;14;8;478

    PUBMED: 27396565; DOI: 10.1038/nrmicro.2016.109

  • Using a Human Challenge Model of Infection to Measure Vaccine Efficacy: A Randomised, Controlled Trial Comparing the Typhoid Vaccines M01ZH09 with Placebo and Ty21a.

    Darton TC, Jones C, Blohmke CJ, Waddington CS, Zhou L, Peters A, Haworth K, Sie R, Green CA, Jeppesen CA et al.

    PLoS neglected tropical diseases 2016;10;8;e0004926

    PUBMED: 27533046; PMC: 4988630; DOI: 10.1371/journal.pntd.0004926

  • Deep learning for computational biology.

    Angermueller C, Pärnamaa T, Parts L and Stegle O

    Molecular systems biology 2016;12;7;878

    PUBMED: 27474269; PMC: 4965871; DOI: 10.15252/msb.20156651

  • Human Rhinovirus B and C Genomes from Rural Coastal Kenya.

    Agoti CN, Kiyuka PK, Kamau E, Munywoki PK, Bett A, van der Hoek L, Kellam P, Nokes DJ and Cotten M

    Genome announcements 2016;4;4

    PUBMED: 27469941; PMC: 4966474; DOI: 10.1128/genomeA.00751-16

  • Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.

    Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Alemán Resto Y, Alsibaee A, Alzualde A et al.

    PLoS pathogens 2016;12;7;e1005763

    PUBMED: 27467575; PMC: 4965013; DOI: 10.1371/journal.ppat.1005763

  • Clonal analysis of stem cells in differentiation and disease.

    Colom B and Jones PH

    Current opinion in cell biology 2016;43;14-21

    PUBMED: 27472647; DOI: 10.1016/j.ceb.2016.07.002

  • The structure of sperm Izumo1 reveals unexpected similarities with Plasmodium invasion proteins.

    Nishimura K, Han L, Bianchi E, Wright GJ, de Sanctis D and Jovine L

    Current biology : CB 2016;26;14;R661-2

    PUBMED: 27374339; PMC: 4963209; DOI: 10.1016/j.cub.2016.06.028

  • BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription.

    Dias C, Estruch SB, Graham SA, McRae J, Sawiak SJ, Hurst JA, Joss SK, Holder SE, Morton JE, Turner C et al.

    American journal of human genetics 2016;99;2;253-74

    PUBMED: 27453576; PMC: 4974071; DOI: 10.1016/j.ajhg.2016.05.030

  • Interleukin-13 Activates Distinct Cellular Pathways Leading to Ductular Reaction, Steatosis, and Fibrosis.

    Gieseck RL, Ramalingam TR, Hart KM, Vannella KM, Cantu DA, Lu WY, Ferreira-González S, Forbes SJ, Vallier L and Wynn TA

    Immunity 2016;45;1;145-58

    PUBMED: 27421703; PMC: 4956513; DOI: 10.1016/j.immuni.2016.06.009

  • Evolutionary dynamics of Anolis sex chromosomes revealed by sequencing of flow sorting-derived microchromosome-specific DNA.

    Kichigin IG, Giovannotti M, Makunin AI, Ng BL, Kabilov MR, Tupikin AE, Barucchi VC, Splendiani A, Ruggeri P, Rens W et al.

    Molecular genetics and genomics : MGG 2016;291;5;1955-66

    PUBMED: 27431992; DOI: 10.1007/s00438-016-1230-z

  • Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland.

    Moradigaravand D, Boinett CJ, Martin V, Peacock SJ and Parkhill J

    Genome research 2016;26;8;1101-9

    PUBMED: 27432456; PMC: 4971767; DOI: 10.1101/gr.205245.116

  • The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization.

    Unemo M, Golparian D, Sánchez-Busó L, Grad Y, Jacobsson S, Ohnishi M, Lahra MM, Limnios A, Sikora AE, Wi T and Harris SR

    The Journal of antimicrobial chemotherapy 2016;71;11;3096-3108

    PUBMED: 27432602; PMC: 5079299; DOI: 10.1093/jac/dkw288

  • G9a inhibition potentiates the anti-tumour activity of DNA double-strand break inducing agents by impairing DNA repair independent of p53 status.

    Agarwal P and Jackson SP

    Cancer letters 2016;380;2;467-475

    PUBMED: 27431310; DOI: 10.1016/j.canlet.2016.07.009

  • Chromatin remodeling inactivates activity genes and regulates neural coding.

    Yang Y, Yamada T, Hill KK, Hemberg M, Reddy NC, Cho HY, Guthrie AN, Oldenborg A, Heiney SA, Ohmae S et al.

    Science (New York, N.Y.) 2016;353;6296;300-305

    PUBMED: 27418512; PMC: 4993111; DOI: 10.1126/science.aad4225

  • Mutations specific to the Rac-GEF domain of TRIO cause intellectual disability and microcephaly.

    Pengelly RJ, Greville-Heygate S, Schmidt S, Seaby EG, Jabalameli MR, Mehta SG, Parker MJ, Goudie D, Fagotto-Kaufmann C, Mercer C et al.

    Journal of medical genetics 2016;53;11;735-742

    PUBMED: 27418539; PMC: 5264232; DOI: 10.1136/jmedgenet-2016-103942

  • A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers.

    Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G et al.

    Nature communications 2016;7;12222

    PUBMED: 27406316; PMC: 4947184; DOI: 10.1038/ncomms12222

  • Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice.

    Miyata H, Castaneda JM, Fujihara Y, Yu Z, Archambeault DR, Isotani A, Kiyozumi D, Kriseman ML, Mashiko D, Matsumura T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;28;7704-10

    PUBMED: 27357688; PMC: 4948324; DOI: 10.1073/pnas.1608458113

  • Germline MC1R status influences somatic mutation burden in melanoma.

    Robles-Espinoza CD, Roberts ND, Chen S, Leacy FP, Alexandrov LB, Pornputtapong N, Halaban R, Krauthammer M, Cui R, Timothy Bishop D and Adams DJ

    Nature communications 2016;7;12064

    PUBMED: 27403562; PMC: 4945874; DOI: 10.1038/ncomms12064

  • A Landscape of Pharmacogenomic Interactions in Cancer.

    Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H et al.

    Cell 2016;166;3;740-754

    PUBMED: 27397505; PMC: 4967469; DOI: 10.1016/j.cell.2016.06.017

  • S1PR2 variants associated with auditory function in humans and endocochlear potential decline in mouse.

    Ingham NJ, Carlisle F, Pearson S, Lewis MA, Buniello A, Chen J, Isaacson RL, Pass J, White JK, Dawson SJ and Steel KP

    Scientific reports 2016;6;28964

    PUBMED: 27383011; PMC: 4935955; DOI: 10.1038/srep28964

  • Resolving early mesoderm diversification through single-cell expression profiling.

    Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC and Göttgens B

    Nature 2016;535;7611;289-293

    PUBMED: 27383781; PMC: 4947525; DOI: 10.1038/nature18633

  • Linear mixed model for heritability estimation that explicitly addresses environmental variation.

    Heckerman D, Gurdasani D, Kadie C, Pomilla C, Carstensen T, Martin H, Ekoru K, Nsubuga RN, Ssenyomo G, Kamali A et al.

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;27;7377-82

    PUBMED: 27382152; PMC: 4941438; DOI: 10.1073/pnas.1510497113

  • Parity, breastfeeding and risk of coronary heart disease: A pan-European case-cohort study.

    Peters SA, van der Schouw YT, Wood AM, Sweeting MJ, Moons KG, Weiderpass E, Arriola L, Benetou V, Boeing H, Bonnet F et al.

    European journal of preventive cardiology 2016;23;16;1755-1765

    PUBMED: 27378766; PMC: 6217919; DOI: 10.1177/2047487316658571

  • Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

    Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J et al.

    Genome biology and evolution 2016;8;6;2020-30

    PUBMED: 27345955; PMC: 4943195; DOI: 10.1093/gbe/evw124

  • Multigenomic Delineation of Plasmodium Species of the Laverania Subgenus Infecting Wild-Living Chimpanzees and Gorillas.

    Liu W, Sundararaman SA, Loy DE, Learn GH, Li Y, Plenderleith LJ, Ndjango JB, Speede S, Atencia R, Cox D et al.

    Genome biology and evolution 2016;8;6;1929-39

    PUBMED: 27289102; PMC: 4943199; DOI: 10.1093/gbe/evw128

  • The acquisition of mechano-electrical transducer current adaptation in auditory hair cells requires myosin VI.

    Marcotti W, Corns LF, Goodyear RJ, Rzadzinska AK, Avraham KB, Steel KP, Richardson GP and Kros CJ

    The Journal of physiology 2016;594;13;3667-81

    PUBMED: 27111754; PMC: 4929313; DOI: 10.1113/JP272220

  • Alkaline ceramidase 1 is essential for mammalian skin homeostasis and regulating whole-body energy expenditure.

    Liakath-Ali K, Vancollie VE, Lelliott CJ, Speak AO, Lafont D, Protheroe HJ, Ingvorsen C, Galli A, Green A, Gleeson D et al.

    The Journal of pathology 2016;239;3;374-83

    PUBMED: 27126290; PMC: 4924601; DOI: 10.1002/path.4737

  • Bacterial GWAS: not just gilding the lily.

    Lees JA and Bentley SD

    Nature reviews. Microbiology 2016;14;7;406

    PUBMED: 27241043; DOI: 10.1038/nrmicro.2016.82

  • Cytokine Profiles during Invasive Nontyphoidal Salmonella Disease Predict Outcome in African Children.

    Gilchrist JJ, Heath JN, Msefula CL, Gondwe EN, Naranbhai V, Mandala W, MacLennan JM, Molyneux EM, Graham SM, Drayson MT et al.

    Clinical and vaccine immunology : CVI 2016;23;7;601-9

    PUBMED: 27170644; PMC: 4933780; DOI: 10.1128/CVI.00128-16

  • Genetic identification of thiosulfate sulfurtransferase as an adipocyte-expressed antidiabetic target in mice selected for leanness.

    Morton NM, Beltram J, Carter RN, Michailidou Z, Gorjanc G, McFadden C, Barrios-Llerena ME, Rodriguez-Cuenca S, Gibbins MT, Aird RE et al.

    Nature medicine 2016;22;7;771-9

    PUBMED: 27270587; PMC: 5524189; DOI: 10.1038/nm.4115

  • GFI1(36N) as a therapeutic and prognostic marker for myelodysplastic syndrome.

    Botezatu L, Michel LC, Makishima H, Schroeder T, Germing U, Haas R, van der Reijden B, Marneth AE, Bergevoet SM, Jansen JH et al.

    Experimental hematology 2016;44;7;590-595.e1

    PUBMED: 27080012; PMC: 4917888; DOI: 10.1016/j.exphem.2016.04.001

  • Goldilocks: a tool for identifying genomic regions that are 'just right'.

    Nicholls SM, Clare A and Randall JC

    Bioinformatics (Oxford, England) 2016;32;13;2047-9

    PUBMED: 27153673; PMC: 4920124; DOI: 10.1093/bioinformatics/btw116

  • New native South American Y chromosome lineages.

    Jota MS, Lacerda DR, Sandoval JR, Vieira PP, Ohasi D, Santos-Júnior JE, Acosta O, Cuellar C, Revollo S, Paz-Y-Miño C et al.

    Journal of human genetics 2016;61;7;593-603

    PUBMED: 27030145; DOI: 10.1038/jhg.2016.26

  • Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants.

    Bronner IF, Otto TD, Zhang M, Udenze K, Wang C, Quail MA, Jiang RH, Adams JH and Rayner JC

    Genome research 2016;26;7;980-9

    PUBMED: 27197223; PMC: 4937560; DOI: 10.1101/gr.200279.115

  • Saturation analysis for whole-genome bisulfite sequencing data.

    Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Herrero J, Czyz A, Ruotti V, Stunnenberg HG, Frontini M et al.

    Nature biotechnology 2016;34;7;691-693

    PUBMED: 27347755; DOI: 10.1038/nbt.3524

  • Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana.

    Lamelas A, Ampah KA, Aboagye S, Kerber S, Danso E, Asante-Poku A, Asare P, Parkhill J, Harris SR, Pluschke G et al.

    PLoS neglected tropical diseases 2016;10;7;e0004856

    PUBMED: 27434064; PMC: 4951013; DOI: 10.1371/journal.pntd.0004856

  • Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection.

    Phan MVT, Anh PH, Cuong NV, Munnink BBO, van der Hoek L, My PT, Tri TN, Bryant JE, Baker S, Thwaites G et al.

    Virus evolution 2016;2;2;vew027

    PUBMED: 28748110; PMC: 5522372; DOI: 10.1093/ve/vew027

  • Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid.

    Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J, Walker AW and Flint HJ

    Environmental microbiology 2016;18;7;2214-25

    PUBMED: 26636660; DOI: 10.1111/1462-2920.13158

  • Whole-genome sequencing of a quarter-century melioidosis outbreak in temperate Australia uncovers a region of low-prevalence endemicity.

    Chapple SNJ, Sarovich DS, Holden MTG, Peacock SJ, Buller N, Golledge C, Mayo M, Currie BJ and Price EP

    Microbial genomics 2016;2;7;e000067

    PUBMED: 28348862; PMC: 5343139; DOI: 10.1099/mgen.0.000067

  • A Stem Cell Strategy Identifies Glycophorin C as a Major Erythrocyte Receptor for the Rodent Malaria Parasite Plasmodium berghei.

    Yiangou L, Montandon R, Modrzynska K, Rosen B, Bushell W, Hale C, Billker O, Rayner JC and Pance A

    PloS one 2016;11;6;e0158238

    PUBMED: 27362409; PMC: 4928779; DOI: 10.1371/journal.pone.0158238

  • Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3.

    Van Haute L, Dietmann S, Kremer L, Hussain S, Pearce SF, Powell CA, Rorbach J, Lantaff R, Blanco S, Sauer S et al.

    Nature communications 2016;7;12039

    PUBMED: 27356879; PMC: 4931328; DOI: 10.1038/ncomms12039

  • The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics.

    Lufino MM, Edser PA, Quail MA, Rice S, Adams DJ and Wade-Martins R

    Scientific reports 2016;6;28644

    PUBMED: 27353647; PMC: 4926088; DOI: 10.1038/srep28644

  • In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine.

    Iurlaro M, McInroy GR, Burgess HE, Dean W, Raiber EA, Bachman M, Beraldi D, Balasubramanian S and Reik W

    Genome biology 2016;17;1;141

    PUBMED: 27356509; PMC: 4928330; DOI: 10.1186/s13059-016-1001-5

  • Sleeping Beauty screen reveals Pparg activation in metastatic prostate cancer.

    Ahmad I, Mui E, Galbraith L, Patel R, Tan EH, Salji M, Rust AG, Repiscak P, Hedley A, Markert E et al.

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;29;8290-5

    PUBMED: 27357679; PMC: 4961202; DOI: 10.1073/pnas.1601571113

  • BRAF(V600E) Kinase Domain Duplication Identified in Therapy-Refractory Melanoma Patient-Derived Xenografts.

    Kemper K, Krijgsman O, Kong X, Cornelissen-Steijger P, Shahrabi A, Weeber F, van der Velden DL, Bleijerveld OB, Kuilman T, Kluin RJC et al.

    Cell reports 2016;16;1;263-277

    PUBMED: 27320919; PMC: 4929150; DOI: 10.1016/j.celrep.2016.05.064

  • Genomic Analysis and Comparison of Two Gonorrhea Outbreaks.

    Didelot X, Dordel J, Whittles LK, Collins C, Bilek N, Bishop CJ, White PJ, Aanensen DM, Parkhill J, Bentley SD et al.

    mBio 2016;7;3

    PUBMED: 27353752; PMC: 4937209; DOI: 10.1128/mBio.00525-16

  • Molecular Insights into Division of Single Human Cancer Cells in On-Chip Transparent Microtubes.

    Xi W, Schmidt CK, Sanchez S, Gracias DH, Carazo-Salas RE, Butler R, Lawrence N, Jackson SP and Schmidt OG

    ACS nano 2016;10;6;5835-46

    PUBMED: 27267364; PMC: 4961266; DOI: 10.1021/acsnano.6b00461

  • DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics.

    Wright JC and Choudhary JS

    Journal of proteomics & bioinformatics 2016;9;6;176-180

    PUBMED: 27418748; PMC: 4941923; DOI: 10.4172/jpb.1000404

  • Genomic analysis of local variation and recent evolution in Plasmodium vivax.

    Pearson RD, Amato R, Auburn S, Miotto O, Almagro-Garcia J, Amaratunga C, Suon S, Mao S, Noviyanti R, Trimarsanto H et al.

    Nature genetics 2016;48;8;959-964

    PUBMED: 27348299; PMC: 4966634; DOI: 10.1038/ng.3599

  • Information recovery from low coverage whole-genome bisulfite sequencing.

    Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH et al.

    Nature communications 2016;7;11306

    PUBMED: 27346250; PMC: 4931220; DOI: 10.1038/ncomms11306

  • Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.

    Rensch T, Villar D, Horvath J, Odom DT and Flicek P

    Genome biology 2016;17;1;139

    PUBMED: 27349964; PMC: 4922064; DOI: 10.1186/s13059-016-0996-y

  • A note on the evaluation of mutation prioritization algorithms

    Popovic,D., Davis,J., SIFRIM,A. and Moor,B.D.

    Proceedings - 2015 IEEE Symposium Series on Computational Intelligence, SSCI 2015 2016;Art. No.: 7376769;1351-7

    DOI: 10.1109/SSCI.2015.193

  • Functional annotation of rare genetic variants

    RITCHIE,G.R.S. and FLICEK,P.;

    Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies 2016;57-70

    DOI: 10.1007/978-1-4939-2824-8_5

  • LINE-1 retrotransposons and their role in cancer

    RAHBARI,R., Habibi,L., Garcia-Puche,J.L., Badge,R.M. and Garcia-Perez,J

    Epigenetics Territory and Cancer 2016;51-99

    DOI: 10.1007/978-94-017-9639-2_3

  • Meta-analysis of rare variants

    TACHMAZIDOU,I. and ZEGGINI,E.;

    Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies 2016;215-226

    DOI: 10.1007/978-1-4939-2824-8_15

  • Natural selection at rare variants

    XUE,Y. and TYLER-SMITH,C.

    Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies 2016;123-33

    DOI: 10.1007/978-1-4939-2824-8_9

  • Population isolates

    Zara, I.

    Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies 2016;107-22

    DOI: 10.1007/978-1-4939-2824-8_8

  • Preface

    ZEGGINI,E. and Morris,A.

    Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies 2016

    DOI: 10.1007/978-1-4939-2824-8

  • The Ensembl gene annotation system.

    Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T et al.

    Database : the journal of biological databases and curation 2016;2016

    PUBMED: 27337980; PMC: 4919035; DOI: 10.1093/database/baw093

  • Complete Genome Sequence of the First KPC-Type Carbapenemase-Positive Proteus mirabilis Strain from a Bloodstream Infection.

    Di Pilato V, Chiarelli A, Boinett CJ, Riccobono E, Harris SR, D'Andrea MM, Thomson NR, Rossolini GM and Giani T

    Genome announcements 2016;4;3

    PUBMED: 27340072; PMC: 4919411; DOI: 10.1128/genomeA.00607-16

  • Making sense of big data in health research: Towards an EU action plan.

    Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A et al.

    Genome medicine 2016;8;1;71

    PUBMED: 27338147; PMC: 4919856; DOI: 10.1186/s13073-016-0323-y

  • Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

    Arias A, Watson SJ, Asogun D, Tobin EA, Lu J, Phan MVT, Jah U, Wadoum REG, Meredith L, Thorne L et al.

    Virus evolution 2016;2;1;vew016

    PUBMED: 28694998; PMC: 5499387; DOI: 10.1093/ve/vew016

  • Admixture into and within sub-Saharan Africa.

    Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM et al.

    eLife 2016;5

    PUBMED: 27324836; PMC: 4915815; DOI: 10.7554/eLife.15266

  • Infection Susceptibility in Gastric Intrinsic Factor (Vitamin B12)-Defective Mice Is Subject to Maternal Influences.

    Mottram L, Speak AO, Selek RM, Cambridge EL, McIntyre Z, Kane L, Mukhopadhyay S, Grove C, Colin A, Brandt C et al.

    mBio 2016;7;3

    PUBMED: 27329747; PMC: 4916386; DOI: 10.1128/mBio.00830-16

  • FANCD2 limits replication stress and genome instability in cells lacking BRCA2.

    Michl J, Zimmer J, Buffa FM, McDermott U and Tarsounas M

    Nature structural & molecular biology 2016;23;8;755-757

    PUBMED: 27322732; PMC: 4973888; DOI: 10.1038/nsmb.3252

  • Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

    Barquist L, Burge SW and Gardner PP

    Current protocols in bioinformatics 2016;54;12.13.1-12.13.25

    PUBMED: 27322404; PMC: 5010141; DOI: 10.1002/cpbi.4

  • PhenoScanner: a database of human genotype-phenotype associations.

    Staley JR, Blackshaw J, Kamat MA, Ellis S, Surendran P, Sun BB, Paul DS, Freitag D, Burgess S, Danesh J et al.

    Bioinformatics (Oxford, England) 2016;32;20;3207-3209

    PUBMED: 27318201; PMC: 5048068; DOI: 10.1093/bioinformatics/btw373

  • DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression.

    Dorman CJ and Dorman MJ

    Biophysical reviews 2016;8;3;209-220

    PUBMED: 28510224; PMC: 5425793; DOI: 10.1007/s12551-016-0205-y

  • Public health interventions to protect against falsified medicines: a systematic review of international, national and local policies.

    Hamilton WL, Doyle C, Halliwell-Ewen M and Lambert G

    Health policy and planning 2016;31;10;1448-1466

    PUBMED: 27311827; DOI: 10.1093/heapol/czw062

  • Taking forward a 'One Health' approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential.

    Zumla A, Dar O, Kock R, Muturi M, Ntoumi F, Kaleebu P, Eusebio M, Mfinanga S, Bates M, Mwaba P et al.

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2016

    PUBMED: 27321961; DOI: 10.1016/j.ijid.2016.06.012

  • Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family.

    Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW, Strugnell RA, Dougan G and Lithgow T

    Genome biology and evolution 2016;8;6;1690-705

    PUBMED: 27190006; PMC: 4943183; DOI: 10.1093/gbe/evw112

  • Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

    Aigrain L, Gu Y and Quail MA

    BMC genomics 2016;17;458

    PUBMED: 27297323; PMC: 4906846; DOI: 10.1186/s12864-016-2757-4

  • The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

    Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EG, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A et al.

    Genome biology 2016;17;1;124

    PUBMED: 27286965; PMC: 4901422; DOI: 10.1186/s13059-016-0985-1

  • Dysfunction of the Voltage-Gated K+ Channel β2 Subunit in a Familial Case of Brugada Syndrome.

    Portero V, Le Scouarnec S, Es-Salah-Lamoureux Z, Burel S, Gourraud JB, Bonnaud S, Lindenbaum P, Simonet F, Violleau J, Baron E et al.

    Journal of the American Heart Association 2016;5;6

    PUBMED: 27287695; PMC: 4937261; DOI: 10.1161/JAHA.115.003122

  • Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens.

    Timms RT, Menzies SA, Tchasovnikarova IA, Christensen LC, Williamson JC, Antrobus R, Dougan G, Ellgaard L and Lehner PJ

    Nature communications 2016;7;11786

    PUBMED: 27283361; PMC: 4906395; DOI: 10.1038/ncomms11786

  • GENOMICS. A federated ecosystem for sharing genomic, clinical data.

    Global Alliance for Genomics and Health

    Science (New York, N.Y.) 2016;352;6291;1278-80

    PUBMED: 27284183; DOI: 10.1126/science.aaf6162

  • A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders.

    Simeoni I, Stephens JC, Hu F, Deevi SV, Megy K, Bariana TK, Lentaigne C, Schulman S, Sivapalaratnam S, Vries MJ et al.

    Blood 2016;127;23;2791-803

    PUBMED: 27084890; PMC: 5016734; DOI: 10.1182/blood-2015-12-688267

  • Genomic Classification and Prognosis in Acute Myeloid Leukemia.

    Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N et al.

    The New England journal of medicine 2016;374;23;2209-2221

    PUBMED: 27276561; PMC: 4979995; DOI: 10.1056/NEJMoa1516192

  • Inherited platelet disorders: toward DNA-based diagnosis.

    Lentaigne C, Freson K, Laffan MA, Turro E, Ouwehand WH and BRIDGE-BPD Consortium and the ThromboGenomics Consortium

    Blood 2016;127;23;2814-23

    PUBMED: 27095789; PMC: 4972611; DOI: 10.1182/blood-2016-03-378588

  • Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines.

    David S, Mentasti M, Tewolde R, Aslett M, Harris SR, Afshar B, Underwood A, Fry NK, Parkhill J and Harrison TG

    Journal of clinical microbiology 2016;54;8;2135-48

    PUBMED: 27280420; PMC: 4963484; DOI: 10.1128/JCM.00432-16

  • Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

    Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW et al.

    BMC genomics 2016;17;440

    PUBMED: 27277524; PMC: 4898365; DOI: 10.1186/s12864-016-2777-0

  • Chromosomal phylogeny of Vampyressine bats (Chiroptera, Phyllostomidae) with description of two new sex chromosome systems.

    Gomes AJ, Nagamachi CY, Rodrigues LR, Benathar TC, Ribas TF, O'Brien PC, Yang F, Ferguson-Smith MA and Pieczarka JC

    BMC evolutionary biology 2016;16;1;119

    PUBMED: 27260645; PMC: 4893233; DOI: 10.1186/s12862-016-0689-x

  • DNA REPAIR. Drugging DNA repair.

    Jackson SP and Helleday T

    Science (New York, N.Y.) 2016;352;6290;1178-9

    PUBMED: 27257245; DOI: 10.1126/science.aab0958

  • Nontyphoidal salmonella disease: Current status of vaccine research and development.

    Tennant SM, MacLennan CA, Simon R, Martin LB and Khan MI

    Vaccine 2016;34;26;2907-2910

    PUBMED: 27032517; DOI: 10.1016/j.vaccine.2016.03.072

  • The industrial melanism mutation in British peppered moths is a transposable element.

    Van't Hof AE, Campagne P, Rigden DJ, Yung CJ, Lingley J, Quail MA, Hall N, Darby AC and Saccheri IJ

    Nature 2016;534;7605;102-5

    PUBMED: 27251284; DOI: 10.1038/nature17951

  • Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

    Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS and Harrow J

    Nature communications 2016;7;11778

    PUBMED: 27250503; PMC: 4895710; DOI: 10.1038/ncomms11778

  • Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168.

    Anjum A, Brathwaite KJ, Aidley J, Connerton PL, Cummings NJ, Parkhill J, Connerton I and Bayliss CD

    Nucleic acids research 2016;44;10;4581-94

    PUBMED: 26786317; PMC: 4889913; DOI: 10.1093/nar/gkw019

  • Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children.

    Kenyan Bacteraemia Study Group, Wellcome Trust Case Control Consortium 2 (WTCCC2), Rautanen A, Pirinen M, Mills TC, Rockett KA, Strange A, Ndungu AW, Naranbhai V, Gilchrist JJ et al.

    American journal of human genetics 2016;98;6;1092-100

    PUBMED: 27236921; DOI: 10.1016/j.ajhg.2016.03.025

  • A genomic approach to therapeutic target validation identifies a glucose-lowering GLP1R variant protective for coronary heart disease.

    Scott RA, Freitag DF, Li L, Chu AY, Surendran P, Young R, Grarup N, Stancáková A, Chen Y, Varga TV et al.

    Science translational medicine 2016;8;341;341ra76

    PUBMED: 27252175; PMC: 5219001; DOI: 10.1126/scitranslmed.aad3744

  • The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

    Pham Thanh D, Thompson CN, Rabaa MA, Sona S, Sopheary S, Kumar V, Moore C, Tran Vu Thieu N, Wijedoru L, Holt KE et al.

    PLoS neglected tropical diseases 2016;10;6;e0004785

    PUBMED: 27331909; PMC: 4917249; DOI: 10.1371/journal.pntd.0004785

  • dfrA thyA Double Deletion in para-Aminosalicylic Acid-Resistant Mycobacterium tuberculosis Beijing Strains.

    Moradigaravand D, Grandjean L, Martinez E, Li H, Zheng J, Coronel J, Moore D, Török ME, Sintchenko V, Huang H et al.

    Antimicrobial agents and chemotherapy 2016;60;6;3864-7

    PUBMED: 27021327; PMC: 4879365; DOI: 10.1128/AAC.00253-16

  • Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study.

    Prins BP, Abbasi A, Wong A, Vaez A, Nolte I, Franceschini N, Stuart PE, Guterriez Achury J, Mistry V, Bradfield JP et al.

    PLoS medicine 2016;13;6;e1001976

    PUBMED: 27327646; PMC: 4915710; DOI: 10.1371/journal.pmed.1001976

  • Quality assurance of the gene ontology using abstraction networks.

    Ochs C, Perl Y, Halper M, Geller J and Lomax J

    Journal of bioinformatics and computational biology 2016;14;3;1642001

    PUBMED: 27301779; DOI: 10.1142/S0219720016420014

  • Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale: a meta-analysis of genome-wide association studies.

    Demirkan A, Lahti J, Direk N, Viktorin A, Lunetta KL, Terracciano A, Nalls MA, Tanaka T, Hek K, Fornage M et al.

    Psychological medicine 2016;46;8;1613-23

    PUBMED: 26997408; PMC: 5812462; DOI: 10.1017/S0033291715002081

  • Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic.

    Jamrozy DM, Harris SR, Mohamed N, Peacock SJ, Tan CY, Parkhill J, Anderson AS and Holden MTG

    Microbial genomics 2016;2;5;e000058

    PUBMED: 28348852; PMC: 5320670; DOI: 10.1099/mgen.0.000058

  • Role of Plasmodium vivax Duffy-binding protein 1 in invasion of Duffy-null Africans.

    Gunalan K, Lo E, Hostetler JB, Yewhalaw D, Mu J, Neafsey DE, Yan G and Miller LH

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;22;6271-6

    PUBMED: 27190089; PMC: 4896682; DOI: 10.1073/pnas.1606113113

  • Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies.

    Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DC, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A et al.

    Genome biology 2016;17;1;115

    PUBMED: 27246460; PMC: 4888588; DOI: 10.1186/s13059-016-0971-7

  • Epstein-Barr virus nuclear protein EBNA3C directly induces expression of AID and somatic mutations in B cells.

    Kalchschmidt JS, Bashford-Rogers R, Paschos K, Gillman AC, Styles CT, Kellam P and Allday MJ

    The Journal of experimental medicine 2016;213;6;921-8

    PUBMED: 27217538; PMC: 4886369; DOI: 10.1084/jem.20160120

  • Functional genomics in osteoarthritis: Past, present, and future.

    Steinberg J and Zeggini E

    Journal of orthopaedic research : official publication of the Orthopaedic Research Society 2016;34;7;1105-10

    PUBMED: 27176659; PMC: 4980743; DOI: 10.1002/jor.23296

  • Genome-Wide Association Studies Suggest Limited Immune Gene Enrichment in Schizophrenia Compared to 5 Autoimmune Diseases.

    Pouget JG, Gonçalves VF, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Spain SL, Finucane HK, Raychaudhuri S, Kennedy JL and Knight J

    Schizophrenia bulletin 2016

    PUBMED: 27242348; DOI: 10.1093/schbul/sbw059

  • Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.

    von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z et al.

    Molecular cell 2016;62;6;848-861

    PUBMED: 27237052; PMC: 4914828; DOI: 10.1016/j.molcel.2016.04.025

  • Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC-dependence in intrahepatic cholangiocarcinoma.

    Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT et al.

    Cancer discovery 2016

    PUBMED: 27231123; DOI: 10.1158/2159-8290.CD-15-1442

  • Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.

    Blohmke CJ, Darton TC, Jones C, Suarez NM, Waddington CS, Angus B, Zhou L, Hill J, Clare S, Kane L et al.

    The Journal of experimental medicine 2016;213;6;1061-77

    PUBMED: 27217537; PMC: 4886356; DOI: 10.1084/jem.20151025

  • Mitochondrial genetic diversity, selection and recombination in a canine transmissible cancer.

    Strakova A, Ní Leathlobhair M, Wang GD, Yin TT, Airikkala-Otter I, Allen JL, Allum KM, Bansse-Issa L, Bisson JL, Castillo Domracheva A et al.

    eLife 2016;5

    PUBMED: 27185408; PMC: 4869914; DOI: 10.7554/eLife.14552

  • An Antibody Screen of a Plasmodium vivax Antigen Library Identifies Novel Merozoite Proteins Associated with Clinical Protection.

    França CT, Hostetler JB, Sharma S, White MT, Lin E, Kiniboro B, Waltmann A, Darcy AW, Li Wai Suen CS, Siba P et al.

    PLoS neglected tropical diseases 2016;10;5;e0004639

    PUBMED: 27182597; PMC: 4868274; DOI: 10.1371/journal.pntd.0004639

  • Multilevel models improve precision and speed of IC50 estimates.

    Vis DJ, Bombardelli L, Lightfoot H, Iorio F, Garnett MJ and Wessels LF

    Pharmacogenomics 2016;17;7;691-700

    PUBMED: 27180993; PMC: 6455999; DOI: 10.2217/pgs.16.15

  • A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

    Danecek P, McCarthy SA, HipSci Consortium and Durbin R

    PloS one 2016;11;5;e0155014

    PUBMED: 27176002; PMC: 4866717; DOI: 10.1371/journal.pone.0155014

  • An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

    Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA et al.

    Nature communications 2016;7;11491

    PUBMED: 27173435; PMC: 4869170; DOI: 10.1038/ncomms11491

  • Binding of Plasmodium falciparum Merozoite Surface Proteins DBLMSP and DBLMSP2 to Human Immunoglobulin M Is Conserved among Broadly Diverged Sequence Variants.

    Crosnier C, Iqbal Z, Knuepfer E, Maciuca S, Perrin AJ, Kamuyu G, Goulding D, Bustamante LY, Miles A, Moore SC et al.

    The Journal of biological chemistry 2016;291;27;14285-14299

    PUBMED: 27226583; PMC: 4933183; DOI: 10.1074/jbc.M116.722074

  • Microsatellite genotyping and genome-wide single nucleotide polymorphism-based indices of Plasmodium falciparum diversity within clinical infections.

    Murray L, Mobegi VA, Duffy CW, Assefa SA, Kwiatkowski DP, Laman E, Loua KM and Conway DJ

    Malaria journal 2016;15;1;275

    PUBMED: 27176827; PMC: 4865991; DOI: 10.1186/s12936-016-1324-4

  • Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics.

    Klemm E and Dougan G

    Cell host & microbe 2016;19;5;599-610

    PUBMED: 27173928; DOI: 10.1016/j.chom.2016.04.015

  • Predicting quantitative traits from genome and phenome with near perfect accuracy.

    Märtens K, Hallin J, Warringer J, Liti G and Parts L

    Nature communications 2016;7;11512

    PUBMED: 27160605; PMC: 4866306; DOI: 10.1038/ncomms11512

  • Single-cell genomics: coming of age.

    Linnarsson S and Teichmann SA

    Genome biology 2016;17;97

    PUBMED: 27160975; PMC: 4862185; DOI: 10.1186/s13059-016-0960-x

  • Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates.

    Willems T, Gymrek M, Poznik GD, Tyler-Smith C, 1000 Genomes Project Chromosome Y Group and Erlich Y

    American journal of human genetics 2016;98;5;919-933

    PUBMED: 27126583; PMC: 4863667; DOI: 10.1016/j.ajhg.2016.04.001

  • Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

    Aanensen DM, Feil EJ, Holden MT, Dordel J, Yeats CA, Fedosejev A, Goater R, Castillo-Ramírez S, Corander J, Colijn C et al.

    mBio 2016;7;3

    PUBMED: 27150362; PMC: 4959656; DOI: 10.1128/mBio.00444-16

  • Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers.

    Einarsson GG, Comer DM, McIlreavey L, Parkhill J, Ennis M, Tunney MM and Elborn JS

    Thorax 2016;71;9;795-803

    PUBMED: 27146202; DOI: 10.1136/thoraxjnl-2015-207235

  • Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.

    Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D and Lawley TD

    Nature 2016;533;7604;543-546

    PUBMED: 27144353; PMC: 4890681; DOI: 10.1038/nature17645

  • Understanding mutagenesis through delineation of mutational signatures in human cancer.

    Petljak M and Alexandrov LB

    Carcinogenesis 2016;37;6;531-40

    PUBMED: 27207657; DOI: 10.1093/carcin/bgw055

  • Very low-depth sequencing in a founder population identifies a cardioprotective APOC3 signal missed by genome-wide imputation.

    Gilly A, Ritchie GR, Southam L, Farmaki AE, Tsafantakis E, Dedoussis G and Zeggini E

    Human molecular genetics 2016;25;11;2360-2365

    PUBMED: 27146844; PMC: 5081052; DOI: 10.1093/hmg/ddw088

  • Alternative Splice Forms Influence Functions of Whirlin in Mechanosensory Hair Cell Stereocilia.

    Ebrahim S, Ingham NJ, Lewis MA, Rogers MJ, Cui R, Kachar B, Pass JC and Steel KP

    Cell reports 2016;15;5;935-43

    PUBMED: 27117407; PMC: 4859837; DOI: 10.1016/j.celrep.2016.03.081

  • Antibiotics, gut bugs and the young.

    Browne H

    Nature reviews. Microbiology 2016;14;6;336

    PUBMED: 27140687; DOI: 10.1038/nrmicro.2016.73

  • RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features.

    Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA et al.

    Leukemia 2016;30;11;2160-2168

    PUBMED: 27137476; DOI: 10.1038/leu.2016.126

  • Study of Plasmodium falciparum DHHC palmitoyl transferases identifies a role for PfDHHC9 in gametocytogenesis.

    Tay CL, Jones ML, Hodson N, Theron M, Choudhary JS and Rayner JC

    Cellular microbiology 2016;18;11;1596-1610

    PUBMED: 27060339; PMC: 5091645; DOI: 10.1111/cmi.12599

  • The topography of mutational processes in breast cancer genomes.

    Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M et al.

    Nature communications 2016;7;11383

    PUBMED: 27136393; PMC: 5001788; DOI: 10.1038/ncomms11383

  • Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

    Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC et al.

    Nature 2016;534;7605;47-54

    PUBMED: 27135926; PMC: 4910866; DOI: 10.1038/nature17676

  • The Contribution of GWAS Loci in Familial Dyslipidemias.

    Ripatti P, Rämö JT, Söderlund S, Surakka I, Matikainen N, Pirinen M, Pajukanta P, Sarin AP, Service SK, Laurila PP et al.

    PLoS genetics 2016;12;5;e1006078

    PUBMED: 27227539; PMC: 4882070; DOI: 10.1371/journal.pgen.1006078

  • A Simple Screening Approach To Prioritize Genes for Functional Analysis Identifies a Role for Interferon Regulatory Factor 7 in the Control of Respiratory Syncytial Virus Disease.

    McDonald JU, Kaforou M, Clare S, Hale C, Ivanova M, Huntley D, Dorner M, Wright VJ, Levin M, Martinon-Torres F et al.

    mSystems 2016;1;3

    PUBMED: 27822537; PMC: 5069771; DOI: 10.1128/mSystems.00051-16

  • Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

    Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C and Odom DT

    PLoS genetics 2016;12;5;e1006024

    PUBMED: 27166679; PMC: 4864286; DOI: 10.1371/journal.pgen.1006024

  • Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus.

    Romanenko SA, Lemskaya NA, Trifonov VA, Serdyukova NA, O'Brien PC, Bulatova NSh, Golenishchev FN, Ferguson-Smith MA, Yang F and Graphodatsky AS

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2016;24;2;145-59

    PUBMED: 26611440; DOI: 10.1007/s10577-015-9504-6

  • Genome-wide time-to-event analysis on smoking progression stages in a family-based study.

    He L, Pitkäniemi J, Heikkilä K, Chou YL, Madden PA, Korhonen T, Sarin AP, Ripatti S, Kaprio J and Loukola A

    Brain and behavior 2016;6;5;e00462

    PUBMED: 27134767; PMC: 4842934; DOI: 10.1002/brb3.462

  • Insights into metabolic disease from studying genetics in isolated populations: stories from Greece to Greenland.

    Zeggini E, Gloyn AL and Hansen T

    Diabetologia 2016;59;5;938-41

    PUBMED: 26993633; PMC: 4826421; DOI: 10.1007/s00125-016-3926-3

  • Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

    Cuthbertson L, Rogers GB, Walker AW, Oliver A, Green LE, Daniels TW, Carroll MP, Parkhill J, Bruce KD and van der Gast CJ

    The ISME journal 2016;10;5;1081-91

    PUBMED: 26555248; PMC: 4820042; DOI: 10.1038/ismej.2015.198

  • Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage-stage chimerism and mixoploidy.

    Destouni A, Zamani Esteki M, Catteeuw M, Tšuiko O, Dimitriadou E, Smits K, Kurg A, Salumets A, Van Soom A, Voet T and Vermeesch JR

    Genome research 2016;26;5;567-78

    PUBMED: 27197242; PMC: 4864459; DOI: 10.1101/gr.200527.115

  • The functional O-mannose glycan on α-dystroglycan contains a phospho-ribitol primed for matriglycan addition.

    Praissman JL, Willer T, Sheikh MO, Toi A, Chitayat D, Lin YY, Lee H, Stalnaker SH, Wang S, Prabhakar PK et al.

    eLife 2016;5

    PUBMED: 27130732; PMC: 4924997; DOI: 10.7554/eLife.14473

  • HUWE1 mutations in Juberg-Marsidi and Brooks syndromes: the results of an X-chromosome exome sequencing study.

    Friez MJ, Brooks SS, Stevenson RE, Field M, Basehore MJ, Adès LC, Sebold C, McGee S, Saxon S, Skinner C et al.

    BMJ open 2016;6;4;e009537

    PUBMED: 27130160; PMC: 4854010; DOI: 10.1136/bmjopen-2015-009537

  • SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments.

    Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA and Harris SR

    Microbial genomics 2016;2;4;e000056

    PUBMED: 28348851; PMC: 5320690; DOI: 10.1099/mgen.0.000056

  • Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies.

    McKerrell T, Moreno T, Ponstingl H, Bolli N, Dias JM, Tischler G, Colonna V, Manasse B, Bench A, Bloxham D et al.

    Blood 2016;128;1;e1-9

    PUBMED: 27121471; PMC: 4937362; DOI: 10.1182/blood-2015-11-683334

  • Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

    Lun AT, Bach K and Marioni JC

    Genome biology 2016;17;75

    PUBMED: 27122128; PMC: 4848819; DOI: 10.1186/s13059-016-0947-7

  • Structure and evolutionary history of a large family of NLR proteins in the zebrafish.

    Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F and Leptin M

    Open biology 2016;6;4;160009

    PUBMED: 27248802; PMC: 4852459; DOI: 10.1098/rsob.160009

  • Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

    Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S et al.

    Nature genetics 2016;48;6;593-9

    PUBMED: 27111036; PMC: 4884158; DOI: 10.1038/ng.3559

  • Loss of Mrap2 is associated with Sim 1 deficiency and increased circulating cholesterol.

    Novoselova TV, Larder R, Rimmington D, Lelliott C, Wynn E, Gorrigan RJ, Tate P, Guasti L, Sanger Mouse Genetics Project T, O'Rahilly S et al.

    The Journal of endocrinology 2016

    PUBMED: 27106110; DOI: 10.1530/JOE-16-0057

  • The influence of a short-term gluten-free diet on the human gut microbiome.

    Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C et al.

    Genome medicine 2016;8;1;45

    PUBMED: 27102333; PMC: 4841035; DOI: 10.1186/s13073-016-0295-y

  • A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect.

    McEntagart M, Williamson KA, Rainger JK, Wheeler A, Seawright A, De Baere E, Verdin H, Bergendahl LT, Quigley A, Rainger J et al.

    American journal of human genetics 2016;98;5;981-992

    PUBMED: 27108798; PMC: 4863663; DOI: 10.1016/j.ajhg.2016.03.018

  • Companion: a web server for annotation and analysis of parasite genomes.

    Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M and Otto TD

    Nucleic acids research 2016;44;W1;W29-34

    PUBMED: 27105845; PMC: 4987884; DOI: 10.1093/nar/gkw292

  • Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines.

    Campino S, Benavente ED, Assefa S, Thompson E, Drought LG, Taylor CJ, Gorvett Z, Carret CK, Flueck C, Ivens AC et al.

    Malaria journal 2016;15;229

    PUBMED: 27098483; PMC: 4839107; DOI: 10.1186/s12936-016-1254-1

  • Impact of socioeconomic status on disease phenotype, genomic landscape and outcomes in myelodysplastic syndromes.

    Mastaglio F, Bedair K, Papaemmanuil E, Groves MJ, Hyslop A, Keenan N, Hothersall EJ, Campbell PJ, Bowen DT and Tauro S

    British journal of haematology 2016;174;2;227-34

    PUBMED: 27098194; DOI: 10.1111/bjh.14042

  • Standardized Welfare Terms for the Zebrafish Community.

    Goodwin N, Karp NA, Blackledge S, Clark B, Keeble R, Kovacs C, Murray KN, Price M, Thompson P and Bussell J

    Zebrafish 2016

    PUBMED: 27096380; DOI: 10.1089/zeb.2016.1248

  • Identification of differential PI3K pathway target dependencies in T-cell acute lymphoblastic leukemia through a large cancer cell panel screen.

    Lynch JT, McEwen R, Crafter C, McDermott U, Garnett MJ, Barry ST and Davies BR

    Oncotarget 2016;7;16;22128-39

    PUBMED: 26989080; PMC: 5008349; DOI: 10.18632/oncotarget.8031

  • Chromosome organisation during ageing and senescence.

    Chandra T and Kirschner K

    Current opinion in cell biology 2016;40;161-167

    PUBMED: 27101466; DOI: 10.1016/j.ceb.2016.03.020

  • Palmitoyl Transferases have Critical Roles in the Development of Mosquito and Liver Stages of Plasmodium.

    Hopp CS, Balaban AE, Bushell E, Billker O, Rayner JC and Sinnis P

    Cellular microbiology 2016

    PUBMED: 27084458; DOI: 10.1111/cmi.12601

  • The BAF chromatin remodelling complex is an epigenetic regulator of lineage specification in the early mouse embryo.

    Panamarova M, Cox A, Wicher KB, Butler R, Bulgakova N, Jeon S, Rosen B, Seong RH, Skarnes W, Crabtree G and Zernicka-Goetz M

    Development (Cambridge, England) 2016;143;8;1271-83

    PUBMED: 26952987; DOI: 10.1242/dev.131961

  • The global antigenic diversity of swine influenza A viruses.

    Lewis NS, Russell CA, Langat P, Anderson TK, Berger K, Bielejec F, Burke DF, Dudas G, Fonville JM, Fouchier RA et al.

    eLife 2016;5;e12217

    PUBMED: 27113719; PMC: 4846380; DOI: 10.7554/eLife.12217

  • CRISPR-Cas9(D10A) nickase-based genotypic and phenotypic screening to enhance genome editing.

    Chiang TW, le Sage C, Larrieu D, Demir M and Jackson SP

    Scientific reports 2016;6;24356

    PUBMED: 27079678; PMC: 4832145; DOI: 10.1038/srep24356

  • Pitfalls in genetic testing: the story of missed SCN1A mutations.

    Djémié T, Weckhuysen S, von Spiczak S, Carvill GL, Jaehn J, Anttonen AK, Brilstra E, Caglayan HS, de Kovel CG, Depienne C et al.

    Molecular genetics & genomic medicine 2016;4;4;457-64

    PUBMED: 27465585; PMC: 4947864; DOI: 10.1002/mgg3.217

  • A detailed clinical analysis of 13 patients with AUTS2 syndrome further delineates the phenotypic spectrum and underscores the behavioural phenotype.

    Beunders G, van de Kamp J, Vasudevan P, Morton J, Smets K, Kleefstra T, de Munnik SA, Schuurs-Hoeijmakers J, Ceulemans B, Zollino M et al.

    Journal of medical genetics 2016;53;8;523-32

    PUBMED: 27075013; DOI: 10.1136/jmedgenet-2015-103601

  • Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass.

    Guo G, von Meyenn F, Santos F, Chen Y, Reik W, Bertone P, Smith A and Nichols J

    Stem cell reports 2016;6;4;437-46

    PUBMED: 26947977; DOI: 10.1016/j.stemcr.2016.02.005

  • Pathogen hide-and-'seq'.

    Chewapreecha C, Bénard A and Reuter S

    Nature reviews. Microbiology 2016;14;5;271

    PUBMED: 27067399; DOI: 10.1038/nrmicro.2016.52

  • Status of paratyphoid fever vaccine research and development.

    Martin LB, Simon R, MacLennan CA, Tennant SM, Sahastrabuddhe S and Khan MI

    Vaccine 2016

    PUBMED: 27083427; DOI: 10.1016/j.vaccine.2016.03.106

  • Phenotypic insights into ADCY5-associated disease.

    Chang FC, Westenberger A, Dale RC, Smith M, Pall HS, Perez-Dueñas B, Grattan-Smith P, Ouvrier RA, Mahant N, Hanna BC et al.

    Movement disorders : official journal of the Movement Disorder Society 2016

    PUBMED: 27061943; DOI: 10.1002/mds.26598

  • Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation.

    Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA et al.

    Nature communications 2016;7;10979

    PUBMED: 27052111; PMC: 4829663; DOI: 10.1038/ncomms10979

  • gEVAL - a web-based browser for evaluating genome assemblies.

    Chow W, Brugger K, Caccamo M, Sealy I, Torrance J and Howe K

    Bioinformatics (Oxford, England) 2016;32;16;2508-10

    PUBMED: 27153597; PMC: 4978925; DOI: 10.1093/bioinformatics/btw159

  • Large-scale production of megakaryocytes from human pluripotent stem cells by chemically defined forward programming.

    Moreau T, Evans AL, Vasquez L, Tijssen MR, Yan Y, Trotter MW, Howard D, Colzani M, Arumugam M, Wu WH et al.

    Nature communications 2016;7;11208

    PUBMED: 27052461; PMC: 4829662; DOI: 10.1038/ncomms11208

  • Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.

    Rouhani FJ, Nik-Zainal S, Wuster A, Li Y, Conte N, Koike-Yusa H, Kumasaka N, Vallier L, Yusa K and Bradley A

    PLoS genetics 2016;12;4;e1005932

    PUBMED: 27054363; PMC: 4824386; DOI: 10.1371/journal.pgen.1005932

  • Mutations and altered expression of SERPINF1 in patients with familial otosclerosis.

    Ziff JL, Crompton M, Powell HR, Lavy JA, Aldren CP, Steel KP, Saeed SR and Dawson SJ

    Human molecular genetics 2016

    PUBMED: 27056980; DOI: 10.1093/hmg/ddw106

  • Oct-1, to go or not to go? That is the PolII question.

    Pance A

    Biochimica et biophysica acta 2016;1859;6;820-4

    PUBMED: 27063953; DOI: 10.1016/j.bbagrm.2016.04.003

  • Rapid parallel acquisition of somatic mutations after NPM1 in acute myeloid leukaemia evolution.

    Grove CS, Bolli N, Manes N, Varela I, Van't Veer M, Bench A, Eldaly H, Wedge D, Van Loo P and Vassiliou GS

    British journal of haematology 2016

    PUBMED: 27062498; DOI: 10.1111/bjh.13999

  • Adipose tissue plasticity: how fat depots respond differently to pathophysiological cues.

    Pellegrinelli V, Carobbio S and Vidal-Puig A

    Diabetologia 2016

    PUBMED: 27039901; DOI: 10.1007/s00125-016-3933-4

  • The genomic signatures of Shigella evolution, adaptation and geographical spread.

    The HC, Thanh DP, Holt KE, Thomson NR and Baker S

    Nature reviews. Microbiology 2016;14;4;235-50

    PUBMED: 26923111; DOI: 10.1038/nrmicro.2016.10

  • An Integrated Genome-Wide Systems Genetics Screen for Breast Cancer Metastasis Susceptibility Genes.

    Bai L, Yang HH, Hu Y, Shukla A, Ha NH, Doran A, Faraji F, Goldberger N, Lee MP, Keane T and Hunter KW

    PLoS genetics 2016;12;4;e1005989

    PUBMED: 27074153; PMC: 4830524; DOI: 10.1371/journal.pgen.1005989

  • A multiple-phenotype imputation method for genetic studies.

    Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A and Marchini J

    Nature genetics 2016;48;4;466-72

    PUBMED: 26901065; PMC: 4817234; DOI: 10.1038/ng.3513

  • A secreted WNT-ligand-binding domain of FZD5 generated by a frameshift mutation causes autosomal dominant coloboma.

    Liu C, Widen SA, Williamson KA, Ratnapriya R, Gerth-Kahlert C, Rainger J, Alur RP, Strachan E, Manjunath SH, Balakrishnan A et al.

    Human molecular genetics 2016;25;7;1382-91

    PUBMED: 26908622; PMC: 4787907; DOI: 10.1093/hmg/ddw020

  • De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects.

    Priest JR, Osoegawa K, Mohammed N, Nanda V, Kundu R, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D et al.

    PLoS genetics 2016;12;4;e1005963

    PUBMED: 27058611; PMC: 4825975; DOI: 10.1371/journal.pgen.1005963

  • Do Genetic Factors Modify the Relationship Between Obesity and Hypertriglyceridemia? Findings From the GLACIER and the MDC Studies.

    Ali A, Varga TV, Stojkovic IA, Schulz CA, Hallmans G, Barroso I, Poveda A, Renström F, Orho-Melander M and Franks PW

    Circulation. Cardiovascular genetics 2016;9;2;162-71

    PUBMED: 26865658; DOI: 10.1161/CIRCGENETICS.115.001218

  • Dynamic spatio-temporal contribution of single β5t+ cortical epithelial precursors to the thymus medulla.

    Mayer CE, Žuklys S, Zhanybekova S, Ohigashi I, Teh HY, Sansom SN, Shikama-Dorn N, Hafen K, Macaulay IC, Deadman ME et al.

    European journal of immunology 2016;46;4;846-56

    PUBMED: 26694097; PMC: 4832341; DOI: 10.1002/eji.201545995

  • Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91-/- phox Mice.

    Grant AJ, Oshota O, Chaudhuri RR, Mayho M, Peters SE, Clare S, Maskell DJ and Mastroeni P

    Infection and immunity 2016;84;4;989-97

    PUBMED: 26787719; PMC: 4807482; DOI: 10.1128/IAI.01423-15

  • Genome-wide rare copy number variation screening in ulcerative colitis identifies potential susceptibility loci.

    Saadati HR, Wittig M, Helbig I, Häsler R, Anderson CA, Mathew CG, Kupcinskas L, Parkes M, Karlsen TH, Rosenstiel P et al.

    BMC medical genetics 2016;17;26

    PUBMED: 27037036; PMC: 4818401; DOI: 10.1186/s12881-016-0289-z

  • Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal.

    Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C and Jobling MA

    Genome research 2016;26;4;427-39

    PUBMED: 26883546; PMC: 4817767; DOI: 10.1101/gr.198754.115

  • Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research.

    Spjuth O, Krestyaninova M, Hastings J, Shen HY, Heikkinen J, Waldenberger M, Langhammer A, Ladenvall C, Esko T, Persson MÅ et al.

    European journal of human genetics : EJHG 2016;24;4;521-8

    PUBMED: 26306643; DOI: 10.1038/ejhg.2015.165

  • Human Knockout Carriers: Dead, Diseased, Healthy, or Improved?

    Narasimhan VM, Xue Y and Tyler-Smith C

    Trends in molecular medicine 2016;22;4;341-351

    PUBMED: 26988438; PMC: 4826344; DOI: 10.1016/j.molmed.2016.02.006

  • Malaria Vaccine Development: Focusing Field Erythrocyte Invasion Studies on Phenotypic Diversity: The West African Merozoite Invasion Network (WAMIN).

    WAMIN Consortium Authors, Ahouidi AD, Amambua-Ngwa A, Awandare GA, Bei AK, Conway DJ, Diakite M, Duraisingh MT, Rayner JC and Zenonos ZA

    Trends in parasitology 2016;32;4;274-83

    PUBMED: 26725306; DOI: 10.1016/j.pt.2015.11.009

  • Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels.

    van Leeuwen EM, Sabo A, Bis JC, Huffman JE, Manichaikul A, Smith AV, Feitosa MF, Demissie S, Joshi PK, Duan Q et al.

    Journal of medical genetics 2016

    PUBMED: 27036123; DOI: 10.1136/jmedgenet-2015-103439

  • Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

    Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR, Connor T, Hopkins KL, Underwood A, Lettini AA, Page A et al.

    Emerging infectious diseases 2016;22;4;617-24

    PUBMED: 26982594; PMC: 4806966; DOI: 10.3201/eid2204.150531

  • Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain.

    Pérez-Vázquez M, Oteo J, García-Cobos S, Aracil B, Harris SR, Ortega A, Fontanals D, Hernández JM, Solís S, Campos J et al.

    The Journal of antimicrobial chemotherapy 2016;71;4;887-96

    PUBMED: 26769896; PMC: 4790626; DOI: 10.1093/jac/dkv458

  • Population and assay thresholds for the predictive value of lipoprotein (a) for coronary artery disease: the EPIC-Norfolk Prospective Population Study.

    Verbeek R, Boekholdt SM, Stoekenbroek RM, Hovingh GK, Witztum JL, Wareham NJ, Sandhu MS, Khaw KT and Tsimikas S

    Journal of lipid research 2016;57;4;697-705

    PUBMED: 26828068; PMC: 4808778; DOI: 10.1194/jlr.P066258

  • Structure-function integrity of the adult hippocampus depends on the transcription factor Bcl11b/Ctip2.

    Simon R, Baumann L, Fischer J, Seigfried FA, De Bruyckere E, Liu P, Jenkins NA, Copeland NG, Schwegler H and Britsch S

    Genes, brain, and behavior 2016;15;4;405-19

    PUBMED: 26915960; PMC: 4832350; DOI: 10.1111/gbb.12287

  • tRNA fragments: novel players in intergenerational inheritance.

    Gapp K and Miska EA

    Cell research 2016;26;4;395-6

    PUBMED: 26902286; PMC: 4822125; DOI: 10.1038/cr.2016.24

  • Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally.

    Zumla A, Goodfellow I, Kasolo F, Ntoumi F, Buchy P, Bates M, Azhar EI, Cotten M and Petersen E

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2016;45;92-4

    PUBMED: 26952389; DOI: 10.1016/j.ijid.2016.02.1007

  • Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments.

    McInroy GR, Beraldi D, Raiber EA, Modrzynska K, van Delft P, Billker O and Balasubramanian S

    PloS one 2016;11;3;e0152322

    PUBMED: 27031619; PMC: 4816320; DOI: 10.1371/journal.pone.0152322

  • Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells.

    Kulbe H, Iorio F, Chakravarty P, Milagre CS, Moore R, Thompson RG, Everitt G, Canosa M, Montoya A, Drygin D et al.

    Oncotarget 2016;7;13;15648-61

    PUBMED: 26871292; PMC: 4941267; DOI: 10.18632/oncotarget.7255

  • Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential.

    Bolton H, Graham SJL, Van der Aa N, Kumar P, Theunis K, Fernandez Gallardo E, Voet T and Zernicka-Goetz M

    Nature communications 2016;7;11165

    PUBMED: 27021558; PMC: 4820631; DOI: 10.1038/ncomms11165

  • Diagnostic Yield of Sequencing Familial Hypercholesterolemia Genes in Patients with Severe Hypercholesterolemia.

    Khera AV, Won HH, Peloso GM, Lawson KS, Bartz TM, Deng X, van Leeuwen EM, Natarajan P, Emdin CA, Bick AG et al.

    Journal of the American College of Cardiology 2016

    PUBMED: 27050191; DOI: 10.1016/j.jacc.2016.03.520

  • RESEARCH ETHICS. Ethics review for international data-intensive research.

    Dove ES, Townend D, Meslin EM, Bobrow M, Littler K, Nicol D, de Vries J, Junker A, Garattini C, Bovenberg J et al.

    Science (New York, N.Y.) 2016;351;6280;1399-400

    PUBMED: 27013718; PMC: 4838154; DOI: 10.1126/science.aad5269

  • Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza.

    Xu H, Song J, Luo H, Zhang Y, Li Q, Zhu Y, Xu J, Li Y, Song C, Wang B et al.

    Molecular plant 2016

    PUBMED: 27018390; DOI: 10.1016/j.molp.2016.03.010

  • Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease.

    Myocardial Infarction Genetics and CARDIoGRAM Exome Consortia Investigators

    The New England journal of medicine 2016;374;12;1134-44

    PUBMED: 26934567; DOI: 10.1056/NEJMoa1507652

  • Comparative genomics of carriage and disease isolates of Streptococcus pneumoniae serotype 22F reveals lineage specific divergence and niche adaptation.

    Cleary DW, Devine VT, Jefferies J, Webb JS, Bentley SD, Gladstone RA, Faust SN and Clarke SC

    Genome biology and evolution 2016

    PUBMED: 27016484; DOI: 10.1093/gbe/evw066

  • Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish.

    Brocal I, White RJ, Dooley CM, Carruthers SN, Clark R, Hall A, Busch-Nentwich EM, Stemple DL and Kettleborough RN

    BMC genomics 2016;17;259

    PUBMED: 27009152; PMC: 4806435; DOI: 10.1186/s12864-016-2563-z

  • Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

    Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC and Zernicka-Goetz M

    Cell 2016;165;1;61-74

    PUBMED: 27015307; PMC: 4819611; DOI: 10.1016/j.cell.2016.01.047

  • Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent.

    Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G et al.

    eLife 2016;5

    PUBMED: 27003289; PMC: 4811772; DOI: 10.7554/eLife.12613

  • Genomes of cryptic chimpanzee Plasmodium species reveal key evolutionary events leading to human malaria.

    Sundararaman SA, Plenderleith LJ, Liu W, Loy DE, Learn GH, Li Y, Shaw KS, Ayouba A, Peeters M, Speede S et al.

    Nature communications 2016;7;11078

    PUBMED: 27002652; PMC: 4804174; DOI: 10.1038/ncomms11078

  • Heterozygous KIDINS220/ARMS nonsense variants cause spastic paraplegia, intellectual disability, nystagmus, and obesity.

    Josifova DJ, Monroe GR, Tessadori F, de Graaff E, van der Zwaag B, Mehta SG, DDD Study, Harakalova M, Duran KJ, Savelberg SM et al.

    Human molecular genetics 2016;25;11;2158-2167

    PUBMED: 27005418; DOI: 10.1093/hmg/ddw082

  • New insights into sex chromosome evolution in anole lizards (Reptilia, Dactyloidae).

    Giovannotti M, Trifonov VA, Paoletti A, Kichigin IG, O'Brien PC, Kasai F, Giovagnoli G, Ng BL, Ruggeri P, Cerioni PN et al.

    Chromosoma 2016;126;2;245-260

    PUBMED: 27001473; DOI: 10.1007/s00412-016-0585-6

  • Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development.

    Takeda H, Rust AG, Ward JM, Yew CC, Jenkins NA and Copeland NG

    Proceedings of the National Academy of Sciences of the United States of America 2016

    PUBMED: 27006499; PMC: 4833248; DOI: 10.1073/pnas.1603223113

  • Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

    Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R et al.

    Nature microbiology 2016;1;16027

    PUBMED: 27572446; DOI: 10.1038/nmicrobiol.2016.27

  • The Relationship Between Invasive Nontyphoidal Salmonella Disease, Other Bacterial Bloodstream Infections, and Malaria in Sub-Saharan Africa.

    Park SE, Pak GD, Aaby P, Adu-Sarkodie Y, Ali M, Aseffa A, Biggs HM, Bjerregaard-Andersen M, Breiman RF, Crump JA et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016;62 Suppl 1;S23-31

    PUBMED: 26933016; PMC: 4772835; DOI: 10.1093/cid/civ893

  • Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence.

    Kumar N, Miyajima F, He M, Roberts P, Swale A, Ellison L, Pickard D, Smith G, Molyneux R, Dougan G et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016;62;6;746-752

    PUBMED: 26683317; PMC: 4772841; DOI: 10.1093/cid/civ1031

  • Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism.

    Fung TC, Bessman NJ, Hepworth MR, Kumar N, Shibata N, Kobuley D, Wang K, Ziegler CGK, Goc J, Shima T et al.

    Immunity 2016;44;3;634-646

    PUBMED: 26982365; PMC: 4845739; DOI: 10.1016/j.immuni.2016.02.019

  • Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci.

    Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park YR, Raychaudhuri S, Pouget JG, Hübenthal M et al.

    Nature genetics 2016

    PUBMED: 26974007; DOI: 10.1038/ng.3528

  • Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders.

    Singh T, Kurki MI, Curtis D, Purcell SM, Crooks L, McRae J, Suvisaari J, Chheda H, Blackwood D, Breen G et al.

    Nature neuroscience 2016;19;4;571-7

    PUBMED: 26974950; PMC: 6689268; DOI: 10.1038/nn.4267

  • Rare variant in scavenger receptor BI raises HDL cholesterol and increases risk of coronary heart disease.

    Zanoni P, Khetarpal SA, Larach DB, Hancock-Cerutti WF, Millar JS, Cuchel M, DerOhannessian S, Kontush A, Surendran P, Saleheen D et al.

    Science (New York, N.Y.) 2016;351;6278;1166-71

    PUBMED: 26965621; DOI: 10.1126/science.aad3517

  • Voices of biotech.

    Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF et al.

    Nature biotechnology 2016;34;3;270-5

    PUBMED: 26963549; DOI: 10.1038/nbt.3502

  • Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989-2013.

    du Plessis M, Allam M, Tempia S, Wolter N, de Gouveia L, Mollendorf CV, Jolley KA, Mbelle N, Wadula J, Cornick JE et al.

    Journal of clinical microbiology 2016

    PUBMED: 26962082; DOI: 10.1128/JCM.00055-16

  • H3Africa multi-centre study of the prevalence and environmental and genetic determinants of type 2 diabetes in sub-Saharan Africa: study protocol.

    Ekoru K, Young EH, Adebamowo C, Balde N, Hennig BJ, Kaleebu P, Kapiga S, Levitt NS, Mayige M, Mbanya JC et al.

    Global health, epidemiology and genomics 2016;1;e5

    PUBMED: 29276615; PMC: 5732581; DOI: 10.1017/gheg.2015.6

  • The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

    Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J et al.

    Nature genetics 2016

    PUBMED: 26950095; DOI: 10.1038/ng.3526

  • EPEC: a cocktail of virulence.

    Kallonen T and Boinett CJ

    Nature reviews. Microbiology 2016;14;4;196

    PUBMED: 26949047; DOI: 10.1038/nrmicro.2016.33

  • T cell fate and clonality inference from single-cell transcriptomes.

    Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G and Teichmann SA

    Nature methods 2016;13;4;329-332

    PUBMED: 26950746; PMC: 4835021; DOI: 10.1038/nmeth.3800

  • Further defining the phenotypic spectrum of B4GALT7 mutations.

    Salter CG, Davies JH, Moon RJ, Fairhurst J, Bunyan D, DDD Study and Foulds N

    American journal of medical genetics. Part A 2016;170;6;1556-63

    PUBMED: 26940150; DOI: 10.1002/ajmg.a.37604

  • Genomic epidemiology of artemisinin resistant malaria.

    MalariaGEN Plasmodium falciparum Community Project

    eLife 2016;5

    PUBMED: 26943619; PMC: 4786412; DOI: 10.7554/eLife.08714

  • Transmission Clusters of Methicillin-Resistant Staphylococcus Aureus in Long-Term Care Facilities Based on Whole-Genome Sequencing.

    Stine OC, Burrowes S, David S, Johnson JK and Roghmann MC

    Infection control and hospital epidemiology 2016;37;6;685-91

    PUBMED: 26941060; DOI: 10.1017/ice.2016.41

  • Deriving functional beige fat from capillaries.

    Pellegrinelli V and Vidal-Puig A

    Nature medicine 2016;22;3;234-6

    PUBMED: 26937616; DOI: 10.1038/nm.4056

  • Health and population effects of rare gene knockouts in adult humans with related parents.

    Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ, Barnes MR, Barnett AH, Bates C, Bellary S, Bockett NA et al.

    Science (New York, N.Y.) 2016;352;6284;474-7

    PUBMED: 26940866; PMC: 4985238; DOI: 10.1126/science.aac8624

  • A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies.

    Turro E, Greene D, Wijgaerts A, Thys C, Lentaigne C, Bariana TK, Westbury SK, Kelly AM, Selleslag D, Stephens JC et al.

    Science translational medicine 2016;8;328;328ra30

    PUBMED: 26936507; PMC: 5903547; DOI: 10.1126/scitranslmed.aad7666

  • The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations.

    Sandoval JR, Lacerda DR, Acosta O, Jota MS, Robles-Ruiz P, Salazar-Granara A, Vieira PP, Paz-Y-Miño C, Fujita R, Santos FR and Genographic Project Consortium

    Annals of human genetics 2016;80;2;88-101

    PUBMED: 26879156; DOI: 10.1111/ahg.12145

  • The ORFeome Collaboration: a genome-scale human ORF-clone resource.

    ORFeome Collaboration

    Nature methods 2016;13;3;191-2

    PUBMED: 26914201; DOI: 10.1038/nmeth.3776

  • Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.

    Torondel B, Ensink JH, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW and Quince C

    Microbial biotechnology 2016;9;2;209-23

    PUBMED: 26875588; PMC: 4767293; DOI: 10.1111/1751-7915.12334

  • Catalog of genetic progression of human cancers: breast cancer.

    Desmedt C, Yates L and Kulka J

    Cancer metastasis reviews 2016;35;1;49-62

    PUBMED: 26951551; DOI: 10.1007/s10555-016-9609-1

  • Chronic subordination stress selectively downregulates the insulin signaling pathway in liver and skeletal muscle but not in adipose tissue of male mice.

    Sanghez V, Cubuk C, Sebastián-Leon P, Carobbio S, Dopazo J, Vidal-Puig A and Bartolomucci A

    Stress (Amsterdam, Netherlands) 2016;19;2;214-24

    PUBMED: 26946982; DOI: 10.3109/10253890.2016.1151491

  • Desmoplastic melanoma: C>Ts and NF-κB.

    Rabbie R and Adams DJ

    Pigment cell & melanoma research 2016;29;2;120-1

    PUBMED: 26663830; PMC: 4864442; DOI: 10.1111/pcmr.12451

  • Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes.

    Teumer A, Tin A, Sorice R, Gorski M, Yeo NC, Chu AY, Li M, Li Y, Mijatovic V, Ko YA et al.

    Diabetes 2016;65;3;803-17

    PUBMED: 26631737; PMC: 4764151; DOI: 10.2337/db15-1313

  • Genomes on ice.

    Parkhill J

    Nature reviews. Microbiology 2016;14;3;134

    PUBMED: 26853114; DOI: 10.1038/nrmicro.2016.13

  • HLA class II sequence variants influence tuberculosis risk in populations of European ancestry.

    Sveinbjornsson G, Gudbjartsson DF, Halldorsson BV, Kristinsson KG, Gottfredsson M, Barrett JC, Gudmundsson LJ, Blondal K, Gylfason A, Gudjonsson SA et al.

    Nature genetics 2016;48;3;318-22

    PUBMED: 26829749; PMC: 5081101; DOI: 10.1038/ng.3498

  • Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

    Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD and Fraser C

    PLoS biology 2016;14;3;e1002394

    PUBMED: 26934590; PMC: 4774983; DOI: 10.1371/journal.pbio.1002394

  • Identification, Validation, and Application of Molecular Diagnostics for Insecticide Resistance in Malaria Vectors.

    Donnelly MJ, Isaacs AT and Weetman D

    Trends in parasitology 2016;32;3;197-206

    PUBMED: 26750864; DOI: 10.1016/j.pt.2015.12.001

  • In vitro selection of miltefosine resistance in promastigotes of Leishmania donovani from Nepal: genomic and metabolomic characterization.

    Shaw CD, Lonchamp J, Downing T, Imamura H, Freeman TM, Cotton JA, Sanders M, Blackburn G, Dujardin JC, Rijal S et al.

    Molecular microbiology 2016;99;6;1134-48

    PUBMED: 26713880; PMC: 4832254; DOI: 10.1111/mmi.13291

  • Innate biology versus lifestyle behaviour in the aetiology of obesity and type 2 diabetes: the GLACIER Study.

    Poveda A, Koivula RW, Ahmad S, Barroso I, Hallmans G, Johansson I, Renström F and Franks PW

    Diabetologia 2016;59;3;462-71

    PUBMED: 26625858; PMC: 4742501; DOI: 10.1007/s00125-015-3818-y

  • Mechanisms of fate decision and lineage commitment during haematopoiesis.

    Cvejic A

    Immunology and cell biology 2016;94;3;230-5

    PUBMED: 26526619; DOI: 10.1038/icb.2015.96

  • Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium.

    van den Berg SM, de Moor MH, Verweij KJ, Krueger RF, Luciano M, Arias Vasquez A, Matteson LK, Derringer J, Esko T, Amin N et al.

    Behavior genetics 2016;46;2;170-82

    PUBMED: 26362575; PMC: 4751159; DOI: 10.1007/s10519-015-9735-5

  • Nitroheterocyclic drug resistance mechanisms in Trypanosoma brucei.

    Wyllie S, Foth BJ, Kelner A, Sokolova AY, Berriman M and Fairlamb AH

    The Journal of antimicrobial chemotherapy 2016;71;3;625-34

    PUBMED: 26581221; PMC: 4743696; DOI: 10.1093/jac/dkv376

  • Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation.

    Rawlings ND

    Biochimie 2016;122;5-30

    PUBMED: 26455268; DOI: 10.1016/j.biochi.2015.10.003

  • Reconstructing transmission trees for communicable diseases using densely sampled genetic data.

    Worby CJ, O'Neill PD, Kypraios T, Robotham JV, De Angelis D, Cartwright EJ, Peacock SJ and Cooper BS

    The annals of applied statistics 2016;10;1;395-417

    PUBMED: 27042253; PMC: 4817375

  • Significant impact of miRNA-target gene networks on genetics of human complex traits.

    Okada Y, Muramatsu T, Suita N, Kanai M, Kawakami E, Iotchkova V, Soranzo N, Inazawa J and Tanaka T

    Scientific reports 2016;6;22223

    PUBMED: 26927695; PMC: 4772006; DOI: 10.1038/srep22223

  • Single-cell technologies are revolutionizing the approach to rare cells.

    Proserpio V and Lönnberg T

    Immunology and cell biology 2016;94;3;225-9

    PUBMED: 26620630; PMC: 4796591; DOI: 10.1038/icb.2015.106

  • Wbp2 is required for normal glutamatergic synapses in the cochlea and is crucial for hearing.

    Buniello A, Ingham NJ, Lewis MA, Huma AC, Martinez-Vega R, Varela-Nieto I, Vizcay-Barrena G, Fleck RA, Houston O, Bardhan T et al.

    EMBO molecular medicine 2016;8;3;191-207

    PUBMED: 26881968; PMC: 4772953; DOI: 10.15252/emmm.201505523

  • Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data.

    Delmans M and Hemberg M

    BMC bioinformatics 2016;17;110

    PUBMED: 26927822; PMC: 4772470; DOI: 10.1186/s12859-016-0944-6

  • Divergence in gene expression within and between two closely related flycatcher species.

    Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B et al.

    Molecular ecology 2016

    PUBMED: 26928872; DOI: 10.1111/mec.13596

  • Genomic Characterization of Primary Invasive Lobular Breast Cancer.

    Desmedt C, Zoppoli G, Gundem G, Pruneri G, Larsimont D, Fornili M, Fumagalli D, Brown D, Rothé F, Vincent D et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2016;34;16;1872-81

    PUBMED: 26926684; DOI: 10.1200/JCO.2015.64.0334

  • Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice.

    Maresch R, Mueller S, Veltkamp C, Öllinger R, Friedrich M, Heid I, Steiger K, Weber J, Engleitner T, Barenboim M et al.

    Nature communications 2016;7;10770

    PUBMED: 26916719; PMC: 4773438; DOI: 10.1038/ncomms10770

  • Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.

    Andersson P, Harris SR, Smith HMBS, Hadfield J, O'Neill C, Cutcliffe LT, Douglas FP, Asche LV, Mathews JD, Hutton SI et al.

    Nature communications 2016;7;10688

    PUBMED: 26912299; PMC: 4773424; DOI: 10.1038/ncomms10688

  • Deep Roots for Aboriginal Australian Y Chromosomes.

    Bergström A, Nagle N, Chen Y, McCarthy S, Pollard MO, Ayub Q, Wilcox S, Wilcox L, van Oorschot RA, McAllister P et al.

    Current biology : CB 2016;26;6;809-13

    PUBMED: 26923783; PMC: 4819516; DOI: 10.1016/j.cub.2016.01.028

  • Evaluating and Optimizing Fish Health and Welfare During Experimental Procedures.

    Goodwin N, Westall L, Karp NA, Hazlehurst D, Kovacs C, Keeble R, Thompson P, Collins R and Bussell J

    Zebrafish 2016

    PUBMED: 26914790; DOI: 10.1089/zeb.2015.1165

  • Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog.

    Davison A, McDowell GS, Holden JM, Johnson HF, Koutsovoulos GD, Liu MM, Hulpiau P, Van Roy F, Wade CM, Banerjee R et al.

    Current biology : CB 2016;26;5;654-60

    PUBMED: 26923788; PMC: 4791482; DOI: 10.1016/j.cub.2015.12.071

  • Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms.

    Horikoshi M, Pasquali L, Wiltshire S, Huyghe JR, Mahajan A, Asimit JL, Ferreira T, Locke AE, Robertson NR, Wang X et al.

    Human molecular genetics 2016

    PUBMED: 26911676; DOI: 10.1093/hmg/ddw048

  • Ensembl comparative genomics resources.

    Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S et al.

    Database : the journal of biological databases and curation 2016;2016

    PUBMED: 26896847; PMC: 4761110; DOI: 10.1093/database/bav096

  • metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis.

    Cichonska A, Rousu J, Marttinen P, Kangas AJ, Soininen P, Lehtimäki T, Raitakari OT, Järvelin MR, Salomaa V, Ala-Korpela M et al.

    Bioinformatics (Oxford, England) 2016

    PUBMED: 27153689; DOI: 10.1093/bioinformatics/btw052

  • Classification of low quality cells from single-cell RNA-seq data.

    Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC and Teichmann SA

    Genome biology 2016;17;29

    PUBMED: 26887813; PMC: 4758103; DOI: 10.1186/s13059-016-0888-1

  • Ensembl regulation resources.

    Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D et al.

    Database : the journal of biological databases and curation 2016;2016

    PUBMED: 26888907; PMC: 4756621; DOI: 10.1093/database/bav119

  • Constrained positive selection on cancer mutations in normal skin.

    Martincorena I, Jones PH and Campbell PJ

    Proceedings of the National Academy of Sciences of the United States of America 2016;113;9;E1128-9

    PUBMED: 26884187; PMC: 4780655; DOI: 10.1073/pnas.1600910113

  • Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection.

    Crellen T, Allan F, David S, Durrant C, Huckvale T, Holroyd N, Emery AM, Rollinson D, Aanensen DM, Berriman M et al.

    Scientific reports 2016;6;20954

    PUBMED: 26879532; PMC: 4754680; DOI: 10.1038/srep20954

  • Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas.

    Hackinger S, Kraaijenbrink T, Xue Y, Mezzavilla M, Asan, van Driem G, Jobling MA, de Knijff P, Tyler-Smith C and Ayub Q

    Human genetics 2016;135;4;393-402

    PUBMED: 26883865; PMC: 4796332; DOI: 10.1007/s00439-016-1641-2

  • 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution.

    McNally A, Thomson NR, Reuter S and Wren BW

    Nature reviews. Microbiology 2016;14;3;177-90

    PUBMED: 26876035; DOI: 10.1038/nrmicro.2015.29

  • Detection of pup odors by non-canonical adult vomeronasal neurons expressing an odorant receptor gene is influenced by sex and parenting status.

    Nakahara TS, Cardozo LM, Ibarra-Soria X, Bard AD, Carvalho VM, Trintinalia GZ, Logan DW and Papes F

    BMC biology 2016;14;12

    PUBMED: 26878847; PMC: 4753656; DOI: 10.1186/s12915-016-0234-9

  • Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin D.

    Pauklin S, Madrigal P, Bertero A and Vallier L

    Genes & development 2016;30;4;421-33

    PUBMED: 26883361; PMC: 4762427; DOI: 10.1101/gad.271452.115

  • A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.

    Makendi C, Page AJ, Wren BW, Le Thi Phuong T, Clare S, Hale C, Goulding D, Klemm EJ, Pickard D, Okoro C et al.

    PLoS neglected tropical diseases 2016;10;2;e0004446

    PUBMED: 26867150; PMC: 4750946; DOI: 10.1371/journal.pntd.0004446

  • Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes.

    O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K and J Flint H

    Microbial genomics 2016;2;2;e000043

    PUBMED: 28348841; PMC: 5320581; DOI: 10.1099/mgen.0.000043

  • Reporting phenotypes in mouse models when considering body size as a potential confounder.

    Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK and Karp NA

    Journal of biomedical semantics 2016;7;2

    PUBMED: 26865945; PMC: 4748495; DOI: 10.1186/s13326-016-0050-8

  • Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intra-Host HIV Infection.

    Dialdestoro K, Sibbesen JA, Maretty L, Raghwani J, Gall A, Kellam P, Pybus OG, Hein J and Jenkins PA

    Genetics 2016

    PUBMED: 26857628; DOI: 10.1534/genetics.115.177931

  • Divergent evolution of vitamin B9 binding underlies Juno-mediated adhesion of mammalian gametes.

    Han L, Nishimura K, Sadat Al Hosseini H, Bianchi E, Wright GJ and Jovine L

    Current biology : CB 2016;26;3;R100-1

    PUBMED: 26859261; PMC: 4751342; DOI: 10.1016/j.cub.2015.12.034

  • Exploitation of the Apoptosis-Primed State of MYCN-Amplified Neuroblastoma to Develop a Potent and Specific Targeted Therapy Combination.

    Ham J, Costa C, Sano R, Lochmann TL, Sennott EM, Patel NU, Dastur A, Gomez-Caraballo M, Krytska K, Hata AN et al.

    Cancer cell 2016;29;2;159-72

    PUBMED: 26859456; DOI: 10.1016/j.ccell.2016.01.002

  • Genome-based characterization of hospital-adapted Enterococcus faecalis lineages.

    Raven KE, Reuter S, Gouliouris T, Reynolds R, Russell JE, Brown NM, Török ME, Parkhill J and Peacock SJ

    Nature microbiology 2016;1;15033

    PUBMED: 27572164; DOI: 10.1038/nmicrobiol.2015.33

  • Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria.

    Seth-Smith HM, Dourala N, Fehr A, Qi W, Katharios P, Ruetten M, Mateos JM, Nufer L, Weilenmann R, Ziegler U et al.

    The ISME journal 2016

    PUBMED: 26849311; DOI: 10.1038/ismej.2015.223

  • Bi-allelic Truncating Mutations in TANGO2 Cause Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy.

    Kremer LS, Distelmaier F, Alhaddad B, Hempel M, Iuso A, Küpper C, Mühlhausen C, Kovacs-Nagy R, Satanovskij R, Graf E et al.

    American journal of human genetics 2016;98;2;358-62

    PUBMED: 26805782; PMC: 4746337; DOI: 10.1016/j.ajhg.2015.12.009

  • Targeting BRCA1 and BRCA2 Deficiencies with G-Quadruplex-Interacting Compounds.

    Zimmer J, Tacconi EM, Folio C, Badie S, Porru M, Klare K, Tumiati M, Markkanen E, Halder S, Ryan A et al.

    Molecular cell 2016;61;3;449-60

    PUBMED: 26748828; DOI: 10.1016/j.molcel.2015.12.004

  • Clinical delineation of the PACS1-related syndrome--Report on 19 patients.

    Schuurs-Hoeijmakers JH, Landsverk ML, Foulds N, Kukolich MK, Gavrilova RH, Greville-Heygate S, Hanson-Kahn A, Bernstein JA, Glass J, Chitayat D et al.

    American journal of medical genetics. Part A 2016;170;3;670-5

    PUBMED: 26842493; DOI: 10.1002/ajmg.a.37476

  • Trans-ethnic study design approaches for fine-mapping.

    Asimit JL, Hatzikotoulas K, McCarthy M, Morris AP and Zeggini E

    European journal of human genetics : EJHG 2016;24;9;1330-6

    PUBMED: 26839038; PMC: 4856879; DOI: 10.1038/ejhg.2016.1

  • Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

    Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F, Voet T, Teichmann SA and Cvejic A

    Cell reports 2016;14;4;966-977

    PUBMED: 26804912; PMC: 4742565; DOI: 10.1016/j.celrep.2015.12.082

  • Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations.

    Lorenz S, Barøy T, Sun J, Nome T, Vodák D, Bryne JC, Håkelien AM, Fernandez-Cuesta L, Möhlendick B, Rieder H et al.

    Oncotarget 2016;7;5;5273-88

    PUBMED: 26672768; PMC: 4868685; DOI: 10.18632/oncotarget.6567

  • The Genetic Epidemiological Landscape of Hip and Knee Osteoarthritis: Where Are We Now and Where Are We Going?

    Zengini E, Finan C and Wilkinson JM

    The Journal of rheumatology 2016;43;2;260-6

    PUBMED: 26628593; DOI: 10.3899/jrheum.150710

  • The genomic basis of parasitism in the Strongyloides clade of nematodes.

    Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H et al.

    Nature genetics 2016;48;3;299-307

    PUBMED: 26829753; PMC: 4948059; DOI: 10.1038/ng.3495

  • Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

    Reuter S, Török ME, Holden MT, Reynolds R, Raven KE, Blane B, Donker T, Bentley SD, Aanensen DM, Grundmann H et al.

    Genome research 2016;26;2;263-70

    PUBMED: 26672018; PMC: 4728378; DOI: 10.1101/gr.196709.115

  • Common polygenic variation in coeliac disease and confirmation of ZNF335 and NIFA as disease susceptibility loci.

    Coleman C, Quinn EM, Ryan AW, Conroy J, Trimble V, Mahmud N, Kennedy N, Corvin AP, Morris DW, Donohoe G et al.

    European journal of human genetics : EJHG 2016;24;2;291-7

    PUBMED: 25920553; PMC: 4717209; DOI: 10.1038/ejhg.2015.87

  • Dysfunctional ADAM22 implicated in progressive encephalopathy with cortical atrophy and epilepsy.

    Muona M, Fukata Y, Anttonen AK, Laari A, Palotie A, Pihko H, Lönnqvist T, Valanne L, Somer M, Fukata M and Lehesjoki AE

    Neurology. Genetics 2016;2;1;e46

    PUBMED: 27066583; PMC: 4817901; DOI: 10.1212/NXG.0000000000000046

  • Exome sequencing identifies rare variants in multiple genes in atrioventricular septal defect.

    D'Alessandro LC, Al Turki S, Manickaraj AK, Manase D, Mulder BJ, Bergin L, Rosenberg HC, Mondal T, Gordon E, Lougheed J et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2016;18;2;189-98

    PUBMED: 25996639; PMC: 5988035; DOI: 10.1038/gim.2015.60

  • Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.

    Holt K, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ, Dougan G and Hall R

    Microbial genomics 2016;2;2;e000052

    PUBMED: 28348844; PMC: 5320584; DOI: 10.1099/mgen.0.000052

  • Genome-Wide Association Analysis of Young-Onset Stroke Identifies a Locus on Chromosome 10q25 Near HABP2.

    Cheng YC, Stanne TM, Giese AK, Ho WK, Traylor M, Amouyel P, Holliday EG, Malik R, Xu H, Kittner SJ et al.

    Stroke; a journal of cerebral circulation 2016;47;2;307-16

    PUBMED: 26732560; DOI: 10.1161/STROKEAHA.115.011328

  • Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.

    Kilpeläinen TO, Carli JF, Skowronski AA, Sun Q, Kriebel J, Feitosa MF, Hedman ÅK, Drong AW, Hayes JE, Zhao J et al.

    Nature communications 2016;7;10494

    PUBMED: 26833098; PMC: 4740377; DOI: 10.1038/ncomms10494

  • GWAS for executive function and processing speed suggests involvement of the CADM2 gene.

    Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C et al.

    Molecular psychiatry 2016;21;2;189-97

    PUBMED: 25869804; PMC: 4722802; DOI: 10.1038/mp.2015.37

  • Invasive Group A Streptococcus Infection among Children, Rural Kenya.

    Seale AC, Davies MR, Anampiu K, Morpeth SC, Nyongesa S, Mwarumba S, Smeesters PR, Efstratiou A, Karugutu R, Mturi N et al.

    Emerging infectious diseases 2016;22;2;224-32

    PUBMED: 26811918; DOI: 10.3201/eid2202.151358

  • New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk.

    Lu Y, Day FR, Gustafsson S, Buchkovich ML, Na J, Bataille V, Cousminer DL, Dastani Z, Drong AW, Esko T et al.

    Nature communications 2016;7;10495

    PUBMED: 26833246; PMC: 4740398; DOI: 10.1038/ncomms10495

  • Single-cell technologies to study the immune system.

    Proserpio V and Mahata B

    Immunology 2016;147;2;133-40

    PUBMED: 26551575; PMC: 4717243; DOI: 10.1111/imm.12553

  • BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

    Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C and Durbin R

    Bioinformatics (Oxford, England) 2016;32;11;1749-51

    PUBMED: 26826718; PMC: 4892413; DOI: 10.1093/bioinformatics/btw044

  • Beegle: from literature mining to disease-gene discovery.

    ElShal S, Tranchevent LC, Sifrim A, Ardeshirdavani A, Davis J and Moreau Y

    Nucleic acids research 2016;44;2;e18

    PUBMED: 26384564; PMC: 4737179; DOI: 10.1093/nar/gkv905

  • Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites.

    Ponsuwanna P, Kochakarn T, Bunditvorapoom D, Kümpornsin K, Otto TD, Ridenour C, Chotivanich K, Wilairat P, White NJ, Miotto O and Chookajorn T

    Malaria journal 2016;15;51

    PUBMED: 26821618; PMC: 4731938; DOI: 10.1186/s12936-016-1097-9

  • Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells.

    Butcher LM, Ito M, Brimpari M, Morris TJ, Soares FAC, Ährlund-Richter L, Carey N, Vallier L, Ferguson-Smith AC and Beck S

    Nature communications 2016;7;10458

    PUBMED: 26822956; PMC: 4740175; DOI: 10.1038/ncomms10458

  • Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases.

    Steger M, Tonelli F, Ito G, Davies P, Trost M, Vetter M, Wachter S, Lorentzen E, Duddy G, Wilson S et al.

    eLife 2016;5

    PUBMED: 26824392; DOI: 10.7554/eLife.12813

  • Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae.

    Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R, Coupland P, Holden MT, Bazzolli DM, Maskell DJ, Tucker AW et al.

    Genome announcements 2016;4;1

    PUBMED: 26823596; PMC: 4732349; DOI: 10.1128/genomeA.01667-15

  • Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes.

    Imamura M, Takahashi A, Yamauchi T, Hara K, Yasuda K, Grarup N, Zhao W, Wang X, Huerta-Chagoya A, Hu C et al.

    Nature communications 2016;7;10531

    PUBMED: 26818947; PMC: 4738362; DOI: 10.1038/ncomms10531

  • USF1 deficiency activates brown adipose tissue and improves cardiometabolic health.

    Laurila PP, Soronen J, Kooijman S, Forsström S, Boon MR, Surakka I, Kaiharju E, Coomans CP, Van Den Berg SA, Autio A et al.

    Science translational medicine 2016;8;323;323ra13

    PUBMED: 26819196; DOI: 10.1126/scitranslmed.aad0015

  • A survey of best practices for RNA-seq data analysis.

    Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X and Mortazavi A

    Genome biology 2016;17;13

    PUBMED: 26813401; PMC: 4728800; DOI: 10.1186/s13059-016-0881-8

  • Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

    Bryant JM, Thibault VC, Smith DG, McLuckie J, Heron I, Sevilla IA, Biet F, Harris SR, Maskell DJ, Bentley SD et al.

    BMC genomics 2016;17;79

    PUBMED: 26813574; PMC: 4729121; DOI: 10.1186/s12864-015-2234-5

  • Population genomics reveals the origin and asexual evolution of human infective trypanosomes.

    Weir W, Capewell P, Foth B, Clucas C, Pountain A, Steketee P, Veitch N, Koffi M, De Meeûs T, Kaboré J et al.

    eLife 2016;5;e11473

    PUBMED: 26809473; PMC: 4739771; DOI: 10.7554/eLife.11473

  • Chromosome engineering in zygotes with CRISPR/Cas9.

    Boroviak K, Doe B, Banerjee R, Yang F and Bradley A

    Genesis (New York, N.Y. : 2000) 2016;54;2;78-85

    PUBMED: 26742453; PMC: 4819711; DOI: 10.1002/dvg.22915

  • Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR, Hale C, Heath JN, Wileman T, Clare S, Kane L et al.

    Nature microbiology 2016;1;15023

    PUBMED: 27572160; DOI: 10.1038/nmicrobiol.2015.23

  • Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism.

    Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F, Schlacht A, Hartley C, Sanders M, Wastling JM, Dacks JB et al.

    Current biology : CB 2016;26;2;161-172

    PUBMED: 26725202; PMC: 4728078; DOI: 10.1016/j.cub.2015.11.055

  • Maternal DNA Methylation Regulates Early Trophoblast Development.

    Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ, Dean W, Hemberger M and Reik W

    Developmental cell 2016;36;2;152-63

    PUBMED: 26812015; PMC: 4729543; DOI: 10.1016/j.devcel.2015.12.027

  • SeqTools: visual tools for manual analysis of sequence alignments.

    Barson G and Griffiths E

    BMC research notes 2016;9;39

    PUBMED: 26801397; PMC: 4724122; DOI: 10.1186/s13104-016-1847-3

  • The mechanisms shaping the single-cell transcriptional landscape.

    Martinez-Jimenez CP and Odom DT

    Current opinion in genetics & development 2016;37;27-35

    PUBMED: 26803530; DOI: 10.1016/j.gde.2015.11.004

  • The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.

    Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA and Parkhill J

    Bioinformatics (Oxford, England) 2016;32;7;1109-11

    PUBMED: 26794317; PMC: 4896371; DOI: 10.1093/bioinformatics/btw022

  • Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

    Pattaro C, Teumer A, Gorski M, Chu AY, Li M, Mijatovic V, Garnaas M, Tin A, Sorice R, Li Y et al.

    Nature communications 2016;7;10023

    PUBMED: 26831199; PMC: 4735748; DOI: 10.1038/ncomms10023

  • Iron Age and Anglo-Saxon genomes from East England reveal British migration history.

    Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D et al.

    Nature communications 2016;7;10408

    PUBMED: 26783965; PMC: 4735688; DOI: 10.1038/ncomms10408

  • Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants.

    Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ, Azzopardi KI, Amarasena T, Bennett-Wood V, Pearson JS, Tamboura B et al.

    Nature microbiology 2016;1;15010

    PUBMED: 27571974; DOI: 10.1038/nmicrobiol.2015.10

  • Plasma urate concentration and risk of coronary heart disease: a Mendelian randomisation analysis.

    White J, Sofat R, Hemani G, Shah T, Engmann J, Dale C, Shah S, Kruger FA, Giambartolomei C, Swerdlow DI et al.

    The lancet. Diabetes & endocrinology 2016;4;4;327-36

    PUBMED: 26781229; PMC: 4805857; DOI: 10.1016/S2213-8587(15)00386-1

  • A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration.

    de Vries PS, Chasman DI, Sabater-Lleal M, Chen MH, Huffman JE, Steri M, Tang W, Teumer A, Marioni RE, Grossmann V et al.

    Human molecular genetics 2016;25;2;358-70

    PUBMED: 26561523; PMC: 4715256; DOI: 10.1093/hmg/ddv454

  • Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration.

    Joyce PI, Fratta P, Landman AS, Mcgoldrick P, Wackerhage H, Groves M, Busam BS, Galino J, Corrochano S, Beskina OA et al.

    Human molecular genetics 2016;25;2;291-307

    PUBMED: 26604141; DOI: 10.1093/hmg/ddv471

  • Genome-wide association analysis identifies three new susceptibility loci for childhood body mass index.

    Felix JF, Bradfield JP, Monnereau C, van der Valk RJ, Stergiakouli E, Chesi A, Gaillard R, Feenstra B, Thiering E, Kreiner-Møller E et al.

    Human molecular genetics 2016;25;2;389-403

    PUBMED: 26604143; DOI: 10.1093/hmg/ddv472

  • FINEMAP: efficient variable selection using summary data from genome-wide association studies.

    Benner C, Spencer CC, Havulinna AS, Salomaa V, Ripatti S and Pirinen M

    Bioinformatics (Oxford, England) 2016;32;10;1493-501

    PUBMED: 26773131; PMC: 4866522; DOI: 10.1093/bioinformatics/btw018

  • Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network.

    Brodrick HJ, Raven KE, Harrison EM, Blane B, Reuter S, Török ME, Parkhill J and Peacock SJ

    Genome medicine 2016;8;1;4

    PUBMED: 26759031; PMC: 4709893; DOI: 10.1186/s13073-015-0259-7

  • Ancient DNA and the rewriting of human history: be sparing with Occam's razor.

    Haber M, Mezzavilla M, Xue Y and Tyler-Smith C

    Genome biology 2016;17;1

    PUBMED: 26753840; PMC: 4707776; DOI: 10.1186/s13059-015-0866-z

  • Modulation of the human gut microbiota by dietary fibres occurs at the species level.

    Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH and Flint HJ

    BMC biology 2016;14;3

    PUBMED: 26754945; PMC: 4709873; DOI: 10.1186/s12915-015-0224-3

  • Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

    Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T et al.

    Nature methods 2016;13;3;229-232

    PUBMED: 26752769; PMC: 4770512; DOI: 10.1038/nmeth.3728

  • Dihydroartemisinin-piperaquine resistance in Plasmodium falciparum malaria in Cambodia: a multisite prospective cohort study.

    Amaratunga C, Lim P, Suon S, Sreng S, Mao S, Sopha C, Sam B, Dek D, Try V, Amato R et al.

    The Lancet. Infectious diseases 2016;16;3;357-65

    PUBMED: 26774243; PMC: 4792715; DOI: 10.1016/S1473-3099(15)00487-9

  • Calcium signalling in malaria parasites.

    Brochet M and Billker O

    Molecular microbiology 2016

    PUBMED: 26748879; DOI: 10.1111/mmi.13324

  • Heterogeneous alleles comprising G6PD deficiency trait in West Africa exert contrasting effects on two major clinical presentations of severe malaria.

    Shah SS, Rockett KA, Jallow M, Sisay-Joof F, Bojang KA, Pinder M, Jeffreys A, Craik R, Hubbart C, Wellems TE et al.

    Malaria journal 2016;15;13

    PUBMED: 26738565; PMC: 4704392; DOI: 10.1186/s12936-015-1045-0

  • A multi-factorial analysis of response to warfarin in a UK prospective cohort.

    Bourgeois S, Jorgensen A, Zhang EJ, Hanson A, Gillman MS, Bumpstead S, Toh CH, Williamson P, Daly AK, Kamali F et al.

    Genome medicine 2016;8;1;2

    PUBMED: 26739746; PMC: 4702374; DOI: 10.1186/s13073-015-0255-y

  • Environmental Correlation Analysis for Genes Associated with Protection against Malaria.

    Mackinnon MJ, Ndila C, Uyoga S, Macharia A, Snow RW, Band G, Rautanen A, Rockett KA, Kwiatkowski DP and Williams TN

    Molecular biology and evolution 2016

    PUBMED: 26744416; PMC: 4839215; DOI: 10.1093/molbev/msw004

  • Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.

    Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV, DDD Study and Wright CF

    Human molecular genetics 2016;25;5;927-35

    PUBMED: 26740553; PMC: 4754046; DOI: 10.1093/hmg/ddv625

  • Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.

    Michaut M, Chin SF, Majewski I, Severson TM, Bismeijer T, de Koning L, Peeters JK, Schouten PC, Rueda OM, Bosma AJ et al.

    Scientific reports 2016;6;18517

    PUBMED: 26729235; PMC: 4700448; DOI: 10.1038/srep18517

  • The Pfam protein families database: towards a more sustainable future.

    Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A et al.

    Nucleic acids research 2016;44;D1;D279-85

    PUBMED: 26673716; PMC: 4702930; DOI: 10.1093/nar/gkv1344

  • Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits.

    Deming Y, Xia J, Cai Y, Lord J, Del-Aguila JL, Fernandez MV, Carrell D, Black K, Budde J, Ma S et al.

    Scientific reports 2016;6;1;18092

    PUBMED: 36647296; PMC: 4698720; DOI: 10.1038/srep18092

  • Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.

    Rawlings ND, Barrett AJ and Finn R

    Nucleic acids research 2016;44;D1;D343-50

    PUBMED: 26527717; PMC: 4702814; DOI: 10.1093/nar/gkv1118

  • The challenges involved in elucidating the molecular basis of sperm-egg recognition in mammals and approaches to overcome them.

    Wright GJ and Bianchi E

    Cell and tissue research 2016;363;1;227-235

    PUBMED: 26224538; PMC: 4700105; DOI: 10.1007/s00441-015-2243-3

  • The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water.

    Karkey A, Jombart T, Walker AW, Thompson CN, Torres A, Dongol S, Tran Vu Thieu N, Pham Thanh D, Tran Thi Ngoc D, Voong Vinh P et al.

    PLoS neglected tropical diseases 2016;10;1;e0004346

    PUBMED: 26735696; PMC: 4703202; DOI: 10.1371/journal.pntd.0004346

  • The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity.

    Warne B, Harkins CP, Harris SR, Vatsiou A, Stanley-Wall N, Parkhill J, Peacock SJ, Palmer T and Holden MT

    BMC genomics 2016;17;1;222

    PUBMED: 26969225; PMC: 4788903; DOI: 10.1186/s12864-016-2426-7

  • The ethics of sustainable genomic research in Africa.

    Parker M and Kwiatkowski DP

    Genome biology 2016;17;1;44

    PUBMED: 26956719; PMC: 4782358; DOI: 10.1186/s13059-016-0914-3

  • A forum for global population health, technological advances and implementation science.

    Sandhu MS

    Global health, epidemiology and genomics 2016;1;e1

    PUBMED: 29868196; PMC: 5870244; DOI: 10.1017/gheg.2015.2

  • The genetic associations of acute anterior uveitis and their overlap with the genetics of ankylosing spondylitis.

    Robinson PC, Leo PJ, Pointon JJ, Harris J, Cremin K, Bradbury LA, Wellcome Trust Case Control Consortium, Australasian Osteoporosis Genetics Consortium (AOGC), Stebbings S, Harrison AA et al.

    Genes and immunity 2016;17;1;46-51

    PUBMED: 26610302; DOI: 10.1038/gene.2015.49

  • A graph extension of the positional burrows-wheeler transform and its applications

    Novak,A.M, GARRISON,E and Paten,B

    Lecture Notes in Computer Science 2016;9383;246

    DOI: 10.1007/978-3-319-43681-4_20

  • The Human Gut Microbiota.

    Harmsen HJ and de Goffau MC

    Advances in experimental medicine and biology 2016;902;95-108

    PUBMED: 27161353; DOI: 10.1007/978-3-319-31248-4_7

  • A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure.

    Pham Thanh D, Karkey A, Dongol S, Ho Thi N, Thompson CN, Rabaa MA, Arjyal A, Holt KE, Wong V, Tran Vu Thieu N et al.

    eLife 2016;5

    PUBMED: 26974227; PMC: 4805543; DOI: 10.7554/eLife.14003

  • A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

    Lun AT, McCarthy DJ and Marioni JC

    F1000Research 2016;5;2122

    PUBMED: 27909575; PMC: 5112579; DOI: 10.12688/f1000research.9501.2

  • A Toll-like receptor-1 variant and its characteristic cellular phenotype is associated with severe malaria in Papua New Guinean children.

    Manning L, Cutts J, Stanisic DI, Laman M, Carmagnac A, Allen S, O'Donnell A, Karunajeewa H, Rosanas-Urgell A, Siba P et al.

    Genes and immunity 2016;17;1;52-9

    PUBMED: 26633000; DOI: 10.1038/gene.2015.50

  • αv Integrins combine with LC3 and atg5 to regulate Toll-like receptor signalling in B cells.

    Acharya M, Sokolovska A, Tam JM, Conway KL, Stefani C, Raso F, Mukhopadhyay S, Feliu M, Paul E, Savill J et al.

    Nature communications 2016;7;10917

    PUBMED: 26965188; PMC: 4792966; DOI: 10.1038/ncomms10917

  • Analysis of TcdB Proteins within the Hypervirulent Clade 2 Reveals an Impact of RhoA Glucosylation on Clostridium difficile Proinflammatory Activities.

    Quesada-Gómez C, López-Ureña D, Chumbler N, Kroh HK, Castro-Peña C, Rodríguez C, Orozco-Aguilar J, González-Camacho S, Rucavado A, Guzmán-Verri C et al.

    Infection and immunity 2016;84;3;856-65

    PUBMED: 26755157; PMC: 4771349; DOI: 10.1128/IAI.01291-15

  • Anti-GPC3-CAR T Cells Suppress the Growth of Tumor Cells in Patient-Derived Xenografts of Hepatocellular Carcinoma.

    Jiang Z, Jiang X, Chen S, Lai Y, Wei X, Li B, Lin S, Wang S, Wu Q, Liang Q et al.

    Frontiers in immunology 2016;7;690

    PUBMED: 28123387; PMC: 5225101; DOI: 10.3389/fimmu.2016.00690

  • Association of Forced Vital Capacity with the Developmental Gene NCOR2.

    Minelli C, Dean CH, Hind M, Alves AC, Amaral AF, Siroux V, Huikari V, Soler Artigas M, Evans DM, Loth DW et al.

    PloS one 2016;11;2;e0147388

    PUBMED: 26836265; PMC: 4737618; DOI: 10.1371/journal.pone.0147388

  • Burden of Diabetes and First Evidence for the Utility of HbA1c for Diagnosis and Detection of Diabetes in Urban Black South Africans: The Durban Diabetes Study.

    Hird TR, Pirie FJ, Esterhuizen TM, O'Leary B, McCarthy MI, Young EH, Sandhu MS and Motala AA

    PloS one 2016;11;8;e0161966

    PUBMED: 27560687; PMC: 4999239; DOI: 10.1371/journal.pone.0161966

  • Canalization of genetic and pharmacological perturbations in developing primary neuronal activity patterns.

    Charlesworth P, Morton A, Eglen SJ, Komiyama NH and Grant SG

    Neuropharmacology 2016;100;47-55

    PUBMED: 26211975; PMC: 4726661; DOI: 10.1016/j.neuropharm.2015.07.027

  • Carriage of Extended-Spectrum Beta-Lactamase-Plasmids Does Not Reduce Fitness but Enhances Virulence in Some Strains of Pandemic E. coli Lineages.

    Schaufler K, Semmler T, Pickard DJ, de Toro M, de la Cruz F, Wieler LH, Ewers C and Guenther S

    Frontiers in microbiology 2016;7;336

    PUBMED: 27014251; PMC: 4794485; DOI: 10.3389/fmicb.2016.00336

  • Characterization and Immunoregulatory Properties of Innate Pro-B-Cell Progenitors.

    Zavala F, Korniotis S and Montandon R

    Methods in molecular biology (Clifton, N.J.) 2016;1371;79-88

    PUBMED: 26530795; DOI: 10.1007/978-1-4939-3139-2_5

  • Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon.

    Bernardo D, Durant L, Mann ER, Bassity E, Montalvillo E, Man R, Vora R, Reddi D, Bayiroglu F, Fernández-Salazar L et al.

    Cellular and molecular gastroenterology and hepatology 2016;2;1;22-39.e5

    PUBMED: 26866054; PMC: 4705905; DOI: 10.1016/j.jcmgh.2015.08.006

  • Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing.

    Rahbari R and Badge RM

    Methods in molecular biology (Clifton, N.J.) 2016;1400;95-106

    PUBMED: 26895048; DOI: 10.1007/978-1-4939-3372-3_6

  • Commitment issues in Plasmodium.

    Gomes AR and Talman AM

    Nature reviews. Microbiology 2016;14;1;4

    PUBMED: 26639781; DOI: 10.1038/nrmicro.2015.9

  • Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak.

    Oude Munnink BB, Phan MV, Kellam P, Cotten M and VIZIONS Consortium

    Genome announcements 2016;4;2

    PUBMED: 27081130; DOI: 10.1128/genomeA.00250-16

  • Consent Codes: Upholding Standard Data Use Conditions.

    Dyke SO, Philippakis AA, Rambla De Argila J, Paltoo DN, Luetkemeier ES, Knoppers BM, Brookes AJ, Spalding JD, Thompson M, Roos M et al.

    PLoS genetics 2016;12;1;e1005772

    PUBMED: 26796797; PMC: 4721915; DOI: 10.1371/journal.pgen.1005772

  • Cross-species models of human melanoma.

    van der Weyden L, Patton EE, Wood GA, Foote AK, Brenn T, Arends MJ and Adams DJ

    The Journal of pathology 2016;238;2;152-65

    PUBMED: 26354726; PMC: 4832391; DOI: 10.1002/path.4632

  • Differential Killing of Salmonella enterica Serovar Typhi by Antibodies Targeting Vi and Lipopolysaccharide O:9 Antigen.

    Hart PJ, O'Shaughnessy CM, Siggins MK, Bobat S, Kingsley RA, Goulding DA, Crump JA, Reyburn H, Micoli F, Dougan G et al.

    PloS one 2016;11;1;e0145945

    PUBMED: 26741681; PMC: 4712142; DOI: 10.1371/journal.pone.0145945

  • Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes.

    Thomsen PF, Møller PR, Sigsgaard EE, Knudsen SW, Jørgensen OA and Willerslev E

    PloS one 2016;11;11;e0165252

    PUBMED: 27851757; PMC: 5112899; DOI: 10.1371/journal.pone.0165252

  • Exploring regulatory networks of miR-96 in the developing inner ear.

    Lewis MA, Buniello A, Hilton JM, Zhu F, Zhang WI, Evans S, van Dongen S, Enright AJ and Steel KP

    Scientific reports 2016;6;23363

    PUBMED: 26988146; PMC: 4796898; DOI: 10.1038/srep23363

  • Filling in the Gap of Human Chromosome 4: Single Molecule Real Time Sequencing of Macrosatellite Repeats in the Facioscapulohumeral Muscular Dystrophy Locus.

    Morioka MS, Kitazume M, Osaki K, Wood J and Tanaka Y

    PloS one 2016;11;3;e0151963

    PUBMED: 27002334; PMC: 4803325; DOI: 10.1371/journal.pone.0151963

  • Functional analysis of an unusual type IV pilus in the Gram-positive Streptococcus sanguinis.

    Gurung I, Spielman I, Davies MR, Lala R, Gaustad P, Biais N and Pelicic V

    Molecular microbiology 2016;99;2;380-92

    PUBMED: 26435398; PMC: 4832360; DOI: 10.1111/mmi.13237

  • Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis.

    Gutierrez-Achury J, Zorro MM, Ricaño-Ponce I, Zhernakova DV, Coeliac Disease Immunochip Consortium, RACI Consortium, Diogo D, Raychaudhuri S, Franke L, Trynka G et al.

    Human molecular genetics 2016;25;1;180-90

    PUBMED: 26546613; PMC: 4690494; DOI: 10.1093/hmg/ddv455

  • Generation and Characterisation of a Pax8-CreERT2 Transgenic Line and a Slc22a6-CreERT2 Knock-In Line for Inducible and Specific Genetic Manipulation of Renal Tubular Epithelial Cells.

    Espana-Agusti J, Zou X, Wong K, Fu B, Yang F, Tuveson DA, Adams DJ and Matakidou A

    PloS one 2016;11;2;e0148055

    PUBMED: 26866916; PMC: 4751286; DOI: 10.1371/journal.pone.0148055

  • Genetic Influences on Metabolite Levels: A Comparison across Metabolomic Platforms.

    Yet I, Menni C, Shin SY, Mangino M, Soranzo N, Adamski J, Suhre K, Spector TD, Kastenmüller G and Bell JT

    PloS one 2016;11;4;e0153672

    PUBMED: 27073872; PMC: 4830611; DOI: 10.1371/journal.pone.0153672

  • Genome wide conditional mouse knockout resources

    Kaloff, C, Anastassiadis, K, Ayadi, A, Baldock, R, Beig, J et al.

    Drug Discovery Today: Disease Models 2016;20;3;12

    DOI: 10.1016/j.ddmod.2017.08.002

  • Genome-Wide Meta-Analysis of Sciatica in Finnish Population.

    Lemmelä S, Solovieva S, Shiri R, Benner C, Heliövaara M, Kettunen J, Anttila V, Ripatti S, Perola M, Seppälä I et al.

    PloS one 2016;11;10;e0163877

    PUBMED: 27764105; PMC: 5072673; DOI: 10.1371/journal.pone.0163877

  • Genome-wide study for circulating metabolites identifies 62 loci and reveals novel systemic effects of LPA.

    Kettunen J, Demirkan A, Würtz P, Draisma HH, Haller T, Rawal R, Vaarhorst A, Kangas AJ, Lyytikäinen LP, Pirinen M et al.

    Nature communications 2016;7;11122

    PUBMED: 27005778; DOI: 10.1038/ncomms11122

  • Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization.

    Singchat W, Hitakomate E, Rerkarmnuaychoke B, Suntronpong A, Fu B, Bodhisuwan W, Peyachoknagul S, Yang F, Koontongkaew S and Srikulnath K

    PloS one 2016;11;8;e0160901

    PUBMED: 27501229; PMC: 4976893; DOI: 10.1371/journal.pone.0160901

  • Genomic Analysis of Companion Rabbit Staphylococcus aureus.

    Holmes MA, Harrison EM, Fisher EA, Graham EM, Parkhill J, Foster G and Paterson GK

    PloS one 2016;11;3;e0151458

    PUBMED: 26963381; PMC: 4786088; DOI: 10.1371/journal.pone.0151458

  • Genomic and Molecular Characterization of Miltefosine Resistance in Leishmania infantum Strains with Either Natural or Acquired Resistance through Experimental Selection of Intracellular Amastigotes.

    Mondelaers A, Sanchez-Cañete MP, Hendrickx S, Eberhardt E, Garcia-Hernandez R, Lachaud L, Cotton J, Sanders M, Cuypers B, Imamura H et al.

    PloS one 2016;11;4;e0154101

    PUBMED: 27123924; PMC: 4849676; DOI: 10.1371/journal.pone.0154101

  • Germline TERT promoter mutations are rare in familial melanoma.

    Harland M, Petljak M, Robles-Espinoza CD, Ding Z, Gruis NA, van Doorn R, Pooley KA, Dunning AM, Aoude LG, Wadt KA et al.

    Familial cancer 2016;15;1;139-44

    PUBMED: 26433962; PMC: 4698275; DOI: 10.1007/s10689-015-9841-9

  • Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

    Laing R, Martinelli A, Tracey A, Holroyd N, Gilleard JS and Cotton JA

    Advances in parasitology 2016;93;569-98

    PUBMED: 27238013; DOI: 10.1016/bs.apar.2016.02.016

  • ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae.

    Bossé JT, Li Y, Fernandez Crespo R, Chaudhuri RR, Rogers J, Holden MT, Maskell DJ, Tucker AW, Wren BW, Rycroft AN et al.

    Frontiers in microbiology 2016;7;810

    PUBMED: 27379024; PMC: 4908127; DOI: 10.3389/fmicb.2016.00810

  • Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus.

    Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS and Lipsitch M

    Genome medicine 2016;8;1;18

    PUBMED: 26873713; PMC: 4752745; DOI: 10.1186/s13073-016-0274-3

  • Immune dysfunction in Niemann-Pick disease type C.

    Platt N, Speak AO, Colaco A, Gray J, Smith DA, Williams IM, Wallom KL and Platt FM

    Journal of neurochemistry 2016;136 Suppl 1;74-80

    PUBMED: 25946402; PMC: 4833189; DOI: 10.1111/jnc.13138

  • Loss of Multicellular Behavior in Epidemic African Nontyphoidal Salmonella enterica Serovar Typhimurium ST313 Strain D23580.

    Singletary LA, Karlinsey JE, Libby SJ, Mooney JP, Lokken KL, Tsolis RM, Byndloss MX, Hirao LA, Gaulke CA, Crawford RW et al.

    mBio 2016;7;2

    PUBMED: 26933058; PMC: 4810497; DOI: 10.1128/mBio.02265-15

  • Brucella abortus Strain 2308 Wisconsin Genome: Importance of the Definition of Reference Strains.

    Suárez-Esquivel M, Ruiz-Villalobos N, Castillo-Zeledón A, Jiménez-Rojas C, Roop Ii RM, Comerci DJ, Barquero-Calvo E, Chacón-Díaz C, Caswell CC, Baker KS et al.

    Frontiers in microbiology 2016;7;1557

    PUBMED: 27746773; PMC: 5041503; DOI: 10.3389/fmicb.2016.01557

  • MLL1: the thin red line divides naïve and primed pluripotency.

    Yang J and Liu P

    Stem cell investigation 2016;3;63

    PUBMED: 27868045; DOI: 10.21037/sci.2016.09.18

  • Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution.

    Jelocnik M, Bachmann NL, Seth-Smith H, Thomson NR, Timms P and Polkinghorne AM

    PeerJ 2016;4;e1661

    PUBMED: 26870613; PMC: 4748734; DOI: 10.7717/peerj.1661

  • Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents.

    Merlevede J, Droin N, Qin T, Meldi K, Yoshida K, Morabito M, Chautard E, Auboeuf D, Fenaux P, Braun T et al.

    Nature communications 2016;7;10767

    PUBMED: 26908133; PMC: 4770084; DOI: 10.1038/ncomms10767

  • Mutation Rates and Discriminating Power for 13 Rapidly-Mutating Y-STRs between Related and Unrelated Individuals.

    Boattini A, Sarno S, Bini C, Pesci V, Barbieri C, De Fanti S, Quagliariello A, Pagani L, Ayub Q, Ferri G et al.

    PloS one 2016;11;11;e0165678

    PUBMED: 27802306; PMC: 5089551; DOI: 10.1371/journal.pone.0165678

  • ncRNA orthologies in the vertebrate lineage.

    Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P and Herrero J

    Database : the journal of biological databases and curation 2016;2016

    PUBMED: 26980512; PMC: 4792531; DOI: 10.1093/database/bav127

  • Practical Experience of the Application of a Weighted Burden Test to Whole Exome Sequence Data for Obesity and Schizophrenia.

    Curtis D and UK10K Consortium

    Annals of human genetics 2016;80;1;38-49

    PUBMED: 26474449; PMC: 4833177; DOI: 10.1111/ahg.12135

  • Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis.

    Skipp PJ, Hughes C, McKenna T, Edwards R, Langridge J, Thomson NR and Clarke IN

    PloS one 2016;11;2;e0149011

    PUBMED: 26871455; PMC: 4752267; DOI: 10.1371/journal.pone.0149011

  • Rapid Karyotype Evolution in Lasiopodomys Involved at Least Two Autosome - Sex Chromosome Translocations.

    Gladkikh OL, Romanenko SA, Lemskaya NA, Serdyukova NA, O'Brien PC, Kovalskaya JM, Smorkatcheva AV, Golenishchev FN, Perelman PL, Trifonov VA et al.

    PloS one 2016;11;12;e0167653

    PUBMED: 27936177; PMC: 5147937; DOI: 10.1371/journal.pone.0167653

  • Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase Gene.

    Jones-Dias D, Clemente L, Egas C, Froufe H, Sampaio DA, Vieira L, Fookes M, Thomson NR, Manageiro V and Caniça M

    Frontiers in microbiology 2016;7;1130

    PUBMED: 27536269; PMC: 4971094; DOI: 10.3389/fmicb.2016.01130

  • Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.

    Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X et al.

    Genome biology 2016;17;103

    PUBMED: 27176874; PMC: 4866375; DOI: 10.1186/s13059-016-0957-5

  • Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.

    Clark SJ, Lee HJ, Smallwood SA, Kelsey G and Reik W

    Genome biology 2016;17;1;72

    PUBMED: 27091476; PMC: 4834828; DOI: 10.1186/s13059-016-0944-x

  • Stability of the Encoding Plasmids and Surface Expression of CS6 Differs in Enterotoxigenic Escherichia coli (ETEC) Encoding Different Heat-Stable (ST) Enterotoxins (STh and STp).

    Tobias J, Von Mentzer A, Loayza Frykberg P, Aslett M, Page AJ, Sjöling Å and Svennerholm AM

    PloS one 2016;11;4;e0152899

    PUBMED: 27054573; PMC: 4824445; DOI: 10.1371/journal.pone.0152899

  • Stearoyl-CoA Desaturase 1 Is a Key Determinant of Membrane Lipid Composition in 3T3-L1 Adipocytes.

    Rodriguez-Cuenca S, Whyte L, Hagen R, Vidal-Puig A and Fuller M

    PloS one 2016;11;9;e0162047

    PUBMED: 27632198; PMC: 5025088; DOI: 10.1371/journal.pone.0162047

  • Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis.

    Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ, Dopazo J, Vidal-Puig A et al.

    Molecular metabolism 2016;5;1;19-33

    PUBMED: 26844204; PMC: 4703853; DOI: 10.1016/j.molmet.2015.10.005

  • Study profile: the Durban Diabetes Study (DDS): a platform for chronic disease research.

    Hird TR, Young EH, Pirie FJ, Riha J, Esterhuizen TM, O'Leary B, McCarthy MI, Sandhu MS and Motala AA

    Global health, epidemiology and genomics 2016;1;e2

    PUBMED: 29276614; PMC: 5732575; DOI: 10.1017/gheg.2015.3

  • TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

    Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K et al.

    Nature genetics 2016;48;1;36-43

    PUBMED: 26595769; PMC: 4697364; DOI: 10.1038/ng.3451

2015

  • Genes Regulated by Vitamin D in Bone Cells Are Positively Selected in East Asians.

    Arciero E, Biagini SA, Chen Y, Xue Y, Luiselli D, Tyler-Smith C, Pagani L and Ayub Q

    PloS one 2015;10;12;e0146072

    PUBMED: 26719974; PMC: 4697808; DOI: 10.1371/journal.pone.0146072

  • Viral fossils.

    Gall A

    Nature reviews. Microbiology 2015;14;2;66

    PUBMED: 26714433; DOI: 10.1038/nrmicro.2015.22

  • A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data.

    Kim YJ, Lee J, Kim BJ, T2D-Genes Consortium and Park T

    BMC genomics 2015;16;1109

    PUBMED: 26715385; PMC: 4696174; DOI: 10.1186/s12864-015-2192-y

  • Characterization of Two Distinct Nucleosome Remodeling and Deacetylase (NuRD) Complex Assemblies in Embryonic Stem Cells.

    Bode D, Yu L, Tate P, Pardo M and Choudhary J

    Molecular & cellular proteomics : MCP 2015;15;3;878-91

    PUBMED: 26714524; PMC: 4813707; DOI: 10.1074/mcp.M115.053207

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

    PUBMED: 26714481; PMC: 4699355; DOI: 10.1186/s13059-015-0849-0

  • A Library of Plasmodium vivax Recombinant Merozoite Proteins Reveals New Vaccine Candidates and Protein-Protein Interactions.

    Hostetler JB, Sharma S, Bartholdson SJ, Wright GJ, Fairhurst RM and Rayner JC

    PLoS neglected tropical diseases 2015;9;12;e0004264

    PUBMED: 26701602; PMC: 4689532; DOI: 10.1371/journal.pntd.0004264

  • Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.

    Maggiore L, Yu L, Omasits U, Rossi O, Dougan G, Thomson NR, Saul A, Choudhary JS and Gerke C

    International journal of medical microbiology : IJMM 2015;306;2;99-108

    PUBMED: 26746581; PMC: 4820968; DOI: 10.1016/j.ijmm.2015.12.003

  • Genomic perspectives on the evolution and spread of bacterial pathogens.

    Bentley SD and Parkhill J

    Proceedings. Biological sciences / The Royal Society 2015;282;1821;20150488

    PUBMED: 26702036; PMC: 4707741; DOI: 10.1098/rspb.2015.0488

  • Patterns of Local and Systemic Cytokines in Bacterial Meningitis and its Relation with Severity and Long-Term Sequelae.

    Perdomo-Celis F, Torres MA, Ostos H, Gutierrez-Achury J, Molano V, Durán LF, González G and Narváez CF

    Biomarker insights 2015;10;125-31

    PUBMED: 26715831; PMC: 4687976; DOI: 10.4137/BMI.S35005

  • Ensembl 2016.

    Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L et al.

    Nucleic acids research 2015;44;D1;D710-6

    PUBMED: 26687719; PMC: 4702834; DOI: 10.1093/nar/gkv1157

  • Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

    Malinsky M, Challis RJ, Tyers AM, Schiffels S, Terai Y, Ngatunga BP, Miska EA, Durbin R, Genner MJ and Turner GF

    Science (New York, N.Y.) 2015;350;6267;1493-1498

    PUBMED: 26680190; PMC: 4700518; DOI: 10.1126/science.aac9927

  • cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing.

    Raine KM, Hinton J, Butler AP, Teague JW, Davies H, Tarpey P, Nik-Zainal S and Campbell PJ

    Current protocols in bioinformatics 2015;52;15.7.1-15.7.12

    PUBMED: 26678382; PMC: 6097606; DOI: 10.1002/0471250953.bi1507s52

  • Chromothripsis and Kataegis Induced by Telomere Crisis.

    Maciejowski J, Li Y, Bosco N, Campbell PJ and de Lange T

    Cell 2015;163;7;1641-54

    PUBMED: 26687355; PMC: 4687025; DOI: 10.1016/j.cell.2015.11.054

  • VAGrENT: Variation Annotation Generator.

    Menzies A, Teague JW, Butler AP, Davies H, Tarpey P, Nik-Zainal S and Campbell PJ

    Current protocols in bioinformatics 2015;52;15.8.1-15.8.11

    PUBMED: 26678383; PMC: 6101192; DOI: 10.1002/0471250953.bi1508s52

  • Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in The Gambia.

    Roca A, Bojang A, Bottomley C, Gladstone RA, Adetifa JU, Egere U, Burr S, Antonio M, Bentley S, Kampmann B et al.

    Vaccine 2015;33;51;7144-51

    PUBMED: 26592141; DOI: 10.1016/j.vaccine.2015.11.012

  • Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.

    Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC and Logan DW

    Scientific reports 2015;5;18178

    PUBMED: 26670777; PMC: 4680959; DOI: 10.1038/srep18178

  • Brown Adipose Tissue Thermogenic Capacity Is Regulated by Elovl6.

    Tan CY, Virtue S, Bidault G, Dale M, Hagen R, Griffin JL and Vidal-Puig A

    Cell reports 2015;13;10;2039-47

    PUBMED: 26628376; PMC: 4688035; DOI: 10.1016/j.celrep.2015.11.004

  • Fine-mapping cellular QTLs with RASQUAL and ATAC-seq.

    Kumasaka N, Knights AJ and Gaffney DJ

    Nature genetics 2015;48;2;206-13

    PUBMED: 26656845; PMC: 5098600; DOI: 10.1038/ng.3467

  • Timing, rates and spectra of human germline mutation.

    Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B et al.

    Nature genetics 2015;48;2;126-133

    PUBMED: 26656846; PMC: 4731925; DOI: 10.1038/ng.3469

  • Principles of assembly reveal a periodic table of protein complexes.

    Ahnert SE, Marsh JA, Hernández H, Robinson CV and Teichmann SA

    Science (New York, N.Y.) 2015;350;6266;aaa2245

    PUBMED: 26659058; DOI: 10.1126/science.aaa2245

  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

    Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L et al.

    Nature communications 2015;6;10001

    PUBMED: 26647970; PMC: 4682041; DOI: 10.1038/ncomms10001

  • Human keratinocytes have two interconvertible modes of proliferation.

    Roshan A, Murai K, Fowler J, Simons BD, Nikolaidou-Neokosmidou V and Jones PH

    Nature cell biology 2015;18;2;145-56

    PUBMED: 26641719; PMC: 4872834; DOI: 10.1038/ncb3282

  • Involvement of astrocyte and oligodendrocyte gene sets in migraine.

    Eising E, de Leeuw C, Min JL, Anttila V, Verheijen MH, Terwindt GM, Dichgans M, Freilinger T, Kubisch C, International Headache Genetics Consortium et al.

    Cephalalgia : an international journal of headache 2015;36;7;640-7

    PUBMED: 26646788; DOI: 10.1177/0333102415618614

  • Devising a Consensus Framework for Validation of Novel Human Coding Loci.

    Bruford EA, Lane L and Harrow J

    Journal of proteome research 2015;14;12;4945-8

    PUBMED: 26367542; PMC: 4765950; DOI: 10.1021/acs.jproteome.5b00688

  • The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish.

    Bielczyk-Maczyńska E, Lam Hung L, Ferreira L, Fleischmann T, Weis F, Fernández-Pevida A, Harvey SA, Wali N, Warren AJ, Barroso I et al.

    PLoS genetics 2015;11;12;e1005677

    PUBMED: 26624285; PMC: 4666468; DOI: 10.1371/journal.pgen.1005677

  • Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis.

    Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA, Luan SL, Chaudhuri RR, Angen Ø, Aragon V, Williamson SM et al.

    Journal of clinical microbiology 2015;53;12;3812-21

    PUBMED: 26424843; PMC: 4652097; DOI: 10.1128/JCM.01991-15

  • Discovery of a novel neuroprotectant, BHDPC, that protects against MPP+/MPTP-induced neuronal death in multiple experimental models.

    Chong CM, Ma D, Zhao C, Franklin RJ, Zhou ZY, Ai N, Li C, Yu H, Hou T, Sa F and Lee SM

    Free radical biology & medicine 2015;89;1057-66

    PUBMED: 26415025; DOI: 10.1016/j.freeradbiomed.2015.08.013

  • Effect of Smoking on Blood Pressure and Resting Heart Rate: A Mendelian Randomization Meta-Analysis in the CARTA Consortium.

    Linneberg A, Jacobsen RK, Skaaby T, Taylor AE, Fluharty ME, Jeppesen JL, Bjorngaard JH, Åsvold BO, Gabrielsen ME, Campbell A et al.

    Circulation. Cardiovascular genetics 2015;8;6;832-41

    PUBMED: 26538566; PMC: 4684098; DOI: 10.1161/CIRCGENETICS.115.001225

  • Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers.

    McCreery MQ, Halliwill KD, Chin D, Delrosario R, Hirst G, Vuong P, Jen KY, Hewinson J, Adams DJ and Balmain A

    Nature medicine 2015;21;12;1514-20

    PUBMED: 26523969; PMC: 5094808; DOI: 10.1038/nm.3979

  • Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

    Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, Rayner NW, Robertson N et al.

    Nature genetics 2015;47;12;1415-25

    PUBMED: 26551672; PMC: 4666734; DOI: 10.1038/ng.3437

  • Genome-Wide Analysis of Evolutionary Markers of Human Influenza A(H1N1)pdm09 and A(H3N2) Viruses May Guide Selection of Vaccine Strain Candidates.

    Belanov SS, Bychkov D, Benner C, Ripatti S, Ojala T, Kankainen M, Kai Lee H, Wei-Tze Tang J and Kainov DE

    Genome biology and evolution 2015;7;12;3472-83

    PUBMED: 26615216; PMC: 4700966; DOI: 10.1093/gbe/evv240

  • Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome.

    Jones DC, Foth BJ, Urbaniak MD, Patterson S, Ong HB, Berriman M and Fairlamb AH

    PLoS neglected tropical diseases 2015;9;12;e0004299

    PUBMED: 26684831; PMC: 4689576; DOI: 10.1371/journal.pntd.0004299

  • Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study.

    Hill DM, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB et al.

    The Lancet. Infectious diseases 2015;15;12;1420-8

    PUBMED: 26515523; PMC: 4655307; DOI: 10.1016/S1473-3099(15)00267-4

  • Next-generation sequencing and empowering personalised cancer medicine.

    McDermott U

    Drug discovery today 2015;20;12;1470-5

    PUBMED: 26494142; DOI: 10.1016/j.drudis.2015.10.008

  • Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

    Ba X, Harrison EM, Lovering AL, Gleadall N, Zadoks R, Parkhill J, Peacock SJ, Holden MT, Paterson GK and Holmes MA

    Antimicrobial agents and chemotherapy 2015;59;12;7396-404

    PUBMED: 26392513; PMC: 4649192; DOI: 10.1128/AAC.01469-15

  • Over-expression of Plk4 induces centrosome amplification, loss of primary cilia and associated tissue hyperplasia in the mouse.

    Coelho PA, Bury L, Shahbazi MN, Liakath-Ali K, Tate PH, Wormald S, Hindley CJ, Huch M, Archer J, Skarnes WC et al.

    Open biology 2015;5;12;150209

    PUBMED: 26701933; PMC: 4703062; DOI: 10.1098/rsob.150209

  • Recurrent duplications of 17q12 associated with variable phenotypes.

    Mitchell E, Douglas A, Kjaegaard S, Callewaert B, Vanlander A, Janssens S, Yuen AL, Skinner C, Failla P, Alberti A et al.

    American journal of medical genetics. Part A 2015;167A;12;3038-45

    PUBMED: 26420380; DOI: 10.1002/ajmg.a.37351

  • Simultaneous impairment of neuronal and metabolic function of mutated gephyrin in a patient with epileptic encephalopathy.

    Dejanovic B, Djémié T, Grünewald N, Suls A, Kress V, Hetsch F, Craiu D, Zemel M, Gormley P, Lal D et al.

    EMBO molecular medicine 2015;7;12;1580-94

    PUBMED: 26613940; PMC: 4693503; DOI: 10.15252/emmm.201505323

  • Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability.

    Grozeva D, Carss K, Spasic-Boskovic O, Tejada MI, Gecz J, Shaw M, Corbett M, Haan E, Thompson E, Friend K et al.

    Human mutation 2015;36;12;1197-204

    PUBMED: 26350204; PMC: 4833192; DOI: 10.1002/humu.22901

  • Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study.

    Roberts Ch, Franklin CS, Makalo P, Joof H, Sarr I, Mahdi OS, Sillah A, Bah M, Payne F, Jeffreys AE et al.

    Scientific reports 2015;5;17447

    PUBMED: 26616738; PMC: 4663496; DOI: 10.1038/srep17447

  • Pregnancy and estrogen enhance neural progenitor-cell proliferation in the vomeronasal sensory epithelium.

    Oboti L, Ibarra-Soria X, Pérez-Gómez A, Schmid A, Pyrski M, Paschek N, Kircher S, Logan DW, Leinders-Zufall T, Zufall F and Chamero P

    BMC biology 2015;13;104

    PUBMED: 26621367; PMC: 4665882; DOI: 10.1186/s12915-015-0211-8

  • Recommendations for minimum information for publication of experimental pathology data: MINPEPA guidelines.

    Scudamore CL, Soilleux EJ, Karp NA, Smith K, Poulsom R, Herrington CS, Day MJ, Brayton CF, Bolon B, Whitelaw B et al.

    The Journal of pathology 2015;238;2;359-67

    PUBMED: 26387837; DOI: 10.1002/path.4642

  • A high-content platform to characterise human induced pluripotent stem cell lines.

    Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A et al.

    Methods (San Diego, Calif.) 2015;96;85-96

    PUBMED: 26608109; PMC: 4773406; DOI: 10.1016/j.ymeth.2015.11.012

  • Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load.

    McLaren PJ, Coulonges C, Bartha I, Lenz TL, Deutsch AJ, Bashirova A, Buchbinder S, Carrington MN, Cossarizza A, Dalmau J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;47;14658-63

    PUBMED: 26553974; PMC: 4664299; DOI: 10.1073/pnas.1514867112

  • HLA-DRB1*11 and variants of the MHC class II locus are strong risk factors for systemic juvenile idiopathic arthritis.

    Ombrello MJ, Remmers EF, Tachmazidou I, Grom A, Foell D, Haas JP, Martini A, Gattorno M, Özen S, Prahalad S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;52;15970-5

    PUBMED: 26598658; PMC: 4702958; DOI: 10.1073/pnas.1520779112

  • Principle of proportionality in genomic data sharing.

    Wright CF, Hurles ME and Firth HV

    Nature reviews. Genetics 2015;17;1;1-2

    PUBMED: 26593419; DOI: 10.1038/nrg.2015.5

  • Using genomics to combat infectious diseases on a global scale.

    Cain AK and Lees JA

    Genome biology 2015;16;250

    PUBMED: 26581564; PMC: 4652341; DOI: 10.1186/s13059-015-0822-y

  • Evaluation of power of the Illumina HumanOmni5M-4v1 BeadChip to detect risk variants for human complex diseases.

    Xing C, Huang J, Hsu YH, DeStefano AL, Heard-Costa NL, Wolf PA, Seshadri S, Kiel DP, Cupples LA and Dupuis J

    European journal of human genetics : EJHG 2015

    PUBMED: 26577045; DOI: 10.1038/ejhg.2015.244

  • The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation.

    Zaiss MM, Rapin A, Lebon L, Dubey LK, Mosconi I, Sarter K, Piersigilli A, Menin L, Walker AW, Rougemont J et al.

    Immunity 2015;43;5;998-1010

    PUBMED: 26522986; PMC: 4658337; DOI: 10.1016/j.immuni.2015.09.012

  • The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences.

    Kensche PR, Hoeijmakers WA, Toenhake CG, Bras M, Chappell L, Berriman M and Bártfai R

    Nucleic acids research 2015;44;5;2110-24

    PUBMED: 26578577; PMC: 4797266; DOI: 10.1093/nar/gkv1214

  • HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

    Forster SC, Browne HP, Kumar N, Hunt M, Denise H, Mitchell A, Finn RD and Lawley TD

    Nucleic acids research 2015;44;D1;D604-9

    PUBMED: 26578596; PMC: 4702862; DOI: 10.1093/nar/gkv1216

  • LIM kinase inhibitors disrupt mitotic microtubule organization and impair tumor cell proliferation.

    Mardilovich K, Baugh M, Crighton D, Kowalczyk D, Gabrielsen M, Munro J, Croft DR, Lourenco F, James D, Kalna G et al.

    Oncotarget 2015;6;36;38469-86

    PUBMED: 26540348; DOI: 10.18632/oncotarget.6288

  • WormBase 2016: expanding to enable helminth genomic research.

    Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C et al.

    Nucleic acids research 2015;44;D1;D774-80

    PUBMED: 26578572; PMC: 4702863; DOI: 10.1093/nar/gkv1217

  • Pharmacogenomic agreement between two cancer cell line data sets.

    Cancer Cell Line Encyclopedia Consortium and Genomics of Drug Sensitivity in Cancer Consortium

    Nature 2015;528;7580;84-7

    PUBMED: 26570998; PMC: 6343827; DOI: 10.1038/nature15736

  • Ptpn22 and Cd2 Variations Are Associated with Altered Protein Expression and Susceptibility to Type 1 Diabetes in Nonobese Diabetic Mice.

    Fraser HI, Howlett S, Clark J, Rainbow DB, Stanford SM, Wu DJ, Hsieh YW, Maine CJ, Christensen M, Kuchroo V et al.

    Journal of immunology (Baltimore, Md. : 1950) 2015;195;10;4841-52

    PUBMED: 26438525; PMC: 4635565; DOI: 10.4049/jimmunol.1402654

  • Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

    Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G et al.

    Genetics in medicine : official journal of the American College of Medical Genetics 2015;18;6;608-17

    PUBMED: 26562225; PMC: 4916229; DOI: 10.1038/gim.2015.137

  • Next-generation diagnostics and disease-gene discovery with the Exomiser.

    Smedley D, Jacobsen JO, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL et al.

    Nature protocols 2015;10;12;2004-15

    PUBMED: 26562621; PMC: 5467691; DOI: 10.1038/nprot.2015.124

  • SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair.

    Kanu N, Grönroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrík M, Rowan AJ, Patel H et al.

    Oncogene 2015;34;46;5699-708

    PUBMED: 25728682; DOI: 10.1038/onc.2015.24

  • The pig X and Y Chromosomes: structure, sequence, and evolution.

    Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W et al.

    Genome research 2015;26;1;130-9

    PUBMED: 26560630; PMC: 4691746; DOI: 10.1101/gr.188839.114

  • Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

    Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira PG, Asher CL, Jurkowski TP, Segonds-Pichon A, Bachman M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;45;13970-5

    PUBMED: 26483466; PMC: 4653166; DOI: 10.1073/pnas.1515937112

  • Clock-like mutational processes in human somatic cells.

    Alexandrov LB, Jones PH, Wedge DC, Sale JE, Campbell PJ, Nik-Zainal S and Stratton MR

    Nature genetics 2015;47;12;1402-7

    PUBMED: 26551669; PMC: 4783858; DOI: 10.1038/ng.3441

  • Discovery and Characterization of Human-Urine Utilization by Asymptomatic-Bacteriuria-Causing Streptococcus agalactiae.

    Ipe DS, Ben Zakour NL, Sullivan MJ, Beatson SA, Ulett KB, Benjamin WH, Davies MR, Dando SJ, King NP, Cripps AW et al.

    Infection and immunity 2015;84;1;307-19

    PUBMED: 26553467; PMC: 4694007; DOI: 10.1128/IAI.00938-15

  • It's diversity all the way down.

    David S and Hadfield J

    Nature reviews. Microbiology 2015;13;12;740

    PUBMED: 26548911; DOI: 10.1038/nrmicro3587

  • High-density P300 enhancers control cell state transitions.

    Witte S, Bradley A, Enright AJ and Muljo SA

    BMC genomics 2015;16;903

    PUBMED: 26546038; PMC: 4636788; DOI: 10.1186/s12864-015-1905-6

  • USP4 Auto-Deubiquitylation Promotes Homologous Recombination.

    Wijnhoven P, Konietzny R, Blackford AN, Travers J, Kessler BM, Nishi R and Jackson SP

    Molecular cell 2015;60;3;362-73

    PUBMED: 26455393; PMC: 4643306; DOI: 10.1016/j.molcel.2015.09.019

  • Adenoma development in familial adenomatous polyposis and MUTYH-associated polyposis: somatic landscape and driver genes.

    Rashid M, Fischer A, Wilson CH, Tiffen J, Rust AG, Stevens P, Idziaszczyk S, Maynard J, Williams GT, Mustonen V et al.

    The Journal of pathology 2015;238;1;98-108

    PUBMED: 26414517; PMC: 4832337; DOI: 10.1002/path.4643

  • A novel genus in the order Picornavirales detected in human stool.

    Oude Munnink BB, Cotten M, Deijs M, Jebbink MF, Bakker M, Jazaeri Farsani SM, Canuti M, Kellam P and van der Hoek L

    The Journal of general virology 2015;96;11;3440-3443

    PUBMED: 26354795; DOI: 10.1099/jgv.0.000279

  • Antimicrobial Resistance Profiles and Diversity in Salmonella from Humans and Cattle, 2004-2011.

    Afema JA, Mather AE and Sischo WM

    Zoonoses and public health 2015;62;7;506-17

    PUBMED: 25414062; DOI: 10.1111/zph.12172

  • Early maturation and distinct tau pathology in induced pluripotent stem cell-derived neurons from patients with MAPT mutations.

    Iovino M, Agathou S, González-Rueda A, Del Castillo Velasco-Herrera M, Borroni B, Alberici A, Lynch T, O'Dowd S, Geti I, Gaffney D et al.

    Brain : a journal of neurology 2015;138;Pt 11;3345-59

    PUBMED: 26220942; PMC: 4620511; DOI: 10.1093/brain/awv222

  • Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers.

    Sidore C, Busonero F, Maschio A, Porcu E, Naitza S, Zoledziewska M, Mulas A, Pistis G, Steri M, Danjou F et al.

    Nature genetics 2015;47;11;1272-81

    PUBMED: 26366554; PMC: 4627508; DOI: 10.1038/ng.3368

  • Mechanism of eIF6 release from the nascent 60S ribosomal subunit.

    Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR and Warren AJ

    Nature structural & molecular biology 2015;22;11;914-9

    PUBMED: 26479198; DOI: 10.1038/nsmb.3112

  • On the identification of low allele frequency mosaic mutations in the brains of Alzheimer's disease patients.

    Sala Frigerio C, Lau P, Troakes C, Deramecourt V, Gele P, Van Loo P, Voet T and De Strooper B

    Alzheimer's & dementia : the journal of the Alzheimer's Association 2015;11;11;1265-76

    PUBMED: 25937274; DOI: 10.1016/j.jalz.2015.02.007

  • Population genetic differentiation of height and body mass index across Europe.

    Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S et al.

    Nature genetics 2015;47;11;1357-62

    PUBMED: 26366552; PMC: 4984852; DOI: 10.1038/ng.3401

  • Putting induced pluripotent stem cells to the test.

    Vallier L

    Nature biotechnology 2015;33;11;1145-6

    PUBMED: 26544143; DOI: 10.1038/nbt.3401

  • Systematic E2 screening reveals a UBE2D-RNF138-CtIP axis promoting DNA repair.

    Schmidt CK, Galanty Y, Sczaniecka-Clift M, Coates J, Jhujh S, Demir M, Cornwell M, Beli P and Jackson SP

    Nature cell biology 2015;17;11;1458-70

    PUBMED: 26502057; PMC: 4894550; DOI: 10.1038/ncb3260

  • Three Epidemics of Invasive Multidrug-Resistant Salmonella Bloodstream Infection in Blantyre, Malawi, 1998-2014.

    Feasey NA, Masesa C, Jassi C, Faragher EB, Mallewa J, Mallewa M, MacLennan CA, Msefula C, Heyderman RS and Gordon MA

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015;61 Suppl 4;S363-71

    PUBMED: 26449953; PMC: 4596930; DOI: 10.1093/cid/civ691

  • True Blood: dengue virus evolution.

    Wash R and Soria CD

    Nature reviews. Microbiology 2015;13;11;662

    PUBMED: 26439086; DOI: 10.1038/nrmicro3570

  • Understanding inflammatory bowel disease via immunogenetics.

    de Lange KM and Barrett JC

    Journal of autoimmunity 2015;64;91-100

    PUBMED: 26257098; DOI: 10.1016/j.jaut.2015.07.013

  • Uric Acid and Cardiovascular Events: A Mendelian Randomization Study.

    Kleber ME, Delgado G, Grammer TB, Silbernagel G, Huang J, Krämer BK, Ritz E and März W

    Journal of the American Society of Nephrology : JASN 2015;26;11;2831-8

    PUBMED: 25788527; DOI: 10.1681/ASN.2014070660

  • Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014.

    Chowdhury F, Mather AE, Begum YA, Asaduzzaman M, Baby N, Sharmin S, Biswas R, Uddin MI, LaRocque RC, Harris JB et al.

    PLoS neglected tropical diseases 2015;9;11;e0004183

    PUBMED: 26562418; PMC: 4642977; DOI: 10.1371/journal.pntd.0004183

  • Cardiomyocytes from human pluripotent stem cells: From laboratory curiosity to industrial biomedical platform.

    Denning C, Borgdorff V, Crutchley J, Firth KS, George V, Kalra S, Kondrashov A, Hoang MD, Mosqueira D, Patel A et al.

    Biochimica et biophysica acta 2015

    PUBMED: 26524115; DOI: 10.1016/j.bbamcr.2015.10.014

  • Comparative genomic analysis of the swine pathogen Bordetella bronchisepticastrain KM22.

    Nicholson TL, Shore SM, Register KB, Bayles DO, Kingsley RA and Brunelle BW

    Veterinary microbiology 2015;182;87-94

    PUBMED: 26711033; DOI: 10.1016/j.vetmic.2015.10.026

  • Antiquity and diversity of aboriginal Australian Y-chromosomes.

    Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA et al.

    American journal of physical anthropology 2015;159;3;367-81

    PUBMED: 26515539; DOI: 10.1002/ajpa.22886

  • A mutational signature in gastric cancer suggests therapeutic strategies.

    Alexandrov LB, Nik-Zainal S, Siu HC, Leung SY and Stratton MR

    Nature communications 2015;6;8683

    PUBMED: 26511885; PMC: 4918743; DOI: 10.1038/ncomms9683

  • CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice.

    Weber J, Öllinger R, Friedrich M, Ehmer U, Barenboim M, Steiger K, Heid I, Mueller S, Maresch R, Engleitner T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;45;13982-7

    PUBMED: 26508638; PMC: 4653208; DOI: 10.1073/pnas.1512392112

  • Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.

    Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M and Hanage WP

    Scientific data 2015;2;150058

    PUBMED: 26528397; PMC: 4622223; DOI: 10.1038/sdata.2015.58

  • Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

    Kim JK, Kolodziejczyk AA, Ilicic T, Illicic T, Teichmann SA and Marioni JC

    Nature communications 2015;6;8687

    PUBMED: 26489834; PMC: 4627577; DOI: 10.1038/ncomms9687

  • Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations.

    Haber M, Mezzavilla M, Xue Y, Comas D, Gasparini P, Zalloua P and Tyler-Smith C

    European journal of human genetics : EJHG 2015;24;6;931-6

    PUBMED: 26486470; PMC: 4820045; DOI: 10.1038/ejhg.2015.206

  • Pathogen Resistance Mediated by IL-22 Signaling at the Epithelial-Microbiota Interface.

    Schreiber F, Arasteh JM and Lawley TD

    Journal of molecular biology 2015;427;23;3676-82

    PUBMED: 26497621; DOI: 10.1016/j.jmb.2015.10.013

  • Artemisinin-resistant Plasmodium falciparum clinical isolates can infect diverse mosquito vectors of Southeast Asia and Africa.

    St Laurent B, Miller B, Burton TA, Amaratunga C, Men S, Sovannaroth S, Fay MP, Miotto O, Gwadz RW, Anderson JM and Fairhurst RM

    Nature communications 2015;6;8614

    PUBMED: 26485448; PMC: 4616032; DOI: 10.1038/ncomms9614

  • What role could organoids play in the personalization of cancer treatment?

    Francies HE and Garnett MJ

    Pharmacogenomics 2015;16;14;1523-6

    PUBMED: 26485224; DOI: 10.2217/pgs.15.114

  • The utility of transposon mutagenesis for cancer studies in the era of genome editing.

    DeNicola GM, Karreth FA, Adams DJ and Wong CC

    Genome biology 2015;16;229

    PUBMED: 26481584; PMC: 4612416; DOI: 10.1186/s13059-015-0794-y

  • Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

    Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S et al.

    Nucleic acids research 2015;44;D1;D746-52

    PUBMED: 26481351; PMC: 4702781; DOI: 10.1093/nar/gkv1045

  • Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study.

    Cleynen I, Boucher G, Jostins L, Schumm LP, Zeissig S, Ahmad T, Andersen V, Andrews JM, Annese V, Brand S et al.

    Lancet (London, England) 2015;387;10014;156-67

    PUBMED: 26490195; PMC: 4714968; DOI: 10.1016/S0140-6736(15)00465-1

  • Processing of Plasmodium falciparum Merozoite Surface Protein MSP1 Activates a Spectrin-Binding Function Enabling Parasite Egress from RBCs.

    Das S, Hertrich N, Perrin AJ, Withers-Martinez C, Collins CR, Jones ML, Watermeyer JM, Fobes ET, Martin SR, Saibil HR et al.

    Cell host & microbe 2015;18;4;433-44

    PUBMED: 26468747; PMC: 4608996; DOI: 10.1016/j.chom.2015.09.007

  • Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae.

    Redmond SN, Eiglmeier K, Mitri C, Markianos K, Guelbeogo WM, Gneme A, Isaacs AT, Coulibaly B, Brito-Fravallo E, Maslen G et al.

    BMC genomics 2015;16;779

    PUBMED: 26462916; PMC: 4603968; DOI: 10.1186/s12864-015-2009-z

  • Mondo-Mlx Mediates Organismal Sugar Sensing through the Gli-Similar Transcription Factor Sugarbabe.

    Mattila J, Havula E, Suominen E, Teesalu M, Surakka I, Hynynen R, Kilpinen H, Väänänen J, Hovatta I, Käkelä R et al.

    Cell reports 2015;13;2;350-64

    PUBMED: 26440885; DOI: 10.1016/j.celrep.2015.08.081

  • Ape parasite origins of human malaria virulence genes.

    Larremore DB, Sundararaman SA, Liu W, Proto WR, Clauset A, Loy DE, Speede S, Plenderleith LJ, Sharp PM, Hahn BH et al.

    Nature communications 2015;6;8368

    PUBMED: 26456841; PMC: 4633637; DOI: 10.1038/ncomms9368

  • PBP2a substitutions linked to ceftaroline resistance in MRSA isolates from the UK.

    Harrison EM, Ba X, Blane B, Ellington MJ, Loeffler A, Hill RL, Holmes MA and Peacock SJ

    The Journal of antimicrobial chemotherapy 2015;71;1;268-9

    PUBMED: 26462986; PMC: 4681373; DOI: 10.1093/jac/dkv317

  • When the Snake Lost Its Limbs, What Did the Mouse and Lizard Say?

    Villar D and Odom DT

    Developmental cell 2015;35;1;3-4

    PUBMED: 26460939; DOI: 10.1016/j.devcel.2015.09.022

  • A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions.

    Iorio F, Shrestha RL, Levin N, Boilot V, Garnett MJ, Saez-Rodriguez J and Draviam VM

    PloS one 2015;10;10;e0139446

    PUBMED: 26452147; PMC: 4599732; DOI: 10.1371/journal.pone.0139446

  • From GWAS to function: lessons from blood cells.

    Vasquez LJ, Mann AL, Chen L and Soranzo N

    ISBT science series 2015;11;Suppl Suppl 1;211-219

    PUBMED: 27347004; PMC: 4916502; DOI: 10.1111/voxs.12217

  • The genome as a record of environmental exposure.

    Nik-Zainal S, Kucab JE, Morganella S, Glodzik D, Alexandrov LB, Arlt VM, Weninger A, Hollstein M, Stratton MR and Phillips DH

    Mutagenesis 2015;30;6;763-70

    PUBMED: 26443852; PMC: 4637815; DOI: 10.1093/mutage/gev073

  • Estimating malaria transmission from humans to mosquitoes in a noisy landscape.

    Reiner RC, Guerra C, Donnelly MJ, Bousema T, Drakeley C and Smith DL

    Journal of the Royal Society, Interface / the Royal Society 2015;12;111;20150478

    PUBMED: 26400195; PMC: 4614487; DOI: 10.1098/rsif.2015.0478

  • Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae).

    Sotero-Caio CG, Volleth M, Hoffmann FG, Scott L, Wichman HA, Yang F and Baker RJ

    BMC evolutionary biology 2015;15;220

    PUBMED: 26444412; PMC: 4594642; DOI: 10.1186/s12862-015-0494-y

  • Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families.

    Akawi N, McRae J, Ansari M, Balasubramanian M, Blyth M, Brady AF, Clayton S, Cole T, Deshpande C, Fitzgerald TW et al.

    Nature genetics 2015;47;11;1363-9

    PUBMED: 26437029; PMC: 5988033; DOI: 10.1038/ng.3410

  • Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage.

    Peltier J, Shaw HA, Couchman EC, Dawson LF, Yu L, Choudhary JS, Kaever V, Wren BW and Fairweather NF

    The Journal of biological chemistry 2015;290;40;24453-69

    PUBMED: 26283789; PMC: 4591827; DOI: 10.1074/jbc.M115.665091

  • A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants.

    Lenassi E, Vincent A, Li Z, Saihan Z, Coffey AJ, Steele-Stallard HB, Moore AT, Steel KP, Luxon LM, Héon E et al.

    European journal of human genetics : EJHG 2015;23;10;1318-27

    PUBMED: 25649381; PMC: 4592079; DOI: 10.1038/ejhg.2014.283

  • An extended Tajima's D neutrality test incorporating SNP calling and imputation uncertainties.

    Zhang Q, Tyler-Smith C and Long Q

    Statistics and its interface 2015;8;4;447-456

    PUBMED: 26681995; PMC: 4678577; DOI: 10.4310/SII.2015.v8.n4.a4

  • A global reference for human genetic variation.

    1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA and Abecasis GR

    Nature 2015;526;7571;68-74

    PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393

  • The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

    Winkler TW, Justice AE, Graff M, Barata L, Feitosa MF, Chu S, Czajkowski J, Esko T, Fall T, Kilpeläinen TO et al.

    PLoS genetics 2015;11;10;e1005378

    PUBMED: 26426971; PMC: 4591371; DOI: 10.1371/journal.pgen.1005378

  • An integrated map of structural variation in 2,504 human genomes.

    Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH et al.

    Nature 2015;526;7571;75-81

    PUBMED: 26432246; PMC: 4617611; DOI: 10.1038/nature15394

  • The Matchmaker Exchange: a platform for rare disease gene discovery.

    Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C et al.

    Human mutation 2015;36;10;915-21

    PUBMED: 26295439; PMC: 4610002; DOI: 10.1002/humu.22858

  • The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles.

    Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C and Brudno M

    Human mutation 2015;36;10;922-7

    PUBMED: 26255989; PMC: 4775166; DOI: 10.1002/humu.22850

  • A mouse informatics platform for phenotypic and translational discovery.

    Ring N, Meehan TF, Blake A, Brown J, Chen CK, Conte N, Di Fenza A, Fiegel T, Horner N, Jacobsen JO et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;413-21

    PUBMED: 26314589; PMC: 4602054; DOI: 10.1007/s00335-015-9599-2

  • Alternative Splice in Alternative Lice.

    Tovar-Corona JM, Castillo-Morales A, Chen L, Olds BP, Clark JM, Reynolds SE, Pittendrigh BR, Feil EJ and Urrutia AO

    Molecular biology and evolution 2015;32;10;2749-59

    PUBMED: 26169943; PMC: 4576711; DOI: 10.1093/molbev/msv151

  • Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes.

    Rosen B, Schick J and Wurst W

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;456-66

    PUBMED: 26340938; DOI: 10.1007/s00335-015-9598-3

  • Class II HLA interactions modulate genetic risk for multiple sclerosis.

    Moutsianas L, Jostins L, Beecham AH, Dilthey AT, Xifara DK, Ban M, Shah TS, Patsopoulos NA, Alfredsson L, Anderson CA et al.

    Nature genetics 2015;47;10;1107-13

    PUBMED: 26343388; PMC: 4874245; DOI: 10.1038/ng.3395

  • Concomitant inactivation of the p53- and pRB- functional pathways predicts resistance to DNA damaging drugs in breast cancer in vivo.

    Knappskog S, Berge EO, Chrisanthar R, Geisler S, Staalesen V, Leirvaag B, Yndestad S, de Faveri E, Karlsen BO, Wedge DC et al.

    Molecular oncology 2015;9;8;1553-64

    PUBMED: 26004085; DOI: 10.1016/j.molonc.2015.04.008

  • Disease insights through cross-species phenotype comparisons.

    Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;548-55

    PUBMED: 26092691; PMC: 4602072; DOI: 10.1007/s00335-015-9577-8

  • Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index.

    Yang J, Bakshi A, Zhu Z, Hemani G, Vinkhuyzen AA, Lee SH, Robinson MR, Perry JR, Nolte IM, van Vliet-Ostaptchouk JV et al.

    Nature genetics 2015;47;10;1114-20

    PUBMED: 26323059; PMC: 4589513; DOI: 10.1038/ng.3390

  • Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England.

    Cairns MD, Preston MD, Lawley TD, Clark TG, Stabler RA and Wren BW

    Journal of clinical microbiology 2015;53;10;3141-7

    PUBMED: 26179308; PMC: 4572532; DOI: 10.1128/JCM.00648-15

  • Glucose-6-phosphate dehydrogenase deficiency and the risk of malaria and other diseases in children in Kenya: a case-control and a cohort study.

    Uyoga S, Ndila CM, Macharia AW, Nyutu G, Shah S, Peshu N, Clarke GM, Kwiatkowski DP, Rockett KA, Williams TN and MalariaGEN Consortium

    The Lancet. Haematology 2015;2;10;e437-44

    PUBMED: 26686045; PMC: 4703047; DOI: 10.1016/S2352-3026(15)00152-0

  • Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

    Kaiser VB, Svinti V, Prendergast JG, Chau YY, Campbell A, Patarcic I, Barroso I, Joshi PK, Hastie ND, Miljkovic A et al.

    Human molecular genetics 2015;24;19;5464-74

    PUBMED: 26173456; PMC: 4572071; DOI: 10.1093/hmg/ddv272

  • How apicomplexans became free-riders.

    Owusu CK and Bennett HM

    Nature reviews. Microbiology 2015;13;10;603

    PUBMED: 26373370; DOI: 10.1038/nrmicro3551

  • Human genomics: The end of the start for population sequencing.

    Birney E and Soranzo N

    Nature 2015;526;7571;52-3

    PUBMED: 26432243; DOI: 10.1038/526052a

  • Immunofluorescence Analysis and Diagnosis of Primary Ciliary Dyskinesia with Radial Spoke Defects.

    Frommer A, Hjeij R, Loges NT, Edelbusch C, Jahnke C, Raidt J, Werner C, Wallmeier J, Große-Onnebrink J, Olbrich H et al.

    American journal of respiratory cell and molecular biology 2015;53;4;563-73

    PUBMED: 25789548; PMC: 5306451; DOI: 10.1165/rcmb.2014-0483OC

  • Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank.

    Wain LV, Shrine N, Miller S, Jackson VE, Ntalla I, Soler Artigas M, Billington CK, Kheirallah AK, Allen R, Cook JP et al.

    The Lancet. Respiratory medicine 2015;3;10;769-81

    PUBMED: 26423011; PMC: 4593935; DOI: 10.1016/S2213-2600(15)00283-0

  • Novel loci associated with usual sleep duration: the CHARGE Consortium Genome-Wide Association Study.

    Gottlieb DJ, Hek K, Chen TH, Watson NF, Eiriksdottir G, Byrne EM, Cornelis M, Warby SC, Bandinelli S, Cherkas L et al.

    Molecular psychiatry 2015;20;10;1232-9

    PUBMED: 25469926; PMC: 4430294; DOI: 10.1038/mp.2014.133

  • PhenoMiner: from text to a database of phenotypes associated with OMIM diseases.

    Collier N, Groza T, Smedley D, Robinson PN, Oellrich A and Rebholz-Schuhmann D

    Database : the journal of biological databases and curation 2015;2015

    PUBMED: 26507285; PMC: 4622021; DOI: 10.1093/database/bav104

  • Positive selection of AS3MT to arsenic water in Andean populations.

    Eichstaedt CA, Antao T, Cardona A, Pagani L, Kivisild T and Mormina M

    Mutation research 2015;780;97-102

    PUBMED: 26366667; PMC: 4896383; DOI: 10.1016/j.mrfmmm.2015.07.007

  • Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome.

    Fumagalli D, Gacquer D, Rothé F, Lefort A, Libert F, Brown D, Kheddoumi N, Shlien A, Konopka T, Salgado R et al.

    Cell reports 2015;13;2;277-89

    PUBMED: 26440892; PMC: 5326813; DOI: 10.1016/j.celrep.2015.09.032

  • Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

    Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P et al.

    Cell stem cell 2015;17;4;471-85

    PUBMED: 26431182; PMC: 4595712; DOI: 10.1016/j.stem.2015.09.011

  • SpeedSeq: ultra-fast personal genome analysis and interpretation.

    Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR and Hall IM

    Nature methods 2015;12;10;966-8

    PUBMED: 26258291; PMC: 4589466; DOI: 10.1038/nmeth.3505

  • Talking welfare: the importance of a common language.

    Bussell J and Wells SE

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;482-5

    PUBMED: 26286857; PMC: 4602052; DOI: 10.1007/s00335-015-9591-x

  • Truncation of POC1A associated with short stature and extreme insulin resistance.

    Chen JH, Segni M, Payne F, Huang-Doran I, Sleigh A, Adams C, UK10K Consortium, Savage DB, O'Rahilly S, Semple RK and Barroso I

    Journal of molecular endocrinology 2015;55;2;147-58

    PUBMED: 26336158; PMC: 4722288; DOI: 10.1530/JME-15-0090

  • Use of model organism and disease databases to support matchmaking for human disease gene discovery.

    Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN et al.

    Human mutation 2015;36;10;979-84

    PUBMED: 26269093; DOI: 10.1002/humu.22857

  • A novel locus of resistance to severe malaria in a region of ancient balancing selection.

    Malaria Genomic Epidemiology Network, Band G, Rockett KA, Spencer CC and Kwiatkowski DP

    Nature 2015;526;7572;253-7

    PUBMED: 26416757; PMC: 4629224; DOI: 10.1038/nature15390

  • Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management.

    Woolhouse ME, Rambaut A and Kellam P

    Science translational medicine 2015;7;307;307rv5

    PUBMED: 26424572; PMC: 5819730; DOI: 10.1126/scitranslmed.aab0191

  • The digital revolution in phenotyping.

    Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K et al.

    Briefings in bioinformatics 2015;17;5;819-30

    PUBMED: 26420780; PMC: 5036847; DOI: 10.1093/bib/bbv083

  • Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

    Sun Z, Harris HM, McCann A, Guo C, Argimón S, Zhang W, Yang X, Jeffery IB, Cooney JC, Kagawa TF et al.

    Nature communications 2015;6;8322

    PUBMED: 26415554; PMC: 4667430; DOI: 10.1038/ncomms9322

  • A Bayesian Approach to the Overlap Analysis of Epidemiologically Linked Traits.

    Asimit JL, Panoutsopoulou K, Wheeler E, Berndt SI, GIANT consortium, the arcOGEN consortium, Cordell HJ, Morris AP, Zeggini E and Barroso I

    Genetic epidemiology 2015;39;8;624-34

    PUBMED: 26411566; PMC: 4832282; DOI: 10.1002/gepi.21919

  • The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource.

    Baker KS, Burnett E, McGregor H, Deheer-Graham A, Boinett C, Langridge GC, Wailan AM, Cain AK, Thomson NR, Russell JE and Parkhill J

    Genome medicine 2015;7;97

    PUBMED: 26411565; PMC: 4584482; DOI: 10.1186/s13073-015-0222-7

  • 'Pop-Up' Governance: developing internal governance frameworks for consortia: the example of UK10K.

    Kaye J, Muddyman D, Smee C, Kennedy K, Bell J and UK10K

    Life sciences, society and policy 2015;11;10

    PUBMED: 26412243; PMC: 4584211; DOI: 10.1186/s40504-015-0028-9

  • Partitioning heritability by functional annotation using genome-wide association summary statistics.

    Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, Loh PR, Anttila V, Xu H, Zang C, Farh K et al.

    Nature genetics 2015;47;11;1228-35

    PUBMED: 26414678; PMC: 4626285; DOI: 10.1038/ng.3404

  • A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant.

    Hamidian M, Holt KE, Pickard D and Hall RM

    The Journal of antimicrobial chemotherapy 2015;71;1;269-71

    PUBMED: 26416779; PMC: 4681370; DOI: 10.1093/jac/dkv293

  • Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes.

    Nie W, O'Brien PC, Fu B, Wang J, Su W, He K, Bed'Hom B, Volobouev V, Ferguson-Smith MA, Dobigny G and Yang F

    BMC evolutionary biology 2015;15;205

    PUBMED: 26409465; PMC: 4583764; DOI: 10.1186/s12862-015-0484-0

  • AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.

    Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann SA and Swint-Kruse L

    Journal of molecular biology 2015;428;4;671-678

    PUBMED: 26410588; PMC: 4783282; DOI: 10.1016/j.jmb.2015.09.015

  • The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases.

    Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HD, Cuong NV, Pham HA et al.

    EcoHealth 2015;12;4;726-35

    PUBMED: 26403795; PMC: 4700077; DOI: 10.1007/s10393-015-1061-0

  • Somatic mutation in cancer and normal cells.

    Martincorena I and Campbell PJ

    Science (New York, N.Y.) 2015;349;6255;1483-9

    PUBMED: 26404825; DOI: 10.1126/science.aab4082

  • Aging as a driver of leukemogenesis.

    McKerrell T and Vassiliou GS

    Science translational medicine 2015;7;306;306fs38

    PUBMED: 26400908; PMC: 4916992; DOI: 10.1126/scitranslmed.aac4428

  • The effect of genetic structure on molecular dating and tests for temporal signal.

    Murray GG, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A and Welch JJ

    Methods in ecology and evolution 2015;7;1;80-89

    PUBMED: 27110344; PMC: 4832290; DOI: 10.1111/2041-210X.12466

  • International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

    Cordell HJ, Han Y, Mells GF, Li Y, Hirschfield GM, Greene CS, Xie G, Juran BD, Zhu D, Qian DC et al.

    Nature communications 2015;6;8019

    PUBMED: 26394269; PMC: 4580981; DOI: 10.1038/ncomms9019

  • Mutational Analysis of Ionizing Radiation Induced Neoplasms.

    Sherborne AL, Davidson PR, Yu K, Nakamura AO, Rashid M and Nakamura JL

    Cell reports 2015;12;11;1915-26

    PUBMED: 26344771; DOI: 10.1016/j.celrep.2015.08.015

  • On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions.

    Madrigal P

    Frontiers in bioengineering and biotechnology 2015;3;144

    PUBMED: 26442258; PMC: 4585268; DOI: 10.3389/fbioe.2015.00144

  • Population, genetic, and antigenic diversity of the apicomplexan Eimeria tenella and their relevance to vaccine development.

    Blake DP, Clark EL, Macdonald SE, Thenmozhi V, Kundu K, Garg R, Jatau ID, Ayoade S, Kawahara F, Moftah A et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;38;E5343-50

    PUBMED: 26354122; PMC: 4586875; DOI: 10.1073/pnas.1506468112

  • The impact of environmental and climatic variation on the spatiotemporal trends of hospitalized pediatric diarrhea in Ho Chi Minh City, Vietnam.

    Thompson CN, Zelner JL, Nhu TD, Phan MV, Hoang Le P, Nguyen Thanh H, Vu Thuy D, Minh Nguyen N, Ha Manh T, Van Hoang Minh T et al.

    Health & place 2015;35;147-154

    PUBMED: 26402922; DOI: 10.1016/j.healthplace.2015.08.001

  • A novel mouse model identifies cooperating mutations and therapeutic targets critical for chronic myeloid leukemia progression.

    Giotopoulos G, van der Weyden L, Osaki H, Rust AG, Gallipoli P, Meduri E, Horton SJ, Chan WI, Foster D, Prinjha RK et al.

    The Journal of experimental medicine 2015;212;10;1551-69

    PUBMED: 26304963; PMC: 4577832; DOI: 10.1084/jem.20141661

  • Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

    Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L and Liu P

    Genome biology 2015;16;178

    PUBMED: 26387834; PMC: 4576406; DOI: 10.1186/s13059-015-0739-5

  • Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation.

    Kato N, Loh M, Takeuchi F, Verweij N, Wang X, Zhang W, Kelly TN, Saleheen D, Lehne B, Leach IM et al.

    Nature genetics 2015;47;11;1282-1293

    PUBMED: 26390057; PMC: 4719169; DOI: 10.1038/ng.3405

  • Successful Generation of Human Induced Pluripotent Stem Cell Lines from Blood Samples Held at Room Temperature for up to 48 hr.

    Agu CA, Soares FA, Alderton A, Patel M, Ansari R, Patel S, Forrest S, Yang F, Lineham J, Vallier L and Kirton CM

    Stem cell reports 2015;5;4;660-71

    PUBMED: 26388286; PMC: 4624992; DOI: 10.1016/j.stemcr.2015.08.012

  • Using human genetics to make new medicines.

    Barrett JC, Dunham I and Birney E

    Nature reviews. Genetics 2015;16;10;561-2

    PUBMED: 26370900; DOI: 10.1038/nrg3998

  • The UK10K project identifies rare variants in health and disease.

    UK10K Consortium, Walter K, Min JL, Huang J, Crooks L, Memari Y, McCarthy S, Perry JR, Xu C, Futema M et al.

    Nature 2015;526;7571;82-90

    PUBMED: 26367797; PMC: 4773891; DOI: 10.1038/nature14962

  • Height-reducing variants and selection for short stature in Sardinia.

    Zoledziewska M, Sidore C, Chiang CW, Sanna S, Mulas A, Steri M, Busonero F, Marcus JH, Marongiu M, Maschio A et al.

    Nature genetics 2015

    PUBMED: 26366551; DOI: 10.1038/ng.3403

  • Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.

    Huang J, Howie B, McCarthy S, Memari Y, Walter K, Min JL, Danecek P, Malerba G, Trabetti E, Zheng HF et al.

    Nature communications 2015;6;8111

    PUBMED: 26368830; PMC: 4579394; DOI: 10.1038/ncomms9111

  • Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

    Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, Dahia CL, Park-Min KH, Tobias JH, Kooperberg C et al.

    Nature 2015;526;7571;112-7

    PUBMED: 26367794; PMC: 4755714; DOI: 10.1038/nature14878

  • Strain features and distributions in pneumococci from children with invasive disease before and after 13-valent conjugate vaccine implementation in the USA.

    Metcalf BJ, Gertz RE, Gladstone RA, Walker H, Sherwood LK, Jackson D, Li Z, Law C, Hawkins PA, Chochua S et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2015;22;1;60.e9-60.e29

    PUBMED: 26363404; PMC: 4721534; DOI: 10.1016/j.cmi.2015.08.027

  • Evaluation of conjunctival swab sampling in the diagnosis of canine leishmaniasis: A two-year follow-up study in Çukurova Plain, Turkey.

    Karakuş M, Töz S, Ertabaklar H, Paşa S, Atasoy A, Arserim SK, Ölgen MK, Alkan MZ, Durrant C and Özbel Y

    Veterinary parasitology 2015;214;3-4;295-302

    PUBMED: 26415899; DOI: 10.1016/j.vetpar.2015.09.009

  • A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.

    Nikpay M, Goel A, Won HH, Hall LM, Willenborg C, Kanoni S, Saleheen D, Kyriakou T, Nelson CP, Hopewell JC et al.

    Nature genetics 2015;47;10;1121-1130

    PUBMED: 26343387; PMC: 4589895; DOI: 10.1038/ng.3396

  • Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals.

    Hoehn KB, Gall A, Bashford-Rogers R, Fidler SJ, Kaye S, Weber JN, McClure MO, SPARTAC Trial Investigators, Kellam P and Pybus OG

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2015;370;1676

    PUBMED: 26194755; PMC: 4528418; DOI: 10.1098/rstb.2014.0241

  • Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

    Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC and Odom DT

    PloS one 2015;10;9;e0137367

    PUBMED: 26339903; PMC: 4560434; DOI: 10.1371/journal.pone.0137367

  • Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder.

    Schneider A, Puechberty J, Ng BL, Coubes C, Gatinois V, Tournaire M, Girard M, Dumont B, Bouret P, Magnetto J et al.

    American journal of medical genetics. Part A 2015;167A;12;3031-7

    PUBMED: 26333717; DOI: 10.1002/ajmg.a.37350

  • When two is not enough: a CtIP tetramer is required for DNA repair by Homologous Recombination.

    Forment JV, Jackson SP and Pellegrini L

    Nucleus (Austin, Tex.) 2015;6;5;344-8

    PUBMED: 26305173; DOI: 10.1080/19491034.2015.1086050

  • Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data.

    Kushniarevich A, Utevska O, Chuhryaeva M, Agdzhoyan A, Dibirova K, Uktveryte I, Möls M, Mulahasanovic L, Pshenichnov A, Frolova S et al.

    PloS one 2015;10;9;e0135820

    PUBMED: 26332464; PMC: 4558026; DOI: 10.1371/journal.pone.0135820

  • The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.

    Chiang Z, Vastermark A, Punta M, Coggill PC, Mistry J, Finn RD and Saier MH

    Briefings in bioinformatics 2015;16;5;865-72

    PUBMED: 25614388; PMC: 4570203; DOI: 10.1093/bib/bbu053

  • A flow cytometry-based method to simplify the analysis and quantification of protein association to chromatin in mammalian cells.

    Forment JV and Jackson SP

    Nature protocols 2015;10;9;1297-307

    PUBMED: 26226461; PMC: 4743064; DOI: 10.1038/nprot.2015.066

  • Computational assignment of cell-cycle stage from single-cell transcriptome data.

    Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC and Buettner F

    Methods (San Diego, Calif.) 2015;85;54-61

    PUBMED: 26142758; DOI: 10.1016/j.ymeth.2015.06.021

  • Entomological Monitoring and Evaluation: Diverse Transmission Settings of ICEMR Projects Will Require Local and Regional Malaria Elimination Strategies.

    Conn JE, Norris DE, Donnelly MJ, Beebe NW, Burkot TR, Coulibaly MB, Chery L, Eapen A, Keven JB, Kilama M et al.

    The American journal of tropical medicine and hygiene 2015;93;3 Suppl;28-41

    PUBMED: 26259942; PMC: 4574272; DOI: 10.4269/ajtmh.15-0009

  • High Throughput Sequencing Analysis of the Immunoglobulin Heavy Chain Gene from Flow-Sorted B Cell Sub-Populations Define the Dynamics of Follicular Lymphoma Clonal Evolution.

    Carlotti E, Wrench D, Rosignoli G, Marzec J, Sangaralingam A, Hazanov L, Michaeli M, Hallam S, Chaplin T, Iqbal S et al.

    PloS one 2015;10;9;e0134833

    PUBMED: 26325507; PMC: 4556522; DOI: 10.1371/journal.pone.0134833

  • Interplay between Gliotoxin Resistance, Secretion, and the Methyl/Methionine Cycle in Aspergillus fumigatus.

    Owens RA, O'Keeffe G, Smith EB, Dolan SK, Hammel S, Sheridan KJ, Fitzpatrick DA, Keane TM, Jones GW and Doyle S

    Eukaryotic cell 2015;14;9;941-57

    PUBMED: 26150413; PMC: 4551589; DOI: 10.1128/EC.00055-15

  • Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts.

    Kemper K, Krijgsman O, Cornelissen-Steijger P, Shahrabi A, Weeber F, Song JY, Kuilman T, Vis DJ, Wessels LF, Voest EE et al.

    EMBO molecular medicine 2015;7;9;1104-18

    PUBMED: 26105199; PMC: 4568946; DOI: 10.15252/emmm.201404914

  • Looking at Beijing's skyline.

    Jamrozy D and Kallonen T

    Nature reviews. Microbiology 2015;13;9;528

    PUBMED: 26505047

  • Monoclonal Antibodies of a Diverse Isotype Induced by an O-Antigen Glycoconjugate Vaccine Mediate In Vitro and In Vivo Killing of African Invasive Nontyphoidal Salmonella.

    Goh YS, Clare S, Micoli F, Saul A, Mastroeni P and MacLennan CA

    Infection and immunity 2015;83;9;3722-31

    PUBMED: 26169269; PMC: 4534659; DOI: 10.1128/IAI.00547-15

  • Plasmodium Infection Is Associated with Impaired Hepatic Dimethylarginine Dimethylaminohydrolase Activity and Disruption of Nitric Oxide Synthase Inhibitor/Substrate Homeostasis.

    Chertow JH, Alkaitis MS, Nardone G, Ikeda AK, Cunnington AJ, Okebe J, Ebonyi AO, Njie M, Correa S, Jayasooriya S et al.

    PLoS pathogens 2015;11;9;e1005119

    PUBMED: 26407009; PMC: 4583463; DOI: 10.1371/journal.ppat.1005119

  • Plasmodium malariae Malaria: From Monkey to Man?

    Rayner JC

    EBioMedicine 2015;2;9;1023-4

    PUBMED: 26501096; PMC: 4588403; DOI: 10.1016/j.ebiom.2015.08.035

  • ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons.

    May M, Hwang KS, Miles J, Williams C, Niranjan T, Kahler SG, Chiurazzi P, Steindl K, Van Der Spek PJ, Swagemakers S et al.

    Human molecular genetics 2015;24;17;4848-61

    PUBMED: 26056227; PMC: 4527488; DOI: 10.1093/hmg/ddv208

  • Zebrafish models for nemaline myopathy reveal a spectrum of nemaline bodies contributing to reduced muscle function.

    Sztal TE, Zhao M, Williams C, Oorschot V, Parslow AC, Giousoh A, Yuen M, Hall TE, Costin A, Ramm G et al.

    Acta neuropathologica 2015;130;3;389-406

    PUBMED: 25931053; PMC: 4541704; DOI: 10.1007/s00401-015-1430-3

  • An interactive genome browser of association results from the UK10K cohorts project.

    Geihs M, Yan Y, Walter K, Huang J, Memari Y, Min JL, Mead D, UK10K Consortium, Hubbard TJ, Timpson NJ et al.

    Bioinformatics (Oxford, England) 2015;31;24;4029-31

    PUBMED: 26315906; PMC: 4673976; DOI: 10.1093/bioinformatics/btv491

  • A gene expression resource generated by genome-wide lacZ profiling in the mouse.

    Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H et al.

    Disease models & mechanisms 2015;8;11;1467-78

    PUBMED: 26398943; PMC: 4631787; DOI: 10.1242/dmm.021238

  • Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.

    van Dorp L, Balding D, Myers S, Pagani L, Tyler-Smith C, Bekele E, Tarekegn A, Thomas MG, Bradman N and Hellenthal G

    PLoS genetics 2015;11;8;e1005397

    PUBMED: 26291793; PMC: 4546361; DOI: 10.1371/journal.pgen.1005397

  • Facilitating collaboration in rare genetic disorders through effective matchmaking in DECIPHER.

    Chatzimichali EA, Brent S, Hutton B, Perrett D, Wright CF, Bevan AP, Hurles ME, Firth HV and Swaminathan GJ

    Human mutation 2015;36;10;941-9

    PUBMED: 26220709; PMC: 4832335; DOI: 10.1002/humu.22842

  • Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs.

    Wong SF, Agarwal V, Mansfield JH, Denans N, Schwartz MG, Prosser HM, Pourquié O, Bartel DP, Tabin CJ and McGlinn E

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;35;E4884-93

    PUBMED: 26283362; PMC: 4568285; DOI: 10.1073/pnas.1512655112

  • Gene × dietary pattern interactions in obesity: analysis of up to 68 317 adults of European ancestry.

    Nettleton JA, Follis JL, Ngwa JS, Smith CE, Ahmad S, Tanaka T, Wojczynski MK, Voortman T, Lemaitre RN, Kristiansson K et al.

    Human molecular genetics 2015;24;16;4728-38

    PUBMED: 25994509; PMC: 4512626; DOI: 10.1093/hmg/ddv186

  • Novel Insights Into the Protective Role of Hemoglobin S and C Against Plasmodium falciparum Parasitemia.

    Mangano VD, Kabore Y, Bougouma EC, Verra F, Sepulveda N, Bisseye C, Santolamazza F, Avellino P, Tiono AB, Diarra A et al.

    The Journal of infectious diseases 2015;212;4;626-34

    PUBMED: 25712976; PMC: 4512610; DOI: 10.1093/infdis/jiv098

  • Oct-2 forms a complex with Oct-1 on the iNOS promoter and represses transcription by interfering with recruitment of RNA PolII by Oct-1.

    Bentrari F, Chantôme A, Knights A, Jeannin JF and Pance A

    Nucleic acids research 2015;43;20;9757-65

    PUBMED: 26271992; PMC: 4787767; DOI: 10.1093/nar/gkv829

  • Somatic drivers of B-ALL in a model of ETV6-RUNX1; Pax5(+/-) leukemia.

    van der Weyden L, Giotopoulos G, Wong K, Rust AG, Robles-Espinoza CD, Osaki H, Huntly BJ and Adams DJ

    BMC cancer 2015;15;585

    PUBMED: 26269126; PMC: 4542115; DOI: 10.1186/s12885-015-1586-1

  • Essential roles of methionine and S-adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis.

    Berney M, Berney-Meyer L, Wong KW, Chen B, Chen M, Kim J, Wang J, Harris D, Parkhill J, Chan J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;32;10008-13

    PUBMED: 26221021; PMC: 4538671; DOI: 10.1073/pnas.1513033112

  • WAC loss-of-function mutations cause a recognisable syndrome characterised by dysmorphic features, developmental delay and hypotonia and recapitulate 10p11.23 microdeletion syndrome.

    DeSanto C, D'Aco K, Araujo GC, Shannon N, DDD Study, Vernon H, Rahrig A, Monaghan KG, Niu Z, Vitazka P et al.

    Journal of medical genetics 2015;52;11;754-61

    PUBMED: 26264232; DOI: 10.1136/jmedgenet-2015-103069

  • Aberrant splicing of genes involved in haemoglobin synthesis and impaired terminal erythroid maturation in SF3B1 mutated refractory anaemia with ring sideroblasts.

    Conte S, Katayama S, Vesterlund L, Karimi M, Dimitriou M, Jansson M, Mortera-Blanco T, Unneberg P, Papaemmanuil E, Sander B et al.

    British journal of haematology 2015;171;4;478-90

    PUBMED: 26255870; PMC: 4832260; DOI: 10.1111/bjh.13610

  • Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome.

    Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR, Gray KJ, Kiran AM, Molyneux E, French N, Parkhill J et al.

    Infection and immunity 2015;83;10;4165-73

    PUBMED: 26259813; PMC: 4567637; DOI: 10.1128/IAI.00814-15

  • Cell Cycle Rules Pluripotency.

    Vallier L

    Cell stem cell 2015;17;2;131-2

    PUBMED: 26253197; DOI: 10.1016/j.stem.2015.07.019

  • DNMT3A mutations occur early or late in patients with myeloproliferative neoplasms and mutation order influences phenotype.

    Nangalia J, Nice FL, Wedge DC, Godfrey AL, Grinfeld J, Thakker C, Massie CE, Baxter J, Sewell D, Silber Y et al.

    Haematologica 2015;100;11;e438-42

    PUBMED: 26250577; PMC: 4825297; DOI: 10.3324/haematol.2015.129510

  • Global diversity, population stratification, and selection of human copy-number variation.

    Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M et al.

    Science (New York, N.Y.) 2015;349;6253;aab3761

    PUBMED: 26249230; PMC: 4568308; DOI: 10.1126/science.aab3761

  • Runs of Homozygosity: Association with Coronary Artery Disease and Gene Expression in Monocytes and Macrophages.

    Christofidou P, Nelson CP, Nikpay M, Qu L, Li M, Loley C, Debiec R, Braund PS, Denniff M, Charchar FJ et al.

    American journal of human genetics 2015;97;2;228-37

    PUBMED: 26166477; PMC: 4573243; DOI: 10.1016/j.ajhg.2015.06.001

  • Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae.

    Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MT, Maskell DJ et al.

    Veterinary microbiology 2015;178;3-4;279-82

    PUBMED: 26049592; PMC: 4503812; DOI: 10.1016/j.vetmic.2015.05.020

  • High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping.

    Collins JE, Wali N, Sealy IM, Morris JA, White RJ, Leonard SR, Jackson DK, Jones MC, Smerdon NC, Zamora J et al.

    BMC genomics 2015;16;578

    PUBMED: 26238335; PMC: 4524448; DOI: 10.1186/s12864-015-1788-6

  • Multicohort analysis of the maternal age effect on recombination.

    Martin HC, Christ R, Hussin JG, O'Connell J, Gordon S, Mbarek H, Hottenga JJ, McAloney K, Willemsen G, Gasparini P et al.

    Nature communications 2015;6;7846

    PUBMED: 26242864; PMC: 4580993; DOI: 10.1038/ncomms8846

  • Rare coding variants and X-linked loci associated with age at menarche.

    Lunetta KL, Day FR, Sulem P, Ruth KS, Tung JY, Hinds DA, Esko T, Elks CE, Altmaier E, He C et al.

    Nature communications 2015;6;7756

    PUBMED: 26239645; PMC: 4538850; DOI: 10.1038/ncomms8756

  • Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

    Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I et al.

    eLife 2015;4;e07335

    PUBMED: 26238191; PMC: 4522646; DOI: 10.7554/eLife.07335

  • A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed in Echinococcus multilocularis Stem Cells.

    Koziol U, Radio S, Smircich P, Zarowiecki M, Fernández C and Brehm K

    Genome biology and evolution 2015;7;8;2136-53

    PUBMED: 26133390; PMC: 4558846; DOI: 10.1093/gbe/evv126

  • The presence of prolines in the flanking region of an immunodominant HIV-2 gag epitope influences the quality and quantity of the epitope generated.

    Jallow S, Leligdowicz A, Kramer HB, Onyango C, Cotten M, Wright C, Whittle HC, McMichael A, Dong T, Kessler BM and Rowland-Jones SL

    European journal of immunology 2015;45;8;2232-42

    PUBMED: 26018465; DOI: 10.1002/eji.201545451

  • An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes.

    Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TM, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA et al.

    Nature cell biology 2015;17;8;1074-87

    PUBMED: 26167768; PMC: 4536769; DOI: 10.1038/ncb3201

  • 5-Formylcytosine can be a stable DNA modification in mammals.

    Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, Murrell A and Balasubramanian S

    Nature chemical biology 2015;11;8;555-7

    PUBMED: 26098680; DOI: 10.1038/nchembio.1848

  • Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci.

    Demerath EW, Guan W, Grove ML, Aslibekyan S, Mendelson M, Zhou YH, Hedman ÅK, Sandling JK, Li LA, Irvin MR et al.

    Human molecular genetics 2015;24;15;4464-79

    PUBMED: 25935004; PMC: 4492394; DOI: 10.1093/hmg/ddv161

  • Genetic characterization of three qnrS1-harbouring multidrug-resistance plasmids and qnrS1-containing transposons circulating in Ho Chi Minh City, Vietnam.

    Le V, Nhu NT, Cerdeno-Tarraga A, Campbell JI, Tuyen HT, Nhu Tdo H, Tam PT, Schultsz C, Thwaites G, Thomson NR and Baker S

    Journal of medical microbiology 2015;64;8;869-78

    PUBMED: 26272054; PMC: 4635468; DOI: 10.1099/jmm.0.000100

  • Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax.

    Jackson AP, Goyard S, Xia D, Foth BJ, Sanders M, Wastling JM, Minoprio P and Berriman M

    PLoS neglected tropical diseases 2015;9;8;e0003975

    PUBMED: 26266535; PMC: 4534299; DOI: 10.1371/journal.pntd.0003975

  • Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae.

    Bossé JT, Li Y, Walker S, Atherton T, Fernandez Crespo R, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Oshota O et al.

    The Journal of antimicrobial chemotherapy 2015;70;8;2217-22

    PUBMED: 25957382; PMC: 4500777; DOI: 10.1093/jac/dkv121

  • Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation.

    Powell N, Lo JW, Biancheri P, Vossenkämper A, Pantazi E, Walker AW, Stolarczyk E, Ammoscato F, Goldberg R, Scott P et al.

    Gastroenterology 2015;149;2;456-67.e15

    PUBMED: 25917784; PMC: 4539618; DOI: 10.1053/j.gastro.2015.04.017

  • Metabolomic identification of a novel pathway of blood pressure regulation involving hexadecanedioate.

    Menni C, Graham D, Kastenmüller G, Alharbi NH, Alsanosi SM, McBride M, Mangino M, Titcombe P, Shin SY, Psatha M et al.

    Hypertension (Dallas, Tex. : 1979) 2015;66;2;422-9

    PUBMED: 26034203; PMC: 4490909; DOI: 10.1161/HYPERTENSIONAHA.115.05544

  • Monoamine Oxidase A gene polymorphisms and self reported aggressive behaviour in a Pakistani ethnic group.

    Shah SS, Mohyuddin A, Colonna V, Mehdi SQ and Ayub Q

    JPMA. The Journal of the Pakistan Medical Association 2015;65;8;818-24

    PUBMED: 26228323

  • Mouse models of colorectal cancer as preclinical models.

    McIntyre RE, Buczacki SJ, Arends MJ and Adams DJ

    BioEssays : news and reviews in molecular, cellular and developmental biology 2015;37;8;909-20

    PUBMED: 26115037; PMC: 4755199; DOI: 10.1002/bies.201500032

  • Recessive nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum is caused by homozygous protein-truncating mutations of WDR73.

    Jinks RN, Puffenberger EG, Baple E, Harding B, Crino P, Fogo AB, Wenger O, Xin B, Koehler AE, McGlincy MH et al.

    Brain : a journal of neurology 2015;138;Pt 8;2173-90

    PUBMED: 26070982; PMC: 4511861; DOI: 10.1093/brain/awv153

  • Widespread Reassortment Shapes the Evolution and Epidemiology of Bluetongue Virus following European Invasion.

    Nomikou K, Hughes J, Wash R, Kellam P, Breard E, Zientara S, Palmarini M, Biek R and Mertens P

    PLoS pathogens 2015;11;8;e1005056

    PUBMED: 26252219; PMC: 4529188; DOI: 10.1371/journal.ppat.1005056

  • Phenotype-driven strategies for exome prioritization of human Mendelian disease genes.

    Smedley D and Robinson PN

    Genome medicine 2015;7;1;81

    PUBMED: 26229552; PMC: 4520011; DOI: 10.1186/s13073-015-0199-2

  • Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription.

    Alasoo K, Martinez FO, Hale C, Gordon S, Powrie F, Dougan G, Mukhopadhyay S and Gaffney DJ

    Scientific reports 2015;5;12524

    PUBMED: 26224331; PMC: 4519778; DOI: 10.1038/srep12524

  • Where Next for Genetics and Genomics?

    Tyler-Smith C, Yang H, Landweber LF, Dunham I, Knoppers BM, Donnelly P, Mardis ER, Snyder M and McVean G

    PLoS biology 2015;13;7;e1002216

    PUBMED: 26225775; PMC: 4520474; DOI: 10.1371/journal.pbio.1002216

  • Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes.

    Judge K, Harris SR, Reuter S, Parkhill J and Peacock SJ

    The Journal of antimicrobial chemotherapy 2015;70;10;2775-8

    PUBMED: 26221019; PMC: 4566964; DOI: 10.1093/jac/dkv206

  • Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

    de Angelis MH, Nicholson G, Selloum M, White J, Morgan H, Ramirez-Solis R, Sorg T, Wells S, Fuchs H, Fray M et al.

    Nature genetics 2015;47;9;969-978

    PUBMED: 26214591; PMC: 4564951; DOI: 10.1038/ng.3360

  • Regulation of mitochondrial morphology and function by stearoylation of TFR1.

    Senyilmaz D, Virtue S, Xu X, Tan CY, Griffin JL, Miller AK, Vidal-Puig A and Teleman AA

    Nature 2015;525;7567;124-8

    PUBMED: 26214738; PMC: 4561519; DOI: 10.1038/nature14601

  • Principles and application of LIMS in mouse clinics.

    Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;467-81

    PUBMED: 26208973; PMC: 4602070; DOI: 10.1007/s00335-015-9586-7

  • Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells.

    Latos PA, Goncalves A, Oxley D, Mohammed H, Turro E and Hemberger M

    Nature communications 2015;6;7776

    PUBMED: 26206133; PMC: 4525203; DOI: 10.1038/ncomms8776

  • Precision medicine: Look to the mice.

    Lloyd KC, Meehan T, Beaudet A, Murray S, Svenson K, McKerlie C, West D, Morse I, Parkinson H, Brown S et al.

    Science (New York, N.Y.) 2015;349;6246;390

    PUBMED: 26206923; DOI: 10.1126/science.349.6246.390-a

  • Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013.

    Watson SJ, Langat P, Reid SM, Lam TT, Cotten M, Kelly M, Van Reeth K, Qiu Y, Simon G, Bonin E et al.

    Journal of virology 2015;89;19;9920-31

    PUBMED: 26202246; PMC: 4577897; DOI: 10.1128/JVI.00840-15

  • POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

    Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS et al.

    Science (New York, N.Y.) 2015;349;6250;aab3884

    PUBMED: 26198033; PMC: 4733658; DOI: 10.1126/science.aab3884

  • Potent organo-osmium compound shifts metabolism in epithelial ovarian cancer cells.

    Hearn JM, Romero-Canelón I, Munro AF, Fu Y, Pizarro AM, Garnett MJ, McDermott U, Carragher NO and Sadler PJ

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;29;E3800-5

    PUBMED: 26162681; PMC: 4517206; DOI: 10.1073/pnas.1500925112

  • Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.

    Liu JZ, van Sommeren S, Huang H, Ng SC, Alberts R, Takahashi A, Ripke S, Lee JC, Jostins L, Shah T et al.

    Nature genetics 2015;47;9;979-986

    PUBMED: 26192919; PMC: 4881818; DOI: 10.1038/ng.3359

  • Basigin is a druggable target for host-oriented antimalarial interventions.

    Zenonos ZA, Dummler SK, Müller-Sienerth N, Chen J, Preiser PR, Rayner JC and Wright GJ

    The Journal of experimental medicine 2015;212;8;1145-51

    PUBMED: 26195724; PMC: 4516795; DOI: 10.1084/jem.20150032

  • Roary: rapid large-scale prokaryote pan genome analysis.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA and Parkhill J

    Bioinformatics (Oxford, England) 2015;31;22;3691-3

    PUBMED: 26198102; PMC: 4817141; DOI: 10.1093/bioinformatics/btv421

  • Creating reference gene annotation for the mouse C57BL6/J genome assembly.

    Mudge JM and Harrow J

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;366-78

    PUBMED: 26187010; PMC: 4602055; DOI: 10.1007/s00335-015-9583-x

  • A putative, novel coli surface antigen 8B (CS8B) of enterotoxigenic Escherichia coli.

    Njoroge SM, Boinett CJ, Madé LF, Ouko TT, Fèvre EM, Thomson NR and Kariuki S

    Pathogens and disease 2015;73;7

    PUBMED: 26187892; PMC: 4535451; DOI: 10.1093/femspd/ftv047

  • Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and Legal Requirements.

    Sariyar M, Schluender I, Smee C and Suhr S

    Biopreservation and biobanking 2015;13;4;263-70

    PUBMED: 26186169; PMC: 4559154; DOI: 10.1089/bio.2015.0014

  • Blastocyst genotyping for quality control of mouse mutant archives: an ethical and economical approach.

    Scavizzi F, Ryder E, Newman S, Raspa M, Gleeson D, Wardle-Jones H, Montoliu L, Fernandez A, Dessain ML, Larrigaldie V et al.

    Transgenic research 2015;24;5;921-7

    PUBMED: 26178246; PMC: 4569667; DOI: 10.1007/s11248-015-9897-1

  • Comparison of genomic signatures of selection on Plasmodium falciparum between different regions of a country with high malaria endemicity.

    Duffy CW, Assefa SA, Abugri J, Amoako N, Owusu-Agyei S, Anyorigiya T, MacInnis B, Kwiatkowski DP, Conway DJ and Awandare GA

    BMC genomics 2015;16;527

    PUBMED: 26173872; PMC: 4502944; DOI: 10.1186/s12864-015-1746-3

  • Bcl11a (Ctip1) Controls Migration of Cortical Projection Neurons through Regulation of Sema3c.

    Wiegreffe C, Simon R, Peschkes K, Kling C, Strehle M, Cheng J, Srivatsa S, Liu P, Jenkins NA, Copeland NG et al.

    Neuron 2015;87;2;311-25

    PUBMED: 26182416; DOI: 10.1016/j.neuron.2015.06.023

  • Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites.

    Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A et al.

    eLife 2015;4;e06974

    PUBMED: 26175406; PMC: 4501334; DOI: 10.7554/eLife.06974

  • Generation of Distal Airway Epithelium from Multipotent Human Foregut Stem Cells.

    Hannan NR, Sampaziotis F, Segeritz CP, Hanley NA and Vallier L

    Stem cells and development 2015;24;14;1680-90

    PUBMED: 25758640; DOI: 10.1089/scd.2014.0512

  • Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.

    Sealey KL, Harris SR, Fry NK, Hurst LD, Gorringe AR, Parkhill J and Preston A

    The Journal of infectious diseases 2015;212;2;294-301

    PUBMED: 25489002; DOI: 10.1093/infdis/jiu665

  • Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom.

    Turner CE, Abbott J, Lamagni T, Holden MT, David S, Jones MD, Game L, Efstratiou A and Sriskandan S

    mBio 2015;6;4;e00622

    PUBMED: 26173696; PMC: 4502227; DOI: 10.1128/mBio.00622-15

  • B56δ-related protein phosphatase 2A dysfunction identified in patients with intellectual disability.

    Houge G, Haesen D, Vissers LE, Mehta S, Parker MJ, Wright M, Vogt J, McKee S, Tolmie JL, Cordeiro N et al.

    The Journal of clinical investigation 2015;125;8;3051-62

    PUBMED: 26168268; PMC: 4623570; DOI: 10.1172/JCI79860

  • Cholangiocytes derived from human induced pluripotent stem cells for disease modeling and drug validation.

    Sampaziotis F, de Brito MC, Madrigal P, Bertero A, Saeb-Parsy K, Soares FAC, Schrumpf E, Melum E, Karlsen TH, Bradley JA et al.

    Nature biotechnology 2015;33;8;845-852

    PUBMED: 26167629; PMC: 4768345; DOI: 10.1038/nbt.3275

  • Genome watch: The chronicles of virus-host affairs.

    Langat P and Petrova V

    Nature reviews. Microbiology 2015;13;8;460

    PUBMED: 26165707; DOI: 10.1038/nrmicro3529

  • Data analysis: Create a cloud commons.

    Stein LD, Knoppers BM, Campbell P, Getz G and Korbel JO

    Nature 2015;523;7559;149-51

    PUBMED: 26156357; DOI: 10.1038/523149a

  • Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection.

    Harris SR, Robinson C, Steward KF, Webb KS, Paillot R, Parkhill J, Holden MT and Waller AS

    Genome research 2015;25;9;1360-71

    PUBMED: 26160165; PMC: 4561494; DOI: 10.1101/gr.189803.115

  • Calcium Builds Strong Host-Parasite Interactions.

    Billker O and Rayner JC

    Cell host & microbe 2015;18;1;9-10

    PUBMED: 26159715; DOI: 10.1016/j.chom.2015.06.012

  • MicroRNA as Type I Interferon-Regulated Transcripts and Modulators of the Innate Immune Response.

    Forster SC, Tate MD and Hertzog PJ

    Frontiers in immunology 2015;6;334

    PUBMED: 26217335; PMC: 4495342; DOI: 10.3389/fimmu.2015.00334

  • Strategies for fine-mapping complex traits.

    Spain SL and Barrett JC

    Human molecular genetics 2015;24;R1;R111-9

    PUBMED: 26157023; PMC: 4572002; DOI: 10.1093/hmg/ddv260

  • PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.

    Kurbatova N, Mason JC, Morgan H, Meehan TF and Karp NA

    PloS one 2015;10;7;e0131274

    PUBMED: 26147094; PMC: 4493137; DOI: 10.1371/journal.pone.0131274

  • A Synergistic Interaction between Chk1- and MK2 Inhibitors in KRAS-Mutant Cancer.

    Dietlein F, Kalb B, Jokic M, Noll EM, Strong A, Tharun L, Ozretić L, Künstlinger H, Kambartel K, Randerath WJ et al.

    Cell 2015;162;1;146-59

    PUBMED: 26140595; DOI: 10.1016/j.cell.2015.05.053

  • Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci.

    Trynka G, Westra HJ, Slowikowski K, Hu X, Xu H, Stranger BE, Klein RJ, Han B and Raychaudhuri S

    American journal of human genetics 2015;97;1;139-52

    PUBMED: 26140449; PMC: 4572568; DOI: 10.1016/j.ajhg.2015.05.016

  • The Bangladesh Risk of Acute Vascular Events (BRAVE) Study: objectives and design.

    Chowdhury R, Alam DS, Fakir II, Adnan SD, Naheed A, Tasmin I, Monower MM, Hossain F, Hossain FM, Rahman MM et al.

    European journal of epidemiology 2015;30;7;577-87

    PUBMED: 25930055; PMC: 4516898; DOI: 10.1007/s10654-015-0037-2

  • Analysis of mutational signatures in exomes from B-cell lymphoma cell lines suggest APOBEC3 family members to be involved in the pathogenesis of primary effusion lymphoma.

    Wagener R, Alexandrov LB, Montesinos-Rongen M, Schlesner M, Haake A, Drexler HG, Richter J, Bignell GR, McDermott U and Siebert R

    Leukemia 2015;29;7;1612-5

    PUBMED: 25650088; DOI: 10.1038/leu.2015.22

  • Characterization of pre-antibiotic era Klebsiella pneumoniae isolates with respect to antibiotic/disinfectant susceptibility and virulence in Galleria mellonella.

    Wand ME, Baker KS, Benthall G, McGregor H, McCowen JW, Deheer-Graham A and Sutton JM

    Antimicrobial agents and chemotherapy 2015;59;7;3966-72

    PUBMED: 25896708; PMC: 4468732; DOI: 10.1128/AAC.05009-14

  • Design and validation of a qPCR assay for accurate detection and initial serogrouping of Legionella pneumophila in clinical specimens by the ESCMID Study Group for Legionella Infections (ESGLI).

    Mentasti M, Kese D, Echahidi F, Uldum SA, Afshar B, David S, Mrazek J, De Mendonça R, Harrison TG and Chalker VJ

    European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2015;34;7;1387-93

    PUBMED: 25851812; DOI: 10.1007/s10096-015-2363-4

  • Dietary Intake, FTO Genetic Variants, and Adiposity: A Combined Analysis of Over 16,000 Children and Adolescents.

    Qi Q, Downer MK, Kilpeläinen TO, Taal HR, Barton SJ, Ntalla I, Standl M, Boraska V, Huikari V, Kiefte-de Jong JC et al.

    Diabetes 2015;64;7;2467-76

    PUBMED: 25720386; PMC: 4876751; DOI: 10.2337/db14-1629

  • Directional dominance on stature and cognition in diverse human populations.

    Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, Jackson AU, Schurmann C, Smith AV, Zhang W et al.

    Nature 2015;523;7561;459-462

    PUBMED: 26131930; PMC: 4516141; DOI: 10.1038/nature14618

  • Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

    Horikoshi M, Mӓgi R, van de Bunt M, Surakka I, Sarin AP, Mahajan A, Marullo L, Thorleifsson G, Hӓgg S, Hottenga JJ et al.

    PLoS genetics 2015;11;7;e1005230

    PUBMED: 26132169; PMC: 4488845; DOI: 10.1371/journal.pgen.1005230

  • Genetic susceptibility to invasive Salmonella disease.

    Gilchrist JJ, MacLennan CA and Hill AV

    Nature reviews. Immunology 2015;15;7;452-63

    PUBMED: 26109132; DOI: 10.1038/nri3858

  • Genome watch. Adaptation: it's a bug's race.

    Wangwiwatsin A and Protasio AV

    Nature reviews. Microbiology 2015;13;7;401

    PUBMED: 26075359; DOI: 10.1038/nrmicro3514

  • Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses.

    Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hoffman LR, Carroll MP, Parkhill J, Bruce KD and van der Gast CJ

    Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2015;14;4;464-7

    PUBMED: 25459563; PMC: 4793934; DOI: 10.1016/j.jcf.2014.10.004

  • Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment.

    Trampush JW, Lencz T, Knowles E, Davies G, Guha S, Pe'er I, Liewald DC, Starr JM, Djurovic S, Melle I et al.

    American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2015;168B;5;363-73

    PUBMED: 25951819; PMC: 4500051; DOI: 10.1002/ajmg.b.32319

  • Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia.

    Swaminathan S, Klemm L, Park E, Papaemmanuil E, Ford A, Kweon SM, Trageser D, Hasselfeld B, Henke N, Mooster J et al.

    Nature immunology 2015;16;7;766-74

    PUBMED: 25985233; PMC: 4475638; DOI: 10.1038/ni.3160

  • Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder.

    Genetics of Personality Consortium, de Moor MH, van den Berg SM, Verweij KJ, Krueger RF, Luciano M, Arias Vasquez A, Matteson LK, Derringer J, Esko T et al.

    JAMA psychiatry 2015;72;7;642-50

    PUBMED: 25993607; PMC: 4667957; DOI: 10.1001/jamapsychiatry.2015.0554

  • Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

    Panagea T, Pincus DH, Grogono D, Jones M, Bryant J, Parkhill J, Floto RA and Gilligan P

    Journal of clinical microbiology 2015;53;7;2355-8

    PUBMED: 25948607; PMC: 4473197; DOI: 10.1128/JCM.00494-15

  • Nonadditive Effects of Genes in Human Metabolomics.

    Tsepilov YA, Shin SY, Soranzo N, Spector TD, Prehn C, Adamski J, Kastenmüller G, Wang-Sattler R, Strauch K, Gieger C et al.

    Genetics 2015;200;3;707-18

    PUBMED: 25977471; PMC: 4512538; DOI: 10.1534/genetics.115.175760

  • Pathway and network analysis of cancer genomes.

    Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C et al.

    Nature methods 2015;12;7;615-621

    PUBMED: 26125594; PMC: 4717906; DOI: 10.1038/nmeth.3440

  • Potential of human induced pluripotent stem cells in studies of liver disease.

    Sampaziotis F, Segeritz CP and Vallier L

    Hepatology (Baltimore, Md.) 2015;62;1;303-11

    PUBMED: 25502113; DOI: 10.1002/hep.27651

  • The genomic evolution of human prostate cancer.

    Mitchell T and Neal DE

    British journal of cancer 2015;113;2;193-8

    PUBMED: 26125442; PMC: 4506396; DOI: 10.1038/bjc.2015.234

  • The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.

    Adams DJ, Doran AG, Lilue J and Keane TM

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;403-12

    PUBMED: 26123534; DOI: 10.1007/s00335-015-9579-6

  • Deubiquitinase MYSM1 Is Essential for Normal Fetal Liver Hematopoiesis and for the Maintenance of Hematopoietic Stem Cells in Adult Bone Marrow.

    Förster M, Belle JI, Petrov JC, Ryder EJ, Clare S and Nijnik A

    Stem cells and development 2015;24;16;1865-77

    PUBMED: 26125289; DOI: 10.1089/scd.2015.0058

  • Disease progression despite protective HLA expression in an HIV-infected transmission pair.

    Brener J, Gall A, Batorsky R, Riddell L, Buus S, Leitman E, Kellam P, Allen T, Goulder P and Matthews PC

    Retrovirology 2015;12;55

    PUBMED: 26123575; PMC: 4487201; DOI: 10.1186/s12977-015-0179-z

  • GENE SILENCING. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells.

    Tchasovnikarova IA, Timms RT, Matheson NJ, Wals K, Antrobus R, Göttgens B, Dougan G, Dawson MA and Lehner PJ

    Science (New York, N.Y.) 2015;348;6242;1481-5

    PUBMED: 26022416; PMC: 4487827; DOI: 10.1126/science.aaa7227

  • Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.

    Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI and Logan DW

    Scientific reports 2015;5;11487

    PUBMED: 26108469; PMC: 4480006; DOI: 10.1038/srep11487

  • Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates.

    Moore S, Miwanda B, Sadji AY, Thefenne H, Jeddi F, Rebaudet S, de Boeck H, Bidjada B, Depina JJ, Bompangue D et al.

    PLoS neglected tropical diseases 2015;9;6;e0003817

    PUBMED: 26110870; PMC: 4482140; DOI: 10.1371/journal.pntd.0003817

  • Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

    Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C, Bradley P, Iqbal Z, Feuerriegel S, Niehaus KE, Wilson DJ et al.

    The Lancet. Infectious diseases 2015;15;10;1193-1202

    PUBMED: 26116186; PMC: 4579482; DOI: 10.1016/S1473-3099(15)00062-6

  • Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.

    Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;27;E3574-81

    PUBMED: 26100894; PMC: 4500264; DOI: 10.1073/pnas.1501049112

  • Subclonal diversification of primary breast cancer revealed by multiregion sequencing.

    Yates LR, Gerstung M, Knappskog S, Desmedt C, Gundem G, Van Loo P, Aas T, Alexandrov LB, Larsimont D, Davies H et al.

    Nature medicine 2015;21;7;751-9

    PUBMED: 26099045; PMC: 4500826; DOI: 10.1038/nm.3886

  • High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children.

    Kamng'ona AW, Hinds J, Bar-Zeev N, Gould KA, Chaguza C, Msefula C, Cornick JE, Kulohoma BW, Gray K, Bentley SD et al.

    BMC infectious diseases 2015;15;234

    PUBMED: 26088623; PMC: 4474563; DOI: 10.1186/s12879-015-0980-2

  • Antimicrobial resistance and management of invasive Salmonella disease.

    Kariuki S, Gordon MA, Feasey N and Parry CM

    Vaccine 2015;33 Suppl 3;C21-9

    PUBMED: 25912288; PMC: 4469558; DOI: 10.1016/j.vaccine.2015.03.102

  • A novel multiple-stage antimalarial agent that inhibits protein synthesis.

    Baragaña B, Hallyburton I, Lee MC, Norcross NR, Grimaldi R, Otto TD, Proto WR, Blagborough AM, Meister S, Wirjanata G et al.

    Nature 2015;522;7556;315-20

    PUBMED: 26085270; PMC: 4700930; DOI: 10.1038/nature14451

  • Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

    Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R and Harrow J

    BMC genomics 2015;16 Suppl 8;S2

    PUBMED: 26110515; PMC: 4502323; DOI: 10.1186/1471-2164-16-S8-S2

  • Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015.

    Hadjirin NF, Lay EM, Paterson GK, Harrison EM, Peacock SJ, Parkhill J, Zadoks RN and Holmes MA

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2015;20;24

    PUBMED: 26111237; PMC: 4841384; DOI: 10.2807/1560-7917.es2015.20.24.21156

  • Artificial membrane-binding proteins stimulate oxygenation of stem cells during engineering of large cartilage tissue.

    Armstrong JPK, Shakur R, Horne JP, Dickinson SC, Armstrong CT, Lau K, Kadiwala J, Lowe R, Seddon A, Mann S et al.

    Nature communications 2015;6;7405

    PUBMED: 26080734; PMC: 4557285; DOI: 10.1038/ncomms8405

  • Genetic Stabilization of the Drug-Resistant PMEN1 Pneumococcus Lineage by Its Distinctive DpnIII Restriction-Modification System.

    Eutsey RA, Powell E, Dordel J, Salter SJ, Clark TA, Korlach J, Ehrlich GD and Hiller NL

    mBio 2015;6;3;e00173

    PUBMED: 26081630; PMC: 4471560; DOI: 10.1128/mBio.00173-15

  • De novo, heterozygous, loss-of-function mutations in SYNGAP1 cause a syndromic form of intellectual disability.

    Parker MJ, Fryer AE, Shears DJ, Lachlan KL, McKee SA, Magee AC, Mohammed S, Vasudevan PC, Park SM, Benoit V et al.

    American journal of medical genetics. Part A 2015;167A;10;2231-7

    PUBMED: 26079862; PMC: 4744742; DOI: 10.1002/ajmg.a.37189

  • Complete Genome Sequence of Bordetella pertussis D420.

    Boinett CJ, Harris SR, Langridge GC, Trainor EA, Merkel TJ and Parkhill J

    Genome announcements 2015;3;3

    PUBMED: 26067980; PMC: 4463544; DOI: 10.1128/genomeA.00657-15

  • Expansion of the HSFY gene family in pig lineages : HSFY expansion in suids.

    Skinner BM, Lachani K, Sargent CA, Yang F, Ellis P, Hunt T, Fu B, Louzada S, Churcher C, Tyler-Smith C and Affara NA

    BMC genomics 2015;16;442

    PUBMED: 26055083; PMC: 4460688; DOI: 10.1186/s12864-015-1650-x

  • A minimally invasive, lentiviral based method for the rapid and sustained genetic manipulation of renal tubules.

    Espana-Agusti J, Tuveson DA, Adams DJ and Matakidou A

    Scientific reports 2015;5;11061

    PUBMED: 26046460; PMC: 4457145; DOI: 10.1038/srep11061

  • P-selectin is a host receptor for Plasmodium MSP7 ligands.

    Perrin AJ, Bartholdson SJ and Wright GJ

    Malaria journal 2015;14;238

    PUBMED: 26045295; PMC: 4478713; DOI: 10.1186/s12936-015-0750-z

  • Cyclic Regulation of Sensory Perception by a Female Hormone Alters Behavior.

    Dey S, Chamero P, Pru JK, Chien MS, Ibarra-Soria X, Spencer KR, Logan DW, Matsunami H, Peluso JJ and Stowers L

    Cell 2015;161;6;1334-44

    PUBMED: 26046438; PMC: 4501503; DOI: 10.1016/j.cell.2015.04.052

  • Draft genomes of Shigella strains used by the STOPENTERICS consortium.

    Rossi O, Baker KS, Phalipon A, Weill FX, Citiulo F, Sansonetti P, Gerke C and Thomson NR

    Gut pathogens 2015;7;14

    PUBMED: 26042182; PMC: 4454270; DOI: 10.1186/s13099-015-0061-5

  • Forget the Parents: Epigenetic Reprogramming in Human Germ Cells.

    von Meyenn F and Reik W

    Cell 2015;161;6;1248-51

    PUBMED: 26046435; DOI: 10.1016/j.cell.2015.05.039

  • Defining the Roles of TcdA and TcdB in Localized Gastrointestinal Disease, Systemic Organ Damage, and the Host Response during Clostridium difficile Infections.

    Carter GP, Chakravorty A, Pham Nguyen TA, Mileto S, Schreiber F, Li L, Howarth P, Clare S, Cunningham B, Sambol SP et al.

    mBio 2015;6;3;e00551

    PUBMED: 26037121; PMC: 4453007; DOI: 10.1128/mBio.00551-15

  • Investigation of GRIN2A in common epilepsy phenotypes.

    Lal D, Steinbrücker S, Schubert J, Sander T, Becker F, Weber Y, Lerche H, Thiele H, Krause R, Lehesjoki AE et al.

    Epilepsy research 2015;115;95-9

    PUBMED: 26220384; DOI: 10.1016/j.eplepsyres.2015.05.010

  • The impact of low-frequency and rare variants on lipid levels.

    Surakka I, Horikoshi M, Mägi R, Sarin AP, Mahajan A, Lagou V, Marullo L, Ferreira T, Miraglio B, Timonen S et al.

    Nature genetics 2015;47;6;589-97

    PUBMED: 25961943; DOI: 10.1038/ng.3300

  • ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.

    Cybis GB, Sinsheimer JS, Bedford T, Mather AE, Lemey P and Suchard MA

    The annals of applied statistics 2015;9;2;969-991

    PUBMED: 27053974; PMC: 4820077; DOI: 10.1214/15-AOAS821

  • Bcl11b is essential for group 2 innate lymphoid cell development.

    Walker JA, Oliphant CJ, Englezakis A, Yu Y, Clare S, Rodewald HR, Belz G, Liu P, Fallon PG and McKenzie AN

    The Journal of experimental medicine 2015;212;6;875-82

    PUBMED: 25964370; PMC: 4451131; DOI: 10.1084/jem.20142224

  • Ceftriaxone-resistant Salmonella enterica serotype typhimurium sequence type 313 from Kenyan patients is associated with the blaCTX-M-15 gene on a novel IncHI2 plasmid.

    Kariuki S, Okoro C, Kiiru J, Njoroge S, Omuse G, Langridge G, Kingsley RA, Dougan G and Revathi G

    Antimicrobial agents and chemotherapy 2015;59;6;3133-9

    PUBMED: 25779570; PMC: 4432211; DOI: 10.1128/AAC.00078-15

  • Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR.

    Vizoso M, Ferreira HJ, Lopez-Serra P, Carmona FJ, Martínez-Cardús A, Girotti MR, Villanueva A, Guil S, Moutinho C, Liz J et al.

    Nature medicine 2015;21;7;741-50

    PUBMED: 26030178; PMC: 4968631; DOI: 10.1038/nm.3863

  • Fine mapping in the MHC region accounts for 18% additional genetic risk for celiac disease.

    Gutierrez-Achury J, Zhernakova A, Pulit SL, Trynka G, Hunt KA, Romanos J, Raychaudhuri S, van Heel DA, Wijmenga C and de Bakker PI

    Nature genetics 2015;47;6;577-8

    PUBMED: 25894500; PMC: 4449296; DOI: 10.1038/ng.3268

  • Genetic and hypoxic alterations of the microRNA-210-ISCU1/2 axis promote iron-sulfur deficiency and pulmonary hypertension.

    White K, Lu Y, Annis S, Hale AE, Chau BN, Dahlman JE, Hemann C, Opotowsky AR, Vargas SO, Rosas I et al.

    EMBO molecular medicine 2015;7;6;695-713

    PUBMED: 25825391; PMC: 4459813; DOI: 10.15252/emmm.201404511

  • Genetic background of extreme violent behavior.

    Tiihonen J, Rautiainen MR, Ollila HM, Repo-Tiihonen E, Virkkunen M, Palotie A, Pietiläinen O, Kristiansson K, Joukamaa M, Lauerma H et al.

    Molecular psychiatry 2015;20;6;786-92

    PUBMED: 25349169; PMC: 4776744; DOI: 10.1038/mp.2014.130

  • Genetics in PSC: what do the "risk genes" teach us?

    Folseraas T, Liaskou E, Anderson CA and Karlsen TH

    Clinical reviews in allergy & immunology 2015;48;2-3;154-64

    PUBMED: 24736995; DOI: 10.1007/s12016-014-8417-z

  • Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon.

    Bolz M, Bratschi MW, Kerber S, Minyem JC, Um Boock A, Vogel M, Bayi PF, Junghanss T, Brites D, Harris SR et al.

    PLoS neglected tropical diseases 2015;9;6;e0003802

    PUBMED: 26046531; PMC: 4457821; DOI: 10.1371/journal.pntd.0003802

  • Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritis.

    Carden S, Okoro C, Dougan G and Monack D

    Pathogens and disease 2015;73;4

    PUBMED: 25808600; PMC: 4399442; DOI: 10.1093/femspd/ftu023

  • Off-target mutations are rare in Cas9-modified mice.

    Iyer V, Shen B, Zhang W, Hodgkins A, Keane T, Huang X and Skarnes WC

    Nature methods 2015;12;6;479

    PUBMED: 26020497; DOI: 10.1038/nmeth.3408

  • Oral Wild-Type Salmonella Typhi Challenge Induces Activation of Circulating Monocytes and Dendritic Cells in Individuals Who Develop Typhoid Disease.

    Toapanta FR, Bernal PJ, Fresnay S, Darton TC, Jones C, Waddington CS, Blohmke CJ, Dougan G, Angus B, Levine MM et al.

    PLoS neglected tropical diseases 2015;9;6;e0003837

    PUBMED: 26065687; PMC: 4465829; DOI: 10.1371/journal.pntd.0003837

  • Structural variation on the human Y chromosome from population-scale resequencing.

    Espinosa JR, Ayub Q, Chen Y, Xue Y and Tyler-Smith C

    Croatian medical journal 2015;56;3;194-207

    PUBMED: 26088844; PMC: 4500966; DOI: 10.3325/cmj.2015.56.194

  • There's no place like home.

    Mather AE

    Nature reviews. Microbiology 2015;13;6;331

    PUBMED: 25978705; DOI: 10.1038/nrmicro3497

  • Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

    Allum F, Shao X, Guénard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman ÅK et al.

    Nature communications 2015;6;7211

    PUBMED: 26021296; PMC: 4544751; DOI: 10.1038/ncomms8211

  • Quantitative evaluation of the immunodeficiency of a mouse strain by tumor engraftments.

    Ye W, Jiang Z, Li GX, Xiao Y, Lin S, Lai Y, Wang S, Li B, Jia B, Li Y et al.

    Journal of hematology & oncology 2015;8;59

    PUBMED: 26022250; PMC: 4478639; DOI: 10.1186/s13045-015-0156-y

  • Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.

    Baker KS, Parkhill J and Thomson NR

    Genome announcements 2015;3;3

    PUBMED: 26021915; PMC: 4447900; DOI: 10.1128/genomeA.00393-15

  • Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

    Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, Chen Y, Xue Y, Haber M, Ekong R, Oljira T et al.

    American journal of human genetics 2015;96;6;986-91

    PUBMED: 26027499; PMC: 4457944; DOI: 10.1016/j.ajhg.2015.04.019

  • As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.

    Hargreaves KR, Otieno JR, Thanki A, Blades MJ, Millard AD, Browne HP, Lawley TD and Clokie MR

    Genome biology and evolution 2015;7;7;1842-55

    PUBMED: 26019165; PMC: 4524475; DOI: 10.1093/gbe/evv094

  • A First Generation Comparative Chromosome Map between Guinea Pig (Cavia porcellus) and Humans.

    Romanenko SA, Perelman PL, Trifonov VA, Serdyukova NA, Li T, Fu B, O'Brien PC, Ng BL, Nie W, Liehr T et al.

    PloS one 2015;10;5;e0127937

    PUBMED: 26010445; PMC: 4444286; DOI: 10.1371/journal.pone.0127937

  • Shared genetic basis for migraine and ischemic stroke: A genome-wide analysis of common variants.

    Malik R, Freilinger T, Winsvold BS, Anttila V, Vander Heiden J, Traylor M, de Vries B, Holliday EG, Terwindt GM, Sturm J et al.

    Neurology 2015;84;21;2132-45

    PUBMED: 25934857; PMC: 4451048; DOI: 10.1212/WNL.0000000000001606

  • Genetic stability of pneumococcal isolates during 35 days of human experimental carriage.

    Gladstone RA, Gritzfeld JF, Coupland P, Gordon SB and Bentley SD

    Vaccine 2015;33;29;3342-5

    PUBMED: 26006086; PMC: 4503797; DOI: 10.1016/j.vaccine.2015.05.021

  • Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.

    Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM et al.

    Science (New York, N.Y.) 2015;348;6237;880-6

    PUBMED: 25999502; PMC: 4471149; DOI: 10.1126/science.aaa6806

  • The technology and biology of single-cell RNA sequencing.

    Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC and Teichmann SA

    Molecular cell 2015;58;4;610-20

    PUBMED: 26000846; DOI: 10.1016/j.molcel.2015.04.005

  • Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.

    Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, Sánchez Castillo M, Oedekoven CA, Diamanti E, Schulte R et al.

    Cell stem cell 2015;16;6;712-24

    PUBMED: 26004780; PMC: 4460190; DOI: 10.1016/j.stem.2015.04.004

  • Applying the ARRIVE Guidelines to an In Vivo Database.

    Karp NA, Meehan TF, Morgan H, Mason JC, Blake A, Kurbatova N, Smedley D, Jacobsen J, Mott RF, Iyer V et al.

    PLoS biology 2015;13;5;e1002151

    PUBMED: 25992600; PMC: 4439173; DOI: 10.1371/journal.pbio.1002151

  • Potential research participants support the return of raw sequence data.

    Middleton A, Wright CF, Morley KI, Bragin E, Firth HV, Hurles ME, Parker M and DDD study

    Journal of medical genetics 2015;52;8;571-4

    PUBMED: 25995218; PMC: 4518751; DOI: 10.1136/jmedgenet-2015-103119

  • Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES).

    Relton CL, Gaunt T, McArdle W, Ho K, Duggirala A, Shihab H, Woodward G, Lyttleton O, Evans DM, Reik W et al.

    International journal of epidemiology 2015;44;4;1181-90

    PUBMED: 25991711; PMC: 5593097; DOI: 10.1093/ije/dyv072

  • Clostridium sordellii genome analysis reveals plasmid localized toxin genes encoded within pathogenicity loci.

    Couchman EC, Browne HP, Dunn M, Lawley TD, Songer JG, Hall V, Petrovska L, Vidor C, Awad M, Lyras D and Fairweather NF

    BMC genomics 2015;16;392

    PUBMED: 25981746; PMC: 4434542; DOI: 10.1186/s12864-015-1613-2

  • Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus.

    Steinig EJ, Andersson P, Harris SR, Sarovich DS, Manoharan A, Coupland P, Holden MT, Parkhill J, Bentley SD, Robinson DA and Tong SY

    BMC genomics 2015;16;388

    PUBMED: 25981586; PMC: 4432960; DOI: 10.1186/s12864-015-1599-9

  • Concurrent whole-genome haplotyping and copy-number profiling of single cells.

    Zamani Esteki M, Dimitriadou E, Mateiu L, Melotte C, Van der Aa N, Kumar P, Das R, Theunis K, Cheng J, Legius E et al.

    American journal of human genetics 2015;96;6;894-912

    PUBMED: 25983246; PMC: 4473724; DOI: 10.1016/j.ajhg.2015.04.011

  • Contemporary evolution of resistance at the major insecticide target site gene Ace-1 by mutation and copy number variation in the malaria mosquito Anopheles gambiae.

    Weetman D, Mitchell SN, Wilding CS, Birks DP, Yawson AE, Essandoh J, Mawejje HD, Djogbenou LS, Steen K, Rippon EJ et al.

    Molecular ecology 2015;24;11;2656-72

    PUBMED: 25865270; PMC: 4447564; DOI: 10.1111/mec.13197

  • WGE: a CRISPR database for genome engineering.

    Hodgkins A, Farne A, Perera S, Grego T, Parry-Smith DJ, Skarnes WC and Iyer V

    Bioinformatics (Oxford, England) 2015;31;18;3078-80

    PUBMED: 25979474; PMC: 4565030; DOI: 10.1093/bioinformatics/btv308

  • Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci.

    van Tonder AJ, Bray JE, Roalfe L, White R, Zancolli M, Quirk SJ, Haraldsson G, Jolley KA, Maiden MC, Bentley SD et al.

    Journal of clinical microbiology 2015;53;7;2271-85

    PUBMED: 25972423; PMC: 4473186; DOI: 10.1128/JCM.00744-15

  • The transcription factor Bcl11b is specifically expressed in group 2 innate lymphoid cells and is essential for their development.

    Yu Y, Wang C, Clare S, Wang J, Lee SC, Brandt C, Burke S, Lu L, He D, Jenkins NA et al.

    The Journal of experimental medicine 2015;212;6;865-74

    PUBMED: 25964371; PMC: 4451136; DOI: 10.1084/jem.20142318

  • Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.

    Ju YS, Tubio JM, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS et al.

    Genome research 2015;25;6;814-24

    PUBMED: 25963125; PMC: 4448678; DOI: 10.1101/gr.190470.115

  • Identification of the inflammasome Nlrp1b as the candidate gene conferring diabetes risk at the Idd4.1 locus in the nonobese diabetic mouse.

    Motta VN, Markle JG, Gulban O, Mortin-Toth S, Liao KC, Mogridge J, Steward CA and Danska JS

    Journal of immunology (Baltimore, Md. : 1950) 2015;194;12;5663-73

    PUBMED: 25964492; DOI: 10.4049/jimmunol.1400913

  • Interaction of Salmonella enterica Serovar Typhimurium with Intestinal Organoids Derived from Human Induced Pluripotent Stem Cells.

    Forbester JL, Goulding D, Vallier L, Hannan N, Hale C, Pickard D, Mukhopadhyay S and Dougan G

    Infection and immunity 2015;83;7;2926-34

    PUBMED: 25964470; PMC: 4468523; DOI: 10.1128/IAI.00161-15

  • Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX et al.

    Nature genetics 2015;47;6;632-9

    PUBMED: 25961941; PMC: 4921243; DOI: 10.1038/ng.3281

  • Copy number variation in the human Y chromosome in the UK population.

    Wei W, Fitzgerald TW, Fitzgerald T, Ayub Q, Massaia A, Smith BH, Smith BB, Dominiczak AF, Dominiczak AA, Morris AD et al.

    Human genetics 2015;134;7;789-800

    PUBMED: 25957587; PMC: 4460274; DOI: 10.1007/s00439-015-1562-5

  • SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts.

    Malcovati L, Karimi M, Papaemmanuil E, Ambaglio I, Jädersten M, Jansson M, Elena C, Gallì A, Walldin G, Della Porta MG et al.

    Blood 2015;126;2;233-41

    PUBMED: 25957392; PMC: 4528082; DOI: 10.1182/blood-2015-03-633537

  • NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.

    Xia J, Gill EE and Hancock RE

    Nature protocols 2015;10;6;823-44

    PUBMED: 25950236; DOI: 10.1038/nprot.2015.052

  • Prospective derivation of a living organoid biobank of colorectal cancer patients.

    van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L et al.

    Cell 2015;161;4;933-45

    PUBMED: 25957691; PMC: 6428276; DOI: 10.1016/j.cell.2015.03.053

  • Uncovering the genomic heterogeneity of multifocal breast cancer.

    Desmedt C, Fumagalli D, Pietri E, Zoppoli G, Brown D, Nik-Zainal S, Gundem G, Rothé F, Majjaj S, Garuti A et al.

    The Journal of pathology 2015;236;4;457-66

    PUBMED: 25850943; PMC: 4691324; DOI: 10.1002/path.4540

  • Identification of a plant isoflavonoid that causes biliary atresia.

    Lorent K, Gong W, Koo KA, Waisbourd-Zinman O, Karjoo S, Zhao X, Sealy I, Kettleborough RN, Stemple DL, Windsor PA et al.

    Science translational medicine 2015;7;286;286ra67

    PUBMED: 25947162; DOI: 10.1126/scitranslmed.aaa1652

  • Induced pluripotent stem cell derived macrophages as a cellular system to study salmonella and other pathogens.

    Hale C, Yeung A, Goulding D, Pickard D, Alasoo K, Powrie F, Dougan G and Mukhopadhyay S

    PloS one 2015;10;5;e0124307

    PUBMED: 25946027; PMC: 4422593; DOI: 10.1371/journal.pone.0124307

  • Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci.

    Tsoi LC, Spain SL, Ellinghaus E, Stuart PE, Capon F, Knight J, Tejasvi T, Kang HM, Allen MH, Lambert S et al.

    Nature communications 2015;6;7001

    PUBMED: 25939698; PMC: 4422106; DOI: 10.1038/ncomms8001

  • The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.

    Wang Y, Lu Y, Zhang Y, Ning Z, Li Y, Zhao Q, Lu H, Huang R, Xia X, Feng Q et al.

    Nature genetics 2015;47;6;625-31

    PUBMED: 25938946; DOI: 10.1038/ng.3280

  • Connecting genotypes to medically relevant phenotypes in major vector mosquitoes

    LAWNICZAK,M.K.N

    Current Opinion in Insect Science 2015;10;59–64

    DOI: 10.1016/j.cois.2015.04.008; URL: https://dx.doi.org/10.1016/j....cois.2015.04.008

  • A Human Platelet Receptor Protein Microarray Identifies the High Affinity Immunoglobulin E Receptor Subunit α (FcεR1α) as an Activating Platelet Endothelium Aggregation Receptor 1 (PEAR1) Ligand.

    Sun Y, Vandenbriele C, Kauskot A, Verhamme P, Hoylaerts MF and Wright GJ

    Molecular & cellular proteomics : MCP 2015;14;5;1265-74

    PUBMED: 25713122; PMC: 4424398; DOI: 10.1074/mcp.M114.046946

  • A prospective multi-center observational study of children hospitalized with diarrhea in Ho Chi Minh City, Vietnam.

    Thompson CN, Phan MV, Hoang NV, Minh PV, Vinh NT, Thuy CT, Nga TT, Rabaa MA, Duy PT, Dung TT et al.

    The American journal of tropical medicine and hygiene 2015;92;5;1045-52

    PUBMED: 25802437; PMC: 4426562; DOI: 10.4269/ajtmh.14-0655

  • Activation of Salmonella Typhi-specific regulatory T cells in typhoid disease in a wild-type S. Typhi challenge model.

    McArthur MA, Fresnay S, Magder LS, Darton TC, Jones C, Waddington CS, Blohmke CJ, Dougan G, Angus B, Levine MM et al.

    PLoS pathogens 2015;11;5;e1004914

    PUBMED: 26001081; PMC: 4441490; DOI: 10.1371/journal.ppat.1004914

  • ANGPTL7 regulates the expansion and repopulation of human hematopoietic stem and progenitor cells.

    Xiao Y, Jiang Z, Li Y, Ye W, Jia B, Zhang M, Xu Y, Wu D, Lai L, Chen Y et al.

    Haematologica 2015;100;5;585-94

    PUBMED: 25637050; PMC: 4420207; DOI: 10.3324/haematol.2014.118612

  • Antimicrobial Drug Resistance of Vibrio cholerae, Democratic Republic of the Congo.

    Miwanda B, Moore S, Muyembe JJ, Nguefack-Tsague G, Kabangwa IK, Ndjakani DY, Mutreja A, Thomson N, Thefenne H, Garnotel E et al.

    Emerging infectious diseases 2015;21;5;847-51

    PUBMED: 25897570; PMC: 4412219; DOI: 10.3201/eid2105.141233

  • Bugs full of viruses.

    Gall A

    Nature reviews. Microbiology 2015;13;5;253

    PUBMED: 25874842; DOI: 10.1038/nrmicro3479

  • Cell Specific eQTL Analysis without Sorting Cells.

    Westra HJ, Arends D, Esko T, Peters MJ, Schurmann C, Schramm K, Kettunen J, Yaghootkar H, Fairfax BP, Andiappan AK et al.

    PLoS genetics 2015;11;5;e1005223

    PUBMED: 25955312; PMC: 4425538; DOI: 10.1371/journal.pgen.1005223

  • CHD2 variants are a risk factor for photosensitivity in epilepsy.

    Galizia EC, Myers CT, Leu C, de Kovel CG, Afrikanova T, Cordero-Maldonado ML, Martins TG, Jacmin M, Drury S, Krishna Chinthapalli V et al.

    Brain : a journal of neurology 2015;138;Pt 5;1198-207

    PUBMED: 25783594; PMC: 4407192; DOI: 10.1093/brain/awv052

  • Colony morphology variation of Burkholderia pseudomallei is associated with antigenic variation and O-polysaccharide modification.

    Wikraiphat C, Saiprom N, Tandhavanant S, Heiss C, Azadi P, Wongsuvan G, Tuanyok A, Holden MT, Burtnick MN, Brett PJ et al.

    Infection and immunity 2015;83;5;2127-38

    PUBMED: 25776750; PMC: 4399047; DOI: 10.1128/IAI.02785-14

  • Conversion of non-adipogenic fibroblasts into adipocytes by a defined hormone mixture.

    Nie T, Hui X, Gao X, Nie B, Mao L, Tang X, Yuan R, Li K, Li P, Xu A et al.

    The Biochemical journal 2015;467;3;487-94

    PUBMED: 25730278; DOI: 10.1042/BJ20140727

  • Deficiency of ECHS1 causes mitochondrial encephalopathy with cardiac involvement.

    Haack TB, Jackson CB, Murayama K, Kremer LS, Schaller A, Kotzaeridou U, de Vries MC, Schottmann G, Santra S, Büchner B et al.

    Annals of clinical and translational neurology 2015;2;5;492-509

    PUBMED: 26000322; PMC: 4435704; DOI: 10.1002/acn3.189

  • Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

    Flegontov P, Michálek J, Janouškovec J, Lai DH, Jirků M, Hajdušková E, Tomčala A, Otto TD, Keeling PJ, Pain A et al.

    Molecular biology and evolution 2015;32;5;1115-31

    PUBMED: 25660376; DOI: 10.1093/molbev/msv021

  • Emergent and evolving antimicrobial resistance cassettes in community-associated fusidic acid and meticillin-resistant Staphylococcus aureus.

    Ellington MJ, Reuter S, Harris SR, Holden MT, Cartwright EJ, Greaves D, Gerver SM, Hope R, Brown NM, Török ME et al.

    International journal of antimicrobial agents 2015;45;5;477-84

    PUBMED: 25769787; PMC: 4415905; DOI: 10.1016/j.ijantimicag.2015.01.009

  • Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets.

    Schulze K, Imbeaud S, Letouzé E, Alexandrov LB, Calderaro J, Rebouissou S, Couchy G, Meiller C, Shinde J, Soysouvanh F et al.

    Nature genetics 2015;47;5;505-11

    PUBMED: 25822088; PMC: 4587544; DOI: 10.1038/ng.3252

  • Genetic and phenotypic differentiation of an Andean intermediate altitude population.

    Eichstaedt CA, Antão T, Cardona A, Pagani L, Kivisild T and Mormina M

    Physiological reports 2015;3;5

    PUBMED: 25948820; PMC: 4463816; DOI: 10.14814/phy2.12376

  • Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.

    Coffee and Caffeine Genetics Consortium, Cornelis MC, Byrne EM, Esko T, Nalls MA, Ganna A, Paynter N, Monda KL, Amin N, Fischer K et al.

    Molecular psychiatry 2015;20;5;647-56

    PUBMED: 25288136; PMC: 4388784; DOI: 10.1038/mp.2014.107

  • Investigation of association between hip osteoarthritis susceptibility loci and radiographic proximal femur shape.

    Lindner C, Thiagarajah S, Wilkinson JM, Panoutsopoulou K, Day-Williams AG, arcOGEN Consortium, Cootes TF and Wallis GA

    Arthritis & rheumatology (Hoboken, N.J.) 2015;67;8;2076-84

    PUBMED: 25939412; PMC: 4864451; DOI: 10.1002/art.39186

  • MacroH2A1 isoforms are associated with epigenetic markers for activation of lipogenic genes in fat-induced steatosis.

    Podrini C, Koffas A, Chokshi S, Vinciguerra M, Lelliott CJ, White JK, Adissu HA, Williams R and Greco A

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2015;29;5;1676-87

    PUBMED: 25526730; DOI: 10.1096/fj.14-262717

  • Mouse slc9a8 mutants exhibit retinal defects due to retinal pigmented epithelium dysfunction.

    Jadeja S, Barnard AR, McKie L, Cross SH, White JK, Sanger Mouse Genetics Project, Robertson M, Budd PS, MacLaren RE and Jackson IJ

    Investigative ophthalmology & visual science 2015;56;5;3015-26

    PUBMED: 25736793; PMC: 4538965; DOI: 10.1167/iovs.14-15735

  • PinR mediates the generation of reversible population diversity in Streptococcus zooepidemicus.

    Steward KF, Harrison T, Robinson C, Slater J, Maskell DJ, Harris SR, Holden MT and Waller AS

    Microbiology (Reading, England) 2015;161;Pt 5;1105-12

    PUBMED: 25701732; DOI: 10.1099/mic.0.000057

  • Signalling Through Retinoic Acid Receptors is Required for Reprogramming of Both Mouse Embryonic Fibroblast Cells and Epiblast Stem Cells to Induced Pluripotent Stem Cells.

    Yang J, Wang W, Ooi J, Campos LS, Lu L and Liu P

    Stem cells (Dayton, Ohio) 2015;33;5;1390-404

    PUBMED: 25546009; PMC: 4863141; DOI: 10.1002/stem.1926

  • Staphylococcus aureus adapts to oxidative stress by producing H2O2-resistant small-colony variants via the SOS response.

    Painter KL, Strange E, Parkhill J, Bamford KB, Armstrong-James D and Edwards AM

    Infection and immunity 2015;83;5;1830-44

    PUBMED: 25690100; PMC: 4399076; DOI: 10.1128/IAI.03016-14

  • Transposon mutagenesis identifies genetic drivers of Braf(V600E) melanoma.

    Mann MB, Black MA, Jones DJ, Ward JM, Yew CC, Newberg JY, Dupuy AJ, Rust AG, Bosenberg MW, McMahon M et al.

    Nature genetics 2015;47;5;486-95

    PUBMED: 25848750; DOI: 10.1038/ng.3275

  • The Kalash genetic isolate: ancient divergence, drift, and selection.

    Ayub Q, Mezzavilla M, Pagani L, Haber M, Mohyuddin A, Khaliq S, Mehdi SQ and Tyler-Smith C

    American journal of human genetics 2015;96;5;775-83

    PUBMED: 25937445; PMC: 4570283; DOI: 10.1016/j.ajhg.2015.03.012

  • Whole genome analysis to detect potential vaccine-induced changes on Shigella sonnei genome.

    Behar A, Fookes MC, Goren S, Thomson NR and Cohen D

    Vaccine 2015;33;26;2978-83

    PUBMED: 25936664; DOI: 10.1016/j.vaccine.2015.04.074

  • Attitudes of nearly 7000 health professionals, genomic researchers and publics toward the return of incidental results from sequencing research.

    Middleton A, Morley KI, Bragin E, Firth HV, Hurles ME, Wright CF, Parker M and DDD study

    European journal of human genetics : EJHG 2015;24;1;21-9

    PUBMED: 25920556; PMC: 4795240; DOI: 10.1038/ejhg.2015.58

  • SNES makes sense? Single-cell exome sequencing evolves.

    Voet T and Van Loo P

    Genome biology 2015;16;86

    PUBMED: 25926122; PMC: 4414391; DOI: 10.1186/s13059-015-0650-0

  • Loss of PCLO function underlies pontocerebellar hypoplasia type III.

    Ahmed MY, Chioza BA, Rajab A, Schmitz-Abe K, Al-Khayat A, Al-Turki S, Baple EL, Patton MA, Al-Memar AY, Hurles ME et al.

    Neurology 2015;84;17;1745-50

    PUBMED: 25832664; PMC: 4424132; DOI: 10.1212/WNL.0000000000001523

  • G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

    Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM et al.

    Nature methods 2015;12;6;519-22

    PUBMED: 25915121; DOI: 10.1038/nmeth.3370

  • Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.

    Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G, Crook PD, Gilbart VL, Zittermann S, Allen VG, Howden BP et al.

    The Lancet. Infectious diseases 2015;15;8;913-21

    PUBMED: 25936611; DOI: 10.1016/S1473-3099(15)00002-X

  • TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors.

    Cebola I, Rodríguez-Seguí SA, Cho CH, Bessa J, Rovira M, Luengo M, Chhatriwala M, Berry A, Ponsa-Cobas J, Maestro MA et al.

    Nature cell biology 2015;17;5;615-626

    PUBMED: 25915126; PMC: 4434585; DOI: 10.1038/ncb3160

  • Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

    Hsu LY, Harris SR, Chlebowicz MA, Lindsay JA, Koh TH, Krishnan P, Tan TY, Hon PY, Grubb WB, Bentley SD et al.

    Genome biology 2015;16;1;81

    PUBMED: 25903077; PMC: 4407387; DOI: 10.1186/s13059-015-0643-z

  • Genetically determined height and coronary artery disease.

    Nelson CP, Hamby SE, Saleheen D, Hopewell JC, Zeng L, Assimes TL, Kanoni S, Willenborg C, Burgess S, Amouyel P et al.

    The New England journal of medicine 2015;372;17;1608-18

    PUBMED: 25853659; PMC: 4648271; DOI: 10.1056/NEJMoa1404881

  • A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites.

    Winter AD, Gillan V, Maitland K, Emes RD, Roberts B, McCormack G, Weir W, Protasio AV, Holroyd N, Berriman M et al.

    BMC genomics 2015;16;331

    PUBMED: 25896062; PMC: 4428239; DOI: 10.1186/s12864-015-1536-y

  • Combined Proteomics and Transcriptomics Identifies Carboxypeptidase B1 and Nuclear Factor κB (NF-κB) Associated Proteins as Putative Biomarkers of Metastasis in Low Grade Breast Cancer.

    Bouchal P, Dvořáková M, Roumeliotis T, Bortlíček Z, Ihnatová I, Procházková I, Ho JT, Maryáš J, Imrichová H, Budinská E et al.

    Molecular & cellular proteomics : MCP 2015;14;7;1814-30

    PUBMED: 25903579; PMC: 4587321; DOI: 10.1074/mcp.M114.041335

  • Key challenges for the creation and maintenance of specialist protein resources.

    Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N et al.

    Proteins 2015;83;6;1005-13

    PUBMED: 25820941; PMC: 4446195; DOI: 10.1002/prot.24803

  • MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.

    Vuckovic D, Gasparini P, Soranzo N and Iotchkova V

    Bioinformatics (Oxford, England) 2015;31;16;2754-6

    PUBMED: 25908790; PMC: 4528637; DOI: 10.1093/bioinformatics/btv222

  • Somatic structural variation and cancer.

    Tubio JM

    Briefings in functional genomics 2015;14;5;339-51

    PUBMED: 25903743; DOI: 10.1093/bfgp/elv016

  • Synthetic viability genomic screening defines Sae2 function in DNA repair.

    Puddu F, Oelschlaegel T, Guerini I, Geisler NJ, Niu H, Herzog M, Salguero I, Ochoa-Montaño B, Viré E, Sung P et al.

    The EMBO journal 2015;34;11;1509-22

    PUBMED: 25899817; PMC: 4474527; DOI: 10.15252/embj.201590973

  • The BioMart community portal: an innovative alternative to large, centralized data repositories.

    Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G et al.

    Nucleic acids research 2015;43;W1;W589-98

    PUBMED: 25897122; PMC: 4489294; DOI: 10.1093/nar/gkv350

  • The epigenetic regulators CBP and p300 facilitate leukemogenesis and represent therapeutic targets in acute myeloid leukemia.

    Giotopoulos G, Chan WI, Horton SJ, Ruau D, Gallipoli P, Fowler A, Crawley C, Papaemmanuil E, Campbell PJ, Göttgens B et al.

    Oncogene 2015;35;3;279-89

    PUBMED: 25893291; PMC: 4729186; DOI: 10.1038/onc.2015.92

  • Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.

    Debette S, Ibrahim Verbaas CA, Bressler J, Schuur M, Smith A, Bis JC, Davies G, Wolf C, Gudnason V, Chibnik LB et al.

    Biological psychiatry 2015;77;8;749-63

    PUBMED: 25648963; PMC: 4513651; DOI: 10.1016/j.biopsych.2014.08.027

  • αIIbβ3 variants defined by next-generation sequencing: predicting variants likely to cause Glanzmann thrombasthenia.

    Buitrago L, Rendon A, Liang Y, Simeoni I, Negri A, ThromboGenomics Consortium, Filizola M, Ouwehand WH and Coller BS

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;15;E1898-907

    PUBMED: 25827233; PMC: 4403182; DOI: 10.1073/pnas.1422238112

  • High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.

    Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D and Marioni JC

    Nature biotechnology 2015;33;5;503-9

    PUBMED: 25867922; DOI: 10.1038/nbt.3209

  • Cardiology: Race for healthy hearts.

    Hitz MP and Andelfinger G

    Nature 2015;520;7546;160-1

    PUBMED: 25830886; DOI: 10.1038/nature14379

  • Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

    Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q, Szpak M, Frandsen P, Chen Y, Yngvadottir B, Cooper DN et al.

    Science (New York, N.Y.) 2015;348;6231;242-245

    PUBMED: 25859046; PMC: 4668944; DOI: 10.1126/science.aaa3952

  • PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia.

    Dang J, Wei L, de Ridder J, Su X, Rust AG, Roberts KG, Payne-Turner D, Cheng J, Ma J, Qu C et al.

    Blood 2015;125;23;3609-17

    PUBMED: 25855603; PMC: 4458800; DOI: 10.1182/blood-2015-02-626127

  • Deep phylogenetic analysis of haplogroup G1 provides estimates of SNP and STR mutation rates on the human Y-chromosome and reveals migrations of Iranic speakers.

    Balanovsky O, Zhabagin M, Agdzhoyan A, Chukhryaeva M, Zaporozhchenko V, Utevska O, Highnam G, Sabitov Z, Greenspan E, Dibirova K et al.

    PloS one 2015;10;4;e0122968

    PUBMED: 25849548; PMC: 4388827; DOI: 10.1371/journal.pone.0122968

  • Distinct Commensals Induce Interleukin-1β via NLRP3 Inflammasome in Inflammatory Monocytes to Promote Intestinal Inflammation in Response to Injury.

    Seo SU, Kamada N, Muñoz-Planillo R, Kim YG, Kim D, Koizumi Y, Hasegawa M, Himpsl SD, Browne HP, Lawley TD et al.

    Immunity 2015;42;4;744-55

    PUBMED: 25862092; PMC: 4408263; DOI: 10.1016/j.immuni.2015.03.004

  • Genetic variation at MECOM, TERT, JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms.

    Tapper W, Jones AV, Kralovics R, Harutyunyan AS, Zoi K, Leung W, Godfrey AL, Guglielmelli P, Callaway A, Ward D et al.

    Nature communications 2015;6;6691

    PUBMED: 25849990; PMC: 4396373; DOI: 10.1038/ncomms7691

  • Evolution of the rapidly mutating human salivary agglutinin gene (DMBT1) and population subsistence strategy.

    Polley S, Louzada S, Forni D, Sironi M, Balaskas T, Hains DS, Yang F and Hollox EJ

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;16;5105-10

    PUBMED: 25848046; PMC: 4413317; DOI: 10.1073/pnas.1416531112

  • An atlas of mouse CD4(+) T cell transcriptomes.

    Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG and Teichmann SA

    Biology direct 2015;10;14

    PUBMED: 25886751; PMC: 4384382; DOI: 10.1186/s13062-015-0045-x

  • The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo.

    Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U et al.

    Cell 2015;161;2;319-32

    PUBMED: 25843629; PMC: 6922011; DOI: 10.1016/j.cell.2015.02.043

  • Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process.

    Greenman CD, Cooke SL, Marshall J, Stratton MR and Campbell PJ

    Journal of mathematical biology 2015;72;1-2;47-86

    PUBMED: 25833184; PMC: 4702116; DOI: 10.1007/s00285-015-0875-2

  • The evolutionary history of lethal metastatic prostate cancer.

    Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M et al.

    Nature 2015;520;7547;353-357

    PUBMED: 25830880; PMC: 4413032; DOI: 10.1038/nature14347

  • A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A.

    Corbett MA, Dudding-Byth T, Crock PA, Botta E, Christie LM, Nardo T, Caligiuri G, Hobson L, Boyle J, Mansour A et al.

    Journal of medical genetics 2015;52;4;269-74

    PUBMED: 25612912; DOI: 10.1136/jmedgenet-2014-102418

  • A switch in time.

    Crellen T and Iantorno S

    Nature reviews. Microbiology 2015;13;4;190

    PUBMED: 25749452; DOI: 10.1038/nrmicro3458

  • Cardiometabolic effects of genetic upregulation of the interleukin 1 receptor antagonist: a Mendelian randomisation analysis.

    Interleukin 1 Genetics Consortium

    The lancet. Diabetes & endocrinology 2015;3;4;243-53

    PUBMED: 25726324; PMC: 4648058; DOI: 10.1016/S2213-8587(15)00034-0

  • De novo loss- or gain-of-function mutations in KCNA2 cause epileptic encephalopathy.

    Syrbe S, Hedrich UB, Riesch E, Djémié T, Müller S, Møller RS, Maher B, Hernandez-Hernandez L, Synofzik M, Caglayan HS et al.

    Nature genetics 2015;47;4;393-9

    PUBMED: 25751627; PMC: 4380508; DOI: 10.1038/ng.3239

  • Detection of T-Cadherin Expression in Mouse Embryos.

    Rubina KA, Smutova VA, Semenova ML, Poliakov AA, Gerety S, Wilkinson D, Surkova EI, Semina EV, Sysoeva VY and Tkachuk VA

    Acta naturae 2015;7;2;87-94

    PUBMED: 26085949; PMC: 4463417

  • Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics.

    Presneau N, Baumhoer D, Behjati S, Pillay N, Tarpey P, Campbell PJ, Jundt G, Hamoudi R, Wedge DC, Loo PV et al.

    The journal of pathology. Clinical research 2015;1;2;113-23

    PUBMED: 27499898; PMC: 4858131; DOI: 10.1002/cjp2.13

  • DNA methylation of lipid-related genes affects blood lipid levels.

    Pfeiffer L, Wahl S, Pilling LC, Reischl E, Sandling JK, Kunze S, Holdt LM, Kretschmer A, Schramm K, Adamski J et al.

    Circulation. Cardiovascular genetics 2015;8;2;334-42

    PUBMED: 25583993; DOI: 10.1161/CIRCGENETICS.114.000804

  • Emergence of an outbreak-associated Clostridium difficile variant with increased virulence.

    Quesada-Gómez C, López-Ureña D, Acuña-Amador L, Villalobos-Zúñiga M, Du T, Freire R, Guzmán-Verri C, del Mar Gamboa-Coronado M, Lawley TD, Moreno E et al.

    Journal of clinical microbiology 2015;53;4;1216-26

    PUBMED: 25653402; PMC: 4365207; DOI: 10.1128/JCM.03058-14

  • Gene expression changes in HLA mismatched mixed lymphocyte cultures reveal genes associated with allorecognition.

    Nicolaidou V, Stylianou C, Koumas L, Vassiliou GS, Bodman-Smith KB and Costeas P

    Tissue antigens 2015;85;4;267-77

    PUBMED: 25786571; PMC: 5054849; DOI: 10.1111/tan.12543

  • Identification of a human synaptotagmin-1 mutation that perturbs synaptic vesicle cycling.

    Baker K, Gordon SL, Grozeva D, van Kogelenberg M, Roberts NY, Pike M, Blair E, Hurles ME, Chong WK, Baldeweg T et al.

    The Journal of clinical investigation 2015;125;4;1670-8

    PUBMED: 25705886; PMC: 4396464; DOI: 10.1172/JCI79765

  • Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.

    Baltazar M, Ngandjio A, Holt KE, Lepillet E, Pardos de la Gandara M, Collard JM, Bercion R, Nzouankeu A, Le Hello S, Dougan G et al.

    Emerging infectious diseases 2015;21;4;655-9

    PUBMED: 25811307; PMC: 4378479; DOI: 10.3201/eid2104.141355

  • Palmitoylation and palmitoyl-transferases in Plasmodium parasites.

    Hodson N, Invergo B, Rayner JC and Choudhary JS

    Biochemical Society transactions 2015;43;2;240-5

    PUBMED: 25849924; DOI: 10.1042/BST20140289

  • piggyBac Transposon.

    Yusa K

    Microbiology spectrum 2015;3;2;MDNA3-0028-2014

    PUBMED: 26104701; DOI: 10.1128/microbiolspec.MDNA3-0028-2014

  • Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism.

    Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, Krishna S, Rayner JC and Cox-Singh J

    PloS one 2015;10;4;e0121303

    PUBMED: 25830531; PMC: 4382175; DOI: 10.1371/journal.pone.0121303

  • Rapid emergence of multidrug resistant, H58-lineage Salmonella typhi in Blantyre, Malawi.

    Feasey NA, Gaskell K, Wong V, Msefula C, Selemani G, Kumwenda S, Allain TJ, Mallewa J, Kennedy N, Bennett A et al.

    PLoS neglected tropical diseases 2015;9;4;e0003748

    PUBMED: 25909750; PMC: 4409211; DOI: 10.1371/journal.pntd.0003748

  • Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up.

    Guerra-Assunção JA, Houben RM, Crampin AC, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RP et al.

    The Journal of infectious diseases 2015;211;7;1154-63

    PUBMED: 25336729; PMC: 4354982; DOI: 10.1093/infdis/jiu574

  • Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.

    Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B and Merkenschlager M

    Genome research 2015;25;4;504-13

    PUBMED: 25677180; PMC: 4381522; DOI: 10.1101/gr.184986.114

  • What is "data sharing" and why should biomedical researchers embrace it?

    Bobrow M

    Transplantation 2015;99;4;654-5

    PUBMED: 25769069; DOI: 10.1097/TP.0000000000000714

  • Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission.

    Paterson GK, Harrison EM, Murray GGR, Welch JJ, Warland JH, Holden MTG, Morgan FJE, Ba X, Koop G, Harris SR et al.

    Nature communications 2015;6;6560

    PUBMED: 25814293; PMC: 4389252; DOI: 10.1038/ncomms7560

  • The genome-wide effects of ionizing radiation on mutation induction in the mammalian germline.

    Adewoye AB, Lindsay SJ, Dubrova YE and Hurles ME

    Nature communications 2015;6;6684

    PUBMED: 25809527; PMC: 4389250; DOI: 10.1038/ncomms7684

  • Switching roles: the functional plasticity of adult tissue stem cells.

    Wabik A and Jones PH

    The EMBO journal 2015;34;9;1164-79

    PUBMED: 25812989; PMC: 4426478; DOI: 10.15252/embj.201490386

  • Activin/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark.

    Bertero A, Madrigal P, Galli A, Hubner NC, Moreno I, Burks D, Brown S, Pedersen RA, Gaffney D, Mendjan S et al.

    Genes & development 2015;29;7;702-17

    PUBMED: 25805847; PMC: 4387713; DOI: 10.1101/gad.255984.114

  • Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

    Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ et al.

    PLoS neglected tropical diseases 2015;9;3;e0003611

    PUBMED: 25803844; PMC: 4372345; DOI: 10.1371/journal.pntd.0003611

  • An O antigen capsule modulates bacterial pathogenesis in Shigella sonnei.

    Caboni M, Pédron T, Rossi O, Goulding D, Pickard D, Citiulo F, MacLennan CA, Dougan G, Thomson NR, Saul A et al.

    PLoS pathogens 2015;11;3;e1004749

    PUBMED: 25794007; PMC: 4368438; DOI: 10.1371/journal.ppat.1004749

  • Absence of heterozygosity due to template switching during replicative rearrangements.

    Carvalho CM, Pfundt R, King DA, Lindsay SJ, Zuccherato LW, Macville MV, Liu P, Johnson D, Stankiewicz P, Brown CW et al.

    American journal of human genetics 2015;96;4;555-64

    PUBMED: 25799105; PMC: 4385179; DOI: 10.1016/j.ajhg.2015.01.021

  • TopBP1 interacts with BLM to maintain genome stability but is dispensable for preventing BLM degradation.

    Blackford AN, Nieminuszczy J, Schwab RA, Galanty Y, Jackson SP and Niedzwiedz W

    Molecular cell 2015;57;6;1133-41

    PUBMED: 25794620; PMC: 4374139; DOI: 10.1016/j.molcel.2015.02.012

  • Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection.

    Palser AL, Grayson NE, White RE, Corton C, Correia S, Ba Abdullah MM, Watson SJ, Cotten M, Arrand JR, Murray PG et al.

    Journal of virology 2015;89;10;5222-37

    PUBMED: 25787276; PMC: 4442510; DOI: 10.1128/JVI.03614-14

  • Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes.

    Carpenter D, Dhar S, Mitchell LM, Fu B, Tyson J, Shwan NA, Yang F, Thomas MG and Armour JA

    Human molecular genetics 2015;24;12;3472-80

    PUBMED: 25788522; PMC: 4498156; DOI: 10.1093/hmg/ddv098

  • Using optical mapping data for the improvement of vertebrate genome assemblies.

    Howe K and Wood JM

    GigaScience 2015;4;10

    PUBMED: 25789164; PMC: 4364110; DOI: 10.1186/s13742-015-0052-y

  • Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

    Marsh JA, Rees HA, Ahnert SE and Teichmann SA

    Nature communications 2015;6;6394

    PUBMED: 25775164; DOI: 10.1038/ncomms7394

  • Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration.

    Curtis J, Luo Y, Zenner HL, Cuchet-Lourenço D, Wu C, Lo K, Maes M, Alisaac A, Stebbings E, Liu JZ et al.

    Nature genetics 2015;47;5;523-527

    PUBMED: 25774636; PMC: 4414475; DOI: 10.1038/ng.3248

  • Detection and correction of artefacts in estimation of rare copy number variants and analysis of rare deletions in type 1 diabetes.

    Cooper NJ, Shtir CJ, Smyth DJ, Guo H, Swafford AD, Zanda M, Hurles ME, Walker NM, Plagnol V, Cooper JD et al.

    Human molecular genetics 2015;24;6;1774-90

    PUBMED: 25424174; PMC: 4381751; DOI: 10.1093/hmg/ddu581

  • Quantitative reduction of the TCR adapter protein SLP-76 unbalances immunity and immune regulation.

    Siggs OM, Miosge LA, Daley SR, Asquith K, Foster PS, Liston A and Goodnow CC

    Journal of immunology (Baltimore, Md. : 1950) 2015;194;6;2587-95

    PUBMED: 25662996; PMC: 4355390; DOI: 10.4049/jimmunol.1400326

  • Five winters of pneumococcal serotype replacement in UK carriage following PCV introduction.

    Gladstone RA, Jefferies JM, Tocheva AS, Beard KR, Garley D, Chong WW, Bentley SD, Faust SN and Clarke SC

    Vaccine 2015;33;17;2015-21

    PUBMED: 25776920; PMC: 4392391; DOI: 10.1016/j.vaccine.2015.03.012

  • A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

    Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M et al.

    Genome research 2015;25;4;459-66

    PUBMED: 25770088; PMC: 4381518; DOI: 10.1101/gr.186684.114

  • Prmt5: a guardian of the germline protects future generations.

    Berrens RV and Reik W

    The EMBO journal 2015;34;6;689-90

    PUBMED: 25687507; PMC: 4369307; DOI: 10.15252/embj.201591054

  • Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function.

    Yeung AT, Hale C, Xia J, Tate PH, Goulding D, Keane JA, Mukhopadhyay S, Forrester L, Billker O, Skarnes WC et al.

    Scientific reports 2015;5;8908

    PUBMED: 25752829; PMC: 4354151; DOI: 10.1038/srep08908

  • Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.

    Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E et al.

    Nature genetics 2015;47;4;381-6

    PUBMED: 25751624; PMC: 4380767; DOI: 10.1038/ng.3245

  • Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

    Anand Brown A, Ding Z, Viñuela A, Glass D, Parts L, Spector T, Winn J and Durbin R

    G3 (Bethesda, Md.) 2015;5;5;839-47

    PUBMED: 25758824; PMC: 4426370; DOI: 10.1534/g3.114.011411

  • Whole-genome sequence-based analysis of thyroid function.

    Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M, Brown SJ, Mullin BH, Shihab HA, Min J, Walter K et al.

    Nature communications 2015;6;5681

    PUBMED: 25743335; PMC: 4366514; DOI: 10.1038/ncomms6681

  • Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis.

    Raposo AASF, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DLC, Ettwiller L et al.

    Cell reports 2015;10;9;1544-1556

    PUBMED: 25753420; PMC: 5383937; DOI: 10.1016/j.celrep.2015.02.025

  • Efficiently editing the vaccinia virus genome by using the CRISPR-Cas9 system.

    Yuan M, Zhang W, Wang J, Al Yaghchi C, Ahmed J, Chard L, Lemoine NR and Wang Y

    Journal of virology 2015;89;9;5176-9

    PUBMED: 25741005; PMC: 4403460; DOI: 10.1128/JVI.00339-15

  • Evolution of insecticide resistance diagnostics in malaria vectors.

    Weetman D and Donnelly MJ

    Transactions of the Royal Society of Tropical Medicine and Hygiene 2015;109;5;291-3

    PUBMED: 25740955; DOI: 10.1093/trstmh/trv017

  • Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area.

    Guerra-Assunção JA, Crampin AC, Houben RM, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RP et al.

    eLife 2015;4

    PUBMED: 25732036; PMC: 4384740; DOI: 10.7554/eLife.05166

  • Metabolite profiling and cardiovascular event risk: a prospective study of 3 population-based cohorts.

    Würtz P, Havulinna AS, Soininen P, Tynkkynen T, Prieto-Merino D, Tillin T, Ghorbani A, Artati A, Wang Q, Tiainen M et al.

    Circulation 2015;131;9;774-85

    PUBMED: 25573147; PMC: 4351161; DOI: 10.1161/CIRCULATIONAHA.114.013116

  • Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

    Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N et al.

    Nature genetics 2015;47;4;367-372

    PUBMED: 25730763; PMC: 4380509; DOI: 10.1038/ng.3221

  • The cytochrome P450 family in the parasitic nematode Haemonchus contortus.

    Laing R, Bartley DJ, Morrison AA, Rezansoff A, Martinelli A, Laing ST and Gilleard JS

    International journal for parasitology 2015;45;4;243-51

    PUBMED: 25558056; PMC: 4365919; DOI: 10.1016/j.ijpara.2014.12.001

  • The genomic and phenotypic diversity of Schizosaccharomyces pombe.

    Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM et al.

    Nature genetics 2015;47;3;235-41

    PUBMED: 25665008; PMC: 4645456; DOI: 10.1038/ng.3215

  • A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae.

    Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK, Ellington M, Baker KS, Dongol S, Thompson C, Harris SR et al.

    EMBO molecular medicine 2015;7;3;227-39

    PUBMED: 25712531; PMC: 4364942; DOI: 10.15252/emmm.201404767

  • Decoding the regulatory network of early blood development from single-cell gene expression measurements.

    Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E et al.

    Nature biotechnology 2015;33;3;269-76

    PUBMED: 25664528; PMC: 4374163; DOI: 10.1038/nbt.3154

  • Gain-of-function mutations in the calcium channel CACNA1C (Cav1.2) cause non-syndromic long-QT but not Timothy syndrome.

    Wemhöner K, Friedrich C, Stallmeyer B, Coffey AJ, Grace A, Zumhagen S, Seebohm G, Ortiz-Bonnin B, Rinné S, Sachse FB et al.

    Journal of molecular and cellular cardiology 2015;80;186-95

    PUBMED: 25633834; DOI: 10.1016/j.yjmcc.2015.01.002

  • Genetic counselors and Genomic Counseling in the United Kingdom.

    Middleton A, Hall G and Patch C

    Molecular genetics & genomic medicine 2015;3;2;79-83

    PUBMED: 25802877; PMC: 4367079; DOI: 10.1002/mgg3.123

  • Human T-cell leukemia virus type 1 (HTLV-1) tax requires CADM1/TSLC1 for inactivation of the NF-κB inhibitor A20 and constitutive NF-κB signaling.

    Pujari R, Hunte R, Thomas R, van der Weyden L, Rauch D, Ratner L, Nyborg JK, Ramos JC, Takai Y and Shembade N

    PLoS pathogens 2015;11;3;e1004721

    PUBMED: 25774694; PMC: 4361615; DOI: 10.1371/journal.ppat.1004721

  • Leucophore identity is more gold than silver.

    Dooley CM

    Pigment cell & melanoma research 2015;28;2;131

    PUBMED: 25546351; DOI: 10.1111/pcmr.12349

  • Malaria genomics: tracking a diverse and evolving parasite population.

    Kwiatkowski D

    International health 2015;7;2;82-4

    PUBMED: 25733556; PMC: 4379983; DOI: 10.1093/inthealth/ihv007

  • Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes.

    Lamberton PH, Crellen T, Cotton JA and Webster JP

    Advances in parasitology 2015;87;293-327

    PUBMED: 25765198; DOI: 10.1016/bs.apar.2014.12.006

  • Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next-generation DNA sequencing.

    Manson-Bahr D, Ball R, Gundem G, Sethia K, Mills R, Rochester M, Goody V, Anderson E, O'Meara S, Flather M et al.

    Journal of clinical pathology 2015;68;3;212-7

    PUBMED: 25586381; DOI: 10.1136/jclinpath-2014-202754

  • PANGEA-HIV: phylogenetics for generalised epidemics in Africa.

    Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Brown AL, Kellam P and PANGEA-HIV Consortium

    The Lancet. Infectious diseases 2015;15;3;259-61

    PUBMED: 25749217; PMC: 4968650; DOI: 10.1016/S1473-3099(15)70036-8

  • Phenotypic and functional analyses show stem cell-derived hepatocyte-like cells better mimic fetal rather than adult hepatocytes.

    Baxter M, Withey S, Harrison S, Segeritz CP, Zhang F, Atkinson-Dell R, Rowe C, Gerrard DT, Sison-Young R, Jenkins R et al.

    Journal of hepatology 2015;62;3;581-9

    PUBMED: 25457200; PMC: 4334496; DOI: 10.1016/j.jhep.2014.10.016

  • Post-translational protein modifications in malaria parasites.

    Doerig C, Rayner JC, Scherf A and Tobin AB

    Nature reviews. Microbiology 2015;13;3;160-72

    PUBMED: 25659318; DOI: 10.1038/nrmicro3402

  • Relationship between antibody susceptibility and lipopolysaccharide O-antigen characteristics of invasive and gastrointestinal nontyphoidal Salmonellae isolates from Kenya.

    Onsare RS, Micoli F, Lanzilao L, Alfini R, Okoro CK, Muigai AW, Revathi G, Saul A, Kariuki S, MacLennan CA and Rondini S

    PLoS neglected tropical diseases 2015;9;3;e0003573

    PUBMED: 25739091; PMC: 4352093; DOI: 10.1371/journal.pntd.0003573

  • Selective and genetic constraints on pneumococcal serotype switching.

    Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M and Hanage WP

    PLoS genetics 2015;11;3;e1005095

    PUBMED: 25826208; PMC: 4380333; DOI: 10.1371/journal.pgen.1005095

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P and Otto TD

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

    PUBMED: 25725497; PMC: 4495290; DOI: 10.1093/bioinformatics/btv120

  • CopywriteR: DNA copy number detection from off-target sequence data.

    Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP et al.

    Genome biology 2015;16;49

    PUBMED: 25887352; PMC: 4396974; DOI: 10.1186/s13059-015-0617-1

  • A genome-scale vector resource enables high-throughput reverse genetic screening in a malaria parasite.

    Gomes AR, Bushell E, Schwach F, Girling G, Anar B, Quail MA, Herd C, Pfander C, Modrzynska K, Rayner JC and Billker O

    Cell host & microbe 2015;17;3;404-413

    PUBMED: 25732065; PMC: 4362957; DOI: 10.1016/j.chom.2015.01.014

  • Leukemia-associated somatic mutations drive distinct patterns of age-related clonal hemopoiesis.

    McKerrell T, Park N, Moreno T, Grove CS, Ponstingl H, Stephens J, Understanding Society Scientific Group, Crawley C, Craig J, Scott MA et al.

    Cell reports 2015;10;8;1239-45

    PUBMED: 25732814; PMC: 4542313; DOI: 10.1016/j.celrep.2015.02.005

  • High-throughput analysis of gene essentiality and sporulation in Clostridium difficile.

    Dembek M, Barquist L, Boinett CJ, Cain AK, Mayho M, Lawley TD, Fairweather NF and Fagan RP

    mBio 2015;6;2;e02383

    PUBMED: 25714712; PMC: 4358009; DOI: 10.1128/mBio.02383-14

  • G6PD gene variants and its association with malaria in a Sri Lankan population.

    Dewasurendra RL, Rockett KA, Fernando SD, Carter R, Kwiatkowski DP, Karunaweera ND and MalariaGEN Consortium

    Malaria journal 2015;14;93

    PUBMED: 25885177; PMC: 4343272; DOI: 10.1186/s12936-015-0603-9

  • Quantification of Plasmodium-host protein interactions on intact, unmodified erythrocytes by back-scattering interferometry.

    Saetear P, Perrin AJ, Bartholdson SJ, Wanaguru M, Kussrow A, Bornhop DJ and Wright GJ

    Malaria journal 2015;14;88

    PUBMED: 25889240; PMC: 4349660; DOI: 10.1186/s12936-015-0553-2

  • p53 mediates loss of hematopoietic stem cell function and lymphopenia in Mysm1 deficiency.

    Belle JI, Langlais D, Petrov JC, Pardo M, Jones RG, Gros P and Nijnik A

    Blood 2015;125;15;2344-8

    PUBMED: 25710881; DOI: 10.1182/blood-2014-05-574111

  • The PDZ-domain protein Whirlin facilitates mechanosensory signaling in mammalian proprioceptors.

    de Nooij JC, Simon CM, Simon A, Doobar S, Steel KP, Banks RW, Mentis GZ, Bewick GS and Jessell TM

    The Journal of neuroscience : the official journal of the Society for Neuroscience 2015;35;7;3073-84

    PUBMED: 25698744; PMC: 4331628; DOI: 10.1523/JNEUROSCI.3699-14.2015

  • Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

    Weerdenburg EM, Abdallah AM, Rangkuti F, Abd El Ghany M, Otto TD, Adroub SA, Molenaar D, Ummels R, Ter Veen K, van Stempvoort G et al.

    Infection and immunity 2015;83;5;1778-88

    PUBMED: 25690095; PMC: 4399070; DOI: 10.1128/IAI.03050-14

  • A novel common variant in DCST2 is associated with length in early life and height in adulthood.

    van der Valk RJ, Kreiner-Møller E, Kooijman MN, Guxens M, Stergiakouli E, Sääf A, Bradfield JP, Geller F, Hayes MG, Cousminer DL et al.

    Human molecular genetics 2015;24;4;1155-68

    PUBMED: 25281659; PMC: 4447786; DOI: 10.1093/hmg/ddu510

  • Genome-wide enrichment analysis between endometriosis and obesity-related traits reveals novel susceptibility loci.

    Rahmioglu N, Macgregor S, Drong AW, Hedman ÅK, Harris HR, Randall JC, Prokopenko I, International Endogene Consortium (IEC), The GIANT Consortium, Nyholt DR et al.

    Human molecular genetics 2015;24;4;1185-99

    PUBMED: 25296917; PMC: 4576730; DOI: 10.1093/hmg/ddu516

  • Multi-stage genome-wide association study identifies new susceptibility locus for testicular germ cell tumour on chromosome 3q25.

    Litchfield K, Sultana R, Renwick A, Dudakia D, Seal S, Ramsay E, Powell S, Elliott A, Warren-Perry M, Eeles R et al.

    Human molecular genetics 2015;24;4;1169-76

    PUBMED: 25281660; PMC: 4375409; DOI: 10.1093/hmg/ddu511

  • TLR signaling modulates side effects of anticancer therapy in the small intestine.

    Frank M, Hennenberg EM, Eyking A, Rünzi M, Gerken G, Scott P, Parkhill J, Walker AW and Cario E

    Journal of immunology (Baltimore, Md. : 1950) 2015;194;4;1983-95

    PUBMED: 25589072; PMC: 4338614; DOI: 10.4049/jimmunol.1402481

  • Effect of mutation order on myeloproliferative neoplasms.

    Ortmann CA, Kent DG, Nangalia J, Silber Y, Wedge DC, Grinfeld J, Baxter EJ, Massie CE, Papaemmanuil E, Menon S et al.

    The New England journal of medicine 2015;372;7;601-612

    PUBMED: 25671252; PMC: 4660033; DOI: 10.1056/NEJMoa1412098

  • Genetic studies of body mass index yield new insights for obesity biology.

    Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, Powell C, Vedantam S, Buchkovich ML, Yang J et al.

    Nature 2015;518;7538;197-206

    PUBMED: 25673413; PMC: 4382211; DOI: 10.1038/nature14177

  • Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom.

    Olasz F, Nagy T, Szabó M, Kiss J, Szmolka A, Barta E, van Tonder A, Thomson N, Barrow P and Nagy B

    Genome announcements 2015;3;1

    PUBMED: 25676749; PMC: 4333649; DOI: 10.1128/genomeA.01468-14

  • New genetic loci link adipose and insulin biology to body fat distribution.

    Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Mägi R, Strawbridge RJ, Pers TH, Fischer K, Justice AE et al.

    Nature 2015;518;7538;187-196

    PUBMED: 25673412; PMC: 4338562; DOI: 10.1038/nature14132

  • Cross-species fertilization: the hamster egg receptor, Juno, binds the human sperm ligand, Izumo1.

    Bianchi E and Wright GJ

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2015;370;1661;20140101

    PUBMED: 25533103; PMC: 4275915; DOI: 10.1098/rstb.2014.0101

  • Genome-wide analyses identify KLF4 as an important negative regulator in T-cell acute lymphoblastic leukemia through directly inhibiting T-cell associated genes.

    Li W, Jiang Z, Li T, Wei X, Zheng Y, Wu D, Yang L, Chen S, Xu B, Zhong M et al.

    Molecular cancer 2015;14;26

    PUBMED: 25644173; PMC: 4350611; DOI: 10.1186/s12943-014-0285-x

  • Global reorganization of the nuclear landscape in senescent cells.

    Chandra T, Ewels PA, Schoenfelder S, Furlan-Magaril M, Wingett SW, Kirschner K, Thuret JY, Andrews S, Fraser P and Reik W

    Cell reports 2015;10;4;471-83

    PUBMED: 25640177; PMC: 4542308; DOI: 10.1016/j.celrep.2014.12.055

  • Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers.

    Shlien A, Campbell BB, de Borja R, Alexandrov LB, Merico D, Wedge D, Van Loo P, Tarpey PS, Coupland P, Behjati S et al.

    Nature genetics 2015;47;3;257-62

    PUBMED: 25642631; DOI: 10.1038/ng.3202

  • R-M systems go on the offensive.

    Lees J and Gladstone RA

    Nature reviews. Microbiology 2015;13;3;131

    PUBMED: 25639682; DOI: 10.1038/nrmicro3435

  • The origins of malaria: there are more things in heaven and earth ….

    Keeling PJ and Rayner JC

    Parasitology 2015;142 Suppl 1;S16-25

    PUBMED: 24963725; PMC: 4413824; DOI: 10.1017/S0031182014000766

  • CD200 receptor restriction of myeloid cell responses antagonizes antiviral immunity and facilitates cytomegalovirus persistence within mucosal tissue.

    Stack G, Jones E, Marsden M, Stacey MA, Snelgrove RJ, Lacaze P, Jacques LC, Cuff SM, Stanton RJ, Gallimore AM et al.

    PLoS pathogens 2015;11;2;e1004641

    PUBMED: 25654642; PMC: 4412112; DOI: 10.1371/journal.ppat.1004641

  • Characterization of expression quantitative trait loci in the human colon.

    Singh T, Levine AP, Smith PJ, Smith AM, Segal AW and Barrett JC

    Inflammatory bowel diseases 2015;21;2;251-6

    PUBMED: 25569741; PMC: 4345969; DOI: 10.1097/MIB.0000000000000265

  • Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan.

    Jones LS, Carvalho MJ, Toleman MA, White PL, Connor TR, Mushtaq A, Weeks JL, Kumarasamy KK, Raven KE, Török ME et al.

    Antimicrobial agents and chemotherapy 2015;59;2;923-9

    PUBMED: 25421466; PMC: 4335910; DOI: 10.1128/AAC.03242-14

  • Clinical and pharmacogenomic implications of genetic variation in a Southern Ethiopian population.

    Tekola-Ayele F, Adeyemo A, Aseffa A, Hailu E, Finan C, Davey G, Rotimi CN and Newport MJ

    The pharmacogenomics journal 2015;15;1;101-8

    PUBMED: 25069476; PMC: 4277706; DOI: 10.1038/tpj.2014.39

  • CtIP tetramer assembly is required for DNA-end resection and repair.

    Davies OR, Forment JV, Sun M, Belotserkovskaya R, Coates J, Galanty Y, Demir M, Morton CR, Rzechorzek NJ, Jackson SP and Pellegrini L

    Nature structural & molecular biology 2015;22;2;150-7

    PUBMED: 25558984; PMC: 4564947; DOI: 10.1038/nsmb.2937

  • Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.

    Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT and Flicek P

    Genome research 2015;25;2;167-78

    PUBMED: 25394363; PMC: 4315291; DOI: 10.1101/gr.177840.114

  • Generation of primary human intestinal T cell transcriptomes reveals differential expression at genetic risk loci for immune-mediated disease.

    Raine T, Liu JZ, Anderson CA, Parkes M and Kaser A

    Gut 2015;64;2;250-9

    PUBMED: 24799394; PMC: 4316924; DOI: 10.1136/gutjnl-2013-306657

  • Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N=53949).

    Davies G, Armstrong N, Bis JC, Bressler J, Chouraki V, Giddaluru S, Hofer E, Ibrahim-Verbaas CA, Kirin M, Lahti J et al.

    Molecular psychiatry 2015;20;2;183-92

    PUBMED: 25644384; PMC: 4356746; DOI: 10.1038/mp.2014.188

  • Hierarchical Bayesian model for rare variant association analysis integrating genotype uncertainty in human sequence data.

    He L, Pitkäniemi J, Sarin AP, Salomaa V, Sillanpää MJ and Ripatti S

    Genetic epidemiology 2015;39;2;89-100

    PUBMED: 25395270; DOI: 10.1002/gepi.21871

  • Keeping an eye on P. aeruginosa.

    Salter SJ

    Nature reviews. Microbiology 2015;13;2;69

    PUBMED: 25549963; DOI: 10.1038/nrmicro3422

  • Microbiota that affect risk for shigellosis in children in low-income countries.

    Lindsay B, Oundo J, Hossain MA, Antonio M, Tamboura B, Walker AW, Paulson JN, Parkhill J, Omore R, Faruque AS et al.

    Emerging infectious diseases 2015;21;2;242-50

    PUBMED: 25625766; PMC: 4313639; DOI: 10.3201/eid2101.140795

  • Parallel evolution or purifying selection, not introgression, explains similarity in the pyrethroid detoxification linked GSTE4 of Anopheles gambiae and An. arabiensis.

    Wilding CS, Weetman D, Rippon EJ, Steen K, Mawejje HD, Barsukov I and Donnelly MJ

    Molecular genetics and genomics : MGG 2015;290;1;201-15

    PUBMED: 25213601; PMC: 4312195; DOI: 10.1007/s00438-014-0910-9

  • Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes.

    Prescott NJ, Lehne B, Stone K, Lee JC, Taylor K, Knight J, Papouli E, Mirza MM, Simpson MA, Spain SL et al.

    PLoS genetics 2015;11;2;e1004955

    PUBMED: 25671699; PMC: 4335459; DOI: 10.1371/journal.pgen.1004955

  • Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways.

    Network and Pathway Analysis Subgroup of Psychiatric Genomics Consortium

    Nature neuroscience 2015;18;2;199-209

    PUBMED: 25599223; PMC: 4378867; DOI: 10.1038/nn.3922

  • Public perceptions of bacterial whole-genome sequencing for tuberculosis.

    Davies A, Scott S, Badger S, Török ME and Peacock SJ

    Trends in genetics : TIG 2015;31;2;58-60

    PUBMED: 25640860; DOI: 10.1016/j.tig.2014.08.002

  • Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes.

    Weiss GE, Gilson PR, Taechalertpaisarn T, Tham WH, de Jong NW, Harvey KL, Fowkes FJ, Barlow PN, Rayner JC, Wright GJ et al.

    PLoS pathogens 2015;11;2;e1004670

    PUBMED: 25723550; PMC: 4344246; DOI: 10.1371/journal.ppat.1004670

  • Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5.

    van Eijk E, Anvar SY, Browne HP, Leung WY, Frank J, Schmitz AM, Roberts AP and Smits WK

    BMC genomics 2015;16;31

    PUBMED: 25636331; PMC: 4320837; DOI: 10.1186/s12864-015-1252-7

  • Enhancer evolution across 20 mammalian species.

    Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ et al.

    Cell 2015;160;3;554-66

    PUBMED: 25635462; PMC: 4313353; DOI: 10.1016/j.cell.2015.01.006

  • Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility.

    Wessel J, Chu AY, Willems SM, Wang S, Yaghootkar H, Brody JA, Dauriz M, Hivert MF, Raghavan S, Lipovich L et al.

    Nature communications 2015;6;5897

    PUBMED: 25631608; PMC: 4311266; DOI: 10.1038/ncomms6897

  • Mosaic structural variation in children with developmental disorders.

    King DA, Jones WD, Crow YJ, Dominiczak AF, Foster NA, Gaunt TR, Harris J, Hellens SW, Homfray T, Innes J et al.

    Human molecular genetics 2015;24;10;2733-45

    PUBMED: 25634561; PMC: 4406290; DOI: 10.1093/hmg/ddv033

  • Computational and analytical challenges in single-cell transcriptomics.

    Stegle O, Teichmann SA and Marioni JC

    Nature reviews. Genetics 2015;16;3;133-45

    PUBMED: 25628217; DOI: 10.1038/nrg3833

  • Quantitative differences in developmental profiles of spontaneous activity in cortical and hippocampal cultures.

    Charlesworth P, Cotterill E, Morton A, Grant S and Eglen SJ

    Neural development 2015;10;1;1

    PUBMED: 25626996; PMC: 4320829; DOI: 10.1186/s13064-014-0028-0

  • Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae.

    Hill SC, Murphy AA, Cotten M, Palser AL, Benson P, Lesellier S, Gormley E, Richomme C, Grierson S, Bhuachalla DN et al.

    The Journal of general virology 2015;96;Pt 6;1411-1422

    PUBMED: 25626684; PMC: 4635489; DOI: 10.1099/vir.0.000071

  • BRAF inhibitor resistance mediated by the AKT pathway in an oncogenic BRAF mouse melanoma model.

    Perna D, Karreth FA, Rust AG, Perez-Mancera PA, Rashid M, Iorio F, Alifrangis C, Arends MJ, Bosenberg MW, Bollag G et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;6;E536-45

    PUBMED: 25624498; PMC: 4330752; DOI: 10.1073/pnas.1418163112

  • Drug-resistance mechanisms and tuberculosis drugs.

    Köser CU, Javid B, Liddell K, Ellington MJ, Feuerriegel S, Niemann S, Brown NM, Burman WJ, Abubakar I, Ismail NA et al.

    Lancet (London, England) 2015;385;9965;305-7

    PUBMED: 25706840; PMC: 4374148; DOI: 10.1016/S0140-6736(14)62450-8

  • Extending reference assembly models.

    Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM et al.

    Genome biology 2015;16;13

    PUBMED: 25651527; PMC: 4305238; DOI: 10.1186/s13059-015-0587-3

  • Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus.

    Johnson MR, Behmoaras J, Bottolo L, Krishnan ML, Pernhorst K, Santoscoy PLM, Rossetti T, Speed D, Srivastava PK, Chadeau-Hyam M et al.

    Nature communications 2015;6;6031

    PUBMED: 25615886; PMC: 4627576; DOI: 10.1038/ncomms7031

  • The Hd, Hj, and Hz66 flagella variants of Salmonella enterica serovar Typhi modify host responses and cellular interactions.

    Schreiber F, Kay S, Frankel G, Clare S, Goulding D, van de Vosse E, van Dissel JT, Strugnell R, Thwaites G, Kingsley RA et al.

    Scientific reports 2015;5;7947

    PUBMED: 25609312; PMC: 4302301; DOI: 10.1038/srep07947

  • Bat and pig IFN-induced transmembrane protein 3 restrict cell entry by influenza virus and lyssaviruses.

    Benfield CTO, Smith SE, Wright E, Wash RS, Ferrara F, Temperton NJ and Kellam P

    The Journal of general virology 2015;96;Pt 5;991-1005

    PUBMED: 25614588; PMC: 4631062; DOI: 10.1099/vir.0.000058

  • Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Oellrich A, Collier N, Smedley D and Groza T

    PloS one 2015;10;1;e0116040

    PUBMED: 25607983; PMC: 4301805; DOI: 10.1371/journal.pone.0116040

  • Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing.

    Agoti CN, Otieno JR, Munywoki PK, Mwihuri AG, Cane PA, Nokes DJ, Kellam P and Cotten M

    Journal of virology 2015;89;7;3444-54

    PUBMED: 25609811; PMC: 4403408; DOI: 10.1128/JVI.03391-14

  • Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.

    Kunowska N, Rotival M, Yu L, Choudhary J and Dillon N

    Nucleic acids research 2015;43;3;1418-32

    PUBMED: 25605797; PMC: 4330348; DOI: 10.1093/nar/gku1350

  • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

    Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC and Stegle O

    Nature biotechnology 2015;33;2;155-60

    PUBMED: 25599176; DOI: 10.1038/nbt.3102

  • Genetic architecture of artemisinin-resistant Plasmodium falciparum.

    Miotto O, Amato R, Ashley EA, MacInnis B, Almagro-Garcia J, Amaratunga C, Lim P, Mead D, Oyola SO, Dhorda M et al.

    Nature genetics 2015;47;3;226-34

    PUBMED: 25599401; PMC: 4545236; DOI: 10.1038/ng.3189

  • Identification of a novel human rhinovirus C type by antibody capture VIDISCA-454.

    Jazaeri Farsani SM, Oude Munnink BB, Canuti M, Deijs M, Cotten M, Jebbink MF, Verhoeven J, Kellam P, Loens K, Goossens H et al.

    Viruses 2015;7;1;239-51

    PUBMED: 25606972; PMC: 4306836; DOI: 10.3390/v7010239

  • Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling.

    Kenyon EJ, Campos I, Bull JC, Williams PH, Stemple DL and Clark MD

    Developmental biology 2015;397;2;212-24

    PUBMED: 25478908; PMC: 4294769; DOI: 10.1016/j.ydbio.2014.11.007

  • A PfRH5-based vaccine is efficacious against heterologous strain blood-stage Plasmodium falciparum infection in aotus monkeys.

    Douglas AD, Baldeviano GC, Lucas CM, Lugo-Roman LA, Crosnier C, Bartholdson SJ, Diouf A, Miura K, Lambert LE, Ventocilla JA et al.

    Cell host & microbe 2015;17;1;130-9

    PUBMED: 25590760; PMC: 4297294; DOI: 10.1016/j.chom.2014.11.017

  • The value of monitoring to control evolving populations.

    Fischer A, Vázquez-García I and Mustonen V

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;4;1007-12

    PUBMED: 25587136; PMC: 4313848; DOI: 10.1073/pnas.1409403112

  • Immediate T-Helper 17 Polarization Upon Triggering CD11b/c on HIV-Exposed Dendritic Cells.

    Wilflingseder D, Schroll A, Hackl H, Gallasch R, Frampton D, Lass-Flörl C, Pancino G, Saez-Cirion A, Lambotte O, Weiss L et al.

    The Journal of infectious diseases 2015;212;1;44-56

    PUBMED: 25583169; DOI: 10.1093/infdis/jiv014

  • BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells.

    Khaled WT, Choon Lee S, Stingl J, Chen X, Raza Ali H, Rueda OM, Hadi F, Wang J, Yu Y, Chin SF et al.

    Nature communications 2015;6;5987

    PUBMED: 25574598; PMC: 4338552; DOI: 10.1038/ncomms6987

  • Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes.

    Gerstung M, Pellagatti A, Malcovati L, Giagounidis A, Porta MG, Jädersten M, Dolatshad H, Verma A, Cross NC, Vyas P et al.

    Nature communications 2015;6;5901

    PUBMED: 25574665; PMC: 4338540; DOI: 10.1038/ncomms6901

  • DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair.

    Ochi T, Blackford AN, Coates J, Jhujh S, Mehmood S, Tamura N, Travers J, Wu Q, Draviam VM, Robinson CV et al.

    Science (New York, N.Y.) 2015;347;6218;185-188

    PUBMED: 25574025; PMC: 4338599; DOI: 10.1126/science.1261971

  • High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis.

    Goyette P, Boucher G, Mallon D, Ellinghaus E, Jostins L, Huang H, Ripke S, Gusareva ES, Annese V, Hauser SL et al.

    Nature genetics 2015;47;2;172-9

    PUBMED: 25559196; PMC: 4310771; DOI: 10.1038/ng.3176

  • Transposon mutagenesis identifies genes and evolutionary forces driving gastrointestinal tract tumor progression.

    Takeda H, Wei Z, Koso H, Rust AG, Yew CC, Mann MB, Ward JM, Adams DJ, Copeland NG and Jenkins NA

    Nature genetics 2015;47;2;142-50

    PUBMED: 25559195; DOI: 10.1038/ng.3175

  • The complexity of pheromone-mediated behaviour in mammals

    Logan, D.W

    Current Opinion in Behavioral Sciences 2015;2;96

    DOI: /10.1016/j.cobeha.2014.10.011

  • The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes.

    Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G and Yu F

    BMC genomics 2015;16;143

    PUBMED: 25765891; PMC: 4352271; DOI: 10.1186/s12864-015-1333-7

  • A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism.

    Loukola A, Buchwald J, Gupta R, Palviainen T, Hällfors J, Tikkanen E, Korhonen T, Ollikainen M, Sarin AP, Ripatti S et al.

    PLoS genetics 2015;11;9;e1005498

    PUBMED: 26407342; PMC: 4583245; DOI: 10.1371/journal.pgen.1005498

  • The LRR receptor Islr2 is required for retinal axon routing at the vertebrate optic chiasm.

    Panza P, Sitko AA, Maischein HM, Koch I, Flötenmeyer M, Wright GJ, Mandai K, Mason CA and Söllner C

    Neural development 2015;10;23

    PUBMED: 26492970; PMC: 4618557; DOI: 10.1186/s13064-015-0050-x

  • A marker-free system for highly efficient construction of vaccinia virus vectors using CRISPR Cas9.

    Yuan M, Gao X, Chard LS, Ali Z, Ahmed J, Li Y, Liu P, Lemoine NR and Wang Y

    Molecular therapy. Methods & clinical development 2015;2;15035

    PUBMED: 26417609; PMC: 4571730; DOI: 10.1038/mtm.2015.35

  • A modified R-type bacteriocin specifically targeting Clostridium difficile prevents colonization of mice without affecting gut microbiota diversity.

    Gebhart D, Lok S, Clare S, Tomas M, Stares M, Scholl D, Donskey CJ, Lawley TD and Govoni GR

    mBio 2015;6;2

    PUBMED: 25805733; PMC: 4453579; DOI: 10.1128/mBio.02368-14

  • An ontology approach to comparative phenomics in plants.

    Oellrich A, Walls RL, Cannon EK, Cannon SB, Cooper L, Gardiner J, Gkoutos GV, Harper L, He M, Hoehndorf R et al.

    Plant methods 2015;11;10

    PUBMED: 25774204; PMC: 4359497; DOI: 10.1186/s13007-015-0053-y

  • A Pooled Genome-Wide Association Study of Asperger Syndrome.

    Warrier V, Chakrabarti B, Murphy L, Chan A, Craig I, Mallya U, Lakatošová S, Rehnstrom K, Peltonen L, Wheelwright S et al.

    PloS one 2015;10;7;e0131202

    PUBMED: 26176695; PMC: 4503355; DOI: 10.1371/journal.pone.0131202

  • The post-vaccine microevolution of invasive Streptococcus pneumoniae.

    Cremers AJ, Mobegi FM, de Jonge MI, van Hijum SA, Meis JF, Hermans PW, Ferwerda G, Bentley SD and Zomer AL

    Scientific reports 2015;5;14952

    PUBMED: 26492862; PMC: 4615977; DOI: 10.1038/srep14952

  • A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy.

    Muona M, Berkovic SF, Dibbens LM, Oliver KL, Maljevic S, Bayly MA, Joensuu T, Canafoglia L, Franceschetti S, Michelucci R et al.

    Nature genetics 2015;47;1;39-46

    PUBMED: 25401298; PMC: 4281260; DOI: 10.1038/ng.3144

  • A risk-based approach to reducing exposure of staff to laboratory animal allergens.

    Westall L, Graham IR and Bussell J

    Lab animal 2015;44;1;32-8

    PUBMED: 25526057; DOI: 10.1038/laban.603

  • The structure of an endogenous Drosophila centromere reveals the prevalence of tandemly repeated sequences able to form i-motifs.

    Garavís M, Méndez-Lago M, Gabelica V, Whitehead SL, González C and Villasante A

    Scientific reports 2015;5;13307

    PUBMED: 26289671; PMC: 4542561; DOI: 10.1038/srep13307

  • The transcriptional landscape of age in human peripheral blood.

    Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K et al.

    Nature communications 2015;6;8570

    PUBMED: 26490707; PMC: 4639797; DOI: 10.1038/ncomms9570

  • 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

    Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ and Scott KP

    Microbiome 2015;3;26

    PUBMED: 26120470; PMC: 4482049; DOI: 10.1186/s40168-015-0087-4

  • Adipose tissue fatty acid chain length and mono-unsaturation increases with obesity and insulin resistance.

    Yew Tan C, Virtue S, Murfitt S, Robert LD, Phua YH, Dale M, Griffin JL, Tinahones F, Scherer PE and Vidal-Puig A

    Scientific reports 2015;5;18366

    PUBMED: 26679101; PMC: 4683622; DOI: 10.1038/srep18366

  • Allele variants of enterotoxigenic Escherichia coli heat-labile toxin are globally transmitted and associated with colonization factors.

    Joffré E, von Mentzer A, Abd El Ghany M, Oezguen N, Savidge T, Dougan G, Svennerholm AM and Sjöling Å

    Journal of bacteriology 2015;197;2;392-403

    PUBMED: 25404692; PMC: 4272596; DOI: 10.1128/JB.02050-14

  • Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

    Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M et al.

    Nature communications 2015;6;7256

    PUBMED: 26028266; PMC: 4451611; DOI: 10.1038/ncomms8256

  • Automatic concept recognition using the human phenotype ontology reference and test suite corpora.

    Groza T, Köhler S, Doelken S, Collier N, Oellrich A, Smedley D, Couto FM, Baynam G, Zankl A and Robinson PN

    Database : the journal of biological databases and curation 2015;2015

    PUBMED: 25725061; PMC: 4343077; DOI: 10.1093/database/bav005

  • Avianbase: a community resource for bird genomics.

    Eöry L, Gilbert MT, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P and Burt DW

    Genome biology 2015;16;21

    PUBMED: 25723810; PMC: 4310197; DOI: 10.1186/s13059-015-0588-2

  • Bacterial calpains and the evolution of the calpain (C2) family of peptidases.

    Rawlings ND

    Biology direct 2015;10;66

    PUBMED: 26527411; PMC: 4631099; DOI: 10.1186/s13062-015-0095-0

  • Bridging the translational divide: identical cognitive touchscreen testing in mice and humans carrying mutations in a disease-relevant homologous gene.

    Nithianantharajah J, McKechanie AG, Stewart TJ, Johnstone M, Blackwood DH, St Clair D, Grant SG, Bussey TJ and Saksida LM

    Scientific reports 2015;5;14613

    PUBMED: 26423861; PMC: 4589696; DOI: 10.1038/srep14613

  • Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

    Nandi T, Holden MT, Holden MT, Didelot X, Mehershahi K, Boddey JA, Beacham I, Peak I, Harting J, Baybayan P et al.

    Genome research 2015;25;1;129-41

    PUBMED: 25236617; PMC: 4317168; DOI: 10.1101/gr.177543.114

  • Cancer evolution: mathematical models and computational inference.

    Beerenwinkel N, Schwarz RF, Gerstung M and Markowetz F

    Systematic biology 2015;64;1;e1-25

    PUBMED: 25293804; PMC: 4265145; DOI: 10.1093/sysbio/syu081

  • Canine Mammary Tumours Are Affected by Frequent Copy Number Aberrations, including Amplification of MYC and Loss of PTEN.

    Borge KS, Nord S, Van Loo P, Lingjærde OC, Gunnes G, Alnæs GI, Solvang HK, Lüders T, Kristensen VN, Børresen-Dale AL and Lingaas F

    PloS one 2015;10;5;e0126371

    PUBMED: 25955013; PMC: 4425491; DOI: 10.1371/journal.pone.0126371

  • Characterization of an Additional Splice Acceptor Site Introduced into CYP4B1 in Hominoidae during Evolution.

    Schmidt EM, Wiek C, Parkinson OT, Roellecke K, Freund M, Gombert M, Lottmann N, Steward CA, Kramm CM, Yarov-Yarovoy V et al.

    PloS one 2015;10;9;e0137110

    PUBMED: 26355749; PMC: 4565547; DOI: 10.1371/journal.pone.0137110

  • Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.

    Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L et al.

    Genome research 2015;25;1;41-56

    PUBMED: 25294244; PMC: 4317172; DOI: 10.1101/gr.173435.114

  • Climate induces seasonality in pneumococcal transmission.

    Numminen E, Chewapreecha C, Turner C, Goldblatt D, Nosten F, Bentley SD, Turner P and Corander J

    Scientific reports 2015;5;11344

    PUBMED: 26067932; PMC: 4464306; DOI: 10.1038/srep11344

  • Clinical and molecular characterization of a novel PLIN1 frameshift mutation identified in patients with familial partial lipodystrophy.

    Kozusko K, Tsang V, Bottomley W, Cho YH, Gandotra S, Mimmack ML, Lim K, Isaac I, Patel S, Saudek V et al.

    Diabetes 2015;64;1;299-310

    PUBMED: 25114292; PMC: 4361744; DOI: 10.2337/db14-0104

  • Combinations of PARP Inhibitors with Temozolomide Drive PARP1 Trapping and Apoptosis in Ewing's Sarcoma.

    Gill SJ, Travers J, Pshenichnaya I, Kogera FA, Barthorpe S, Mironenko T, Richardson L, Benes CH, Stratton MR, McDermott U et al.

    PloS one 2015;10;10;e0140988

    PUBMED: 26505995; PMC: 4624427; DOI: 10.1371/journal.pone.0140988

  • Comparative Analysis of Whole-Genome Sequences of Influenza A(H1N1)pdm09 Viruses Isolated from Hospitalized and Nonhospitalized Patients Identifies Missense Mutations That Might Be Associated with Patient Hospital Admissions in Finland during 2009 to 2014.

    Mishel P, Ojala T, Benner C, Lakspere T, Bychkov D, Jalovaara P, Kakkola L, Kallio-Kokko H, Kantele A, Kankainen M et al.

    Genome announcements 2015;3;4

    PUBMED: 26227588; PMC: 4520887; DOI: 10.1128/genomeA.00676-15

  • Comprehensive comparative homeobox gene annotation in human and mouse.

    Wilming LG, Boychenko V and Harrow JL

    Database : the journal of biological databases and curation 2015;2015

    PUBMED: 26412852; PMC: 4584094; DOI: 10.1093/database/bav091

  • Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features.

    Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, Panigrahi A, Vermont SJ, Otto TD, Wastling J and Pain A

    PloS one 2015;10;4;e0124473

    PUBMED: 25875305; PMC: 4395442; DOI: 10.1371/journal.pone.0124473

  • Concept selection for phenotypes and diseases using learn to rank.

    Collier N, Oellrich A and Groza T

    Journal of biomedical semantics 2015;6;24

    PUBMED: 26034558; PMC: 4450611; DOI: 10.1186/s13326-015-0019-z

  • Demystifying Escherichia coli pathovars.

    Baker KS

    Nature reviews. Microbiology 2015;13;1;5

    PUBMED: 25482288; DOI: 10.1038/nrmicro3411

  • Design of a study to determine the impact of insecticide resistance on malaria vector control: a multi-country investigation.

    Kleinschmidt I, Mnzava AP, Kafy HT, Mbogo C, Bashir AI, Bigoga J, Adechoubou A, Raghavendra K, Knox TB, Malik EM et al.

    Malaria journal 2015;14;282

    PUBMED: 26194648; PMC: 4508808; DOI: 10.1186/s12936-015-0782-4

  • Dihydroceramide desaturase 1, the gatekeeper of ceramide induced lipotoxicity.

    Rodriguez-Cuenca S, Barbarroja N and Vidal-Puig A

    Biochimica et biophysica acta 2015;1851;1;40-50

    PUBMED: 25283058; DOI: 10.1016/j.bbalip.2014.09.021

  • Draft Genome Sequence of a Fluconazole-Resistant Candida auris Strain from a Candidemia Patient in India.

    Sharma C, Kumar N, Meis JF, Pandey R and Chowdhary A

    Genome announcements 2015;3;4

    PUBMED: 26184929; PMC: 4505117; DOI: 10.1128/genomeA.00722-15

  • Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66.

    Hahn C, Harrison EM, Parkhill J, Holmes MA and Paterson GK

    Genome announcements 2015;3;3

    PUBMED: 26112793; PMC: 4481291; DOI: 10.1128/genomeA.00697-15

  • Elucidation of the RamA regulon in Klebsiella pneumoniae reveals a role in LPS regulation.

    De Majumdar S, Yu J, Fookes M, McAteer SP, Llobet E, Finn S, Spence S, Monahan A, Monaghan A, Kissenpfennig A et al.

    PLoS pathogens 2015;11;1;e1004627

    PUBMED: 25633080; PMC: 4310594; DOI: 10.1371/journal.ppat.1004627

  • Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp.

    Katharios P, Seth-Smith HM, Fehr A, Mateos JM, Qi W, Richter D, Nufer L, Ruetten M, Guevara Soto M, Ziegler U et al.

    Scientific reports 2015;5;17609

    PUBMED: 26639610; PMC: 4671022; DOI: 10.1038/srep17609

  • Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus.

    Laabei M, Uhlemann AC, Lowy FD, Austin ED, Yokoyama M, Ouadi K, Feil E, Thorpe HA, Williams B, Perkins M et al.

    PLoS biology 2015;13;9;e1002229

    PUBMED: 26331877; PMC: 4558032; DOI: 10.1371/journal.pbio.1002229

  • From sequence mapping to genome assemblies.

    Otto TD

    Methods in molecular biology (Clifton, N.J.) 2015;1201;19-50

    PUBMED: 25388106; DOI: 10.1007/978-1-4939-1438-8_2

  • Fucci2a mouse upgrades live cell cycle imaging.

    Bertero A and Vallier L

    Cell cycle (Georgetown, Tex.) 2015;14;7;948-9

    PUBMED: 25807308; PMC: 4613997; DOI: 10.1080/15384101.2015.1006549

  • Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.

    Wu TJ, Schriml LM, Chen QR, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D et al.

    Database : the journal of biological databases and curation 2015;2015;bav032

    PUBMED: 25841438; PMC: 4385274; DOI: 10.1093/database/bav032

  • Genetic association of fetal-hemoglobin levels in individuals with sickle cell disease in Tanzania maps to conserved regulatory elements within the MYB core enhancer.

    Mtatiro SN, Mgaya J, Singh T, Mariki H, Rooks H, Soka D, Mmbando B, Thein SL, Barrett JC, Makani J et al.

    BMC medical genetics 2015;16;4

    PUBMED: 25928412; PMC: 4422446; DOI: 10.1186/s12881-015-0148-3

  • Genetic determinants of anti-malarial acquired immunity in a large multi-centre study.

    Shelton JM, Corran P, Risley P, Silva N, Hubbart C, Jeffreys A, Rowlands K, Craik R, Cornelius V, Hensmann M et al.

    Malaria journal 2015;14;333

    PUBMED: 26314886; PMC: 4552443; DOI: 10.1186/s12936-015-0833-x

  • Genetic Loci Associated with Allergic Sensitization in Lithuanians.

    Šaulienė I, Greičiuvienė J, Šukienė L, Juškevičiūtė N, Benner C, Zinkevičienė A, Ripatti S, Donner K and Kainov D

    PloS one 2015;10;7;e0134188

    PUBMED: 26214689; PMC: 4516305; DOI: 10.1371/journal.pone.0134188

  • Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.

    Reppe S, Wang Y, Thompson WK, McEvoy LK, Schork AJ, Zuber V, LeBlanc M, Bettella F, Mills IG, Desikan RS et al.

    PloS one 2015;10;12;e0144531

    PUBMED: 26695485; PMC: 4687843; DOI: 10.1371/journal.pone.0144531

  • Genetic Variants on Chromosome 1p13.3 Are Associated with Non-ST Elevation Myocardial Infarction and the Expression of DRAM2 in the Finnish Population.

    Salo PP, Vaara S, Kettunen J, Pirinen M, Sarin AP, Huikuri H, Karhunen PJ, Eskola M, Nikus K, Lokki ML et al.

    PloS one 2015;10;10;e0140576

    PUBMED: 26509668; PMC: 4625034; DOI: 10.1371/journal.pone.0140576

  • Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.

    Holt KE, Hamidian M, Kenyon JJ, Wynn MT, Hawkey J, Pickard D and Hall RM

    Genome announcements 2015;3;2

    PUBMED: 25767221; PMC: 4357743; DOI: 10.1128/genomeA.00032-15

  • Genome-wide mapping of Hif-1α binding sites in zebrafish.

    Greenald D, Jeyakani J, Pelster B, Sealy I, Mathavan S and van Eeden FJ

    BMC genomics 2015;16;923

    PUBMED: 26559940; PMC: 4642629; DOI: 10.1186/s12864-015-2169-x

  • Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations.

    Abdallah AM, Hill-Cawthorne GA, Otto TD, Coll F, Guerra-Assunção JA, Gao G, Naeem R, Ansari H, Malas TB, Adroub SA et al.

    Scientific reports 2015;5;15443

    PUBMED: 26487098; PMC: 4614345; DOI: 10.1038/srep15443

  • Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

    Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N et al.

    Nature communications 2015;6;6740

    PUBMED: 25824154; PMC: 4389249; DOI: 10.1038/ncomms7740

  • Heavier smoking may lead to a relative increase in waist circumference: evidence for a causal relationship from a Mendelian randomisation meta-analysis. The CARTA consortium.

    Morris RW, Taylor AE, Fluharty ME, Bjørngaard JH, Åsvold BO, Elvestad Gabrielsen M, Campbell A, Marioni R, Kumari M, Korhonen T et al.

    BMJ open 2015;5;8;e008808

    PUBMED: 26264275; PMC: 4538266; DOI: 10.1136/bmjopen-2015-008808

  • High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma.

    Linnemann C, van Buuren MM, Bies L, Verdegaal EM, Schotte R, Calis JJ, Behjati S, Velds A, Hilkmann H, Atmioui DE et al.

    Nature medicine 2015;21;1;81-5

    PUBMED: 25531942; DOI: 10.1038/nm.3773

  • How plants manage food reserves at night: quantitative models and open questions.

    Scialdone A and Howard M

    Frontiers in plant science 2015;6;204

    PUBMED: 25873925; PMC: 4379750; DOI: 10.3389/fpls.2015.00204

  • Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders.

    Westbury SK, Turro E, Greene D, Lentaigne C, Kelly AM, Bariana TK, Simeoni I, Pillois X, Attwood A, Austin S et al.

    Genome medicine 2015;7;1;36

    PUBMED: 25949529; PMC: 4422517; DOI: 10.1186/s13073-015-0151-5

  • Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus.

    Mahajan A, Sim X, Ng HJ, Manning A, Rivas MA, Highland HM, Locke AE, Grarup N, Im HK, Cingolani P et al.

    PLoS genetics 2015;11;1;e1004876

    PUBMED: 25625282; PMC: 4307976; DOI: 10.1371/journal.pgen.1004876

  • Identification of antigen-specific B cell receptor sequences using public repertoire analysis.

    Trück J, Ramasamy MN, Galson JD, Rance R, Parkhill J, Lunter G, Pollard AJ and Kelly DF

    Journal of immunology (Baltimore, Md. : 1950) 2015;194;1;252-61

    PUBMED: 25392534; PMC: 4272858; DOI: 10.4049/jimmunol.1401405

  • Improving the Sequence Ontology terminology for genomic variant annotation.

    Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR and Eilbeck K

    Journal of biomedical semantics 2015;6;32

    PUBMED: 26229585; PMC: 4520272; DOI: 10.1186/s13326-015-0030-4

  • INFRAFRONTIER--providing mutant mouse resources as research tools for the international scientific community.

    INFRAFRONTIER Consortium

    Nucleic acids research 2015;43;Database issue;D1171-5

    PUBMED: 25414328; PMC: 4383977; DOI: 10.1093/nar/gku1193

  • Inter-individual variability contrasts with regional homogeneity in the human brain DNA methylome.

    Illingworth RS, Gruenewald-Schneider U, De Sousa D, Webb S, Merusi C, Kerr AR, James KD, Smith C, Walker R, Andrews R and Bird AP

    Nucleic acids research 2015;43;2;732-44

    PUBMED: 25572316; PMC: 4333374; DOI: 10.1093/nar/gku1305

  • Is mouse embryonic stem cell technology obsolete?

    Skarnes WC

    Genome biology 2015;16;109

    PUBMED: 26013980; PMC: 4443626; DOI: 10.1186/s13059-015-0673-6

  • Linking gene expression to phenotypes via pathway information.

    Papatheodorou I, Oellrich A and Smedley D

    Journal of biomedical semantics 2015;6;17

    PUBMED: 25901272; PMC: 4404592; DOI: 10.1186/s13326-015-0013-5

  • Loss of Angiopoietin-like 7 diminishes the regeneration capacity of hematopoietic stem and progenitor cells.

    Xiao Y, Wei X, Jiang Z, Wang X, Ye W, Liu X, Zhang M, Xu Y, Wu D, Lai L et al.

    Journal of hematology & oncology 2015;8;7

    PUBMED: 25652910; PMC: 4353465; DOI: 10.1186/s13045-014-0102-4

  • Lymphocyte Perturbations in Malawian Children with Severe and Uncomplicated Malaria.

    Mandala WL, Msefula CL, Gondwe EN, Gilchrist JJ, Graham SM, Pensulo P, Mwimaniwa G, Banda M, Taylor TE, Molyneux EE et al.

    Clinical and vaccine immunology : CVI 2015;23;2;95-103

    PUBMED: 26581890; PMC: 4744922; DOI: 10.1128/CVI.00564-15

  • microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach.

    Macchiaroli N, Cucher M, Zarowiecki M, Maldonado L, Kamenetzky L and Rosenzvit MC

    Parasites & vectors 2015;8;83

    PUBMED: 25656283; PMC: 4326209; DOI: 10.1186/s13071-015-0686-8

  • Missense Mutation R338W in ARHGEF9 in a Family with X-linked Intellectual Disability with Variable Macrocephaly and Macro-Orchidism.

    Long P, May MM, James VM, Grannò S, Johnson JP, Tarpey P, Stevenson RE, Harvey K, Schwartz CE and Harvey RJ

    Frontiers in molecular neuroscience 2015;8;83

    PUBMED: 26834553; PMC: 4719118; DOI: 10.3389/fnmol.2015.00083

  • Modulation of genetic associations with serum urate levels by body-mass-index in humans.

    Huffman JE, Albrecht E, Teumer A, Mangino M, Kapur K, Johnson T, Kutalik Z, Pirastu N, Pistis G, Lopez LM et al.

    PloS one 2015;10;3;e0119752

    PUBMED: 25811787; PMC: 4374966; DOI: 10.1371/journal.pone.0119752

  • Novel R pipeline for analyzing Biolog Phenotypic MicroArray data.

    Vehkala M, Shubin M, Connor TR, Thomson NR and Corander J

    PloS one 2015;10;3;e0118392

    PUBMED: 25786143; PMC: 4365023; DOI: 10.1371/journal.pone.0118392

  • Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov.

    Tong SY, Schaumburg F, Ellington MJ, Corander J, Pichon B, Leendertz F, Bentley SD, Parkhill J, Holt DC, Peters G and Giffard PM

    International journal of systematic and evolutionary microbiology 2015;65;Pt 1;15-22

    PUBMED: 25269845; PMC: 4298100; DOI: 10.1099/ijs.0.062752-0

  • Pharmacogenomics of hypertension: a genome‐wide, placebo‐controlled cross‐over study, using four classes of antihypertensive drugs.

    Hiltunen TP, Donner KM, Sarin AP, Saarela J, Ripatti S, Chapman AB, Gums JG, Gong Y, Cooper-DeHoff RM, Frau F et al.

    Journal of the American Heart Association 2015;4;1;e001521

    PUBMED: 25622599; PMC: 4330076; DOI: 10.1161/JAHA.115.001778

  • Phylogenetic reconstruction by cross-species chromosome painting and G-banding in four species of Phyllostomini tribe (Chiroptera, Phyllostomidae) in the Brazilian Amazon: an independent evidence for monophyly.

    Ribas TF, Rodrigues LR, Nagamachi CY, Gomes AJ, Rissino Jd, O'Brien PC, Yang F, Ferguson-Smith MA and Pieczarka JC

    PloS one 2015;10;3;e0122845

    PUBMED: 25806812; PMC: 4373847; DOI: 10.1371/journal.pone.0122845

  • PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.

    Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR and Clark TG

    BMC bioinformatics 2015;16;155

    PUBMED: 25968323; PMC: 4429496; DOI: 10.1186/s12859-015-0603-3

  • piggyBac transposon-based insertional mutagenesis in mouse haploid embryonic stem cells.

    Pettitt SJ, Tan EP and Yusa K

    Methods in molecular biology (Clifton, N.J.) 2015;1239;15-28

    PUBMED: 25408399; DOI: 10.1007/978-1-4939-1862-1_2

  • PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

    Schwach F, Bushell E, Gomes AR, Anar B, Girling G, Herd C, Rayner JC and Billker O

    Nucleic acids research 2015;43;Database issue;D1176-82

    PUBMED: 25593348; PMC: 4383951; DOI: 10.1093/nar/gku1143

  • Points to consider in the development of seed stocks of pluripotent stem cells for clinical applications: International Stem Cell Banking Initiative (ISCBI).

    Andrews PW, Baker D, Benvinisty N, Miranda B, Bruce K, Brüstle O, Choi M, Choi YM, Crook JM, de Sousa PA et al.

    Regenerative medicine 2015;10;2 Suppl;1-44

    PUBMED: 25675265; DOI: 10.2217/rme.14.93

  • Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.

    Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM, Multiple Tissue Human Expression Resource et al.

    Genome biology 2015;16;290

    PUBMED: 26699896; PMC: 4699357; DOI: 10.1186/s13059-015-0856-1

  • Prediction and analysis of intrinsically disordered proteins.

    Punta M, Simon I and Dosztányi Z

    Methods in molecular biology (Clifton, N.J.) 2015;1261;35-59

    PUBMED: 25502193; DOI: 10.1007/978-1-4939-2230-7_3

  • Presence of the knockdown resistance mutation, Vgsc-1014F in Anopheles gambiae and An. arabiensis in western Kenya.

    Ochomo E, Subramaniam K, Kemei B, Rippon E, Bayoh NM, Kamau L, Atieli F, Vulule JM, Ouma C, Gimnig J et al.

    Parasites & vectors 2015;8;616

    PUBMED: 26626424; PMC: 4666190; DOI: 10.1186/s13071-015-1223-5

  • Prevalence of dyslipidaemia and associated risk factors in a rural population in South-Western Uganda: a community based survey.

    Asiki G, Murphy GA, Baisley K, Nsubuga RN, Karabarinde A, Newton R, Seeley J, Young EH, Kamali A and Sandhu MS

    PloS one 2015;10;5;e0126166

    PUBMED: 25974077; PMC: 4431752; DOI: 10.1371/journal.pone.0126166

  • Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case.

    Popovic D, Sifrim A, Davis J, Moreau Y and De Moor B

    BMC bioinformatics 2015;16 Suppl 4;S2

    PUBMED: 25734591; PMC: 4347616; DOI: 10.1186/1471-2105-16-S4-S2

  • Regulation of systemic energy homeostasis by serotonin in adipose tissues.

    Oh CM, Namkung J, Go Y, Shong KE, Kim K, Kim H, Park BY, Lee HW, Jeon YH, Song J et al.

    Nature communications 2015;6;6794

    PUBMED: 25864946; PMC: 4403443; DOI: 10.1038/ncomms7794

  • Rfam: annotating families of non-coding RNA sequences.

    Daub J, Eberhardt RY, Tate JG and Burge SW

    Methods in molecular biology (Clifton, N.J.) 2015;1269;349-63

    PUBMED: 25577390; DOI: 10.1007/978-1-4939-2291-8_22

  • RNAcentral: an international database of ncRNA sequences.

    RNAcentral Consortium, Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD et al.

    Nucleic acids research 2015;43;Database issue;D123-9

    PUBMED: 25352543; PMC: 4384043; DOI: 10.1093/nar/gku991

  • Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

    Rowe W, Baker KS, Verner-Jeffreys D, Baker-Austin C, Ryan JJ, Maskell D and Pearce G

    PloS one 2015;10;7;e0133492

    PUBMED: 26197475; PMC: 4510569; DOI: 10.1371/journal.pone.0133492

  • Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo.

    Arand J, Wossidlo M, Lepikhov K, Peat JR, Reik W and Walter J

    Epigenetics & chromatin 2015;8;1;1

    PUBMED: 25621012; PMC: 4304184; DOI: 10.1186/1756-8935-8-1

  • Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation.

    Soler Artigas M, Wain LV, Miller S, Kheirallah AK, Huffman JE, Ntalla I, Shrine N, Obeidat M, Trochet H, McArdle WL et al.

    Nature communications 2015;6;8658

    PUBMED: 26635082; PMC: 4686825; DOI: 10.1038/ncomms9658

  • Soluble LR11/SorLA represses thermogenesis in adipose tissue and correlates with BMI in humans.

    Whittle AJ, Jiang M, Peirce V, Relat J, Virtue S, Ebinuma H, Fukamachi I, Yamaguchi T, Takahashi M, Murano T et al.

    Nature communications 2015;6;8951

    PUBMED: 26584636; PMC: 4673879; DOI: 10.1038/ncomms9951

  • Special issue on bio-ontologies and phenotypes.

    Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M and Shah NH

    Journal of biomedical semantics 2015;6;40

    PUBMED: 26682035; PMC: 4682270; DOI: 10.1186/s13326-015-0040-2

  • Strain Selection for Generation of O-Antigen-Based Glycoconjugate Vaccines against Invasive Nontyphoidal Salmonella Disease.

    Lanzilao L, Stefanetti G, Saul A, MacLennan CA, Micoli F and Rondini S

    PloS one 2015;10;10;e0139847

    PUBMED: 26445460; PMC: 4596569; DOI: 10.1371/journal.pone.0139847

  • Structure, dynamics, assembly, and evolution of protein complexes.

    Marsh JA and Teichmann SA

    Annual review of biochemistry 2015;84;551-75

    PUBMED: 25494300; DOI: 10.1146/annurev-biochem-060614-034142

  • Systematic discovery of probiotics.

    Forster SC and Lawley TD

    Nature biotechnology 2015;33;1;47-9

    PUBMED: 25574637; DOI: 10.1038/nbt.3111

  • Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty.

    Cousminer DL, Leinonen JT, Sarin AP, Chheda H, Surakka I, Wehkalampi K, Ellonen P, Ripatti S, Dunkel L, Palotie A and Widén E

    PloS one 2015;10;6;e0128524

    PUBMED: 26030606; PMC: 4452275; DOI: 10.1371/journal.pone.0128524

  • TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport.

    Schmidts M, Hou Y, Cortés CR, Mans DA, Huber C, Boldt K, Patel M, van Reeuwijk J, Plaza JM, van Beersum SE et al.

    Nature communications 2015;6;7074

    PUBMED: 26044572; PMC: 4468853; DOI: 10.1038/ncomms8074

  • Third Report on Chicken Genes and Chromosomes 2015.

    Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT et al.

    Cytogenetic and genome research 2015;145;2;78-179

    PUBMED: 26282327; PMC: 5120589; DOI: 10.1159/000430927

  • Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer.

    Hong MK, Macintyre G, Wedge DC, Van Loo P, Patel K, Lunke S, Alexandrov LB, Sloggett C, Cmero M, Marass F et al.

    Nature communications 2015;6;6605

    PUBMED: 25827447; PMC: 4396364; DOI: 10.1038/ncomms7605

  • Transfer of scarlet fever-associated elements into the group A Streptococcus M1T1 clone.

    Ben Zakour NL, Davies MR, You Y, Chen JH, Forde BM, Stanton-Cook M, Yang R, Cui Y, Barnett TC, Venturini C et al.

    Scientific reports 2015;5;15877

    PUBMED: 26522788; PMC: 4629146; DOI: 10.1038/srep15877

  • Turner et al. Reply to "Emergence of the Same Successful Clade among Distinct Populations of emm89 Streptococcus pyogenes in Multiple Geographic Regions".

    Turner CE, Lamagni T, Holden MT, David S, Jones MD, Game L, Efstratiou A and Sriskandan S

    mBio 2015;6;6;e01883-15

    PUBMED: 26628727; PMC: 4669389; DOI: 10.1128/mBio.01883-15

  • Ubiquitin specific protease 21 is dispensable for normal development, hematopoiesis and lymphocyte differentiation.

    Pannu J, Belle JI, Förster M, Duerr CU, Shen S, Kane L, Harcourt K, Fritz JH, Clare S and Nijnik A

    PloS one 2015;10;2;e0117304

    PUBMED: 25680095; PMC: 4332479; DOI: 10.1371/journal.pone.0117304

  • Using population data for assessing next-generation sequencing performance.

    Houniet DT, Rahman TJ, Al Turki S, Hurles ME, Xu Y, Goodship J, Keavney B and Santibanez Koref M

    Bioinformatics (Oxford, England) 2015;31;1;56-61

    PUBMED: 25236458; PMC: 4271148; DOI: 10.1093/bioinformatics/btu606

  • Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis.

    Landy J, Walker AW, Li JV, Al-Hassi HO, Ronde E, English NR, Mann ER, Bernardo D, McLaughlin SD, Parkhill J et al.

    Scientific reports 2015;5;12955

    PUBMED: 26264409; PMC: 4532993; DOI: 10.1038/srep12955

  • Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.

    Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MT, Parkhill J, Langford PR, Rycroft AN et al.

    Frontiers in microbiology 2015;6;1191

    PUBMED: 26583006; PMC: 4631834; DOI: 10.3389/fmicb.2015.01191

  • Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy.

    De Smet B, Sarovich DS, Price EP, Mayo M, Theobald V, Kham C, Heng S, Thong P, Holden MT, Parkhill J et al.

    Journal of clinical microbiology 2015;53;1;323-6

    PUBMED: 25392354; PMC: 4290968; DOI: 10.1128/JCM.02574-14

  • Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi.

    Glynn JR, Guerra-Assunção JA, Houben RM, Sichali L, Mzembe T, Mwaungulu LK, Mwaungulu JN, McNerney R, Khan P, Parkhill J et al.

    PloS one 2015;10;7;e0132840

    PUBMED: 26181760; PMC: 4504505; DOI: 10.1371/journal.pone.0132840

2014

  • A high-throughput in vivo micronucleus assay for genome instability screening in mice.

    Balmus G, Karp NA, Ng BL, Jackson SP, Adams DJ and McIntyre RE

    Nature protocols 2014;10;1;205-15

    PUBMED: 25551665; PMC: 4806852; DOI: 10.1038/nprot.2015.010

  • Large-scale discovery of novel genetic causes of developmental disorders.

    Deciphering Developmental Disorders Study

    Nature 2014;519;7542;223-8

    PUBMED: 25533962; PMC: 5955210; DOI: 10.1038/nature14135

  • Sequence-dependent off-target inhibition of TLR7/8 sensing by synthetic microRNA inhibitors.

    Sarvestani ST, Stunden HJ, Behlke MA, Forster SC, McCoy CE, Tate MD, Ferrand J, Lennox KA, Latz E, Williams BR and Gantier MP

    Nucleic acids research 2014;43;2;1177-88

    PUBMED: 25539920; PMC: 4333393; DOI: 10.1093/nar/gku1343

  • Patterns of genome evolution that have accompanied host adaptation in Salmonella.

    Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;112;3;863-8

    PUBMED: 25535353; PMC: 4311825; DOI: 10.1073/pnas.1416707112

  • Complete genome sequence of BS49 and draft genome sequence of BS34A, Bacillus subtilis strains carrying Tn916.

    Browne HP, Anvar SY, Frank J, Lawley TD, Roberts AP and Smits WK

    FEMS microbiology letters 2014;362;3;1-4

    PUBMED: 25673660; DOI: 10.1093/femsle/fnu050

  • FTO genetic variants, dietary intake and body mass index: insights from 177,330 individuals.

    Qi Q, Kilpeläinen TO, Downer MK, Tanaka T, Smith CE, Sluijs I, Sonestedt E, Chu AY, Renström F, Lin X et al.

    Human molecular genetics 2014;23;25;6961-72

    PUBMED: 25104851; PMC: 4271061; DOI: 10.1093/hmg/ddu411

  • A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.

    Bratcher HB, Corton C, Jolley KA, Parkhill J and Maiden MC

    BMC genomics 2014;15;1138

    PUBMED: 25523208; PMC: 4377854; DOI: 10.1186/1471-2164-15-1138

  • Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Claessens A, Hamilton WL, Kekre M, Otto TD, Faizullabhoy A, Rayner JC and Kwiatkowski D

    PLoS genetics 2014;10;12;e1004812

    PUBMED: 25521112; PMC: 4270465; DOI: 10.1371/journal.pgen.1004812

  • Molecular evolution of broadly neutralizing Llama antibodies to the CD4-binding site of HIV-1.

    McCoy LE, Rutten L, Frampton D, Anderson I, Granger L, Bashford-Rogers R, Dekkers G, Strokappe NM, Seaman MS, Koh W et al.

    PLoS pathogens 2014;10;12;e1004552

    PUBMED: 25522326; PMC: 4270772; DOI: 10.1371/journal.ppat.1004552

  • Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data.

    Wright CF, Fitzgerald TW, Jones WD, Clayton S, McRae JF, van Kogelenberg M, King DA, Ambridge K, Barrett DM, Bayzetinova T et al.

    Lancet (London, England) 2014;385;9975;1305-14

    PUBMED: 25529582; PMC: 4392068; DOI: 10.1016/S0140-6736(14)61705-0

  • No expectation to share incidental findings in genomic research.

    Middleton A, Morley KI, Bragin E, Firth HV, Hurles ME, Wright CF, Parker M and Deciphering Developmental Disorders Study

    Lancet (London, England) 2014;385;9975;1289-90

    PUBMED: 25529584; DOI: 10.1016/S0140-6736(14)62119-X

  • Testing the Toxicofera: comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system.

    Hargreaves AD, Swain MT, Logan DW and Mulley JF

    Toxicon : official journal of the International Society on Toxinology 2014;92;140-56

    PUBMED: 25449103; DOI: 10.1016/j.toxicon.2014.10.004

  • Nonsense mutations in the shelterin complex genes ACD and TERF2IP in familial melanoma.

    Aoude LG, Pritchard AL, Robles-Espinoza CD, Wadt K, Harland M, Choi J, Gartside M, Quesada V, Johansson P, Palmer JM et al.

    Journal of the National Cancer Institute 2014;107;2

    PUBMED: 25505254; PMC: 4334787; DOI: 10.1093/jnci/dju408

  • Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

    Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA and Reik W

    Cell reports 2014;9;6;1990-2000

    PUBMED: 25497087; PMC: 4542306; DOI: 10.1016/j.celrep.2014.11.034

  • Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.

    Rawlings ND, Barrett AJ and Bateman A

    Current protocols in bioinformatics 2014;48;1.25.1-1.25.33

    PUBMED: 25501939; DOI: 10.1002/0471250953.bi0125s48

  • Drug resistance. Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance.

    Mok S, Ashley EA, Ferreira PE, Zhu L, Lin Z, Yeo T, Chotivanich K, Imwong M, Pukrittayakamee S, Dhorda M et al.

    Science (New York, N.Y.) 2014;347;6220;431-5

    PUBMED: 25502316; PMC: 5642863; DOI: 10.1126/science.1260403

  • Genome-scale RNAi screens for high-throughput phenotyping in bloodstream-form African trypanosomes.

    Glover L, Alsford S, Baker N, Turner DJ, Sanchez-Flores A, Hutchinson S, Hertz-Fowler C, Berriman M and Horn D

    Nature protocols 2014;10;1;106-33

    PUBMED: 25502887; DOI: 10.1038/nprot.2015.005

  • Off-target assessment of CRISPR-Cas9 guiding RNAs in human iPS and mouse ES cells.

    Tan EP, Li Y, Velasco-Herrera Mdel C, Yusa K and Bradley A

    Genesis (New York, N.Y. : 2000) 2014;53;2;225-36

    PUBMED: 25378133; DOI: 10.1002/dvg.22835

  • Pathogens' exploitation of the intestinal food web.

    Pham N TA and Lawley TD

    Cell host & microbe 2014;16;6;703-5

    PUBMED: 25498340; DOI: 10.1016/j.chom.2014.11.012

  • Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.

    Tong SY, Holden MT, Nickerson EK, Cooper BS, Köser CU, Cori A, Jombart T, Cauchemez S, Fraser C, Wuthiekanun V et al.

    Genome research 2014;25;1;111-8

    PUBMED: 25491771; PMC: 4317166; DOI: 10.1101/gr.174730.114

  • International coordination of large-scale human induced pluripotent stem cell initiatives: Wellcome Trust and ISSCR workshops white paper.

    Soares FA, Sheldon M, Rao M, Mummery C and Vallier L

    Stem cell reports 2014;3;6;931-9

    PUBMED: 25496616; PMC: 4263998; DOI: 10.1016/j.stemcr.2014.11.006

  • Prenatal exome sequencing for fetuses with structural abnormalities: the next step.

    Hillman SC, Willams D, Carss KJ, McMullan DJ, Hurles ME and Kilby MD

    Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology 2014;45;1;4-9

    PUBMED: 25157891; DOI: 10.1002/uog.14653

  • A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.

    Rad R, Rad L, Wang W, Strong A, Ponstingl H, Bronner IF, Mayho M, Steiger K, Weber J, Hieber M et al.

    Nature genetics 2014;47;1;47-56

    PUBMED: 25485836; DOI: 10.1038/ng.3164

  • What helminth genomes have taught us about parasite evolution.

    Zarowiecki M and Berriman M

    Parasitology 2014;142 Suppl 1;S85-97

    PUBMED: 25482650; PMC: 4413821; DOI: 10.1017/S0031182014001449

  • A panel of recombinant monoclonal antibodies against zebrafish neural receptors and secreted proteins suitable for wholemount immunostaining.

    Staudt N, Müller-Sienerth N, Fane-Dremucheva A, Yusaf SP, Millrine D and Wright GJ

    Biochemical and biophysical research communications 2014;456;1;527-33

    PUBMED: 25490391; PMC: 4297863; DOI: 10.1016/j.bbrc.2014.11.123

  • Differential PfEMP1 expression is associated with cerebral malaria pathology.

    Tembo DL, Nyoni B, Murikoli RV, Mukaka M, Milner DA, Berriman M, Rogerson SJ, Taylor TE, Molyneux ME, Mandala WL et al.

    PLoS pathogens 2014;10;12;e1004537

    PUBMED: 25473835; PMC: 4256257; DOI: 10.1371/journal.ppat.1004537

  • Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.

    Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P et al.

    Genome biology and evolution 2014;6;12;3281-94

    PUBMED: 25480686; PMC: 4986459; DOI: 10.1093/gbe/evu263

  • The African Genome Variation Project shapes medical genetics in Africa.

    Gurdasani D, Carstensen T, Tekola-Ayele F, Pagani L, Tachmazidou I, Hatzikotoulas K, Karthikeyan S, Iles L, Pollard MO, Choudhury A et al.

    Nature 2014;517;7534;327-32

    PUBMED: 25470054; PMC: 4297536; DOI: 10.1038/nature13997

  • The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades.

    Hallast P, Batini C, Zadik D, Maisano Delser P, Wetton JH, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Destro Bisol G, Dupuy BM et al.

    Molecular biology and evolution 2014;32;3;661-73

    PUBMED: 25468874; PMC: 4327154; DOI: 10.1093/molbev/msu327

  • Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

    Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;48;17230-5

    PUBMED: 25385592; PMC: 4260561; DOI: 10.1073/pnas.1410083111

  • The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.

    Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M et al.

    Nature biotechnology 2014;32;12;1250-5

    PUBMED: 25402615; PMC: 4262547; DOI: 10.1038/nbt.3079

  • Common genetic variants highlight the role of insulin resistance and body fat distribution in type 2 diabetes, independent of obesity.

    Scott RA, Fall T, Pasko D, Barker A, Sharp SJ, Arriola L, Balkau B, Barricarte A, Barroso I, Boeing H et al.

    Diabetes 2014;63;12;4378-4387

    PUBMED: 24947364; PMC: 4241116; DOI: 10.2337/db14-0319

  • Dysfunction of phospholipase Cγ in immune disorders and cancer.

    Koss H, Bunney TD, Behjati S and Katan M

    Trends in biochemical sciences 2014;39;12;603-11

    PUBMED: 25456276; DOI: 10.1016/j.tibs.2014.09.004

  • Estimation of epistatic variance components and heritability in founder populations and crosses.

    Young AI and Durbin R

    Genetics 2014;198;4;1405-16

    PUBMED: 25326236; PMC: 4256760; DOI: 10.1534/genetics.114.170795

  • Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins.

    Buil A, Brown AA, Lappalainen T, Viñuela A, Davies MN, Zheng HF, Richards JB, Glass D, Small KS, Durbin R et al.

    Nature genetics 2014;47;1;88-91

    PUBMED: 25436857; PMC: 4643454; DOI: 10.1038/ng.3162

  • Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies.

    Kurbasic A, Poveda A, Chen Y, Agren A, Engberg E, Hu FB, Johansson I, Barroso I, Brändström A, Hallmans G et al.

    Current nutrition reports 2014;3;4;400-411

    PUBMED: 25396097; PMC: 4225623; DOI: 10.1007/s13668-014-0100-8

  • Genome-wide association study of sleep duration in the Finnish population.

    Ollila HM, Kettunen J, Pietiläinen O, Aho V, Silander K, Kronholm E, Perola M, Lahti J, Räikkönen K, Widen E et al.

    Journal of sleep research 2014;23;6;609-618

    PUBMED: 25109461; DOI: 10.1111/jsr.12175

  • Insights into cancer biology through next-generation sequencing.

    Nik-Zainal S

    Clinical medicine (London, England) 2014;14 Suppl 6;s71-7

    PUBMED: 25468925; DOI: 10.7861/clinmedicine.14-6-s71

  • Metabolic signatures of adiposity in young adults: Mendelian randomization analysis and effects of weight change.

    Würtz P, Wang Q, Kangas AJ, Richmond RC, Skarp J, Tiainen M, Tynkkynen T, Soininen P, Havulinna AS, Kaakinen M et al.

    PLoS medicine 2014;11;12;e1001765

    PUBMED: 25490400; PMC: 4260795; DOI: 10.1371/journal.pmed.1001765

  • Mutations in PLK4, encoding a master regulator of centriole biogenesis, cause microcephaly, growth failure and retinopathy.

    Martin CA, Ahmad I, Klingseisen A, Hussain MS, Bicknell LS, Leitch A, Nürnberg G, Toliat MR, Murray JE, Hunt D et al.

    Nature genetics 2014;46;12;1283-92

    PUBMED: 25344692; PMC: 4676084; DOI: 10.1038/ng.3122

  • Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia.

    Sansom SN, Shikama-Dorn N, Zhanybekova S, Nusspaumer G, Macaulay IC, Deadman ME, Heger A, Ponting CP and Holländer GA

    Genome research 2014;24;12;1918-31

    PUBMED: 25224068; PMC: 4248310; DOI: 10.1101/gr.171645.113

  • Stratification by smoking status reveals an association of CHRNA5-A3-B4 genotype with body mass index in never smokers.

    Taylor AE, Morris RW, Fluharty ME, Bjorngaard JH, Åsvold BO, Gabrielsen ME, Campbell A, Marioni R, Kumari M, Hällfors J et al.

    PLoS genetics 2014;10;12;e1004799

    PUBMED: 25474695; PMC: 4256159; DOI: 10.1371/journal.pgen.1004799

  • Human post-mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes.

    Bayés À, Collins MO, Galtrey CM, Simonnet C, Roy M, Croning MD, Gou G, van de Lagemaat LN, Milward D, Whittle IR et al.

    Molecular brain 2014;7;88

    PUBMED: 25429717; PMC: 4271336; DOI: 10.1186/s13041-014-0088-4

  • Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.

    Nigro SJ, Holt KE, Pickard D and Hall RM

    The Journal of antimicrobial chemotherapy 2014;70;4;1259-61

    PUBMED: 25433005; PMC: 4356202; DOI: 10.1093/jac/dku486

  • Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells.

    Dolatshad H, Pellagatti A, Fernandez-Mercado M, Yip BH, Malcovati L, Attwood M, Przychodzen B, Sahgal N, Kanapin AA, Lockstone H et al.

    Leukemia 2014;29;5;1092-103

    PUBMED: 25428262; PMC: 4430703; DOI: 10.1038/leu.2014.331

  • Host genetics of Epstein-Barr virus infection, latency and disease.

    Houldcroft CJ and Kellam P

    Reviews in medical virology 2014;25;2;71-84

    PUBMED: 25430668; PMC: 4407908; DOI: 10.1002/rmv.1816

  • Inactivating mutations in NPC1L1 and protection from coronary heart disease.

    Myocardial Infarction Genetics Consortium Investigators

    The New England journal of medicine 2014;371;22;2072-82

    PUBMED: 25390462; PMC: 4335708; DOI: 10.1056/NEJMoa1405386

  • KLF2 mutation is the most frequent somatic change in splenic marginal zone lymphoma and identifies a subset with distinct genotype.

    Clipson A, Wang M, de Leval L, Ashton-Key M, Wotherspoon A, Vassiliou G, Bolli N, Grove C, Moody S, Escudero-Ibarz L et al.

    Leukemia 2014;29;5;1177-85

    PUBMED: 25428260; DOI: 10.1038/leu.2014.330

  • Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

    Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G et al.

    Science (New York, N.Y.) 2014;347;6217;1258522

    PUBMED: 25554792; PMC: 4380271; DOI: 10.1126/science.1258522

  • A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster.

    Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K, Ohnishi M, Hayashi T and Thomson NR

    DNA research : an international journal for rapid publication of reports on genes and genomes 2014;22;1;101-7

    PUBMED: 25428893; PMC: 4379981; DOI: 10.1093/dnares/dsu043

  • Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum.

    Vaidya AB, Morrisey JM, Zhang Z, Das S, Daly TM, Otto TD, Spillman NJ, Wyvratt M, Siegl P, Marfurt J et al.

    Nature communications 2014;5;5521

    PUBMED: 25422853; PMC: 4263321; DOI: 10.1038/ncomms6521

  • Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells.

    Tokunaga M, Kokubu C, Maeda Y, Sese J, Horie K, Sugimoto N, Kinoshita T, Yusa K and Takeda J

    BMC genomics 2014;15;1016

    PUBMED: 25418962; PMC: 4301880; DOI: 10.1186/1471-2164-15-1016

  • A comparative encyclopedia of DNA elements in the mouse genome.

    Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD et al.

    Nature 2014;515;7527;355-64

    PUBMED: 25409824; PMC: 4266106; DOI: 10.1038/nature13992

  • Nongenetic stochastic expansion of JAK2V617F-homozygous subclones in polycythemia vera?

    Godfrey AL, Nangalia J, Baxter EJ, Massie CE, Kent DG, Papaemmanuil E, Campbell PJ and Green AR

    Blood 2014;124;22;3332-4

    PUBMED: 25414437; PMC: 4239339; DOI: 10.1182/blood-2014-09-603043

  • Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

    Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD et al.

    PLoS genetics 2014;10;11;e1004798

    PUBMED: 25411781; PMC: 4238955; DOI: 10.1371/journal.pgen.1004798

  • Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, Parkhill J and Harris SR

    Nucleic acids research 2014;43;3;e15

    PUBMED: 25414349; PMC: 4330336; DOI: 10.1093/nar/gku1196

  • Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation.

    Saksouk N, Barth TK, Ziegler-Birling C, Olova N, Nowak A, Rey E, Mateos-Langerak J, Urbach S, Reik W, Torres-Padilla ME et al.

    Molecular cell 2014;56;4;580-94

    PUBMED: 25457167; DOI: 10.1016/j.molcel.2014.10.001

  • Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping.

    Mezzavilla M, Geppert M, Tyler-Smith C, Roewer L and Xue Y

    Forensic science international. Genetics 2014;15;115-20

    PUBMED: 25435155; PMC: 4312352; DOI: 10.1016/j.fsigen.2014.11.005

  • Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance.

    Davies MR, Holden MT, Coupland P, Chen JH, Venturini C, Barnett TC, Zakour NL, Tse H, Dougan G, Yuen KY and Walker MJ

    Nature genetics 2014;47;1;84-7

    PUBMED: 25401300; DOI: 10.1038/ng.3147

  • Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

    Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A and Tress ML

    Human molecular genetics 2014;23;22;5866-78

    PUBMED: 24939910; PMC: 4204768; DOI: 10.1093/hmg/ddu309

  • Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character.

    Fish MB, Nakayama T, Fisher M, Hirsch N, Cox A, Reeder R, Carruthers S, Hall A, Stemple DL and Grainger RM

    Developmental biology 2014;395;2;317-30

    PUBMED: 25224223; PMC: 4267880; DOI: 10.1016/j.ydbio.2014.09.004

  • Antibiotics and Collateral Damage

    MATHER,A. E.;

    Science 2014;344;6183;472-3

    DOI: 10.1126/science.1252914

  • Differential and limited expression of mutant alleles in multiple myeloma.

    Rashid NU, Sperling AS, Bolli N, Wedge DC, Van Loo P, Tai YT, Shammas MA, Fulciniti M, Samur MK, Richardson PG et al.

    Blood 2014;124;20;3110-7

    PUBMED: 25237203; PMC: 4231420; DOI: 10.1182/blood-2014-04-569327

  • Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011.

    Knetsch CW, Connor TR, Mutreja A, van Dorp SM, Sanders IM, Browne HP, Harris D, Lipman L, Keessen EC, Corver J et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2014;19;45;20954

    PUBMED: 25411691; PMC: 4518193; DOI: 10.2807/1560-7917.es2014.19.45.20954

  • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.

    Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ and Walker AW

    BMC biology 2014;12;87

    PUBMED: 25387460; PMC: 4228153; DOI: 10.1186/s12915-014-0087-z

  • Genome-wide association studies of glycaemic traits: A MAGICal journey

    Florez,J.C.; and BARROSO,I.

    Frontiers in Diabetes 2014;23;42-57

    DOI: 10.1159/000362466

  • Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.

    von Mentzer A, Connor TR, Wieler LH, Semmler T, Iguchi A, Thomson NR, Rasko DA, Joffre E, Corander J, Pickard D et al.

    Nature genetics 2014;46;12;1321-6

    PUBMED: 25383970; DOI: 10.1038/ng.3145

  • Recombination: genomic mix 'n' match.

    Boinett CJ and Cain AK

    Nature reviews. Microbiology 2014;12;12;795

    PUBMED: 25383603; DOI: 10.1038/nrmicro3388

  • Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection.

    Mather AE, Baker KS, McGregor H, Coupland P, Mather PL, Deheer-Graham A, Parkhill J, Bracegirdle P, Russell JE and Thomson NR

    Lancet (London, England) 2014;384;9955;1720

    PUBMED: 25441203; DOI: 10.1016/S0140-6736(14)61790-6

  • Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol.

    Bolli N, Manes N, McKerrell T, Chi J, Park N, Gundem G, Quail MA, Sathiaseelan V, Herman B, Crawley C et al.

    Haematologica 2014;100;2;214-22

    PUBMED: 25381129; PMC: 4803131; DOI: 10.3324/haematol.2014.113381

  • Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants.

    Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE, Ritchie GR, Southam L, Gilly A, Tachmazidou I, Fatumo S et al.

    Nature communications 2014;5;5345

    PUBMED: 25373335; PMC: 4242463; DOI: 10.1038/ncomms6345

  • Genome wide association study of fetal hemoglobin in sickle cell anemia in Tanzania.

    Mtatiro SN, Singh T, Rooks H, Mgaya J, Mariki H, Soka D, Mmbando B, Msaki E, Kolder I, Thein SL et al.

    PloS one 2014;9;11;e111464

    PUBMED: 25372704; PMC: 4221031; DOI: 10.1371/journal.pone.0111464

  • Whole Genome Sequencing of a Methicillin-Resistant Staphylococcus aureus Pseudo-Outbreak in a Professional Football Team.

    Anderson DJ, Harris SR, Godofsky E, Toriscelli T, Rude TH, Elder K, Sexton DJ, Pellman EJ, Mayer T, Fowler VG and Peacock SJ

    Open forum infectious diseases 2014;1;3;ofu096

    PUBMED: 25734164; PMC: 4324220; DOI: 10.1093/ofid/ofu096

  • Conceptual issues for screening in the genomic era - time for an update?

    WRIGHT,C.F. and Zimmern,R.L.

    Epidemiology Biostatistics and Public Health 2014;11;4;1-8

    DOI: 10.2427/9944; URL: https://ebph.it/article/view/9944/10123

  • Human genetics: pre-Columbian Pacific contact.

    Tyler-Smith C

    Current biology : CB 2014;24;21;R1038-40

    PUBMED: 25517365; DOI: 10.1016/j.cub.2014.09.019

  • The mutational landscapes of genetic and chemical models of Kras-driven lung cancer.

    Westcott PM, Halliwill KD, To MD, Rashid M, Rust AG, Keane TM, Delrosario R, Jen KY, Gurley KE, Kemp CJ et al.

    Nature 2014;517;7535;489-92

    PUBMED: 25363767; PMC: 4304785; DOI: 10.1038/nature13898

  • K13-propeller polymorphisms in Plasmodium falciparum parasites from sub-Saharan Africa.

    Kamau E, Campino S, Amenga-Etego L, Drury E, Ishengoma D, Johnson K, Mumba D, Kekre M, Yavo W, Mead D et al.

    The Journal of infectious diseases 2014;211;8;1352-5

    PUBMED: 25367300; PMC: 4827505; DOI: 10.1093/infdis/jiu608

  • An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation.

    Pena OM, Hancock DG, Lyle NH, Linder A, Russell JA, Xia J, Fjell CD, Boyd JH and Hancock RE

    EBioMedicine 2014;1;1;64-71

    PUBMED: 25685830; PMC: 4326653; DOI: 10.1016/j.ebiom.2014.10.003

  • Central genes, pathways and modules that regulate bone mass.

    Quiros-Gonzalez I and Yadav VK

    Archives of biochemistry and biophysics 2014;561;130-6

    PUBMED: 24950023; DOI: 10.1016/j.abb.2014.06.005

  • Defining the role of common variation in the genomic and biological architecture of adult human height.

    Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z et al.

    Nature genetics 2014;46;11;1173-86

    PUBMED: 25282103; PMC: 4250049; DOI: 10.1038/ng.3097

  • Design of clone-specific probes from genome sequences for rapid PCR-typing of outbreak pathogens.

    López-Camacho E, Rentero Z, Ruiz-Carrascoso G, Wesselink JJ, Pérez-Vázquez M, Lusa-Bernal S, Gómez-Puertas P, Kingsley RA, Gómez-Sánchez P, Campos J et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2014;20;11;O891-3

    PUBMED: 24606530; DOI: 10.1111/1469-0691.12616

  • Drug resistance in Salmonella enterica ser. Typhimurium bloodstream infection, Malawi.

    Feasey NA, Cain AK, Msefula CL, Pickard D, Alaerts M, Aslett M, Everett DB, Allain TJ, Dougan G, Gordon MA et al.

    Emerging infectious diseases 2014;20;11;1957-9

    PUBMED: 25340988; PMC: 4214322; DOI: 10.3201/eid2011.141175

  • Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies.

    Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB, Owings AC, Schurr TG and Genographic Consortium

    American journal of physical anthropology 2014;155;3;352-68

    PUBMED: 25043798; DOI: 10.1002/ajpa.22569

  • Genome-wide association study of intracranial aneurysm identifies a new association on chromosome 7.

    Foroud T, Lai D, Koller D, Van't Hof F, Kurki MI, Anderson CS, Brown RD, Connolly ES, Eriksson JG, Flaherty M et al.

    Stroke; a journal of cerebral circulation 2014;45;11;3194-9

    PUBMED: 25256182; PMC: 4213281; DOI: 10.1161/STROKEAHA.114.006096

  • Genomics illuminates parasite biology.

    Foth BJ and Otto TD

    Nature reviews. Microbiology 2014;12;11;727

    PUBMED: 25402362; DOI: 10.1038/nrmicro3368

  • Mutation, clonal fitness and field change in epithelial carcinogenesis.

    Frede J, Adams DJ and Jones PH

    The Journal of pathology 2014;234;3;296-301

    PUBMED: 25046364; DOI: 10.1002/path.4409

  • Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm.

    Chetaille P, Preuss C, Burkhard S, Côté JM, Houde C, Castilloux J, Piché J, Gosset N, Leclerc S, Wünnemann F et al.

    Nature genetics 2014;46;11;1245-9

    PUBMED: 25282101; DOI: 10.1038/ng.3113

  • Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses.

    Ried JS, Shin SY, Krumsiek J, Illig T, Theis FJ, Spector TD, Adamski J, Wichmann HE, Strauch K, Soranzo N et al.

    Human molecular genetics 2014;23;21;5847-57

    PUBMED: 24927737; PMC: 4271073; DOI: 10.1093/hmg/ddu301

  • Regularized machine learning in the genetic prediction of complex traits.

    Okser S, Pahikkala T, Airola A, Salakoski T, Ripatti S and Aittokallio T

    PLoS genetics 2014;10;11;e1004754

    PUBMED: 25393026; PMC: 4230844; DOI: 10.1371/journal.pgen.1004754

  • Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals.

    Cavanagh JP, Hjerde E, Holden MT, Kahlke T, Klingenberg C, Flægstad T, Parkhill J, Bentley SD and Sollid JU

    The Journal of antimicrobial chemotherapy 2014;69;11;2920-7

    PUBMED: 25038069; PMC: 4195474; DOI: 10.1093/jac/dku271

  • Innate immunity. A Spaetzle-like role for nerve growth factor β in vertebrate immunity to Staphylococcus aureus.

    Hepburn L, Prajsnar TK, Klapholz C, Moreno P, Loynes CA, Ogryzko NV, Brown K, Schiebler M, Hegyi K, Antrobus R et al.

    Science (New York, N.Y.) 2014;346;6209;641-6

    PUBMED: 25359976; PMC: 4255479; DOI: 10.1126/science.1258705

  • A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

    Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WA, Religa AA, Robertson L, Sanders M, Ogun SA et al.

    BMC biology 2014;12;86

    PUBMED: 25359557; PMC: 4242472; DOI: 10.1186/s12915-014-0086-0

  • Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

    Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L et al.

    PLoS computational biology 2014;10;10;e1003907

    PUBMED: 25357249; PMC: 4214555; DOI: 10.1371/journal.pcbi.1003907

  • Spinster homolog 2 (spns2) deficiency causes early onset progressive hearing loss.

    Chen J, Ingham N, Kelly J, Jadeja S, Goulding D, Pass J, Mahajan VB, Tsang SH, Nijnik A, Jackson IJ et al.

    PLoS genetics 2014;10;10;e1004688

    PUBMED: 25356849; PMC: 4214598; DOI: 10.1371/journal.pgen.1004688

  • Calreticulin mutations in myeloproliferative neoplasms and new methodology for their detection and monitoring.

    Chi J, Manoloukos M, Pierides C, Nicolaidou V, Nicolaou K, Kleopa M, Vassiliou G and Costeas P

    Annals of hematology 2014;94;3;399-408

    PUBMED: 25349114; DOI: 10.1007/s00277-014-2232-8

  • COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

    Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S et al.

    Nucleic acids research 2014;43;Database issue;D805-11

    PUBMED: 25355519; PMC: 4383913; DOI: 10.1093/nar/gku1075

  • Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis.

    Nones K, Waddell N, Wayte N, Patch AM, Bailey P, Newell F, Holmes O, Fink JL, Quinn MCJ, Tang YH et al.

    Nature communications 2014;5;5224

    PUBMED: 25351503; PMC: 4596003; DOI: 10.1038/ncomms6224

  • Synaptic, transcriptional and chromatin genes disrupted in autism.

    De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S et al.

    Nature 2014;515;7526;209-15

    PUBMED: 25363760; PMC: 4402723; DOI: 10.1038/nature13772

  • Ensembl 2015.

    Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S et al.

    Nucleic acids research 2014;43;Database issue;D662-9

    PUBMED: 25352552; PMC: 4383879; DOI: 10.1093/nar/gku1010

  • Increased dihydroceramide/ceramide ratio mediated by defective expression of degs1 impairs adipocyte differentiation and function.

    Barbarroja N, Rodriguez-Cuenca S, Nygren H, Camargo A, Pirraco A, Relat J, Cuadrado I, Pellegrinelli V, Medina-Gomez G, Lopez-Pedrera C et al.

    Diabetes 2014;64;4;1180-92

    PUBMED: 25352638; DOI: 10.2337/db14-0359

  • Obesity accelerates epigenetic aging of human liver.

    Horvath S, Erhart W, Brosch M, Ammerpohl O, von Schönfels W, Ahrens M, Heits N, Bell JT, Tsai PC, Spector TD et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;43;15538-43

    PUBMED: 25313081; PMC: 4217403; DOI: 10.1073/pnas.1412759111

  • CD28 expression is required after T cell priming for helper T cell responses and protective immunity to infection.

    Linterman MA, Denton AE, Divekar DP, Zvetkova I, Kane L, Ferreira C, Veldhoen M, Clare S, Dougan G, Espéli M and Smith KG

    eLife 2014;3

    PUBMED: 25347065; PMC: 4241536; DOI: 10.7554/eLife.03180

  • Comparative genome analysis of Wolbachia strain wAu.

    Sutton ER, Harris SR, Parkhill J and Sinkins SP

    BMC genomics 2014;15;928

    PUBMED: 25341639; PMC: 4223829; DOI: 10.1186/1471-2164-15-928

  • Impact of temporal variation on design and analysis of mouse knockout phenotyping studies.

    Karp NA, Speak AO, White JK, Adams DJ, Hrabé de Angelis M, Hérault Y and Mott RF

    PloS one 2014;9;10;e111239

    PUBMED: 25343444; PMC: 4208881; DOI: 10.1371/journal.pone.0111239

  • Recurrent ETNK1 mutations in atypical chronic myeloid leukemia.

    Gambacorti-Passerini CB, Donadoni C, Parmiani A, Pirola A, Redaelli S, Signore G, Piazza V, Malcovati L, Fontana D, Spinelli R et al.

    Blood 2014;125;3;499-503

    PUBMED: 25343957; DOI: 10.1182/blood-2014-06-579466

  • A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.

    Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G, Pagani L, Lawson DJ, Antão T, Vicente M, Mitt M et al.

    American journal of human genetics 2014;95;5;584-589

    PUBMED: 25449608; PMC: 4225582; DOI: 10.1016/j.ajhg.2014.09.016

  • Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen.

    Gillespie SH, Ling CL, Oravcova K, Pinheiro M, Wells L, Bryant JM, McHugh TD, Bébéar C, Webster D, Harris SR et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2014;60;3;381-8

    PUBMED: 25344534; PMC: 4293396; DOI: 10.1093/cid/ciu820

  • Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse.

    DiTommaso T, Jones LK, Cottle DL, WTSI Mouse Genetics Program, Gerdin AK, Vancollie VE, Watt FM, Ramirez-Solis R, Bradley A, Steel KP et al.

    PLoS genetics 2014;10;10;e1004705

    PUBMED: 25340873; PMC: 4207618; DOI: 10.1371/journal.pgen.1004705

  • Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability.

    Hunt D, Leventer RJ, Simons C, Taft R, Swoboda KJ, Gawne-Cain M, DDD study, Magee AC, Turnpenny PD and Baralle D

    Journal of medical genetics 2014;51;12;806-13

    PUBMED: 25342064; PMC: 4251168; DOI: 10.1136/jmedgenet-2014-102798

  • Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing.

    Dujardin JC, Mannaert A, Durrant C and Cotton JA

    Trends in parasitology 2014;30;12;554-5

    PUBMED: 25458156; DOI: 10.1016/j.pt.2014.09.004

  • Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels.

    Hall M, Chattaway MA, Reuter S, Savin C, Strauch E, Carniel E, Connor T, Van Damme I, Rajakaruna L, Rajendram D et al.

    Journal of clinical microbiology 2014;53;1;35-42

    PUBMED: 25339391; PMC: 4290955; DOI: 10.1128/JCM.02395-14

  • Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

    Lamelas A, Harris SR, Röltgen K, Dangy JP, Hauser J, Kingsley RA, Connor TR, Sie A, Hodgson A, Dougan G et al.

    mBio 2014;5;5;e01974-14

    PUBMED: 25336458; PMC: 4212839; DOI: 10.1128/mBio.01974-14

  • A next-generation dual-recombinase system for time- and host-specific targeting of pancreatic cancer.

    Schönhuber N, Seidler B, Schuck K, Veltkamp C, Schachtler C, Zukowska M, Eser S, Feyerabend TB, Paul MC, Eser P et al.

    Nature medicine 2014;20;11;1340-1347

    PUBMED: 25326799; PMC: 4270133; DOI: 10.1038/nm.3646

  • A 2.5-kilobase deletion containing a cluster of nine microRNAs in the latency-associated-transcript locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency.

    Mahjoub N, Dhorne-Pollet S, Fuchs W, Endale Ahanda ML, Lange E, Klupp B, Arya A, Loveland JE, Lefevre F, Mettenleiter TC and Giuffra E

    Journal of virology 2014;89;1;428-42

    PUBMED: 25320324; PMC: 4301172; DOI: 10.1128/JVI.02181-14

  • Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder.

    Chaudhry A, Noor A, Degagne B, Baker K, Bok LA, Brady AF, Chitayat D, Chung BH, Cytrynbaum C, Dyment D et al.

    Clinical genetics 2014;88;3;224-33

    PUBMED: 25131214; DOI: 10.1111/cge.12482

  • BRAF/NRAS wild-type melanoma, NF1 status and sensitivity to trametinib.

    Ranzani M, Alifrangis C, Perna D, Dutton-Regester K, Pritchard A, Wong K, Rashid M, Robles-Espinoza CD, Hayward NK, McDermott U et al.

    Pigment cell & melanoma research 2014;28;1;117-9

    PUBMED: 25243813; PMC: 4296225; DOI: 10.1111/pcmr.12316

  • Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing.

    Zhang J, Fujimoto J, Zhang J, Wedge DC, Song X, Zhang J, Seth S, Chow CW, Cao Y, Gumbs C et al.

    Science (New York, N.Y.) 2014;346;6206;256-9

    PUBMED: 25301631; PMC: 4354858; DOI: 10.1126/science.1256930

  • Medicine. Halting harmful helminths.

    Hoffmann KF, Brindley PJ and Berriman M

    Science (New York, N.Y.) 2014;346;6206;168-9

    PUBMED: 25301604; DOI: 10.1126/science.1261139

  • Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.

    de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal-Hanjani M, Shafi S, Murugaesu N, Rowan AJ et al.

    Science (New York, N.Y.) 2014;346;6206;251-6

    PUBMED: 25301630; PMC: 4636050; DOI: 10.1126/science.1253462

  • TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

    Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F et al.

    Nucleic acids research 2014;43;Database issue;D637-44

    PUBMED: 25300491; PMC: 4384016; DOI: 10.1093/nar/gku944

  • Host genetic variants and gene expression patterns associated with Epstein-Barr virus copy number in lymphoblastoid cell lines.

    Houldcroft CJ, Petrova V, Liu JZ, Frampton D, Anderson CA, Gall A and Kellam P

    PloS one 2014;9;10;e108384

    PUBMED: 25290448; PMC: 4188571; DOI: 10.1371/journal.pone.0108384

  • Clinical interpretation of CNVs with cross-species phenotype data.

    Köhler S, Schoeneberg U, Czeschik JC, Doelken SC, Hehir-Kwa JY, Ibn-Salem J, Mungall CJ, Smedley D, Haendel MA and Robinson PN

    Journal of medical genetics 2014;51;11;766-772

    PUBMED: 25280750; PMC: 4501634; DOI: 10.1136/jmedgenet-2014-102633

  • Right Ventricular Epicardial Fibrosis in Mice With Sternal Segment Dislocation.

    Adissu HA, Medhanie GA, Morikawa L, White JK, Newbigging S and McKerlie C

    Veterinary pathology 2014;52;5;967-76

    PUBMED: 25281652; PMC: 4469621; DOI: 10.1177/0300985814552108

  • Evidence for camel-to-human transmission of MERS coronavirus.

    Madani TA, Azhar EI and Hashem AM

    The New England journal of medicine 2014;371;14;1360

    PUBMED: 25271614; DOI: 10.1056/NEJMc1409847

  • A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate.

    Hamidian M, Kenyon JJ, Holt KE, Pickard D and Hall RM

    The Journal of antimicrobial chemotherapy 2014;69;10;2625-8

    PUBMED: 24907141; PMC: 4164139; DOI: 10.1093/jac/dku188

  • A syndromic form of Pierre Robin sequence is caused by 5q23 deletions encompassing FBN2 and PHAX.

    Ansari M, Rainger JK, Murray JE, Hanson I, Firth HV, Mehendale F, Amiel J, Gordon CT, Percesepe A, Mazzanti L et al.

    European journal of medical genetics 2014;57;10;587-95

    PUBMED: 25195018; DOI: 10.1016/j.ejmg.2014.08.007

  • Buzz off, that's my bee!

    Langridge G

    Nature reviews. Microbiology 2014;12;10;659

    PUBMED: 25198139; DOI: 10.1038/nrmicro3353

  • Cellular reprogramming by transcription factor engineering.

    Tsang JC, Gao X, Lu L and Liu P

    Current opinion in genetics & development 2014;28;1-9

    PUBMED: 25151337; DOI: 10.1016/j.gde.2014.07.001

  • Cigarette smoking reduces DNA methylation levels at multiple genomic loci but the effect is partially reversible upon cessation.

    Tsaprouni LG, Yang TP, Bell J, Dick KJ, Kanoni S, Nisbet J, Viñuela A, Grundberg E, Nelson CP, Meduri E et al.

    Epigenetics 2014;9;10;1382-96

    PUBMED: 25424692; PMC: 4623553; DOI: 10.4161/15592294.2014.969637

  • Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

    Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE et al.

    Protein science : a publication of the Protein Society 2014;23;10;1380-91

    PUBMED: 25044324; PMC: 4287006; DOI: 10.1002/pro.2522

  • Hypothalamic control of bone metabolism.

    Sharan K and Yadav VK

    Best practice & research. Clinical endocrinology & metabolism 2014;28;5;713-23

    PUBMED: 25256766; DOI: 10.1016/j.beem.2014.04.003

  • New insights into the maternal to zygotic transition.

    Langley AR, Smith JC, Stemple DL and Harvey SA

    Development (Cambridge, England) 2014;141;20;3834-41

    PUBMED: 25294937; DOI: 10.1242/dev.102368

  • Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer.

    Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, Davies HR, Papaemmanuil E, Gundem G, Shlien A et al.

    eLife 2014;3

    PUBMED: 25271376; PMC: 4371858; DOI: 10.7554/eLife.02935

  • Phenotyping structural abnormalities in mouse embryos using high-resolution episcopic microscopy.

    Weninger WJ, Geyer SH, Martineau A, Galli A, Adams DJ, Wilson R and Mohun TJ

    Disease models & mechanisms 2014;7;10;1143-52

    PUBMED: 25256713; PMC: 4174525; DOI: 10.1242/dmm.016337

  • Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

    Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C and Cohen MS

    Journal of acquired immune deficiency syndromes (1999) 2014;67;2;181-95

    PUBMED: 24977473; PMC: 4304655; DOI: 10.1097/QAI.0000000000000271

  • RASSF1A-LATS1 signalling stabilizes replication forks by restricting CDK2-mediated phosphorylation of BRCA2.

    Pefani DE, Latusek R, Pires I, Grawenda AM, Yee KS, Hamilton G, van der Weyden L, Esashi F, Hammond EM and O'Neill E

    Nature cell biology 2014;16;10;962-71, 1-8

    PUBMED: 25218637; PMC: 4861244; DOI: 10.1038/ncb3035

  • Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification.

    Wilkinson AC, Kawata VK, Schütte J, Gao X, Antoniou S, Baumann C, Woodhouse S, Hannah R, Tanaka Y, Swiers G et al.

    Development (Cambridge, England) 2014;141;20;4018-30

    PUBMED: 25252941; PMC: 4197694; DOI: 10.1242/dev.115709

  • Typhoid fever in Fiji: a reversible plague?

    Thompson CN, Kama M, Acharya S, Bera U, Clemens J, Crump JA, Dawainavesi A, Dougan G, Edmunds WJ, Fox K et al.

    Tropical medicine & international health : TM & IH 2014;19;10;1284-92

    PUBMED: 25066005; PMC: 4285329; DOI: 10.1111/tmi.12367

  • A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.

    Romero DA, Hasan AH, Lin YF, Kime L, Ruiz-Larrabeiti O, Urem M, Bucca G, Mamanova L, Laing EE, van Wezel GP et al.

    Molecular microbiology 2014

    PUBMED: 25266672; PMC: 4681348; DOI: 10.1111/mmi.12810

  • Population distribution and ancestry of the cancer protective MDM2 SNP285 (rs117039649).

    Knappskog S, Gansmo LB, Dibirova K, Metspalu A, Cybulski C, Peterlongo P, Aaltonen L, Vatten L, Romundstad P, Hveem K et al.

    Oncotarget 2014;5;18;8223-34

    PUBMED: 25327560; PMC: 4226679; DOI: 10.18632/oncotarget.1910

  • Identification of new SNPs in native South American populations by resequencing the Y chromosome.

    Geppert M, Ayub Q, Xue Y, Santos S, Ribeiro-dos-Santos Â, Baeta M, Núñez C, Martínez-Jarreta B, Tyler-Smith C and Roewer L

    Forensic science international. Genetics 2014;15;111-4

    PUBMED: 25303787; DOI: 10.1016/j.fsigen.2014.09.014

  • Reappraisal of known malaria resistance loci in a large multicenter study.

    Malaria Genomic Epidemiology Network and Malaria Genomic Epidemiology Network

    Nature genetics 2014;46;11;1197-204

    PUBMED: 25261933; PMC: 4617542; DOI: 10.1038/ng.3107

  • Polygenic in vivo validation of cancer mutations using transposons.

    Chew SK, Lu D, Campos LS, Scott KL, Saci A, Wang J, Collinson A, Raine K, Hinton J, Teague JW et al.

    Genome biology 2014;15;9;455

    PUBMED: 25260652; PMC: 4210617; DOI: 10.1186/s13059-014-0455-6

  • Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa.

    Reid AJ

    Parasitology 2014;142 Suppl 1;S57-70

    PUBMED: 25257746; PMC: 4413850; DOI: 10.1017/S0031182014001528

  • Transcriptional diversity during lineage commitment of human blood progenitors.

    Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S et al.

    Science (New York, N.Y.) 2014;345;6204;1251033

    PUBMED: 25258084; PMC: 4254742; DOI: 10.1126/science.1251033

  • Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

    Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD, Browne HP, Keane JA, Page AJ, Kumasaka N, Kane L et al.

    Cell host & microbe 2014;16;4;504-16

    PUBMED: 25263220; PMC: 4190086; DOI: 10.1016/j.chom.2014.08.017

  • Gray platelet syndrome: proinflammatory megakaryocytes and α-granule loss cause myelofibrosis and confer metastasis resistance in mice.

    Guerrero JA, Bennett C, van der Weyden L, McKinney H, Chin M, Nurden P, McIntyre Z, Cambridge EL, Estabel J, Wardle-Jones H et al.

    Blood 2014;124;24;3624-35

    PUBMED: 25258341; DOI: 10.1182/blood-2014-04-566760

  • MARIMO cells harbor a CALR mutation but are not dependent on JAK2/STAT5 signaling.

    Kollmann K, Nangalia J, Warsch W, Quentmeier H, Bench A, Boyd E, Scott M, Drexler HG and Green AR

    Leukemia 2014;29;2;494-7

    PUBMED: 25249012; PMC: 4320290; DOI: 10.1038/leu.2014.285

  • Telomere-regulating genes and the telomere interactome in familial cancers.

    Robles-Espinoza CD, Velasco-Herrera Mdel C, Hayward NK and Adams DJ

    Molecular cancer research : MCR 2014;13;2;211-22

    PUBMED: 25244922; PMC: 4278843; DOI: 10.1158/1541-7786.MCR-14-0305

  • Optimized whole-genome amplification strategy for extremely AT-biased template.

    Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL, Kekre M, Drury E, Mead D, Gu Y, Miles A et al.

    DNA research : an international journal for rapid publication of reports on genes and genomes 2014;21;6;661-71

    PUBMED: 25240466; PMC: 4263299; DOI: 10.1093/dnares/dsu028

  • The Ensembl REST API: Ensembl Data for Any Language.

    Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GR, Ruffier M, Taylor K, Vullo A and Flicek P

    Bioinformatics (Oxford, England) 2014;31;1;143-5

    PUBMED: 25236461; PMC: 4271150; DOI: 10.1093/bioinformatics/btu613

  • The AURORA initiative for metastatic breast cancer.

    Zardavas D, Maetens M, Irrthum A, Goulioti T, Engelen K, Fumagalli D, Salgado R, Aftimos P, Saini KS, Sotiriou C et al.

    British journal of cancer 2014;111;10;1881-7

    PUBMED: 25225904; PMC: 4229627; DOI: 10.1038/bjc.2014.341

  • A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.

    Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G, Shin SY, Chen L, Futema M, Southam L, Iotchkova V et al.

    Nature communications 2014;5;4871

    PUBMED: 25225788; PMC: 4167609; DOI: 10.1038/ncomms5871

  • Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress.

    Foijer F, Xie SZ, Simon JE, Bakker PL, Conte N, Davis SH, Kregel E, Jonkers J, Bradley A and Sorger PK

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;37;13427-32

    PUBMED: 25197064; PMC: 4169945; DOI: 10.1073/pnas.1400892111

  • A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response.

    Blasius M, Wagner SA, Choudhary C, Bartek J and Jackson SP

    Genes & development 2014;28;18;1977-82

    PUBMED: 25189701; PMC: 4173157; DOI: 10.1101/gad.246272.114

  • Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers.

    Gao X, Tsang JC, Gaba F, Wu D, Lu L and Liu P

    Nucleic acids research 2014;42;20;e155

    PUBMED: 25223790; PMC: 4227760; DOI: 10.1093/nar/gku836

  • Monitoring parasite diversity for malaria elimination in sub-Saharan Africa.

    Ghansah A, Amenga-Etego L, Amambua-Ngwa A, Andagalu B, Apinjoh T, Bouyou-Akotet M, Cornelius V, Golassa L, Andrianaranjaka VH, Ishengoma D et al.

    Science (New York, N.Y.) 2014;345;6202;1297-8

    PUBMED: 25214619; PMC: 4541720; DOI: 10.1126/science.1259423

  • Reading between the lines; understanding drug response in the post genomic era.

    Alifrangis CC and McDermott U

    Molecular oncology 2014;8;6;1112-9

    PUBMED: 24957465; PMC: 5528621; DOI: 10.1016/j.molonc.2014.05.014

  • Resetting transcription factor control circuitry toward ground-state pluripotency in human.

    Takashima Y, Guo G, Loos R, Nichols J, Ficz G, Krueger F, Oxley D, Santos F, Clarke J, Mansfield W et al.

    Cell 2014;158;6;1254-1269

    PUBMED: 25215486; PMC: 4162745; DOI: 10.1016/j.cell.2014.08.029

  • Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom.

    Elderfield RA, Watson SJ, Godlee A, Adamson WE, Thompson CI, Dunning J, Fernandez-Alonso M, Blumenkrantz D, Hussell T, MOSAIC Investigators et al.

    Journal of virology 2014;88;22;13269-83

    PUBMED: 25210166; PMC: 4249111; DOI: 10.1128/JVI.01636-14

  • Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

    Otto TD, Rayner JC, Böhme U, Pain A, Spottiswoode N, Sanders M, Quail M, Ollomo B, Renaud F, Thomas AW et al.

    Nature communications 2014;5;4754

    PUBMED: 25203297; PMC: 4166903; DOI: 10.1038/ncomms5754

  • Systematic characterization of deubiquitylating enzymes for roles in maintaining genome integrity.

    Nishi R, Wijnhoven P, le Sage C, Tjeertes J, Galanty Y, Forment JV, Clague MJ, Urbé S and Jackson SP

    Nature cell biology 2014;16;10;1016-26, 1-8

    PUBMED: 25194926; PMC: 4183562; DOI: 10.1038/ncb3028

  • The olfactory transcriptomes of mice.

    Ibarra-Soria X, Levitin MO, Saraiva LR and Logan DW

    PLoS genetics 2014;10;9;e1004593

    PUBMED: 25187969; PMC: 4154679; DOI: 10.1371/journal.pgen.1004593

  • The genomic substrate for adaptive radiation in African cichlid fish.

    Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E et al.

    Nature 2014;513;7518;375-381

    PUBMED: 25186727; PMC: 4353498; DOI: 10.1038/nature13726

  • Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.

    Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M et al.

    Science translational medicine 2014;6;252;252ra123

    PUBMED: 25186178; PMC: 4512639; DOI: 10.1126/scitranslmed.3009262

  • Generation and characterization of influenza A viruses with altered polymerase fidelity.

    Cheung PP, Watson SJ, Choy KT, Fun Sia S, Wong DD, Poon LL, Kellam P, Guan Y, Malik Peiris JS and Yen HL

    Nature communications 2014;5;4794

    PUBMED: 25183443; PMC: 4155405; DOI: 10.1038/ncomms5794

  • Mouse models of NPM1-mutated acute myeloid leukemia: biological and clinical implications.

    Sportoletti P, Varasano E, Rossi R, Mupo A, Tiacci E, Vassiliou G, Martelli MP and Falini B

    Leukemia 2014;29;2;269-78

    PUBMED: 25179729; DOI: 10.1038/leu.2014.257

  • A framework for the interpretation of de novo mutation in human disease.

    Samocha KE, Robinson EB, Sanders SJ, Stevens C, Sabo A, McGrath LM, Kosmicki JA, Rehnström K, Mallick S, Kirby A et al.

    Nature genetics 2014;46;9;944-50

    PUBMED: 25086666; PMC: 4222185; DOI: 10.1038/ng.3050

  • Barriers to the effective treatment of sepsis: antimicrobial agents, sepsis definitions, and host-directed therapies.

    Lyle NH, Pena OM, Boyd JH and Hancock RE

    Annals of the New York Academy of Sciences 2014;1323;101-14

    PUBMED: 24797961; DOI: 10.1111/nyas.12444

  • Cancer gene discovery goes mobile.

    van der Weyden L, Ranzani M and Adams DJ

    Nature genetics 2014;46;9;928-9

    PUBMED: 25162801; DOI: 10.1038/ng.3072

  • Fast randomization of large genomic datasets while preserving alteration counts.

    Gobbi A, Iorio F, Dawson KJ, Wedge DC, Tamborero D, Alexandrov LB, Lopez-Bigas N, Garnett MJ, Jurman G and Saez-Rodriguez J

    Bioinformatics (Oxford, England) 2014;30;17;i617-23

    PUBMED: 25161255; PMC: 4147926; DOI: 10.1093/bioinformatics/btu474

  • Functional characterization of obesity-associated variants involving the α and β isoforms of human SH2B1.

    Pearce LR, Joe R, Doche ME, Su HW, Keogh JM, Henning E, Argetsinger LS, Bochukova EG, Cline JM, Garg S et al.

    Endocrinology 2014;155;9;3219-26

    PUBMED: 24971614; PMC: 4138566; DOI: 10.1210/en.2014-1264

  • Genetic predisposition to increased blood cholesterol and triglyceride lipid levels and risk of Alzheimer disease: a Mendelian randomization analysis.

    Proitsi P, Lupton MK, Velayudhan L, Newhouse S, Fogh I, Tsolaki M, Daniilidou M, Pritchard M, Kloszewska I, Soininen H et al.

    PLoS medicine 2014;11;9;e1001713

    PUBMED: 25226301; PMC: 4165594; DOI: 10.1371/journal.pmed.1001713

  • Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.

    Takala-Harrison S, Jacob CG, Arze C, Cummings MP, Silva JC, Dondorp AM, Fukuda MM, Hien TT, Mayxay M, Noedl H et al.

    The Journal of infectious diseases 2014;211;5;670-9

    PUBMED: 25180241; PMC: 4334802; DOI: 10.1093/infdis/jiu491

  • Removal of reprogramming transgenes improves the tissue reconstitution potential of keratinocytes generated from human induced pluripotent stem cells.

    Igawa K, Kokubu C, Yusa K, Horie K, Yoshimura Y, Yamauchi K, Suemori H, Yokozeki H, Toyoda M, Kiyokawa N et al.

    Stem cells translational medicine 2014;3;9;992-1001

    PUBMED: 25024429; PMC: 4149296; DOI: 10.5966/sctm.2013-0179

  • Voyage to the bottom of the 'seaquence'.

    Wash R and Soria CD

    Nature reviews. Microbiology 2014;12;9;597

    PUBMED: 25118883; DOI: 10.1038/nrmicro3341

  • Whole-genome sequencing to control antimicrobial resistance.

    Köser CU, Ellington MJ and Peacock SJ

    Trends in genetics : TIG 2014;30;9;401-7

    PUBMED: 25096945; PMC: 4156311; DOI: 10.1016/j.tig.2014.07.003

  • Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

    Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Barrio AM, Pielberg G, Rafati N, Sayyab S, Turner-Maier J et al.

    Science (New York, N.Y.) 2014;345;6200;1074-9

    PUBMED: 25170157; DOI: 10.1126/science.1253714

  • Candidate-gene association study searching for genetic factors involved in migraine chronification.

    Louter MA, Fernandez-Morales J, de Vries B, Winsvold B, Anttila V, Fernandez-Cadenas I, Vila-Pueyo M, Sintas C, van Duijn CM, Cormand B et al.

    Cephalalgia : an international journal of headache 2014;35;6;500-7

    PUBMED: 25169732; DOI: 10.1177/0333102414547141

  • One patient, two lesions, two oncogenic drivers of gastric cancer.

    Alsinet C, Ranzani M and Adams DJ

    Genome biology 2014;15;8;444

    PUBMED: 25222187; PMC: 4281955; DOI: 10.1186/s13059-014-0444-9

  • Comparative analysis of pseudogenes across three phyla.

    Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;37;13361-6

    PUBMED: 25157146; PMC: 4169933; DOI: 10.1073/pnas.1407293111

  • Defining the estimated core genome of bacterial populations using a Bayesian decision model.

    van Tonder AJ, Mistry S, Bray JE, Hill DM, Cody AJ, Farmer CL, Klugman KP, von Gottberg A, Bentley SD, Parkhill J et al.

    PLoS computational biology 2014;10;8;e1003788

    PUBMED: 25144616; PMC: 4140633; DOI: 10.1371/journal.pcbi.1003788

  • International glossina genome initiative 2004-2014: a driver for post-genomic era research on the African continent.

    Christoffels A, Masiga D, Berriman M, Lehane M, Touré Y and Aksoy S

    PLoS neglected tropical diseases 2014;8;8;e3024

    PUBMED: 25144472; PMC: 4140670; DOI: 10.1371/journal.pntd.0003024

  • Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

    Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ et al.

    Nature 2014;514;7523;494-7

    PUBMED: 25141181; PMC: 4550673; DOI: 10.1038/nature13591

  • Quantitation of malaria parasite-erythrocyte cell-cell interactions using optical tweezers.

    Crick AJ, Theron M, Tiffert T, Lew VL, Cicuta P and Rayner JC

    Biophysical journal 2014;107;4;846-53

    PUBMED: 25140419; PMC: 4142257; DOI: 10.1016/j.bpj.2014.07.010

  • Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

    Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;33;E3366

    PUBMED: 25275169; PMC: 4143047

  • Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.

    Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q, Kamatani Y, Bennet AM, Tamm R, Trompet S et al.

    Human molecular genetics 2014;23;16;4420-32

    PUBMED: 24688116; PMC: 4103672; DOI: 10.1093/hmg/ddu139

  • Genome-wide association study of sexual maturation in males and females highlights a role for body mass and menarche loci in male puberty.

    Cousminer DL, Stergiakouli E, Berry DJ, Ang W, Groen-Blokhuis MM, Körner A, Siitonen N, Ntalla I, Marinelli M, Perry JR et al.

    Human molecular genetics 2014;23;16;4452-64

    PUBMED: 24770850; PMC: 4168307; DOI: 10.1093/hmg/ddu150

  • In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism.

    Radford EJ, Ito M, Shi H, Corish JA, Yamazawa K, Isganaitis E, Seisenberger S, Hore TA, Reik W, Erkek S et al.

    Science (New York, N.Y.) 2014;345;6198;1255903

    PUBMED: 25011554; PMC: 4404520; DOI: 10.1126/science.1255903

  • Open-source electronic data capture system offered increased accuracy and cost-effectiveness compared with paper methods in Africa.

    Dillon DG, Pirie F, Rice S, Pomilla C, Sandhu MS, Motala AA, Young EH and African Partnership for Chronic Disease Research (APCDR)

    Journal of clinical epidemiology 2014;67;12;1358-63

    PUBMED: 25135245; PMC: 4271740; DOI: 10.1016/j.jclinepi.2014.06.012

  • Considerations when investigating lncRNA function in vivo.

    Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W et al.

    eLife 2014;3;e03058

    PUBMED: 25124674; PMC: 4132285; DOI: 10.7554/eLife.03058

  • Knowing who to trust: exploring the role of 'ethical metadata' in mediating risk of harm in collaborative genomics research in Africa.

    de Vries J, Williams TN, Bojang K, Kwiatkowski DP, Fitzpatrick R and Parker M

    BMC medical ethics 2014;15;62

    PUBMED: 25124199; PMC: 4146449; DOI: 10.1186/1472-6939-15-62

  • Novel porcine-like human G26P[19] rotavirus identified in hospitalized paediatric diarrhoea patients in Ho Chi Minh City, Vietnam.

    My PVT, Rabaa MA, Donato C, Cowley D, Phat VV, Dung TTN, Anh PH, Vinh H, Bryant JE, Kellam P et al.

    The Journal of general virology 2014;95;Pt 12;2727-2733

    PUBMED: 25121549; PMC: 4233630; DOI: 10.1099/vir.0.068403-0

  • Rolled-up functionalized nanomembranes as three-dimensional cavities for single cell studies.

    Xi W, Schmidt CK, Sanchez S, Gracias DH, Carazo-Salas RE, Jackson SP and Schmidt OG

    Nano letters 2014;14;8;4197-204

    PUBMED: 24598026; PMC: 4133182; DOI: 10.1021/nl4042565

  • A new method to determine in vivo interactomes reveals binding of the Legionella pneumophila effector PieE to multiple rab GTPases.

    Mousnier A, Schroeder GN, Stoneham CA, So EC, Garnett JA, Yu L, Matthews SJ, Choudhary JS, Hartland EL and Frankel G

    mBio 2014;5;4

    PUBMED: 25118235; PMC: 4145681; DOI: 10.1128/mBio.01148-14

  • Disruption of the potassium channel regulatory subunit KCNE2 causes iron-deficient anemia.

    Salsbury G, Cambridge EL, McIntyre Z, Arends MJ, Karp NA, Isherwood C, Shannon C, Hooks Y, Sanger Mouse Genetics Project, Ramirez-Solis R et al.

    Experimental hematology 2014;42;12;1053-8.e1

    PUBMED: 25127743; PMC: 4271779; DOI: 10.1016/j.exphem.2014.07.269

  • A membrane topology model for human interferon inducible transmembrane protein 1.

    Weston S, Czieso S, White IJ, Smith SE, Kellam P and Marsh M

    PloS one 2014;9;8;e104341

    PUBMED: 25105503; PMC: 4126714; DOI: 10.1371/journal.pone.0104341

  • Hypomorphism in human NSMCE2 linked to primordial dwarfism and insulin resistance.

    Payne F, Colnaghi R, Rocha N, Seth A, Harris J, Carpenter G, Bottomley WE, Wheeler E, Wong S, Saudek V et al.

    The Journal of clinical investigation 2014;124;9;4028-38

    PUBMED: 25105364; PMC: 4151221; DOI: 10.1172/JCI73264

  • A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012.

    Byrne L, Fisher I, Peters T, Mather A, Thomson N, Rosner B, Bernard H, McKeown P, Cormican M, Cowden J et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2014;19;31;6-13

    PUBMED: 25138971; PMC: 4516299; DOI: 10.2807/1560-7917.es2014.19.31.20866

  • Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.

    Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C et al.

    PLoS genetics 2014;10;8;e1004547

    PUBMED: 25101644; PMC: 4125147; DOI: 10.1371/journal.pgen.1004547

  • Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods.

    Bashford-Rogers RJ, Palser AL, Idris SF, Carter L, Epstein M, Callard RE, Douek DC, Vassiliou GS, Follows GA, Hubank M and Kellam P

    BMC immunology 2014;15;29

    PUBMED: 25189176; PMC: 4243823; DOI: 10.1186/s12865-014-0029-0

  • TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I.

    van den Boomen DJ, Timms RT, Grice GL, Stagg HR, Skødt K, Dougan G, Nathan JA and Lehner PJ

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;31;11425-30

    PUBMED: 25030448; PMC: 4128144; DOI: 10.1073/pnas.1409099111

  • Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

    Da Cunha V, Davies MR, Douarre PE, Rosinski-Chupin I, Margarit I, Spinali S, Perkins T, Lechat P, Dmytruk N, Sauvage E et al.

    Nature communications 2014;5;4544

    PUBMED: 25088811; PMC: 4538795; DOI: 10.1038/ncomms5544

  • Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.

    Zhou Z, McCann A, Weill FX, Blin C, Nair S, Wain J, Dougan G and Achtman M

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;33;12199-204

    PUBMED: 25092320; PMC: 4143038; DOI: 10.1073/pnas.1411012111

  • The common marmoset genome provides insight into primate biology and evolution.

    Marmoset Genome Sequencing and Analysis Consortium

    Nature genetics 2014;46;8;850-7

    PUBMED: 25038751; PMC: 4138798; DOI: 10.1038/ng.3042

  • The food-borne identity.

    Salter SJ

    Nature reviews. Microbiology 2014;12;8;533

    PUBMED: 24975320; DOI: 10.1038/nrmicro3313

  • The genome sequence of ectromelia virus Naval and Cornell isolates from outbreaks in North America.

    Mavian C, López-Bueno A, Bryant NA, Seeger K, Quail MA, Harris D, Barrell B and Alcami A

    Virology 2014;462-463;218-26

    PUBMED: 24999046; PMC: 4139192; DOI: 10.1016/j.virol.2014.06.010

  • Acute myeloid leukaemia: a paradigm for the clonal evolution of cancer?

    Grove CS and Vassiliou GS

    Disease models & mechanisms 2014;7;8;941-51

    PUBMED: 25056697; PMC: 4107323; DOI: 10.1242/dmm.015974

  • Do you smell what I smell? Genetic variation in olfactory perception.

    Logan DW

    Biochemical Society transactions 2014;42;4;861-5

    PUBMED: 25109969; DOI: 10.1042/BST20140052

  • From genome-wide association study hits to new insights into experimental hematology.

    Cvejic A

    Experimental hematology 2014;42;8;630-6

    PUBMED: 24746874; DOI: 10.1016/j.exphem.2014.04.005

  • Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

    Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J et al.

    Genome biology and evolution 2014;6;8;2096-110

    PUBMED: 25070509; PMC: 4231636; DOI: 10.1093/gbe/evu160

  • Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J et al.

    PLoS biology 2014;12;8;e1001920

    PUBMED: 25093819; PMC: 4122341; DOI: 10.1371/journal.pbio.1001920

  • Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.

    Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K et al.

    Science (New York, N.Y.) 2014;345;6196;1251343

    PUBMED: 25082706; PMC: 4380235; DOI: 10.1126/science.1251343

  • Plasmodium falciparum founder populations in western Cambodia have reduced artemisinin sensitivity in vitro.

    Amaratunga C, Witkowski B, Dek D, Try V, Khim N, Miotto O, Ménard D and Fairhurst RM

    Antimicrobial agents and chemotherapy 2014;58;8;4935-7

    PUBMED: 24867977; PMC: 4136061; DOI: 10.1128/AAC.03055-14

  • Response to 'Predicting the diagnosis of autism spectrum disorder using gene pathway analysis'.

    Robinson EB, Howrigan D, Yang J, Ripke S, Anttila V, Duncan LE, Jostins L, Barrett JC, Medland SE, MacArthur DG et al.

    Molecular psychiatry 2014;19;8;859-61

    PUBMED: 24145379; PMC: 4113933; DOI: 10.1038/mp.2013.125

  • Response to comment on Ye et al. The association between circulating lipoprotein(a) and type 2 diabetes: is it causal? Diabetes 2014;63:332-342.

    Ye Z, Sandhu MS and Forouhi NG

    Diabetes 2014;63;8;e15

    PUBMED: 25060897; DOI: 10.2337/db14-0644

  • Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins.

    Hargreaves AD, Swain MT, Hegarty MJ, Logan DW and Mulley JF

    Genome biology and evolution 2014;6;8;2088-95

    PUBMED: 25079342; PMC: 4231632; DOI: 10.1093/gbe/evu166

  • Structural genomic variation as risk factor for idiopathic recurrent miscarriage.

    Nagirnaja L, Palta P, Kasak L, Rull K, Christiansen OB, Nielsen HS, Steffensen R, Esko T, Remm M and Laan M

    Human mutation 2014;35;8;972-82

    PUBMED: 24827138; PMC: 4285182; DOI: 10.1002/humu.22589

  • Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections.

    Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hafiz T, Hoffman LR, Carroll MP, Parkhill J, Bruce KD and van der Gast CJ

    Journal of clinical microbiology 2014;52;8;3011-6

    PUBMED: 24920767; PMC: 4136140; DOI: 10.1128/JCM.00764-14

  • Epigenetics: Cellular memory erased in human embryos.

    Reik W and Kelsey G

    Nature 2014;511;7511;540-1

    PUBMED: 25079550; DOI: 10.1038/nature13648

  • Identifying selection in the within-host evolution of influenza using viral sequence data.

    Illingworth CJ, Fischer A and Mustonen V

    PLoS computational biology 2014;10;7;e1003755

    PUBMED: 25080215; PMC: 4117419; DOI: 10.1371/journal.pcbi.1003755

  • Spread of artemisinin resistance in Plasmodium falciparum malaria.

    Ashley EA, Dhorda M, Fairhurst RM, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM, Mao S, Sam B et al.

    The New England journal of medicine 2014;371;5;411-23

    PUBMED: 25075834; PMC: 4143591; DOI: 10.1056/NEJMoa1314981

  • New antigens for a multicomponent blood-stage malaria vaccine.

    Osier FH, Mackinnon MJ, Crosnier C, Fegan G, Kamuyu G, Wanaguru M, Ogada E, McDade B, Rayner JC, Wright GJ and Marsh K

    Science translational medicine 2014;6;247;247ra102

    PUBMED: 25080477; PMC: 4856877; DOI: 10.1126/scitranslmed.3008705

  • Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases.

    Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C, Hamosh A, Veldboer J, Zemojtel T and Robinson PN

    Bioinformatics (Oxford, England) 2014;30;22;3215-22

    PUBMED: 25078397; PMC: 4221119; DOI: 10.1093/bioinformatics/btu508

  • Urbanicity and lifestyle risk factors for cardiometabolic diseases in rural Uganda: a cross-sectional study.

    Riha J, Karabarinde A, Ssenyomo G, Allender S, Asiki G, Kamali A, Young EH, Sandhu MS and Seeley J

    PLoS medicine 2014;11;7;e1001683

    PUBMED: 25072243; PMC: 4114555; DOI: 10.1371/journal.pmed.1001683

  • The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.

    Abd El Ghany M, Chander J, Mutreja A, Rashid M, Hill-Cawthorne GA, Ali S, Naeem R, Thomson NR, Dougan G and Pain A

    PLoS neglected tropical diseases 2014;8;7;e2981

    PUBMED: 25058483; PMC: 4109905; DOI: 10.1371/journal.pntd.0002981

  • Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.

    Cotten M, Petrova V, Phan MV, Rabaa MA, Watson SJ, Ong SH, Kellam P and Baker S

    Journal of virology 2014;88;19;11056-69

    PUBMED: 25056894; PMC: 4178781; DOI: 10.1128/JVI.01333-14

  • Meta-analysis identifies loci affecting levels of the potential osteoarthritis biomarkers sCOMP and uCTX-II with genome wide significance.

    Ramos YF, Metrustry S, Arden N, Bay-Jensen AC, Beekman M, de Craen AJ, Cupples LA, Esko T, Evangelou E, Felson DT et al.

    Journal of medical genetics 2014;51;9;596-604

    PUBMED: 25057126; DOI: 10.1136/jmedgenet-2014-102478

  • Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.

    Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W and Kelsey G

    Nature methods 2014;11;8;817-820

    PUBMED: 25042786; PMC: 4117646; DOI: 10.1038/nmeth.3035

  • BCKDH: the missing link in apicomplexan mitochondrial metabolism is required for full virulence of Toxoplasma gondii and Plasmodium berghei.

    Oppenheim RD, Creek DJ, Macrae JI, Modrzynska KK, Pino P, Limenitakis J, Polonais V, Seeber F, Barrett MP, Billker O et al.

    PLoS pathogens 2014;10;7;e1004263

    PUBMED: 25032958; PMC: 4102578; DOI: 10.1371/journal.ppat.1004263

  • C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency.

    Meier B, Cooke SL, Weiss J, Bailly AP, Alexandrov LB, Marshall J, Raine K, Maddison M, Anderson E, Stratton MR et al.

    Genome research 2014;24;10;1624-36

    PUBMED: 25030888; PMC: 4199376; DOI: 10.1101/gr.175547.114

  • Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression.

    Marttinen P, Pirinen M, Sarin AP, Gillberg J, Kettunen J, Surakka I, Kangas AJ, Soininen P, O'Reilly P, Kaakinen M et al.

    Bioinformatics (Oxford, England) 2014;30;14;2026-34

    PUBMED: 24665129; PMC: 4080737; DOI: 10.1093/bioinformatics/btu140

  • Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.

    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B et al.

    Human mutation 2014;35;8;1021-32

    PUBMED: 24917567; PMC: 4145662; DOI: 10.1002/humu.22599

  • Genomic analysis of the causative agents of coccidiosis in domestic chickens.

    Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D et al.

    Genome research 2014;24;10;1676-85

    PUBMED: 25015382; PMC: 4199364; DOI: 10.1101/gr.168955.113

  • Using population isolates in genetic association studies.

    Hatzikotoulas K, Gilly A and Zeggini E

    Briefings in functional genomics 2014;13;5;371-7

    PUBMED: 25009120; PMC: 4168662; DOI: 10.1093/bfgp/elu022

  • The correlation between reading and mathematics ability at age twelve has a substantial genetic component.

    Davis OS, Band G, Pirinen M, Haworth CM, Meaburn EL, Kovas Y, Harlaar N, Docherty SJ, Hanscombe KB, Trzaskowski M et al.

    Nature communications 2014;5;4204

    PUBMED: 25003214; PMC: 4102107; DOI: 10.1038/ncomms5204

  • Exome Sequencing in Fetuses with Structural Malformations.

    Mackie FL, Carss KJ, Hillman SC, Hurles ME and Kilby MD

    Journal of clinical medicine 2014;3;3;747-62

    PUBMED: 26237476; PMC: 4449643; DOI: 10.3390/jcm3030747

  • Histone deacetylase (HDAC) 1 and 2 are essential for accurate cell division and the pluripotency of embryonic stem cells.

    Jamaladdin S, Kelly RD, O'Regan L, Dovey OM, Hodson GE, Millard CJ, Portolano N, Fry AM, Schwabe JW and Cowley SM

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;27;9840-5

    PUBMED: 24958871; PMC: 4103379; DOI: 10.1073/pnas.1321330111

  • Human immunodeficiency virus Tat associates with a specific set of cellular RNAs.

    Bouwman RD, Palser A, Parry CM, Coulter E, Rasaiyaah J, Kellam P and Jenner RG

    Retrovirology 2014;11;53

    PUBMED: 24990269; PMC: 4086691; DOI: 10.1186/1742-4690-11-53

  • Loss-of-function mutations in APOC3, triglycerides, and coronary disease.

    TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute, Crosby J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA et al.

    The New England journal of medicine 2014;371;1;22-31

    PUBMED: 24941081; PMC: 4180269; DOI: 10.1056/NEJMoa1307095

  • Secreted proteomes of different developmental stages of the gastrointestinal nematode Nippostrongylus brasiliensis.

    Sotillo J, Sanchez-Flores A, Cantacessi C, Harcus Y, Pickering D, Bouchery T, Camberis M, Tang SC, Giacomin P, Mulvenna J et al.

    Molecular & cellular proteomics : MCP 2014;13;10;2736-51

    PUBMED: 24994561; PMC: 4188999; DOI: 10.1074/mcp.M114.038950

  • Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples.

    Kwok H, Wu CW, Palser AL, Kellam P, Sham PC, Kwong DL and Chiang AK

    Journal of virology 2014;88;18;10662-72

    PUBMED: 24991008; PMC: 4178900; DOI: 10.1128/JVI.01665-14

  • Identification of structural variation in mouse genomes.

    Keane TM, Wong K, Adams DJ, Flint J, Reymond A and Yalcin B

    Frontiers in genetics 2014;5;192

    PUBMED: 25071822; PMC: 4079067; DOI: 10.3389/fgene.2014.00192

  • A loss of function screen of identified genome-wide association study Loci reveals new genes controlling hematopoiesis.

    Bielczyk-Maczyńska E, Serbanovic-Canic J, Ferreira L, Soranzo N, Stemple DL, Ouwehand WH and Cvejic A

    PLoS genetics 2014;10;7;e1004450

    PUBMED: 25010335; PMC: 4091788; DOI: 10.1371/journal.pgen.1004450

  • Cis and trans effects of human genomic variants on gene expression.

    Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P et al.

    PLoS genetics 2014;10;7;e1004461

    PUBMED: 25010687; PMC: 4091791; DOI: 10.1371/journal.pgen.1004461

  • Distribution and medical impact of loss-of-function variants in the Finnish founder population.

    Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T et al.

    PLoS genetics 2014;10;7;e1004494

    PUBMED: 25078778; PMC: 4117444; DOI: 10.1371/journal.pgen.1004494

  • Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape.

    Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C et al.

    Genome biology and evolution 2014;6;7;1589-602

    PUBMED: 24916661; PMC: 4122920; DOI: 10.1093/gbe/evu120

  • Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay.

    Köser CU, Comas I, Feuerriegel S, Niemann S, Gagneux S and Peacock SJ

    Tuberculosis (Edinburgh, Scotland) 2014;94;4;451-3

    PUBMED: 24870943; PMC: 4075347; DOI: 10.1016/j.tube.2014.04.002

  • Genome-wide association analysis identifies six new loci associated with forced vital capacity.

    Loth DW, Soler Artigas M, Gharib SA, Wain LV, Franceschini N, Koch B, Pottinger TD, Smith AV, Duan Q, Oldmeadow C et al.

    Nature genetics 2014;46;7;669-77

    PUBMED: 24929828; PMC: 4140093; DOI: 10.1038/ng.3011

  • Harmonization of Neuroticism and Extraversion phenotypes across inventories and cohorts in the Genetics of Personality Consortium: an application of Item Response Theory.

    van den Berg SM, de Moor MH, McGue M, Pettersson E, Terracciano A, Verweij KJ, Amin N, Derringer J, Esko T, van Grootheest G et al.

    Behavior genetics 2014;44;4;295-313

    PUBMED: 24828478; PMC: 4057636; DOI: 10.1007/s10519-014-9654-x

  • Human stem cells for craniomaxillofacial reconstruction.

    Jalali M, Kirkpatrick WN, Cameron MG, Pauklin S and Vallier L

    Stem cells and development 2014;23;13;1437-51

    PUBMED: 24564584; PMC: 4066224; DOI: 10.1089/scd.2013.0576

  • Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides.

    Kenyon JJ, Holt KE, Pickard D, Dougan G and Hall RM

    Research in microbiology 2014;165;6;472-5

    PUBMED: 24861001; PMC: 4110982; DOI: 10.1016/j.resmic.2014.05.034

  • Keeping 53BP1 out of focus in mitosis.

    Belotserkovskaya R and Jackson SP

    Cell research 2014;24;7;781-2

    PUBMED: 24810302; PMC: 4085762; DOI: 10.1038/cr.2014.62

  • Luminal microbes promote monocyte-stem cell interactions across a healthy colonic epithelium.

    Skoczek DA, Walczysko P, Horn N, Parris A, Clare S, Williams MR and Sobolewski A

    Journal of immunology (Baltimore, Md. : 1950) 2014;193;1;439-51

    PUBMED: 24907348; PMC: 4067517; DOI: 10.4049/jimmunol.1301497

  • Mechanisms underlying mutational signatures in human cancers.

    Helleday T, Eshtad S and Nik-Zainal S

    Nature reviews. Genetics 2014;15;9;585-98

    PUBMED: 24981601; PMC: 6044419; DOI: 10.1038/nrg3729

  • Multiplex PCR assay for unequivocal differentiation of Actinobacillus pleuropneumoniae serovars 1 to 3, 5 to 8, 10, and 12.

    Bossé JT, Li Y, Angen Ø, Weinert LA, Chaudhuri RR, Holden MT, Williamson SM, Maskell DJ, Tucker AW, Wren BW et al.

    Journal of clinical microbiology 2014;52;7;2380-5

    PUBMED: 24759717; PMC: 4097740; DOI: 10.1128/JCM.00685-14

  • NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration.

    Xia J, Benner MJ and Hancock RE

    Nucleic acids research 2014;42;Web Server issue;W167-74

    PUBMED: 24861621; PMC: 4086107; DOI: 10.1093/nar/gku443

  • PredictProtein--an open resource for online prediction of protein structural and functional features.

    Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M et al.

    Nucleic acids research 2014;42;Web Server issue;W337-43

    PUBMED: 24799431; PMC: 4086098; DOI: 10.1093/nar/gku366

  • Split reality for novel tick virus.

    Bennett HM

    Nature reviews. Microbiology 2014;12;7;464

    PUBMED: 24909108; DOI: 10.1038/nrmicro3297

  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

    Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium et al.

    Genome biology 2014;15;6;R88

    PUBMED: 24980144; PMC: 4197830; DOI: 10.1186/gb-2014-15-6-r88

  • Genome sequencing of normal cells reveals developmental lineages and mutational processes.

    Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G et al.

    Nature 2014;513;7518;422-425

    PUBMED: 25043003; PMC: 4227286; DOI: 10.1038/nature13448

  • Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.

    Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.

    Genome biology 2014;15;6;R76

    PUBMED: 24995464; PMC: 4072981; DOI: 10.1186/gb-2014-15-6-r76

  • A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.

    Rapa RA, Islam A, Monahan LG, Mutreja A, Thomson N, Charles IG, Stokes HW and Labbate M

    Environmental microbiology 2014;17;4;1090-102

    PUBMED: 24889424; PMC: 4405046; DOI: 10.1111/1462-2920.12512

  • Driver somatic mutations identify distinct disease entities within myeloid neoplasms with myelodysplasia.

    Malcovati L, Papaemmanuil E, Ambaglio I, Elena C, Gallì A, Della Porta MG, Travaglino E, Pietra D, Pascutto C, Ubezio M et al.

    Blood 2014;124;9;1513-21

    PUBMED: 24970933; PMC: 4148773; DOI: 10.1182/blood-2014-03-560227

  • Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.

    Clarkson CS, Weetman D, Essandoh J, Yawson AE, Maslen G, Manske M, Field SG, Webster M, Antão T, MacInnis B et al.

    Nature communications 2014;5;4248

    PUBMED: 24963649; PMC: 4086683; DOI: 10.1038/ncomms5248

  • Inferring human population size and separation history from multiple genome sequences.

    Schiffels S and Durbin R

    Nature genetics 2014;46;8;919-25

    PUBMED: 24952747; PMC: 4116295; DOI: 10.1038/ng.3015

  • Whole-genome scans provide evidence of adaptive evolution in Malawian Plasmodium falciparum isolates.

    Ocholla H, Preston MD, Mipando M, Jensen AT, Campino S, MacInnis B, Alcock D, Terlouw A, Zongo I, Oudraogo JB et al.

    The Journal of infectious diseases 2014;210;12;1991-2000

    PUBMED: 24948693; PMC: 4241944; DOI: 10.1093/infdis/jiu349

  • Modification of British Committee for Standards in Haematology diagnostic criteria for essential thrombocythaemia.

    Harrison CN, Butt N, Campbell P, Conneally E, Drummond M, Green AR, Murrin R, Radia DH, Mead A, Reilly JT et al.

    British journal of haematology 2014;167;3;421-3

    PUBMED: 24935860; DOI: 10.1111/bjh.12986

  • Using association rule mining to determine promising secondary phenotyping hypotheses.

    Oellrich A, Jacobsen J, Papatheodorou I, Sanger Mouse Genetics Project and Smedley D

    Bioinformatics (Oxford, England) 2014;30;12;i52-59

    PUBMED: 24932005; PMC: 4059059; DOI: 10.1093/bioinformatics/btu260

  • Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

    Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M et al.

    Nature genetics 2014;46;7;693-700

    PUBMED: 24929830; PMC: 5012510; DOI: 10.1038/ng.3010

  • The Scramble conversion tool.

    Bonfield JK

    Bioinformatics (Oxford, England) 2014;30;19;2818-9

    PUBMED: 24930138; PMC: 4173023; DOI: 10.1093/bioinformatics/btu390

  • Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

    Delaneau O, Marchini J, 1000 Genomes Project Consortium and 1000 Genomes Project Consortium

    Nature communications 2014;5;3934

    PUBMED: 25653097; PMC: 4338501; DOI: 10.1038/ncomms4934

  • The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design.

    van Sorge NM, Cole JN, Kuipers K, Henningham A, Aziz RK, Kasirer-Friede A, Lin L, Berends ETM, Davies MR, Dougan G et al.

    Cell host & microbe 2014;15;6;729-740

    PUBMED: 24922575; PMC: 4078075; DOI: 10.1016/j.chom.2014.05.009

  • Vitamin B₁₂-dependent taurine synthesis regulates growth and bone mass.

    Roman-Garcia P, Quiros-Gonzalez I, Mottram L, Lieben L, Sharan K, Wangwiwatsin A, Tubio J, Lewis K, Wilkinson D, Santhanam B et al.

    The Journal of clinical investigation 2014;124;7;2988-3002

    PUBMED: 24911144; PMC: 4071367; DOI: 10.1172/JCI72606

  • DNA methylation and body-mass index: a genome-wide analysis.

    Dick KJ, Nelson CP, Tsaprouni L, Sandling JK, Aïssi D, Wahl S, Meduri E, Morange PE, Gagnon F, Grallert H et al.

    Lancet (London, England) 2014;383;9933;1990-8

    PUBMED: 24630777; DOI: 10.1016/S0140-6736(13)62674-4

  • The sheep genome illuminates biology of the rumen and lipid metabolism.

    Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W et al.

    Science (New York, N.Y.) 2014;344;6188;1168-73

    PUBMED: 24904168; PMC: 4157056; DOI: 10.1126/science.1252806

  • RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri.

    Vergara-Irigaray M, Fookes MC, Thomson NR and Tang CM

    BMC genomics 2014;15;438

    PUBMED: 24907032; PMC: 4229854; DOI: 10.1186/1471-2164-15-438

  • The different shades of fat.

    Peirce V, Carobbio S and Vidal-Puig A

    Nature 2014;510;7503;76-83

    PUBMED: 24899307; DOI: 10.1038/nature13477

  • Genetic background drives transcriptional variation in human induced pluripotent stem cells.

    Rouhani F, Kumasaka N, de Brito MC, Bradley A, Vallier L and Gaffney D

    PLoS genetics 2014;10;6;e1004432

    PUBMED: 24901476; PMC: 4046971; DOI: 10.1371/journal.pgen.1004432

  • Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations.

    Rainger J, Pehlivan D, Johansson S, Bengani H, Sanchez-Pulido L, Williamson KA, Ture M, Barker H, Rosendahl K, Spranger J et al.

    American journal of human genetics 2014;94;6;915-23

    PUBMED: 24906020; PMC: 4121478; DOI: 10.1016/j.ajhg.2014.05.005

  • Reprogramming the methylome: erasing memory and creating diversity.

    Lee HJ, Hore TA and Reik W

    Cell stem cell 2014;14;6;710-9

    PUBMED: 24905162; PMC: 4051243; DOI: 10.1016/j.stem.2014.05.008

  • CtIP-mediated resection is essential for viability and can operate independently of BRCA1.

    Polato F, Callen E, Wong N, Faryabi R, Bunting S, Chen HT, Kozak M, Kruhlak MJ, Reczek CR, Lee WH et al.

    The Journal of experimental medicine 2014;211;6;1027-36

    PUBMED: 24842372; PMC: 4042650; DOI: 10.1084/jem.20131939

  • Mutations disrupting the Kennedy phosphatidylcholine pathway in humans with congenital lipodystrophy and fatty liver disease.

    Payne F, Lim K, Girousse A, Brown RJ, Kory N, Robbins A, Xue Y, Sleigh A, Cochran E, Adams C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;24;8901-6

    PUBMED: 24889630; PMC: 4066527; DOI: 10.1073/pnas.1408523111

  • The International Cancer Genome Consortium's evolving data-protection policies.

    Milius D, Dove ES, Chalmers D, Dyke SO, Kato K, Nicolás P, Ouellette BF, Ozenberger B, Rodriguez LL, Zeps N and Joly Y

    Nature biotechnology 2014;32;6;519-23

    PUBMED: 24911490; DOI: 10.1038/nbt.2926

  • 27th International Mammalian Genome Conference meeting report.

    Gamache B, Leist SR, Bard AD, Logan DW and Carpanini SM

    Mammalian genome : official journal of the International Mammalian Genome Society 2014;25;5-6;195-201

    PUBMED: 24752582; DOI: 10.1007/s00335-014-9513-3

  • Allele-specific regulation of DISC1 expression by miR-135b-5p.

    Rossi M, Kilpinen H, Muona M, Surakka I, Ingle C, Lahtinen J, Hennah W, Ripatti S and Hovatta I

    European journal of human genetics : EJHG 2014;22;6;840-3

    PUBMED: 24169524; PMC: 4023220; DOI: 10.1038/ejhg.2013.246

  • Common genetic variants do not associate with CAD in familial hypercholesterolemia.

    van Iperen EP, Sivapalaratnam S, Boekholdt SM, Hovingh GK, Maiwald S, Tanck MW, Soranzo N, Stephens JC, Sambrook JG, Levi M et al.

    European journal of human genetics : EJHG 2014;22;6;809-13

    PUBMED: 24219970; PMC: 4023217; DOI: 10.1038/ejhg.2013.242

  • De novo mutations in HCN1 cause early infantile epileptic encephalopathy.

    Nava C, Dalle C, Rastetter A, Striano P, de Kovel CG, Nabbout R, Cancès C, Ville D, Brilstra EH, Gobbi G et al.

    Nature genetics 2014;46;6;640-5

    PUBMED: 24747641; DOI: 10.1038/ng.2952

  • Deciphering the origin of the 2012 cholera epidemic in Guinea by integrating epidemiological and molecular analyses.

    Rebaudet S, Mengel MA, Koivogui L, Moore S, Mutreja A, Kande Y, Yattara O, Sarr Keita V, Njanpop-Lafourcade BM, Fournier PE et al.

    PLoS neglected tropical diseases 2014;8;6;e2898

    PUBMED: 24901522; PMC: 4046952; DOI: 10.1371/journal.pntd.0002898

  • DrsG from Streptococcus dysgalactiae subsp. equisimilis inhibits the antimicrobial peptide LL-37.

    Smyth D, Cameron A, Davies MR, McNeilly C, Hafner L, Sriprakash KS and McMillan DJ

    Infection and immunity 2014;82;6;2337-44

    PUBMED: 24664506; PMC: 4019180; DOI: 10.1128/IAI.01411-13

  • Expression of a single-chain human leukocyte antigen-DRA/DRB3*01:01 molecule and differential binding of a monoclonal antibody in the presence of specifically bound human platelet antigen-1a peptide.

    Bouwmans EE, Smethurst PA, Garner SF, Ouwehand WH and Morley SL

    Transfusion 2014;54;6;1478-85

    PUBMED: 24308361; DOI: 10.1111/trf.12502

  • Genetic determinants of long-term changes in blood lipid concentrations: 10-year follow-up of the GLACIER study.

    Varga TV, Sonestedt E, Shungin D, Koivula RW, Hallmans G, Escher SA, Barroso I, Nilsson P, Melander O, Orho-Melander M et al.

    PLoS genetics 2014;10;6;e1004388

    PUBMED: 24922540; PMC: 4055682; DOI: 10.1371/journal.pgen.1004388

  • Genetic studies of Crohn's disease: past, present and future.

    Liu JZ and Anderson CA

    Best practice & research. Clinical gastroenterology 2014;28;3;373-86

    PUBMED: 24913378; PMC: 4075408; DOI: 10.1016/j.bpg.2014.04.009

  • Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity.

    Mobegi VA, Duffy CW, Amambua-Ngwa A, Loua KM, Laman E, Nwakanma DC, MacInnis B, Aspeling-Jones H, Murray L, Clark TG et al.

    Molecular biology and evolution 2014;31;6;1490-9

    PUBMED: 24644299; PMC: 4032133; DOI: 10.1093/molbev/msu106

  • Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013.

    Memish ZA, Cotten M, Meyer B, Watson SJ, Alsahafi AJ, Al Rabeeah AA, Corman VM, Sieberg A, Makhdoom HQ, Assiri A et al.

    Emerging infectious diseases 2014;20;6;1012-5

    PUBMED: 24857749; PMC: 4036761; DOI: 10.3201/eid2006.140402

  • Lipoprotein(a) levels, genotype, and incident aortic valve stenosis: a prospective Mendelian randomization study and replication in a case-control cohort.

    Arsenault BJ, Boekholdt SM, Dubé MP, Rhéaume E, Wareham NJ, Khaw KT, Sandhu MS and Tardif JC

    Circulation. Cardiovascular genetics 2014;7;3;304-10

    PUBMED: 24704946; DOI: 10.1161/CIRCGENETICS.113.000400

  • OutbreakTools: a new platform for disease outbreak analysis using the R software.

    Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, Colijn C, Collins C, Cori A, Didelot X et al.

    Epidemics 2014;7;28-34

    PUBMED: 24928667; PMC: 4058532; DOI: 10.1016/j.epidem.2014.04.003

  • PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation.

    Preston MD, Assefa SA, Ocholla H, Sutherland CJ, Borrmann S, Nzila A, Michon P, Hien TT, Bousema T, Drakeley CJ et al.

    The Journal of infectious diseases 2014;209;11;1808-15

    PUBMED: 24338354; PMC: 4017360; DOI: 10.1093/infdis/jit812

  • Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns.

    Salomonsen J, Chattaway JA, Chan AC, Parker A, Huguet S, Marston DA, Rogers SL, Wu Z, Smith AL, Staines K et al.

    PLoS genetics 2014;10;6;e1004417

    PUBMED: 24901252; PMC: 4046983; DOI: 10.1371/journal.pgen.1004417

  • TB or not TB? Genomic portraits provide answers.

    Baker KS and Ellington MJ

    Nature reviews. Microbiology 2014;12;6;398

    PUBMED: 24801935; DOI: 10.1038/nrmicro3273

  • USP28 is recruited to sites of DNA damage by the tandem BRCT domains of 53BP1 but plays a minor role in double-strand break metabolism.

    Knobel PA, Belotserkovskaya R, Galanty Y, Schmidt CK, Jackson SP and Stracker TH

    Molecular and cellular biology 2014;34;11;2062-74

    PUBMED: 24687851; PMC: 4019063; DOI: 10.1128/MCB.00197-14

  • Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b.

    Toribio AL, Pickard D, Cerdeño-Tárraga AM, Petty NK, Thomson N, Salmond G and Dougan G

    Genome announcements 2014;2;3

    PUBMED: 24874665; PMC: 4038870; DOI: 10.1128/genomeA.00146-14

  • High-definition reconstruction of clonal composition in cancer.

    Fischer A, Vázquez-García I, Illingworth CJR and Mustonen V

    Cell reports 2014;7;5;1740-1752

    PUBMED: 24882004; PMC: 4062932; DOI: 10.1016/j.celrep.2014.04.055

  • Fibroblastic growth factor receptor 1 amplification in osteosarcoma is associated with poor response to neo-adjuvant chemotherapy.

    Fernanda Amary M, Ye H, Berisha F, Khatri B, Forbes G, Lehovsky K, Frezza AM, Behjati S, Tarpey P, Pillay N et al.

    Cancer medicine 2014;3;4;980-7

    PUBMED: 24861215; PMC: 4303166; DOI: 10.1002/cam4.268

  • Plasmid CDS5 influences infectivity and virulence in a mouse model of Chlamydia trachomatis urogenital infection.

    Ramsey KH, Schripsema JH, Smith BJ, Wang Y, Jham BC, O'Hagan KP, Thomson NR, Murthy AK, Skilton RJ, Chu P and Clarke IN

    Infection and immunity 2014;82;8;3341-9

    PUBMED: 24866804; PMC: 4136204; DOI: 10.1128/IAI.01795-14

  • Genome-wide analysis of cold adaptation in indigenous Siberian populations.

    Cardona A, Pagani L, Antao T, Lawson DJ, Eichstaedt CA, Yngvadottir B, Shwe MT, Wee J, Romero IG, Raj S et al.

    PloS one 2014;9;5;e98076

    PUBMED: 24847810; PMC: 4029955; DOI: 10.1371/journal.pone.0098076

  • Gene-lifestyle interaction and type 2 diabetes: the EPIC interact case-cohort study.

    Langenberg C, Sharp SJ, Franks PW, Scott RA, Deloukas P, Forouhi NG, Froguel P, Groop LC, Hansen T, Palla L et al.

    PLoS medicine 2014;11;5;e1001647

    PUBMED: 24845081; PMC: 4028183; DOI: 10.1371/journal.pmed.1001647

  • Minimal morphological criteria for defining bone marrow dysplasia: a basis for clinical implementation of WHO classification of myelodysplastic syndromes.

    Della Porta MG, Travaglino E, Boveri E, Ponzoni M, Malcovati L, Papaemmanuil E, Rigolin GM, Pascutto C, Croci G, Gianelli U et al.

    Leukemia 2014;29;1;66-75

    PUBMED: 24935723; DOI: 10.1038/leu.2014.161

  • Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.

    Woll PS, Kjällquist U, Chowdhury O, Doolittle H, Wedge DC, Thongjuea S, Erlandsson R, Ngara M, Anderson K, Deng Q et al.

    Cancer cell 2014;25;6;794-808

    PUBMED: 24835589; DOI: 10.1016/j.ccr.2014.03.036

  • Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome.

    Memish ZA, Al-Tawfiq JA, Makhdoom HQ, Assiri A, Alhakeem RF, Albarrak A, Alsubaie S, Al-Rabeeah AA, Hajomar WH, Hussain R et al.

    The Journal of infectious diseases 2014;210;10;1590-4

    PUBMED: 24837403; PMC: 7107391; DOI: 10.1093/infdis/jiu292

  • A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals.

    Harrison EM, Weinert LA, Holden MT, Welch JJ, Wilson K, Morgan FJ, Harris SR, Loeffler A, Boag AK, Peacock SJ et al.

    mBio 2014;5;3;e00985-13

    PUBMED: 24825010; PMC: 4030480; DOI: 10.1128/mBio.00985-13

  • An atlas of genetic influences on human blood metabolites.

    Shin SY, Fauman EB, Petersen AK, Krumsiek J, Santos R, Huang J, Arnold M, Erte I, Forgetta V, Yang TP et al.

    Nature genetics 2014;46;6;543-550

    PUBMED: 24816252; PMC: 4064254; DOI: 10.1038/ng.2982

  • Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.

    Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, Hebenstreit D, Dingler FA, Moignard V, Göttgens B et al.

    Cell reports 2014;7;4;1130-42

    PUBMED: 24813893; PMC: 4039991; DOI: 10.1016/j.celrep.2014.04.011

  • The genetic basis of plasmid tropism between Chlamydia trachomatis and Chlamydia muridarum.

    Wang Y, Cutcliffe LT, Skilton RJ, Ramsey KH, Thomson NR and Clarke IN

    Pathogens and disease 2014;72;1;19-23

    PUBMED: 24700815; PMC: 4314687; DOI: 10.1111/2049-632X.12175

  • A genome wide association study of Plasmodium falciparum susceptibility to 22 antimalarial drugs in Kenya.

    Wendler JP, Okombo J, Amato R, Miotto O, Kiara SM, Mwai L, Pole L, O'Brien J, Manske M, Alcock D et al.

    PloS one 2014;9;5;e96486

    PUBMED: 24809681; PMC: 4014544; DOI: 10.1371/journal.pone.0096486

  • The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

    Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D, Echaide IE, Farber M, Gahlot S, Gamble J, Gupta D et al.

    Nucleic acids research 2014;42;11;7113-31

    PUBMED: 24799432; PMC: 4066756; DOI: 10.1093/nar/gku322

  • Chemical inhibition of NAT10 corrects defects of laminopathic cells.

    Larrieu D, Britton S, Demir M, Rodriguez R and Jackson SP

    Science (New York, N.Y.) 2014;344;6183;527-32

    PUBMED: 24786082; PMC: 4246063; DOI: 10.1126/science.1252651

  • An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution.

    Waddington CS, Darton TC, Jones C, Haworth K, Peters A, John T, Thompson BA, Kerridge SA, Kingsley RA, Zhou L et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2014;58;9;1230-40

    PUBMED: 24519873; PMC: 3982839; DOI: 10.1093/cid/ciu078

  • Bayesian latent variable collapsing model for detecting rare variant interaction effect in twin study.

    He L, Sillanpää MJ, Ripatti S and Pitkäniemi J

    Genetic epidemiology 2014;38;4;310-24

    PUBMED: 24719390; DOI: 10.1002/gepi.21804

  • Dissecting mammalian immunity through mutation.

    Siggs OM

    Immunology and cell biology 2014;92;5;392-9

    PUBMED: 24518983; PMC: 4038135; DOI: 10.1038/icb.2014.8

  • estMOI: estimating multiplicity of infection using parasite deep sequencing data.

    Assefa SA, Preston MD, Campino S, Ocholla H, Sutherland CJ and Clark TG

    Bioinformatics (Oxford, England) 2014;30;9;1292-4

    PUBMED: 24443379; PMC: 3998131; DOI: 10.1093/bioinformatics/btu005

  • Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats.

    Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C and Jobling MA

    Human mutation 2014;35;5;609-17

    PUBMED: 24610746; PMC: 4233959; DOI: 10.1002/humu.22542

  • Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

    Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S and Fraser C

    PLoS genetics 2014;10;5;e1004300

    PUBMED: 24786281; PMC: 4006708; DOI: 10.1371/journal.pgen.1004300

  • Jannovar: a java library for exome annotation.

    Jäger M, Wang K, Bauer S, Smedley D, Krawitz P and Robinson PN

    Human mutation 2014;35;5;548-55

    PUBMED: 24677618; DOI: 10.1002/humu.22531

  • Low copy number of the salivary amylase gene predisposes to obesity.

    Falchi M, El-Sayed Moustafa JS, Takousis P, Pesce F, Bonnefond A, Andersson-Assarsson JC, Sudmant PH, Dorajoo R, Al-Shafai MN, Bottolo L et al.

    Nature genetics 2014;46;5;492-7

    PUBMED: 24686848; PMC: 6485469; DOI: 10.1038/ng.2939

  • Paving the way towards a successful and fulfilling career in computational biology.

    Oluwagbemi O, Adebiyi M, Fatumo S and Macintyre G

    PLoS computational biology 2014;10;5;e1003593

    PUBMED: 24784875; PMC: 4006700; DOI: 10.1371/journal.pcbi.1003593

  • PolyTB: a genomic variation map for Mycobacterium tuberculosis.

    Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S et al.

    Tuberculosis (Edinburgh, Scotland) 2014;94;3;346-54

    PUBMED: 24637013; PMC: 4066953; DOI: 10.1016/j.tube.2014.02.005

  • Predicting the virulence of MRSA from its genome sequence.

    Laabei M, Recker M, Rudkin JK, Aldeljawi M, Gulay Z, Sloan TJ, Williams P, Endres JL, Bayles KW, Fey PD et al.

    Genome research 2014;24;5;839-49

    PUBMED: 24717264; PMC: 4009613; DOI: 10.1101/gr.165415.113

  • Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo-Oriental Region.

    Zarowiecki M, Linton YM, Post RJ, Bangs MJ, Htun PT, Hlaing T, Seng CM, Baimai V, Ding TH, Sochantha T and Walton C

    Molecular ecology 2014;23;10;2573-89

    PUBMED: 24750501; DOI: 10.1111/mec.12761

  • Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction.

    Wain LV, Sayers I, Soler Artigas M, Portelli MA, Zeggini E, Obeidat M, Sin DD, Bossé Y, Nickle D, Brandsma CA et al.

    PLoS genetics 2014;10;5;e1004314

    PUBMED: 24786987; PMC: 4006731; DOI: 10.1371/journal.pgen.1004314

  • Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?

    Török ME, Harris SR, Cartwright EJ, Raven KE, Brown NM, Allison ME, Greaves D, Quail MA, Limmathurotsakul D, Holden MT et al.

    The Journal of antimicrobial chemotherapy 2014;69;8;2238-45

    PUBMED: 24788657; PMC: 4100711; DOI: 10.1093/jac/dku128

  • Defining functional DNA elements in the human genome.

    Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;17;6131-8

    PUBMED: 24753594; PMC: 4035993; DOI: 10.1073/pnas.1318948111

  • Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

    Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Maria Calò C, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P et al.

    Nature communications 2014;5;3513

    PUBMED: 24781250; PMC: 4007635; DOI: 10.1038/ncomms4513

  • Natural selection and infectious disease in human populations.

    Karlsson EK, Kwiatkowski DP and Sabeti PC

    Nature reviews. Genetics 2014;15;6;379-93

    PUBMED: 24776769; PMC: 4912034; DOI: 10.1038/nrg3734

  • A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

    Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SM, Santos LH, Anslinger K, Bayer B et al.

    Forensic science international. Genetics 2014;12;12-23

    PUBMED: 24854874; PMC: 4127773; DOI: 10.1016/j.fsigen.2014.04.008

  • Confinement and deformation of single cells and their nuclei inside size-adapted microtubes.

    Koch B, Sanchez S, Schmidt CK, Swiersy A, Jackson SP and Schmidt OG

    Advanced healthcare materials 2014;3;11;1753-8

    PUBMED: 24764273; PMC: 4227890; DOI: 10.1002/adhm.201300678

  • Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

    Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR et al.

    Molecular ecology 2014;23;10;2442-51

    PUBMED: 24689900; PMC: 4237157; DOI: 10.1111/mec.12742

  • Genetic interactions affecting human gene expression identified by variance association mapping.

    Brown AA, Buil A, Viñuela A, Lappalainen T, Zheng HF, Richards JB, Small KS, Spector TD, Dermitzakis ET and Durbin R

    eLife 2014;3;e01381

    PUBMED: 24771767; PMC: 4017648; DOI: 10.7554/eLife.01381

  • Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.

    International Glossina Genome Initiative

    Science (New York, N.Y.) 2014;344;6182;380-6

    PUBMED: 24763584; PMC: 4077534; DOI: 10.1126/science.1249656

  • Guidelines for investigating causality of sequence variants in human disease.

    MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA et al.

    Nature 2014;508;7497;469-76

    PUBMED: 24759409; PMC: 4180223; DOI: 10.1038/nature13127

  • Global population structure and evolution of Bordetella pertussis and their relationship with vaccination.

    Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D, Bouchez V, Cassiday PK, Chiang CS, Dalby T, Fry NK et al.

    mBio 2014;5;2;e01074

    PUBMED: 24757216; PMC: 3994516; DOI: 10.1128/mBio.01074-14

  • Parallel independent evolution of pathogenicity within the genus Yersinia.

    Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;18;6768-73

    PUBMED: 24753568; PMC: 4020045; DOI: 10.1073/pnas.1317161111

  • Random projection based clustering for population genomics

    Tasoulis,S, Cheng,L, Valimaki,N, Croucher,N.J, HARRIS,S.R, Hanage,W.P, Roos,T and Corander,J

    Proceedings - 2014 IEEE International Conference on Big Data, IEEE Big Data 2014 2014;675-82

    DOI: 10.1109/BigData.2014.7004291

  • Comment on: characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array.

    Köser CU, Bryant JM, Comas I, Feuerriegel S, Niemann S, Gagneux S, Parkhill J and Peacock SJ

    The Journal of antimicrobial chemotherapy 2014;69;8;2298-9

    PUBMED: 24752956; PMC: 4100706; DOI: 10.1093/jac/dku101

  • A general approach for haplotype phasing across the full spectrum of relatedness.

    O'Connell J, Gurdasani D, Delaneau O, Pirastu N, Ulivi S, Cocca M, Traglia M, Huang J, Huffman JE, Rudan I et al.

    PLoS genetics 2014;10;4;e1004234

    PUBMED: 24743097; PMC: 3990520; DOI: 10.1371/journal.pgen.1004234

  • A strategy to identify dominant point mutant modifiers of a quantitative trait.

    Dove WF, Shedlovsky A, Clipson L, Amos-Landgraf JM, Halberg RB, Krentz KJ, Boehm FJ, Newton MA, Adams DJ and Keane TM

    G3 (Bethesda, Md.) 2014;4;6;1113-21

    PUBMED: 24747760; PMC: 4065254; DOI: 10.1534/g3.114.010595

  • Juno is the egg Izumo receptor and is essential for mammalian fertilization.

    Bianchi E, Doe B, Goulding D and Wright GJ

    Nature 2014;508;7497;483-7

    PUBMED: 24739963; PMC: 3998876; DOI: 10.1038/nature13203

  • Epidermal Wnt/β-catenin signaling regulates adipocyte differentiation via secretion of adipogenic factors.

    Donati G, Proserpio V, Lichtenberger BM, Natsuga K, Sinclair R, Fujiwara H and Watt FM

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;15;E1501-9

    PUBMED: 24706781; PMC: 3992657; DOI: 10.1073/pnas.1312880111

  • Global dissemination of a multidrug resistant Escherichia coli clone.

    Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M, Forde BM, Phan MD, Gomes Moriel D, Peters KM, Davies M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;15;5694-9

    PUBMED: 24706808; PMC: 3992628; DOI: 10.1073/pnas.1322678111

  • Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer.

    Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP, Bolli N, Davies HR, Knappskog S, Martin S, Papaemmanuil E et al.

    Nature genetics 2014;46;5;487-91

    PUBMED: 24728294; PMC: 4137149; DOI: 10.1038/ng.2955

  • Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen.

    Liakath-Ali K, Vancollie VE, Heath E, Smedley DP, Estabel J, Sunter D, Ditommaso T, White JK, Ramirez-Solis R, Smyth I et al.

    Nature communications 2014;5;3540

    PUBMED: 24721909; PMC: 3996542; DOI: 10.1038/ncomms4540

  • Neutrophils recruited by IL-22 in peripheral tissues function as TRAIL-dependent antiviral effectors against MCMV.

    Stacey MA, Marsden M, Pham N TA, Clare S, Dolton G, Stack G, Jones E, Klenerman P, Gallimore AM, Taylor PR et al.

    Cell host & microbe 2014;15;4;471-83

    PUBMED: 24721575; PMC: 3989063; DOI: 10.1016/j.chom.2014.03.003

  • Processed pseudogenes acquired somatically during cancer development.

    Cooke SL, Shlien A, Marshall J, Pipinikas CP, Martincorena I, Tubio JM, Li Y, Menzies A, Mudie L, Ramakrishna M et al.

    Nature communications 2014;5;3644

    PUBMED: 24714652; PMC: 3996531; DOI: 10.1038/ncomms4644

  • Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.

    De Chiara M, Hood D, Muzzi A, Pickard DJ, Perkins T, Pizza M, Dougan G, Rappuoli R, Moxon ER, Soriani M and Donati C

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;14;5439-44

    PUBMED: 24706866; PMC: 3986186; DOI: 10.1073/pnas.1403353111

  • A central role for GRB10 in regulation of islet function in man.

    Prokopenko I, Poon W, Mägi R, Prasad B R, Salehi SA, Almgren P, Osmark P, Bouatia-Naji N, Wierup N, Fall T et al.

    PLoS genetics 2014;10;4;e1004235

    PUBMED: 24699409; PMC: 3974640; DOI: 10.1371/journal.pgen.1004235

  • De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability.

    Grozeva D, Carss K, Spasic-Boskovic O, Parker MJ, Archer H, Firth HV, Park SM, Canham N, Holder SE, Wilson M et al.

    American journal of human genetics 2014;94;4;618-24

    PUBMED: 24680889; PMC: 3980521; DOI: 10.1016/j.ajhg.2014.03.006

  • Rare variants in NR2F2 cause congenital heart defects in humans.

    Al Turki S, Manickaraj AK, Mercer CL, Gerety SS, Hitz MP, Lindsay S, D'Alessandro LC, Swaminathan GJ, Bentham J, Arndt AK et al.

    American journal of human genetics 2014;94;4;574-85

    PUBMED: 24702954; PMC: 3980509; DOI: 10.1016/j.ajhg.2014.03.007

  • Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm.

    Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P and van der Hoek L

    PloS one 2014;9;4;e93269

    PUBMED: 24695106; PMC: 3973683; DOI: 10.1371/journal.pone.0093269

  • A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.

    Hamidian M, Holt KE, Pickard D, Dougan G and Hall RM

    The Journal of antimicrobial chemotherapy 2014;69;4;955-8

    PUBMED: 24235096; PMC: 3956371; DOI: 10.1093/jac/dkt454

  • A novel hybrid SCCmec-mecC region in Staphylococcus sciuri.

    Harrison EM, Paterson GK, Holden MT, Ba X, Rolo J, Morgan FJ, Pichon B, Kearns A, Zadoks RN, Peacock SJ et al.

    The Journal of antimicrobial chemotherapy 2014;69;4;911-8

    PUBMED: 24302651; PMC: 3956370; DOI: 10.1093/jac/dkt452

  • The use of anthropometric measures for cardiometabolic risk identification in a rural African population.

    Murphy GA, Asiki G, Nsubuga RN, Young EH, Seeley J, Sandhu MS and Kamali A

    Diabetes care 2014;37;4;e64-5

    PUBMED: 24652731; DOI: 10.2337/dc13-2096

  • Assessment of osteoarthritis candidate genes in a meta-analysis of nine genome-wide association studies.

    Rodriguez-Fontenla C, Calaza M, Evangelou E, Valdes AM, Arden N, Blanco FJ, Carr A, Chapman K, Deloukas P, Doherty M et al.

    Arthritis & rheumatology (Hoboken, N.J.) 2014;66;4;940-9

    PUBMED: 24757145; PMC: 4660891; DOI: 10.1002/art.38300

  • Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection.

    Nwakanma DC, Duffy CW, Amambua-Ngwa A, Oriero EC, Bojang KA, Pinder M, Drakeley CJ, Sutherland CJ, Milligan PJ, Macinnis B et al.

    The Journal of infectious diseases 2014;209;7;1126-35

    PUBMED: 24265439; PMC: 3952670; DOI: 10.1093/infdis/jit618

  • Chromatin landscapes of retroviral and transposon integration profiles.

    de Jong J, Akhtar W, Badhai J, Rust AG, Rad R, Hilkens J, Berns A, van Lohuizen M, Wessels LF and de Ridder J

    PLoS genetics 2014;10;4;e1004250

    PUBMED: 24721906; PMC: 3983033; DOI: 10.1371/journal.pgen.1004250

  • Computational biology and bioinformatics in Nigeria.

    Fatumo SA, Adoga MP, Ojo OO, Oluwagbemi O, Adeoye T, Ewejobi I, Adebiyi M, Adebiyi E, Bewaji C and Nashiru O

    PLoS computational biology 2014;10;4;e1003516

    PUBMED: 24763310; PMC: 3998874; DOI: 10.1371/journal.pcbi.1003516

  • Cross-species analysis of mouse and human cancer genomes.

    Robles-Espinoza CD and Adams DJ

    Cold Spring Harbor protocols 2014;2014;4;350-8

    PUBMED: 24173316; DOI: 10.1101/pdb.top078824

  • Human African trypanosomiasis research gets a boost: unraveling the tsetse genome.

    Aksoy S, Attardo G, Berriman M, Christoffels A, Lehane M, Masiga D and Toure Y

    PLoS neglected tropical diseases 2014;8;4;e2624

    PUBMED: 24762859; PMC: 3998789; DOI: 10.1371/journal.pntd.0002624

  • JAK2V617F homozygosity drives a phenotypic switch in myeloproliferative neoplasms, but is insufficient to sustain disease.

    Li J, Kent DG, Godfrey AL, Manning H, Nangalia J, Aziz A, Chen E, Saeb-Parsy K, Fink J, Sneade R et al.

    Blood 2014;123;20;3139-51

    PUBMED: 24692758; DOI: 10.1182/blood-2013-06-510222

  • Kdm3a lysine demethylase is an Hsp90 client required for cytoskeletal rearrangements during spermatogenesis.

    Kasioulis I, Syred HM, Tate P, Finch A, Shaw J, Seawright A, Fuszard M, Botting CH, Shirran S, Adams IR et al.

    Molecular biology of the cell 2014;25;8;1216-33

    PUBMED: 24554764; PMC: 3982988; DOI: 10.1091/mbc.E13-08-0471

  • Poxviruses in bats … so what?

    Baker KS and Murcia PR

    Viruses 2014;6;4;1564-77

    PUBMED: 24704730; PMC: 4014710; DOI: 10.3390/v6041564

  • Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP.

    Wickramasinghe VO, Andrews R, Ellis P, Langford C, Gurdon JB, Stewart M, Venkitaraman AR and Laskey RA

    Nucleic acids research 2014;42;8;5059-71

    PUBMED: 24510098; PMC: 4005691; DOI: 10.1093/nar/gku095

  • Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks.

    Aymard F, Bugler B, Schmidt CK, Guillou E, Caron P, Briois S, Iacovoni JS, Daburon V, Miller KM, Jackson SP and Legube G

    Nature structural & molecular biology 2014;21;4;366-74

    PUBMED: 24658350; DOI: 10.1038/nsmb.2796

  • Community case clusters of Middle East respiratory syndrome coronavirus in Hafr Al-Batin, Kingdom of Saudi Arabia: a descriptive genomic study.

    Memish ZA, Cotten M, Watson SJ, Kellam P, Zumla A, Alhakeem RF, Assiri A, Rabeeah AA and Al-Tawfiq JA

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2014;23;63-8

    PUBMED: 24699184; PMC: 4441753; DOI: 10.1016/j.ijid.2014.03.1372

  • Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.

    Ashton PM, Baker KS, Gentle A, Wooldridge DJ, Thomson NR, Dallman TJ and Jenkins C

    Gut pathogens 2014;6;1;7

    PUBMED: 24684748; PMC: 3972513; DOI: 10.1186/1757-4749-6-7

  • POT1 loss-of-function variants predispose to familial melanoma.

    Robles-Espinoza CD, Harland M, Ramsay AJ, Aoude LG, Quesada V, Ding Z, Pooley KA, Pritchard AL, Tiffen JC, Petljak M et al.

    Nature genetics 2014;46;5;478-481

    PUBMED: 24686849; PMC: 4266105; DOI: 10.1038/ng.2947

  • Widespread epidemic cholera caused by a restricted subset of Vibrio cholerae clones.

    Moore S, Thomson N, Mutreja A and Piarroux R

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2014;20;5;373-9

    PUBMED: 24575898; DOI: 10.1111/1469-0691.12610

  • Epistasis between the haptoglobin common variant and α+thalassemia influences risk of severe malaria in Kenyan children.

    Atkinson SH, Uyoga SM, Nyatichi E, Macharia AW, Nyutu G, Ndila C, Kwiatkowski DP, Rockett KA and Williams TN

    Blood 2014;123;13;2008-16

    PUBMED: 24478401; PMC: 3968387; DOI: 10.1182/blood-2013-10-533489

  • Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia.

    Li Y, Schwab C, Ryan S, Papaemmanuil E, Robinson HM, Jacobs P, Moorman AV, Dyer S, Borrow J, Griffiths M et al.

    Nature 2014;508;7494;98-102

    PUBMED: 24670643; PMC: 3976272; DOI: 10.1038/nature13115

  • Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.

    Collins MO, Wright JC, Jones M, Rayner JC and Choudhary JS

    Journal of proteomics 2014;103;1-14

    PUBMED: 24657495; PMC: 4047622; DOI: 10.1016/j.jprot.2014.03.010

  • Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen.

    Adissu HA, Estabel J, Sunter D, Tuck E, Hooks Y, Carragher DM, Clarke K, Karp NA, Sanger Mouse Genetics Project, Newbigging S et al.

    Disease models & mechanisms 2014;7;5;515-24

    PUBMED: 24652767; PMC: 4007403; DOI: 10.1242/dmm.015263

  • Optoactivation of locus ceruleus neurons evokes bidirectional changes in thermal nociception in rats.

    Hickey L, Li Y, Fyson SJ, Watson TC, Perrins R, Hewinson J, Teschemacher AG, Furue H, Lumb BM and Pickering AE

    The Journal of neuroscience : the official journal of the Society for Neuroscience 2014;34;12;4148-60

    PUBMED: 24647936; PMC: 3960461; DOI: 10.1523/JNEUROSCI.4835-13.2014

  • Targeting of Slc25a21 is associated with orofacial defects and otitis media due to disrupted expression of a neighbouring gene.

    Maguire S, Estabel J, Ingham N, Pearson S, Ryder E, Carragher DM, Walker N, Sanger MGP Slc25a21 Project Team, Bussell J, Chan WI et al.

    PloS one 2014;9;3;e91807

    PUBMED: 24642684; PMC: 3958370; DOI: 10.1371/journal.pone.0091807

  • Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery.

    Lee EC, Liang Q, Ali H, Bayliss L, Beasley A, Bloomfield-Gerdes T, Bonoli L, Brown R, Campbell J, Carpenter A et al.

    Nature biotechnology 2014;32;4;356-63

    PUBMED: 24633243; DOI: 10.1038/nbt.2825

  • Recurrent PTPRB and PLCG1 mutations in angiosarcoma.

    Behjati S, Tarpey PS, Sheldon H, Martincorena I, Van Loo P, Gundem G, Wedge DC, Ramakrishna M, Cooke SL, Pillay N et al.

    Nature genetics 2014;46;4;376-379

    PUBMED: 24633157; PMC: 4032873; DOI: 10.1038/ng.2921

  • Antibacterial resistance in sub-Saharan Africa: an underestimated emergency.

    Kariuki S and Dougan G

    Annals of the New York Academy of Sciences 2014;1323;43-55

    PUBMED: 24628272; PMC: 4159419; DOI: 10.1111/nyas.12380

  • Linking tissues to phenotypes using gene expression profiles.

    Oellrich A, Sanger Mouse Genetics Project and Smedley D

    Database : the journal of biological databases and curation 2014;2014;bau017

    PUBMED: 24634472; PMC: 3982582; DOI: 10.1093/database/bau017

  • The OMSSAPercolator: an automated tool to validate OMSSA results.

    Wen B, Li G, Wright JC, Du C, Feng Q, Xu X, Choudhary JS and Wang J

    Proteomics 2014;14;9;1011-4

    PUBMED: 24504981; DOI: 10.1002/pmic.201300393

  • Towards a comprehensive Plasmodium falciparum merozoite cell surface and secreted recombinant protein library.

    Zenonos ZA, Rayner JC and Wright GJ

    Malaria journal 2014;13;93

    PUBMED: 24620899; PMC: 3995786; DOI: 10.1186/1475-2875-13-93

  • An Adipocentric View of the Metabolic Syndrome and Cardiovascular Disease

    Michael Conall Dennedy and Antonio Vidal-Puig

    Current Cardiovascular Risk Reports 2014;8;3;1-9

    DOI: 10.1007/s12170-014-0379-4; URL: https://link.springer.com/article.../10.1007%2Fs12170-014-0379-4

  • A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region.

    Kraaijenbrink T, van der Gaag KJ, Zuniga SB, Xue Y, Carvalho-Silva DR, Tyler-Smith C, Jobling MA, Parkin EJ, Su B, Shi H et al.

    PloS one 2014;9;3;e91534

    PUBMED: 24614536; PMC: 3948894; DOI: 10.1371/journal.pone.0091534

  • Found in translation.

    Chappell L

    Nature reviews. Microbiology 2014;12;4;238

    PUBMED: 24608332; DOI: 10.1038/nrmicro3243

  • Investigating the feasibility of scale up and automation of human induced pluripotent stem cells cultured in aggregates in feeder free conditions.

    Soares FA, Chandra A, Thomas RJ, Pedersen RA, Vallier L and Williams DJ

    Journal of biotechnology 2014;173;53-8

    PUBMED: 24440272; PMC: 3969287; DOI: 10.1016/j.jbiotec.2013.12.009

  • Estimating telomere length from whole genome sequence data.

    Ding Z, Mangino M, Aviv A, Spector T, Durbin R and UK10K Consortium

    Nucleic acids research 2014;42;9;e75

    PUBMED: 24609383; PMC: 4027178; DOI: 10.1093/nar/gku181

  • Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression.

    Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C and Knight JC

    Science (New York, N.Y.) 2014;343;6175;1246949

    PUBMED: 24604202; PMC: 4064786; DOI: 10.1126/science.1246949

  • The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age.

    MacArthur JA, Spector TD, Lindsay SJ, Mangino M, Gill R, Small KS and Hurles ME

    PLoS genetics 2014;10;3;e1004195

    PUBMED: 24603440; PMC: 3945173; DOI: 10.1371/journal.pgen.1004195

  • Heps with pep: direct reprogramming into human hepatocytes.

    Vallier L

    Cell stem cell 2014;14;3;267-9

    PUBMED: 24607399; DOI: 10.1016/j.stem.2014.02.010

  • The evolving role of cancer cell line-based screens to define the impact of cancer genomes on drug response.

    Garnett MJ and McDermott U

    Current opinion in genetics & development 2014;24;114-9

    PUBMED: 24607840; PMC: 4003351; DOI: 10.1016/j.gde.2013.12.002

  • Phosphoinositide metabolism links cGMP-dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites.

    Brochet M, Collins MO, Smith TK, Thompson E, Sebastian S, Volkmann K, Schwach F, Chappell L, Gomes AR, Berriman M et al.

    PLoS biology 2014;12;3;e1001806

    PUBMED: 24594931; PMC: 3942320; DOI: 10.1371/journal.pbio.1001806

  • A comprehensive evaluation of assembly scaffolding tools.

    Hunt M, Newbold C, Berriman M and Otto TD

    Genome biology 2014;15;3;R42

    PUBMED: 24581555; PMC: 4053845; DOI: 10.1186/gb-2014-15-3-r42

  • The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

    Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ et al.

    Genome biology 2014;15;3;R43

    PUBMED: 24580726; PMC: 4054857; DOI: 10.1186/gb-2014-15-3-r43

  • Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects.

    Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgkins A, Iyer V, Huang X and Skarnes WC

    Nature methods 2014;11;4;399-402

    PUBMED: 24584192; DOI: 10.1038/nmeth.2857

  • A reduction in Ptprq associated with specific features of the deafness phenotype of the miR-96 mutant mouse diminuendo.

    Chen J, Johnson SL, Lewis MA, Hilton JM, Huma A, Marcotti W and Steel KP

    The European journal of neuroscience 2014;39;5;744-56

    PUBMED: 24446963; PMC: 4065360; DOI: 10.1111/ejn.12484

  • Cancer mouse models: past, present and future.

    Khaled WT and Liu P

    Seminars in cell & developmental biology 2014;27;54-60

    PUBMED: 24718321; DOI: 10.1016/j.semcdb.2014.04.003

  • Characterizing genetic variants for clinical action.

    Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJ, Jarvik GP, O'Donnell C et al.

    American journal of medical genetics. Part C, Seminars in medical genetics 2014;166C;1;93-104

    PUBMED: 24634402; PMC: 4158437; DOI: 10.1002/ajmg.c.31386

  • CYP6 P450 enzymes and ACE-1 duplication produce extreme and multiple insecticide resistance in the malaria mosquito Anopheles gambiae.

    Edi CV, Djogbénou L, Jenkins AM, Regna K, Muskavitch MA, Poupardin R, Jones CM, Essandoh J, Kétoh GK, Paine MJ et al.

    PLoS genetics 2014;10;3;e1004236

    PUBMED: 24651294; PMC: 3961184; DOI: 10.1371/journal.pgen.1004236

  • Detecting Break Points of Insertions and Deletions from Paired-end Short Reads

    Kai Ye and Zemin Ning

    Next-generation Sequencing: Current Technologies and Applications 2014

    URL: https://www.horizonpress.com/nextgenseq

  • Evolution and transmission of drug-resistant tuberculosis in a Russian population.

    Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, Corander J, Bryant J, Parkhill J, Nejentsev S et al.

    Nature genetics 2014;46;3;279-86

    PUBMED: 24464101; PMC: 3939361; DOI: 10.1038/ng.2878

  • Expression of phosphofructokinase in skeletal muscle is influenced by genetic variation and associated with insulin sensitivity.

    Keildson S, Fadista J, Ladenvall C, Hedman ÅK, Elgzyri T, Small KS, Grundberg E, Nica AC, Glass D, Richards JB et al.

    Diabetes 2014;63;3;1154-65

    PUBMED: 24306210; PMC: 3931395; DOI: 10.2337/db13-1301

  • Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

    DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium, South Asian Type 2 Diabetes (SAT2D) Consortium, Mexican American Type 2 Diabetes (MAT2D) Consortium, Type 2 Diabetes Genetic Exploration by Nex-generation sequencing in muylti-Ethnic Samples (T2D-GENES) Consortium, Mahajan A, Go MJ, Zhang W, Below JE, Gaulton KJ et al.

    Nature genetics 2014;46;3;234-44

    PUBMED: 24509480; PMC: 3969612; DOI: 10.1038/ng.2897

  • Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study.

    Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S and Lipsitch M

    The Lancet. Infectious diseases 2014;14;3;220-6

    PUBMED: 24462211; PMC: 4030102; DOI: 10.1016/S1473-3099(13)70693-5

  • Naturally acquired antibodies specific for Plasmodium falciparum reticulocyte-binding protein homologue 5 inhibit parasite growth and predict protection from malaria.

    Tran TM, Ongoiba A, Coursen J, Crosnier C, Diouf A, Huang CY, Li S, Doumbo S, Doumtabe D, Kone Y et al.

    The Journal of infectious diseases 2014;209;5;789-98

    PUBMED: 24133188; PMC: 3923542; DOI: 10.1093/infdis/jit553

  • Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene.

    Ba X, Harrison EM, Edwards GF, Holden MT, Larsen AR, Petersen A, Skov RL, Peacock SJ, Parkhill J, Paterson GK and Holmes MA

    The Journal of antimicrobial chemotherapy 2014;69;3;594-7

    PUBMED: 24216768; PMC: 3922151; DOI: 10.1093/jac/dkt418

  • Plasmodium falciparum erythrocyte invasion: combining function with immune evasion.

    Wright GJ and Rayner JC

    PLoS pathogens 2014;10;3;e1003943

    PUBMED: 24651270; PMC: 3961354; DOI: 10.1371/journal.ppat.1003943

  • Prevalence and properties of mecC methicillin-resistant Staphylococcus aureus (MRSA) in bovine bulk tank milk in Great Britain.

    Paterson GK, Morgan FJ, Harrison EM, Peacock SJ, Parkhill J, Zadoks RN and Holmes MA

    The Journal of antimicrobial chemotherapy 2014;69;3;598-602

    PUBMED: 24155057; PMC: 3922150; DOI: 10.1093/jac/dkt417

  • Reciprocal duplication of the williams-beuren syndrome deletion on chromosome 7q11.23 is associated with schizophrenia.

    Mulle JG, Pulver AE, McGrath JA, Wolyniec PS, Dodd AF, Cutler DJ, Sebat J, Malhotra D, Nestadt G, Conrad DF et al.

    Biological psychiatry 2014;75;5;371-7

    PUBMED: 23871472; PMC: 3838485; DOI: 10.1016/j.biopsych.2013.05.040

  • Trypsin- and Chymotrypsin-like serine proteases in schistosoma mansoni-- 'the undiscovered country'.

    Horn M, Fajtová P, Rojo Arreola L, Ulrychová L, Bartošová-Sojková P, Franta Z, Protasio AV, Opavský D, Vondrášek J, McKerrow JH et al.

    PLoS neglected tropical diseases 2014;8;3;e2766

    PUBMED: 24676141; PMC: 3967958; DOI: 10.1371/journal.pntd.0002766

  • Vying over spilt oil.

    Pham N TA and Anonye BO

    Nature reviews. Microbiology 2014;12;3;156

    PUBMED: 24509784; DOI: 10.1038/nrmicro3224

  • Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2.

    Huang J, Huffman JE, Yamakuchi M, Trompet S, Asselbergs FW, Sabater-Lleal M, Trégouët DA, Chen WM, Smith NL, Kleber ME et al.

    Arteriosclerosis, thrombosis, and vascular biology 2014;34;5;1093-101

    PUBMED: 24578379; PMC: 4009733; DOI: 10.1161/ATVBAHA.113.302088

  • Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.

    Huser CA, Gilroy KL, de Ridder J, Kilbey A, Borland G, Mackay N, Jenkins A, Bell M, Herzyk P, van der Weyden L et al.

    PLoS genetics 2014;10;2;e1004167

    PUBMED: 24586197; PMC: 3937229; DOI: 10.1371/journal.pgen.1004167

  • Single cell analysis of cancer genomes.

    Van Loo P and Voet T

    Current opinion in genetics & development 2014;24;82-91

    PUBMED: 24531336; DOI: 10.1016/j.gde.2013.12.004

  • Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism.

    Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ et al.

    BMC genomics 2014;15;160

    PUBMED: 24568651; PMC: 4028888; DOI: 10.1186/1471-2164-15-160

  • A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium.

    Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C, Dickens NJ, Religa AA, Bushell E, Graham AL, Cameron R et al.

    Nature 2014;507;7491;253-257

    PUBMED: 24572359; PMC: 4105895; DOI: 10.1038/nature12970

  • A transcriptional switch underlies commitment to sexual development in malaria parasites.

    Kafsack BF, Rovira-Graells N, Clark TG, Bancells C, Crowley VM, Campino SG, Williams AE, Drought LG, Kwiatkowski DP, Baker DA et al.

    Nature 2014;507;7491;248-52

    PUBMED: 24572369; PMC: 4040541; DOI: 10.1038/nature12920

  • Obituary: Professor Frederick Sanger:13 August 1918 – 19 November 2013

    Powell, D

    Genetics Society News 2014;70;16-18

    URL: https://www.genetics.org.uk/Portal...s/0/Issue%2070.pdf

  • Using ancestry-informative markers to identify fine structure across 15 populations of European origin.

    Huckins LM, Boraska V, Franklin CS, Floyd JA, Southam L, GCAN, WTCCC3, Sullivan PF, Bulik CM, Collier DA et al.

    European journal of human genetics : EJHG 2014;22;10;1190-200

    PUBMED: 24549058; PMC: 4169539; DOI: 10.1038/ejhg.2014.1

  • The Yersinia pseudotuberculosis complex: characterization and delineation of a new species, Yersinia wautersii.

    Savin C, Martin L, Bouchier C, Filali S, Chenau J, Zhou Z, Becher F, Fukushima H, Thomson NR, Scholz HC and Carniel E

    International journal of medical microbiology : IJMM 2014;304;3-4;452-63

    PUBMED: 24598372; DOI: 10.1016/j.ijmm.2014.02.002

  • Finding people who will tell you their thoughts on genomics-recruitment strategies for social sciences research.

    Middleton A, Bragin E, Parker M and DDD Study

    Journal of community genetics 2014;5;4;291-302

    PUBMED: 24535681; PMC: 4159472; DOI: 10.1007/s12687-014-0184-2

  • Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus.

    Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, Al Rabeeah AA, Alhakeem RF, Assiri A, Al-Tawfiq JA et al.

    mBio 2014;5;1

    PUBMED: 24549846; PMC: 3944817; DOI: 10.1128/mBio.01062-13

  • Estimating genome-wide significance for whole-genome sequencing studies.

    Xu C, Tachmazidou I, Walter K, Ciampi A, Zeggini E, Greenwood CM and UK10K Consortium

    Genetic epidemiology 2014;38;4;281-90

    PUBMED: 24676807; PMC: 4489336; DOI: 10.1002/gepi.21797

  • Open science and community norms: Data retention and publication moratoria policies in genomics projects

    Joly,Y., Dove,E.S., KENNEDY,K.L., Bobrow,M., Ouellette,B.F.F., DYKE,S., Kato,K. and Knoppers,B.M.

    Medical Law International 2014;12;2;92-120

    DOI: 10.1177/0968533212458431; URL: https://mli.sagepub.com/content/12/2/92

  • BioJS: an open source standard for biological visualisation - its status in 2014.

    Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I et al.

    F1000Research 2014;3;55

    PUBMED: 25075290; PMC: 4103492; DOI: 10.12688/f1000research.3-55.v1

  • De novo mutations in schizophrenia implicate synaptic networks.

    Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, Georgieva L, Rees E, Palta P, Ruderfer DM et al.

    Nature 2014;506;7487;179-84

    PUBMED: 24463507; PMC: 4237002; DOI: 10.1038/nature12929

  • A genome-wide association study of anorexia nervosa.

    Boraska V, Franklin CS, Floyd JA, Thornton LM, Huckins LM, Southam L, Rayner NW, Tachmazidou I, Klump KL, Treasure J et al.

    Molecular psychiatry 2014;19;10;1085-94

    PUBMED: 24514567; PMC: 4325090; DOI: 10.1038/mp.2013.187

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ et al.

    Nature genetics 2014;46;3;305-309

    PUBMED: 24509479; PMC: 3970364; DOI: 10.1038/ng.2895

  • SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing.

    Quail MA, Smith M, Jackson D, Leonard S, Skelly T, Swerdlow HP, Gu Y and Ellis P

    BMC genomics 2014;15;110

    PUBMED: 24507442; PMC: 4008303; DOI: 10.1186/1471-2164-15-110

  • Complete Genome Sequence of the WHO International Standard for HIV-1 RNA Determined by Deep Sequencing.

    Gall A, Morris C, Kellam P and Berry N

    Genome announcements 2014;2;1

    PUBMED: 24503998; PMC: 3916492; DOI: 10.1128/genomeA.01254-13

  • Heterozygous loss-of-function mutations in YAP1 cause both isolated and syndromic optic fissure closure defects.

    Williamson KA, Rainger J, Floyd JA, Ansari M, Meynert A, Aldridge KV, Rainger JK, Anderson CA, Moore AT, Hurles ME et al.

    American journal of human genetics 2014;94;2;295-302

    PUBMED: 24462371; PMC: 3928658; DOI: 10.1016/j.ajhg.2014.01.001

  • Loss of FTO antagonises Wnt signaling and leads to developmental defects associated with ciliopathies.

    Osborn DP, Roccasecca RM, McMurray F, Hernandez-Hernandez V, Mukherjee S, Barroso I, Stemple D, Cox R, Beales PL and Christou-Savina S

    PloS one 2014;9;2;e87662

    PUBMED: 24503721; PMC: 3913654; DOI: 10.1371/journal.pone.0087662

  • Functional annotation of noncoding sequence variants.

    Ritchie GR, Dunham I, Zeggini E and Flicek P

    Nature methods 2014;11;3;294-6

    PUBMED: 24487584; PMC: 5015703; DOI: 10.1038/nmeth.2832

  • The genomic basis of vomeronasal-mediated behaviour.

    Ibarra-Soria X, Levitin MO and Logan DW

    Mammalian genome : official journal of the International Mammalian Genome Society 2014;25;1-2;75-86

    PUBMED: 23884334; PMC: 3916702; DOI: 10.1007/s00335-013-9463-1

  • Adding genomic 'foliage' to the tree of life.

    Walker A

    Nature reviews. Microbiology 2014;12;2;78

    PUBMED: 24429416; DOI: 10.1038/nrmicro3203

  • Biomarker profiling by nuclear magnetic resonance spectroscopy for the prediction of all-cause mortality: an observational study of 17,345 persons.

    Fischer K, Kettunen J, Würtz P, Haller T, Havulinna AS, Kangas AJ, Soininen P, Esko T, Tammesoo ML, Mägi R et al.

    PLoS medicine 2014;11;2;e1001606

    PUBMED: 24586121; PMC: 3934819; DOI: 10.1371/journal.pmed.1001606

  • Chromosome X-wide association study identifies Loci for fasting insulin and height and evidence for incomplete dosage compensation.

    Tukiainen T, Pirinen M, Sarin AP, Ladenvall C, Kettunen J, Lehtimäki T, Lokki ML, Perola M, Sinisalo J, Vlachopoulou E et al.

    PLoS genetics 2014;10;2;e1004127

    PUBMED: 24516404; PMC: 3916240; DOI: 10.1371/journal.pgen.1004127

  • Editorial overview: cancer genomics: kill it. Kill it dead.

    Adams D and McDermott U

    Current opinion in genetics & development 2014;24;v-vi

    PUBMED: 24569083; DOI: 10.1016/j.gde.2013.12.006

  • Functional interpretation of non-coding sequence variation: concepts and challenges.

    Paul DS, Soranzo N and Beck S

    BioEssays : news and reviews in molecular, cellular and developmental biology 2014;36;2;191-9

    PUBMED: 24311363; PMC: 3992842; DOI: 10.1002/bies.201300126

  • Genetic screens in mice for genome integrity maintenance and cancer predisposition.

    Balmus G and McIntyre RE

    Current opinion in genetics & development 2014;24;1-7

    PUBMED: 24657530; DOI: 10.1016/j.gde.2013.10.010

  • Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi.

    Cornick JE, Harris SR, Parry CM, Moore MJ, Jassi C, Kamng'ona A, Kulohoma B, Heyderman RS, Bentley SD and Everett DB

    The Journal of antimicrobial chemotherapy 2014;69;2;368-74

    PUBMED: 24080503; PMC: 3886935; DOI: 10.1093/jac/dkt384

  • Identification of novel genetic Loci associated with thyroid peroxidase antibodies and clinical thyroid disease.

    Medici M, Porcu E, Pistis G, Teumer A, Brown SJ, Jensen RA, Rawal R, Roef GL, Plantinga TS, Vermeulen SH et al.

    PLoS genetics 2014;10;2;e1004123

    PUBMED: 24586183; PMC: 3937134; DOI: 10.1371/journal.pgen.1004123

  • In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

    van Hal SJ, Steen JA, Espedido BA, Grimmond SM, Cooper MA, Holden MT, Bentley SD, Gosbell IB and Jensen SO

    The Journal of antimicrobial chemotherapy 2014;69;2;363-7

    PUBMED: 24047554; PMC: 3886930; DOI: 10.1093/jac/dkt354

  • Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling.

    Logan CV, Szabadkai G, Sharpe JA, Parry DA, Torelli S, Childs AM, Kriek M, Phadke R, Johnson CA, Roberts NY et al.

    Nature genetics 2014;46;2;188-93

    PUBMED: 24336167; DOI: 10.1038/ng.2851

  • Molecular genetic evidence for overlap between general cognitive ability and risk for schizophrenia: a report from the Cognitive Genomics consorTium (COGENT).

    Lencz T, Knowles E, Davies G, Guha S, Liewald DC, Starr JM, Djurovic S, Melle I, Sundet K, Christoforou A et al.

    Molecular psychiatry 2014;19;2;168-74

    PUBMED: 24342994; PMC: 3968799; DOI: 10.1038/mp.2013.166

  • Mutational signatures: the patterns of somatic mutations hidden in cancer genomes.

    Alexandrov LB and Stratton MR

    Current opinion in genetics & development 2014;24;52-60

    PUBMED: 24657537; PMC: 3990474; DOI: 10.1016/j.gde.2013.11.014

  • Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.

    Marsh JA and Teichmann SA

    BioEssays : news and reviews in molecular, cellular and developmental biology 2014;36;2;209-18

    PUBMED: 24272815; DOI: 10.1002/bies.201300134

  • Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model.

    Sigar IM, Schripsema JH, Wang Y, Clarke IN, Cutcliffe LT, Seth-Smith HM, Thomson NR, Bjartling C, Unemo M, Persson K and Ramsey KH

    Pathogens and disease 2014;70;1;61-9

    PUBMED: 24022847; PMC: 4300952; DOI: 10.1111/2049-632X.12086

  • Workshops: a great way to enhance and supplement a degree.

    Fatumo S, Shome S and Macintyre G

    PLoS computational biology 2014;10;2;e1003497

    PUBMED: 24586140; PMC: 3937119; DOI: 10.1371/journal.pcbi.1003497

  • Zebrafish models of cancer: progress and future challenges.

    Yen J, White RM and Stemple DL

    Current opinion in genetics & development 2014;24;38-45

    PUBMED: 24657535; PMC: 4003353; DOI: 10.1016/j.gde.2013.11.003

  • RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation.

    Jones M, Dry IR, Frampton D, Singh M, Kanda RK, Yee MB, Kellam P, Hollinshead M, Kinchington PR, O'Toole EA and Breuer J

    PLoS pathogens 2014;10;1;e1003896

    PUBMED: 24497829; PMC: 3907375; DOI: 10.1371/journal.ppat.1003896

  • Single cell genomics: advances and future perspectives.

    Macaulay IC and Voet T

    PLoS genetics 2014;10;1;e1004126

    PUBMED: 24497842; PMC: 3907301; DOI: 10.1371/journal.pgen.1004126

  • Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.

    Carss KJ, Hillman SC, Parthiban V, McMullan DJ, Maher ER, Kilby MD and Hurles ME

    Human molecular genetics 2014;23;12;3269-77

    PUBMED: 24476948; PMC: 4030780; DOI: 10.1093/hmg/ddu038

  • IFITM proteins-cellular inhibitors of viral entry.

    Smith S, Weston S, Kellam P and Marsh M

    Current opinion in virology 2014;4;71-7

    PUBMED: 24480526; PMC: 7185728; DOI: 10.1016/j.coviro.2013.11.004

  • Development of an antigen microarray for high throughput monoclonal antibody selection.

    Staudt N, Müller-Sienerth N and Wright GJ

    Biochemical and biophysical research communications 2014;445;4;785-90

    PUBMED: 24472540; PMC: 3989025; DOI: 10.1016/j.bbrc.2013.12.033

  • Transmissible [corrected] dog cancer genome reveals the origin and history of an ancient cell lineage.

    Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JMC, Werner EI, Allen J, De Nardi AB et al.

    Science (New York, N.Y.) 2014;343;6169;437-440

    PUBMED: 24458646; PMC: 3918581; DOI: 10.1126/science.1247167

  • A polygenic burden of rare disruptive mutations in schizophrenia.

    Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N, Roussos P, O'Dushlaine C, Chambert K, Bergen SE, Kähler A et al.

    Nature 2014;506;7487;185-90

    PUBMED: 24463508; PMC: 4136494; DOI: 10.1038/nature12975

  • Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population.

    Rogers MB, Downing T, Smith BA, Imamura H, Sanders M, Svobodova M, Volf P, Berriman M, Cotton JA and Smith DF

    PLoS genetics 2014;10;1;e1004092

    PUBMED: 24453988; PMC: 3894156; DOI: 10.1371/journal.pgen.1004092

  • Subclonal variant calling with multiple samples and prior knowledge.

    Gerstung M, Papaemmanuil E and Campbell PJ

    Bioinformatics (Oxford, England) 2014;30;9;1198-204

    PUBMED: 24443148; PMC: 3998123; DOI: 10.1093/bioinformatics/btt750

  • A novel RCE1 isoform is required for H-Ras plasma membrane localization and is regulated by USP17.

    Jaworski J, Govender U, McFarlane C, de la Vega M, Greene MK, Rawlings ND, Johnston JA, Scott CJ and Burrows JF

    The Biochemical journal 2014;457;2;289-300

    PUBMED: 24134311; DOI: 10.1042/BJ20131213

  • Managing clinically significant findings in research: the UK10K example.

    Kaye J, Hurles M, Griffin H, Grewal J, Bobrow M, Timpson N, Smee C, Bolton P, Durbin R, Dyke S et al.

    European journal of human genetics : EJHG 2014;22;9;1100-4

    PUBMED: 24424120; PMC: 4026295; DOI: 10.1038/ejhg.2013.290

  • A high-definition view of functional genetic variation from natural yeast genomes.

    Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V et al.

    Molecular biology and evolution 2014;31;4;872-88

    PUBMED: 24425782; PMC: 3969562; DOI: 10.1093/molbev/msu037

  • A systematic review of definitions of extreme phenotypes of HIV control and progression.

    Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P et al.

    AIDS (London, England) 2014;28;2;149-62

    PUBMED: 24149086; PMC: 3882304; DOI: 10.1097/QAD.0000000000000049

  • Expression and replication studies to identify new candidate genes involved in normal hearing function.

    Girotto G, Vuckovic D, Buniello A, Lorente-Cánovas B, Lewis M, Gasparini P and Steel KP

    PloS one 2014;9;1;e85352

    PUBMED: 24454846; PMC: 3891868; DOI: 10.1371/journal.pone.0085352

  • Unexplained diarrhoea in HIV-1 infected individuals.

    Oude Munnink BB, Canuti M, Deijs M, de Vries M, Jebbink MF, Rebers S, Molenkamp R, van Hemert FJ, Chung K, Cotten M et al.

    BMC infectious diseases 2014;14;22

    PUBMED: 24410947; PMC: 3925291; DOI: 10.1186/1471-2334-14-22

  • RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia.

    Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J et al.

    Nature genetics 2014;46;2;116-25

    PUBMED: 24413735; PMC: 3960636; DOI: 10.1038/ng.2874

  • Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).

    Durbin R

    Bioinformatics (Oxford, England) 2014;30;9;1266-72

    PUBMED: 24413527; PMC: 3998136; DOI: 10.1093/bioinformatics/btu014

  • Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes.

    Ayub Q, Moutsianas L, Chen Y, Panoutsopoulou K, Colonna V, Pagani L, Prokopenko I, Ritchie GR, Tyler-Smith C, McCarthy MI et al.

    American journal of human genetics 2014;94;2;176-85

    PUBMED: 24412096; PMC: 3928649; DOI: 10.1016/j.ajhg.2013.12.010

  • Position statement on opportunistic genomic screening from the Association of Genetic Nurses and Counsellors (UK and Ireland).

    Middleton A, Patch C, Wiggins J, Barnes K, Crawford G, Benjamin C, Bruce A and Association of Genetic Nurses and Counsellors in United Kingdom and Ireland

    European journal of human genetics : EJHG 2014;22;8;955-6

    PUBMED: 24398792; PMC: 4350604; DOI: 10.1038/ejhg.2013.301

  • A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.

    Ariey F, Witkowski B, Amaratunga C, Beghain J, Langlois AC, Khim N, Kim S, Duru V, Bouchier C, Ma L et al.

    Nature 2014;505;7481;50-5

    PUBMED: 24352242; PMC: 5007947; DOI: 10.1038/nature12876

  • Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures.

    Baple EL, Maroofian R, Chioza BA, Izadi M, Cross HE, Al-Turki S, Barwick K, Skrzypiec A, Pawlak R, Wagner K et al.

    American journal of human genetics 2014;94;1;87-94

    PUBMED: 24239382; PMC: 3882725; DOI: 10.1016/j.ajhg.2013.10.001

  • A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains.

    Preston MD, Campino S, Assefa SA, Echeverry DF, Ocholla H, Amambua-Ngwa A, Stewart LB, Conway DJ, Borrmann S, Michon P et al.

    Nature communications 2014;5;4052

    PUBMED: 24923250; PMC: 4082634; DOI: 10.1038/ncomms5052

  • The cavefish genome reveals candidate genes for eye loss.

    McGaugh SE, Gross JB, Aken B, Blin M, Borowsky R, Chalopin D, Hinaux H, Jeffery WR, Keene A, Ma L et al.

    Nature communications 2014;5;5307

    PUBMED: 25329095; PMC: 4218959; DOI: 10.1038/ncomms6307

  • The challenges of genome-wide interaction studies: lessons to learn from the analysis of HDL blood levels.

    van Leeuwen EM, Smouter FA, Kam-Thong T, Karbalai N, Smith AV, Harris TB, Launer LJ, Sitlani CM, Li G, Brody JA et al.

    PloS one 2014;9;10;e109290

    PUBMED: 25329471; PMC: 4203717; DOI: 10.1371/journal.pone.0109290

  • A common control group - optimising the experiment design to maximise sensitivity.

    Bate S and Karp NA

    PloS one 2014;9;12;e114872

    PUBMED: 25504147; PMC: 4263717; DOI: 10.1371/journal.pone.0114872

  • A comparison of peak callers used for DNase-Seq data.

    Koohy H, Down TA, Spivakov M and Hubbard T

    PloS one 2014;9;5;e96303

    PUBMED: 24810143; PMC: 4014496; DOI: 10.1371/journal.pone.0096303

  • A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect.

    Lopez-Serra P, Marcilla M, Villanueva A, Ramos-Fernandez A, Palau A, Leal L, Wahi JE, Setien-Baranda F, Szczesna K, Moutinho C et al.

    Nature communications 2014;5;3608

    PUBMED: 24699711; PMC: 3988805; DOI: 10.1038/ncomms4608

  • An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration.

    Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS et al.

    PloS one 2014;9;1;e86719

    PUBMED: 24489776; PMC: 3904947; DOI: 10.1371/journal.pone.0086719

  • The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion.

    Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ, Antoun NM, Coghlan A, Harsha B, Traini A, Ribeiro DM et al.

    Genome biology 2014;15;11;510

    PUBMED: 25413302; PMC: 4265353; DOI: 10.1186/PREACCEPT-2413673241432389

  • A genome-wide assessment of the role of untagged copy number variants in type 1 diabetes.

    Zanda M, Onengut-Gumuscu S, Walker N, Shtir C, Gallo D, Wallace C, Smyth D, Todd JA, Hurles ME, Plagnol V and Rich SS

    PLoS genetics 2014;10;5;e1004367

    PUBMED: 24875393; PMC: 4038470; DOI: 10.1371/journal.pgen.1004367

  • A genome wide association study of mathematical ability reveals an association at chromosome 3q29, a locus associated with autism and learning difficulties: a preliminary study.

    Baron-Cohen S, Murphy L, Chakrabarti B, Craig I, Mallya U, Lakatošová S, Rehnstrom K, Peltonen L, Wheelwright S, Allison C et al.

    PloS one 2014;9;5;e96374

    PUBMED: 24801482; PMC: 4011843; DOI: 10.1371/journal.pone.0096374

  • The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

    Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J et al.

    Nucleic acids research 2014;42;1;D966-74

    PUBMED: 24217912; DOI: 10.1093/nar/gkt1026

  • The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.

    Kennedy NA, Walker AW, Berry SH, Duncan SH, Farquarson FM, Louis P, Thomson JM, UK IBD Genetics Consortium, Satsangi J, Flint HJ et al.

    PloS one 2014;9;2;e88982

    PUBMED: 24586470; PMC: 3933346; DOI: 10.1371/journal.pone.0088982

  • The influence of disease categories on gene candidate predictions from model organism phenotypes.

    Oellrich A, Koehler S, Washington N, Sanger Mouse Genetic Project, Mungall C, Lewis S, Haendel M, Robinson PN and Smedley D

    Journal of biomedical semantics 2014;5;Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G;S4

    PUBMED: 25093073; PMC: 4108905; DOI: 10.1186/2041-1480-5-S1-S4

  • A pathogenic mosaic TP53 mutation in two germ layers detected by next generation sequencing.

    Behjati S, Maschietto M, Williams RD, Side L, Hubank M, West R, Pearson K, Sebire N, Tarpey P, Futreal A et al.

    PloS one 2014;9;5;e96531

    PUBMED: 24810334; PMC: 4014518; DOI: 10.1371/journal.pone.0096531

  • A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells.

    Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR and Lamond AI

    eLife 2014;3;e01630

    PUBMED: 24596151; PMC: 3936288

  • The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis.

    Howell KJ, Weinert LA, Chaudhuri RR, Luan SL, Peters SE, Corander J, Harris D, Angen Ø, Aragon V, Bensaid A et al.

    BMC genomics 2014;15;1179

    PUBMED: 25539682; PMC: 4532294; DOI: 10.1186/1471-2164-15-1179

  • Absence of Appl2 sensitizes endotoxin shock through activation of PI3K/Akt pathway.

    Mao L, Lin W, Nie T, Hui X, Gao X, Li K, Ding M, Tang X, Li P, Wang Y et al.

    Cell & bioscience 2014;4;1;60

    PUBMED: 25328665; PMC: 4201708; DOI: 10.1186/2045-3701-4-60

  • Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen.

    Hargreaves KR, Flores CO, Lawley TD and Clokie MR

    mBio 2014;5;5;e01045-13

    PUBMED: 25161187; PMC: 4173771; DOI: 10.1128/mBio.01045-13

  • African origin of the malaria parasite Plasmodium vivax.

    Liu W, Li Y, Shaw KS, Learn GH, Plenderleith LJ, Malenke JA, Sundararaman SA, Ramirez MA, Crystal PA, Smith AG et al.

    Nature communications 2014;5;3346

    PUBMED: 24557500; PMC: 4089193; DOI: 10.1038/ncomms4346

  • Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.

    Adoue V, Schiavi A, Light N, Almlöf JC, Lundmark P, Ge B, Kwan T, Caron M, Rönnblom L, Wang C et al.

    Molecular systems biology 2014;10;754

    PUBMED: 25326100; PMC: 4299376

  • Bioinformatic analysis of expression data to identify effector candidates.

    Reid AJ and Jones JT

    Methods in molecular biology (Clifton, N.J.) 2014;1127;17-27

    PUBMED: 24643549; DOI: 10.1007/978-1-62703-986-4_2

  • Characterization of Vibrio cholerae bacteriophages isolated from the environmental waters of the Lake Victoria region of Kenya.

    Maina AN, Mwaura FB, Oyugi J, Goulding D, Toribio AL and Kariuki S

    Current microbiology 2014;68;1;64-70

    PUBMED: 23982202; DOI: 10.1007/s00284-013-0447-x

  • Cloning of recombinant monoclonal antibodies from hybridomas in a single mammalian expression plasmid.

    Müller-Sienerth N, Crosnier C, Wright GJ and Staudt N

    Methods in molecular biology (Clifton, N.J.) 2014;1131;229-40

    PUBMED: 24515469; DOI: 10.1007/978-1-62703-992-5_14

  • Collateral damage.

    Hancock RE

    Nature biotechnology 2014;32;1;66-8

    PUBMED: 24406933; DOI: 10.1038/nbt.2779

  • Common variant at 16p11.2 conferring risk of psychosis.

    Steinberg S, de Jong S, Mattheisen M, Costas J, Demontis D, Jamain S, Pietiläinen OP, Lin K, Papiol S, Huttenlocher J et al.

    Molecular psychiatry 2014;19;1;108-14

    PUBMED: 23164818; PMC: 3872086; DOI: 10.1038/mp.2012.157

  • Computational approaches to interpreting genomic sequence variation.

    Ritchie GR and Flicek P

    Genome medicine 2014;6;10;87

    PUBMED: 25473426; PMC: 4254438; DOI: 10.1186/s13073-014-0087-1

  • Contemporary gene flow between wild An. gambiae s.s. and An. arabiensis.

    Weetman D, Steen K, Rippon EJ, Mawejje HD, Donnelly MJ and Wilding CS

    Parasites & vectors 2014;7;345

    PUBMED: 25060488; PMC: 4124135; DOI: 10.1186/1756-3305-7-345

  • Deconstructing pheromone-mediated behavior one layer at a time.

    Sánchez-Andrade G and Logan DW

    BMC biology 2014;12;33

    PUBMED: 24884538; PMC: 4037717; DOI: 10.1186/1741-7007-12-33

  • Deletions of chromosomal regulatory boundaries are associated with congenital disease.

    Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ et al.

    Genome biology 2014;15;9;423

    PUBMED: 25315429; PMC: 4180961; DOI: 10.1186/s13059-014-0423-1

  • Different waves and directions of Neolithic migrations in the Armenian Highland.

    Hovhannisyan A, Khachatryan Z, Haber M, Hrechdakian P, Karafet T, Zalloua P and Yepiskoposyan L

    Investigative genetics 2014;5;1;15

    PUBMED: 25452838; PMC: 4249771; DOI: 10.1186/s13323-014-0015-6

  • Differential methylation of the TRPA1 promoter in pain sensitivity.

    Bell JT, Loomis AK, Butcher LM, Gao F, Zhang B, Hyde CL, Sun J, Wu H, Ward K, Harris J et al.

    Nature communications 2014;5;2978

    PUBMED: 24496475; PMC: 3926001; DOI: 10.1038/ncomms3978

  • Diversification of bacterial genome content through distinct mechanisms over different timescales.

    Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD and Hanage WP

    Nature communications 2014;5;5471

    PUBMED: 25407023; PMC: 4263131; DOI: 10.1038/ncomms6471

  • Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9.

    Han J, Zhang J, Chen L, Shen B, Zhou J, Hu B, Du Y, Tate PH, Huang X and Zhang W

    RNA biology 2014;11;7;829-35

    PUBMED: 25137067; PMC: 4179957; DOI: 10.4161/rna.29624

  • Epigenome-wide DNA methylation in hearing ability: new mechanisms for an old problem.

    Wolber LE, Steves CJ, Tsai PC, Deloukas P, Spector TD, Bell JT and Williams FM

    PloS one 2014;9;9;e105729

    PUBMED: 25184702; PMC: 4153547; DOI: 10.1371/journal.pone.0105729

  • European surveillance network for influenza in pigs: surveillance programs, diagnostic tools and Swine influenza virus subtypes identified in 14 European countries from 2010 to 2013.

    Simon G, Larsen LE, Dürrwald R, Foni E, Harder T, Van Reeth K, Markowska-Daniel I, Reid SM, Dan A, Maldonado J et al.

    PloS one 2014;9;12;e115815

    PUBMED: 25542013; PMC: 4277368; DOI: 10.1371/journal.pone.0115815

  • Extreme growth failure is a common presentation of ligase IV deficiency.

    Murray JE, Bicknell LS, Yigit G, Duker AL, van Kogelenberg M, Haghayegh S, Wieczorek D, Kayserili H, Albert MH, Wise CA et al.

    Human mutation 2014;35;1;76-85

    PUBMED: 24123394; PMC: 3995017; DOI: 10.1002/humu.22461

  • Faster average case low memory semi-external construction of the burrows-wheeler transform

    TISCHLER,G.

    CEUR Workshop Proceedings 2014;1146;61-68

    URL: https://ceur-ws.org/Vol-1146/I...CABD2014-Proceedings.pdf

  • Fc gamma receptor IIa-H131R polymorphism and malaria susceptibility in sympatric ethnic groups, Fulani and Dogon of Mali.

    Maiga B, Dolo A, Touré O, Dara V, Tapily A, Campino S, Sepulveda N, Corran P, Rockett K, Clark TG et al.

    Scandinavian journal of immunology 2014;79;1;43-50

    PUBMED: 24117665; PMC: 3992902; DOI: 10.1111/sji.12122

  • From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.

    Clarke AC, Prost S, Stanton JA, White WT, Kaplan ME, Matisoo-Smith EA and Genographic Consortium

    BMC genomics 2014;15;68

    PUBMED: 24460871; PMC: 3922791; DOI: 10.1186/1471-2164-15-68

  • GENCODE pseudogenes.

    Frankish A and Harrow J

    Methods in molecular biology (Clifton, N.J.) 2014;1167;129-55

    PUBMED: 24823776; DOI: 10.1007/978-1-4939-0835-6_10

  • Genetic determinants of glucose-6-phosphate dehydrogenase activity in Kenya.

    Shah SS, Macharia A, Makale J, Uyoga S, Kivinen K, Craik R, Hubbart C, Wellems TE, Rockett KA, Kwiatkowski DP and Williams TN

    BMC medical genetics 2014;15;93

    PUBMED: 25201310; PMC: 4236593; DOI: 10.1186/s12881-014-0093-6

  • Genetic interaction implicates iRhom2 in the regulation of EGF receptor signalling in mice.

    Siggs OM, Grieve A, Xu H, Bambrough P, Christova Y and Freeman M

    Biology open 2014;3;12;1151-7

    PUBMED: 25395669; PMC: 4265752; DOI: 10.1242/bio.201410116

  • Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

    Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV et al.

    Genome biology 2014;15;9;459

    PUBMED: 25244985; PMC: 4195908; DOI: 10.1186/s13059-014-0459-2

  • Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

    Shah MA, Mutreja A, Thomson N, Baker S, Parkhill J, Dougan G, Bokhari H and Wren BW

    Emerging infectious diseases 2014;20;1;13-20

    PUBMED: 24378019; PMC: 3884714; DOI: 10.3201/.eid2001.130428

  • Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression.

    Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AE and Wardle FC

    BMC biology 2014;12;81

    PUBMED: 25277163; PMC: 4206766; DOI: 10.1186/s12915-014-0081-5

  • Glucose-6-phosphate dehydrogenase polymorphisms and susceptibility to mild malaria in Dogon and Fulani, Mali.

    Maiga B, Dolo A, Campino S, Sepulveda N, Corran P, Rockett KA, Troye-Blomberg M, Doumbo OK and Clark TG

    Malaria journal 2014;13;270

    PUBMED: 25015414; PMC: 4110528; DOI: 10.1186/1475-2875-13-270

  • H3Africa: a tipping point for a revolution in bioinformatics, genomics and health research in Africa.

    Adoga MP, Fatumo SA and Agwale SM

    Source code for biology and medicine 2014;9;10

    PUBMED: 24829612; PMC: 4019950; DOI: 10.1186/1751-0473-9-10

  • Haptoglobin (HP) and Haptoglobin-related protein (HPR) copy number variation, natural selection, and trypanosomiasis.

    Hardwick RJ, Ménard A, Sironi M, Milet J, Garcia A, Sese C, Yang F, Fu B, Courtin D and Hollox EJ

    Human genetics 2014;133;1;69-83

    PUBMED: 24005574; PMC: 3898332; DOI: 10.1007/s00439-013-1352-x

  • Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.

    Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR et al.

    Nature communications 2014;5;2997

    PUBMED: 24429703; PMC: 3905727; DOI: 10.1038/ncomms3997

  • High risk population isolate reveals low frequency variants predisposing to intracranial aneurysms.

    Kurki MI, Gaál EI, Kettunen J, Lappalainen T, Menelaou A, Anttila V, van 't Hof FN, von Und Zu Fraunberg M, Helisalmi S, Hiltunen M et al.

    PLoS genetics 2014;10;1;e1004134

    PUBMED: 24497844; DOI: 10.1371/journal.pgen.1004134

  • High throughput exome coverage of clinically relevant cardiac genes.

    Manase D, D'Alessandro LC, Manickaraj AK, Al Turki S, Hurles ME and Mital S

    BMC medical genomics 2014;7;67

    PUBMED: 25496018; PMC: 4272796; DOI: 10.1186/s12920-014-0067-8

  • How synthetic biology will reconsider natural bioluminescence and its applications.

    Reeve B, Sanderson T, Ellis T and Freemont P

    Advances in biochemical engineering/biotechnology 2014;145;3-30

    PUBMED: 25216951; DOI: 10.1007/978-3-662-43619-6_1

  • Impact of infectious diseases consultation on the management of Staphylococcus aureus bacteraemia in children.

    Saunderson RB, Gouliouris T, Cartwright EJ, Nickerson EJ, Aliyu SH, O'Donnell DR, Kelsall W, Limmathurotsakul D, Peacock SJ and Török ME

    BMJ open 2014;4;7;e004659

    PUBMED: 24989617; PMC: 4091395; DOI: 10.1136/bmjopen-2013-004659

  • Integrating non-coding RNAs in JAK-STAT regulatory networks.

    Witte S and Muljo SA

    JAK-STAT 2014;3;1;e28055

    PUBMED: 24778925; PMC: 3995732; DOI: 10.4161/jkst.28055

  • InterPregGen: genetic studies of pre-eclampsia in three continents.

    Morgan L, McGinnis R, Steinthorsdottir V, Svyatova G, Zakhidova N, Lee WK, Iversen AC, Magnus P, Walker J, Casas JP et al.

    Norsk epidemiologi = Norwegian journal of epidemiology 2014;24;1-2;141-146

    PUBMED: 26568652; PMC: 4641320; DOI: 10.5324/nje.v24i1-2.1815

  • Investigating the possible causal association of smoking with depression and anxiety using Mendelian randomisation meta-analysis: the CARTA consortium.

    Taylor AE, Fluharty ME, Bjørngaard JH, Gabrielsen ME, Skorpen F, Marioni RE, Campbell A, Engmann J, Mirza SS, Loukola A et al.

    BMJ open 2014;4;10;e006141

    PUBMED: 25293386; PMC: 4187451; DOI: 10.1136/bmjopen-2014-006141

  • Izumo meets Juno: preventing polyspermy in fertilization.

    Bianchi E and Wright GJ

    Cell cycle (Georgetown, Tex.) 2014;13;13;2019-20

    PUBMED: 24906131; PMC: 4111690; DOI: 10.4161/cc.29461

  • Long term conservation of human metabolic phenotypes and link to heritability.

    Yousri NA, Kastenmüller G, Gieger C, Shin SY, Erte I, Menni C, Peters A, Meisinger C, Mohney RP, Illig T et al.

    Metabolomics : Official journal of the Metabolomic Society 2014;10;5;1005-1017

    PUBMED: 25177233; PMC: 4145193; DOI: 10.1007/s11306-014-0629-y

  • Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma.

    Müller J, Krijgsman O, Tsoi J, Robert L, Hugo W, Song C, Kong X, Possik PA, Cornelissen-Steijger PD, Foppen MH et al.

    Nature communications 2014;5;5712

    PUBMED: 25502142; PMC: 4428333; DOI: 10.1038/ncomms6712

  • Maturation of induced pluripotent stem cell derived hepatocytes by 3D-culture.

    Gieseck RL, Hannan NR, Bort R, Hanley NA, Drake RA, Cameron GW, Wynn TA and Vallier L

    PloS one 2014;9;1;e86372

    PUBMED: 24466060; PMC: 3899231; DOI: 10.1371/journal.pone.0086372

  • Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae.

    Mitchell SN, Rigden DJ, Dowd AJ, Lu F, Wilding CS, Weetman D, Dadzie S, Jenkins AM, Regna K, Boko P et al.

    PloS one 2014;9;3;e92662

    PUBMED: 24675797; PMC: 3968025; DOI: 10.1371/journal.pone.0092662

  • Microbial sequencing to improve individual and population health.

    Peacock SJ and Weinstock GM

    Genome medicine 2014;6;11;103

    PUBMED: 25505493; PMC: 4262389; DOI: 10.1186/s13073-014-0103-5

  • Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1.

    Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JE, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W and Genographic Consortium

    PloS one 2014;9;2;e87612

    PUBMED: 24503968; PMC: 3913659; DOI: 10.1371/journal.pone.0087612

  • Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

    Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A et al.

    eLife 2014;3;e02626

    PUBMED: 25279814; PMC: 4359374; DOI: 10.7554/eLife.02626

  • Mutation in KERA identified by linkage analysis and targeted resequencing in a pedigree with premature atherosclerosis.

    Maiwald S, Sivapalaratnam S, Motazacker MM, van Capelleveen JC, Bot I, de Jager SC, van Eck M, Jolley J, Kuiper J, Stephens J et al.

    PloS one 2014;9;5;e98289

    PUBMED: 24879339; PMC: 4039470; DOI: 10.1371/journal.pone.0098289

  • Neutralization of Plasmodium falciparum merozoites by antibodies against PfRH5.

    Douglas AD, Williams AR, Knuepfer E, Illingworth JJ, Furze JM, Crosnier C, Choudhary P, Bustamante LY, Zakutansky SE, Awuah DK et al.

    Journal of immunology (Baltimore, Md. : 1950) 2014;192;1;245-58

    PUBMED: 24293631; PMC: 3872115; DOI: 10.4049/jimmunol.1302045

  • New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.

    Trame CB, Chang Y, Axelrod HL, Eberhardt RY, Coggill P, Punta M and Rawlings ND

    BMC bioinformatics 2014;15;1

    PUBMED: 24383880; PMC: 3890501; DOI: 10.1186/1471-2105-15-1

  • Next-generation pathogen genomics.

    Weinstock GM and Peacock SJ

    Genome biology 2014;15;11;528

    PUBMED: 25417942; PMC: 4283783; DOI: 10.1186/s13059-014-0528-6

  • No evidence for genome-wide interactions on plasma fibrinogen by smoking, alcohol consumption and body mass index: results from meta-analyses of 80,607 subjects.

    Baumert J, Huang J, McKnight B, Sabater-Lleal M, Steri M, Chu AY, Trompet S, Lopez LM, Fornage M, Teumer A et al.

    PloS one 2014;9;12;e111156

    PUBMED: 25551457; PMC: 4281156; DOI: 10.1371/journal.pone.0111156

  • Novel determinants of antibiotic resistance: identification of mutated loci in highly methicillin-resistant subpopulations of methicillin-resistant Staphylococcus aureus.

    Dordel J, Kim C, Chung M, Pardos de la Gándara M, Holden MT, Parkhill J, de Lencastre H, Bentley SD and Tomasz A

    mBio 2014;5;2;e01000

    PUBMED: 24713324; PMC: 3993859; DOI: 10.1128/mBio.01000-13

  • Olfactory bulb encoding during learning under anesthesia.

    Nicol AU, Sanchez-Andrade G, Collado P, Segonds-Pichon A and Kendrick KM

    Frontiers in behavioral neuroscience 2014;8;193

    PUBMED: 24926241; PMC: 4046573; DOI: 10.3389/fnbeh.2014.00193

  • OncoCis: annotation of cis-regulatory mutations in cancer.

    Perera D, Chacon D, Thoms JA, Poulos RC, Shlien A, Beck D, Campbell PJ, Pimanda JE and Wong JW

    Genome biology 2014;15;10;485

    PUBMED: 25298093; PMC: 4224696; DOI: 10.1186/s13059-014-0485-0

  • One-step generation of different immunodeficient mice with multiple gene modifications by CRISPR/Cas9 mediated genome engineering.

    Zhou J, Shen B, Zhang W, Wang J, Yang J, Chen L, Zhang N, Zhu K, Xu J, Hu B et al.

    The international journal of biochemistry & cell biology 2014;46;49-55

    PUBMED: 24269190; DOI: 10.1016/j.biocel.2013.10.010

  • Pfam: the protein families database.

    Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J et al.

    Nucleic acids research 2014;42;Database issue;D222-30

    PUBMED: 24288371; PMC: 3965110; DOI: 10.1093/nar/gkt1223

  • Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci.

    Service SK, Teslovich TM, Fuchsberger C, Ramensky V, Yajnik P, Koboldt DC, Larson DE, Zhang Q, Lin L, Welch R et al.

    PLoS genetics 2014;10;1;e1004147

    PUBMED: 24497850; PMC: 3907339; DOI: 10.1371/journal.pgen.1004147

  • RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus.

    O'Keeffe G, Hammel S, Owens RA, Keane TM, Fitzpatrick DA, Jones GW and Doyle S

    BMC genomics 2014;15;894

    PUBMED: 25311525; PMC: 4209032; DOI: 10.1186/1471-2164-15-894

  • Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever.

    Dougan G and Baker S

    Annual review of microbiology 2014;68;317-36

    PUBMED: 25208300; DOI: 10.1146/annurev-micro-091313-103739

  • SDF-1 chemokine signalling modulates the apoptotic responses to iron deprivation of clathrin-depleted DT40 cells.

    Pance A, Morrissey-Wettey FR, Craig H, Downing A, Talbot R and Jackson AP

    PloS one 2014;9;8;e106278

    PUBMED: 25162584; PMC: 4146602; DOI: 10.1371/journal.pone.0106278

  • Single Cell Genomics meeting in Stockholm: from single cells to cell types.

    Scialdone A, Achim K and Marioni JC

    Genome biology 2014;15;10;496

    PUBMED: 25418892; PMC: 4281946; DOI: 10.1186/s13059-014-0496-x

  • Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes.

    Almlöf JC, Lundmark P, Lundmark A, Ge B, Pastinen T, Cardiogenics Consortium, Goodall AH, Cambien F, Deloukas P, Ouwehand WH and Syvänen AC

    PloS one 2014;9;7;e102612

    PUBMED: 25025429; PMC: 4099216; DOI: 10.1371/journal.pone.0102612

  • Single nucleotide variants in the protein C pathway and mortality in dialysis patients.

    Ocak G, Drechsler C, Vossen CY, Vos HL, Rosendaal FR, Reitsma PH, Hoffmann MM, März W, Ouwehand WH, Krediet RT et al.

    PloS one 2014;9;5;e97251

    PUBMED: 24816905; PMC: 4016291; DOI: 10.1371/journal.pone.0097251

  • Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase.

    Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL and Godzik A

    BMC bioinformatics 2014;15;112

    PUBMED: 24742328; PMC: 4032388; DOI: 10.1186/1471-2105-15-112

  • Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.

    Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A and Aravind L

    BMC bioinformatics 2014;15;75

    PUBMED: 24646163; PMC: 4000134; DOI: 10.1186/1471-2105-15-75

  • Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.

    Rigden DJ, Eberhardt RY, Gilbert HJ, Xu Q, Chang Y and Godzik A

    BMC bioinformatics 2014;15;196

    PUBMED: 24938123; PMC: 4071793; DOI: 10.1186/1471-2105-15-196

  • Survival and differentiation of adenovirus-generated induced pluripotent stem cells transplanted into the rat striatum.

    Fink KD, Rossignol J, Lu M, Lévêque X, Hulse TD, Crane AT, Nerriere-Daguin V, Wyse RD, Starski PA, Schloop MT et al.

    Cell transplantation 2014;23;11;1407-23

    PUBMED: 23879897; DOI: 10.3727/096368913X670958

  • Towards a molecular systems model of coronary artery disease.

    Abraham G, Bhalala OG, de Bakker PI, Ripatti S and Inouye M

    Current cardiology reports 2014;16;6;488

    PUBMED: 24743898; PMC: 4050311; DOI: 10.1007/s11886-014-0488-1

  • TreeFam v9: a new website, more species and orthology-on-the-fly.

    Schreiber F, Patricio M, Muffato M, Pignatelli M and Bateman A

    Nucleic acids research 2014;42;Database issue;D922-5

    PUBMED: 24194607; PMC: 3965059; DOI: 10.1093/nar/gkt1055

  • Using genetically isolated populations to understand the genomic basis of disease.

    Zeggini E

    Genome medicine 2014;6;10;83

    PUBMED: 25473423; PMC: 4254420; DOI: 10.1186/s13073-014-0083-5

  • Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone.

    Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B et al.

    BMC biology 2014;12;49

    PUBMED: 24957517; PMC: 4094930; DOI: 10.1186/1741-7007-12-49

  • Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

    Iantorno S, Gori K, Goldman N, Gil M and Dessimoz C

    Methods in molecular biology (Clifton, N.J.) 2014;1079;59-73

    PUBMED: 24170395; DOI: 10.1007/978-1-62703-646-7_4

  • Whole-exome sequencing in an extended family with myocardial infarction unmasks familial hypercholesterolemia.

    Brænne I, Reiz B, Medack A, Kleinecke M, Fischer M, Tuna S, Hengstenberg C, Deloukas P, Erdmann J, Schunkert H and Cardiogenics consortium

    BMC cardiovascular disorders 2014;14;108

    PUBMED: 25154303; PMC: 4243586; DOI: 10.1186/1471-2261-14-108

  • Your gut microbiota are what you eat.

    Chewapreecha C

    Nature reviews. Microbiology 2014;12;1;8

    PUBMED: 24336181; DOI: 10.1038/nrmicro3186

  • Whole-exome sequencing of patients with severe disorders of insulin action

    Semple,R. and BARROSO,I.

    Frontiers in Diabetes 2014;23;87-101

    DOI: 10.1159/000362469; URL: https://www.karger.com/Article/...Abstract/362469

2013

  • Next-generation sequencing of disseminated tumor cells.

    Møller EK, Kumar P, Voet T, Peterson A, Van Loo P, Mathiesen RR, Fjelldal R, Grundstad J, Borgen E, Baumbusch LO et al.

    Frontiers in oncology 2013;3;320

    PUBMED: 24427740; PMC: 3876274; DOI: 10.3389/fonc.2013.00320

  • Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

    Wong VK, Pickard DJ, Barquist L, Sivaraman K, Page AJ, Hart PJ, Arends MJ, Holt KE, Kane L, Mottram LF et al.

    PloS one 2013;8;12;e84567

    PUBMED: 24386394; PMC: 3875573; DOI: 10.1371/journal.pone.0084567

  • Efficacy of a Plasmodium vivax malaria vaccine using ChAd63 and modified vaccinia Ankara expressing thrombospondin-related anonymous protein as assessed with transgenic Plasmodium berghei parasites.

    Bauza K, Malinauskas T, Pfander C, Anar B, Jones EY, Billker O, Hill AV and Reyes-Sandoval A

    Infection and immunity 2013;82;3;1277-86

    PUBMED: 24379295; PMC: 3957994; DOI: 10.1128/IAI.01187-13

  • Emerging insights on intestinal dysbiosis during bacterial infections.

    Pham TA and Lawley TD

    Current opinion in microbiology 2013;17;67-74

    PUBMED: 24581695; PMC: 3969284; DOI: 10.1016/j.mib.2013.12.002

  • Chromosomal evolution among leaf-nosed nectarivorous bats--evidence from cross-species chromosome painting (Phyllostomidae, Chiroptera).

    Sotero-Caio CG, Volleth M, Gollahon LS, Fu B, Cheng W, Ng BL, Yang F and Baker RJ

    BMC evolutionary biology 2013;13;276

    PUBMED: 24369737; PMC: 3880000; DOI: 10.1186/1471-2148-13-276

  • Rapid single-colony whole-genome sequencing of bacterial pathogens.

    Köser CU, Fraser LJ, Ioannou A, Becq J, Ellington MJ, Holden MT, Reuter S, Török ME, Bentley SD, Parkhill J et al.

    The Journal of antimicrobial chemotherapy 2013;69;5;1275-81

    PUBMED: 24370932; PMC: 3977605; DOI: 10.1093/jac/dkt494

  • Calreticulin gene exon 9 frameshift mutations in patients with thrombocytosis.

    Chi J, Nicolaou KA, Nicolaidou V, Koumas L, Mitsidou A, Pierides C, Manoloukos M, Barbouti K, Melanthiou F, Prokopiou C et al.

    Leukemia 2013;28;5;1152-4

    PUBMED: 24365789; PMC: 4017256; DOI: 10.1038/leu.2013.382

  • Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library.

    Koike-Yusa H, Li Y, Tan EP, Velasco-Herrera Mdel C and Yusa K

    Nature biotechnology 2013;32;3;267-73

    PUBMED: 24535568; DOI: 10.1038/nbt.2800

  • Detecting and measuring selection from gene frequency data.

    Vitalis R, Gautier M, Dawson KJ and Beaumont MA

    Genetics 2013;196;3;799-817

    PUBMED: 24361938; PMC: 3948807; DOI: 10.1534/genetics.113.152991

  • Epigenetic regulation of COL15A1 in smooth muscle cell replicative aging and atherosclerosis.

    Connelly JJ, Cherepanova OA, Doss JF, Karaoli T, Lillard TS, Markunas CA, Nelson S, Wang T, Ellis PD, Langford CF et al.

    Human molecular genetics 2013;22;25;5107-20

    PUBMED: 23912340; PMC: 3842173; DOI: 10.1093/hmg/ddt365

  • A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders.

    King DA, Fitzgerald TW, Miller R, Canham N, Clayton-Smith J, Johnson D, Mansour S, Stewart F, Vasudevan P, Hurles ME and DDD Study

    Genome research 2013;24;4;673-87

    PUBMED: 24356988; PMC: 3975066; DOI: 10.1101/gr.160465.113

  • Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.

    Tsai IJ, Hunt M, Holroyd N, Huckvale T, Berriman M and Kikuchi T

    DNA research : an international journal for rapid publication of reports on genes and genomes 2013;21;3;243-54

    PUBMED: 24353264; PMC: 4060946; DOI: 10.1093/dnares/dst054

  • Online questionnaire development: using film to engage participants and then gather attitudes towards the sharing of genomic data.

    Middleton A, Bragin E, Morley KI, Parker M and DDD Study

    Social science research 2013;44;100;211-23

    PUBMED: 24468445; PMC: 3969308; DOI: 10.1016/j.ssresearch.2013.12.004

  • INVEX--a web-based tool for integrative visualization of expression data.

    Xia J, Lyle NH, Mayer ML, Pena OM and Hancock RE

    Bioinformatics (Oxford, England) 2013;29;24;3232-4

    PUBMED: 24078684; PMC: 3842763; DOI: 10.1093/bioinformatics/btt562

  • Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites.

    Valentim CL, Cioli D, Chevalier FD, Cao X, Taylor AB, Holloway SP, Pica-Mattoccia L, Guidi A, Basso A, Tsai IJ et al.

    Science (New York, N.Y.) 2013;342;6164;1385-9

    PUBMED: 24263136; DOI: 10.1126/science.1243106

  • Network based elucidation of drug response: from modulators to targets.

    Iorio F, Saez-Rodriguez J and di Bernardo D

    BMC systems biology 2013;7;139

    PUBMED: 24330611; PMC: 3878740; DOI: 10.1186/1752-0509-7-139

  • Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions.

    Zilbauer M, Rayner TF, Clark C, Coffey AJ, Joyce CJ, Palta P, Palotie A, Lyons PA and Smith KG

    Blood 2013;122;25;e52-60

    PUBMED: 24159175; PMC: 3862273; DOI: 10.1182/blood-2013-05-503201

  • Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure.

    Baker S, Duy PT, Nga TV, Dung TT, Phat VV, Chau TT, Turner AK, Farrar J and Boni MF

    eLife 2013;2;e01229

    PUBMED: 24327559; PMC: 3857714; DOI: 10.7554/eLife.01229

  • Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2.

    Nangalia J, Massie CE, Baxter EJ, Nice FL, Gundem G, Wedge DC, Avezov E, Li J, Kollmann K, Kent DG et al.

    The New England journal of medicine 2013;369;25;2391-2405

    PUBMED: 24325359; PMC: 3966280; DOI: 10.1056/NEJMoa1312542

  • Inactivating CUX1 mutations promote tumorigenesis.

    Wong CC, Martincorena I, Rust AG, Rashid M, Alifrangis C, Alexandrov LB, Tiffen JC, Kober C, Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium, Green AR et al.

    Nature genetics 2013;46;1;33-8

    PUBMED: 24316979; PMC: 3874239; DOI: 10.1038/ng.2846

  • Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model.

    Bard-Chapeau EA, Nguyen AT, Rust AG, Sayadi A, Lee P, Chua BQ, New LS, de Jong J, Ward JM, Chin CK et al.

    Nature genetics 2013;46;1;24-32

    PUBMED: 24316982; PMC: 4131144; DOI: 10.1038/ng.2847

  • The Vertebrate Genome Annotation browser 10 years on.

    Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S and Wilming LG

    Nucleic acids research 2013;42;Database issue;D771-9

    PUBMED: 24316575; PMC: 3964964; DOI: 10.1093/nar/gkt1241

  • Ensembl 2014.

    Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S et al.

    Nucleic acids research 2013;42;Database issue;D749-55

    PUBMED: 24316576; PMC: 3964975; DOI: 10.1093/nar/gkt1196

  • Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents.

    Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ and Keightley PD

    PLoS genetics 2013;9;12;e1003995

    PUBMED: 24339797; PMC: 3854965; DOI: 10.1371/journal.pgen.1003995

  • Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity.

    Dimas AS, Lagou V, Barker A, Knowles JW, Mägi R, Hivert MF, Benazzo A, Rybin D, Jackson AU, Stringham HM et al.

    Diabetes 2013;63;6;2158-71

    PUBMED: 24296717; PMC: 4030103; DOI: 10.2337/db13-0949

  • RH5-Basigin interaction plays a major role in the host tropism of Plasmodium falciparum.

    Wanaguru M, Liu W, Hahn BH, Rayner JC and Wright GJ

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;51;20735-40

    PUBMED: 24297912; PMC: 3870751; DOI: 10.1073/pnas.1320771110

  • Adipogenesis: new insights into brown adipose tissue differentiation.

    Carobbio S, Rosen B and Vidal-Puig A

    Journal of molecular endocrinology 2013;51;3;T75-85

    PUBMED: 24041933; DOI: 10.1530/JME-13-0158

  • Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs.

    Ye K, Beekman M, Lameijer EW, Zhang Y, Moed MH, van den Akker EB, Deelen J, Houwing-Duistermaat JJ, Kremer D, Anvar SY et al.

    Twin research and human genetics : the official journal of the International Society for Twin Studies 2013;16;6;1026-32

    PUBMED: 24182360; DOI: 10.1017/thg.2013.73

  • Association of HIV and ART with cardiometabolic traits in sub-Saharan Africa: a systematic review and meta-analysis.

    Dillon DG, Gurdasani D, Riha J, Ekoru K, Asiki G, Mayanja BN, Levitt NS, Crowther NJ, Nyirenda M, Njelekela M et al.

    International journal of epidemiology 2013;42;6;1754-71

    PUBMED: 24415610; PMC: 3887568; DOI: 10.1093/ije/dyt198

  • Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.

    Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG et al.

    Genome research 2013;23;12;2066-77

    PUBMED: 24002784; PMC: 3847776; DOI: 10.1101/gr.161620.113

  • COX10 mutations resulting in complex multisystem mitochondrial disease that remains stable into adulthood.

    Pitceathly RD, Taanman JW, Rahman S, Meunier B, Sadowski M, Cirak S, Hargreaves I, Land JM, Nanji T, Polke JM et al.

    JAMA neurology 2013;70;12;1556-61

    PUBMED: 24100867; DOI: 10.1001/jamaneurol.2013.3242

  • Mutations in B4GALNT1 (GM2 synthase) underlie a new disorder of ganglioside biosynthesis.

    Harlalka GV, Lehman A, Chioza B, Baple EL, Maroofian R, Cross H, Sreekantan-Nair A, Priestman DA, Al-Turki S, McEntagart ME et al.

    Brain : a journal of neurology 2013;136;Pt 12;3618-24

    PUBMED: 24103911; PMC: 3859217; DOI: 10.1093/brain/awt270

  • Playing fast and loose with mutation.

    Mather AE and Harris SR

    Nature reviews. Microbiology 2013;11;12;822

    PUBMED: 24232567; DOI: 10.1038/nrmicro3164

  • Reduced burden of very large and rare CNVs in bipolar affective disorder.

    Grozeva D, Kirov G, Conrad DF, Barnes CP, Hurles M, Owen MJ, O'Donovan MC and Craddock N

    Bipolar disorders 2013;15;8;893-8

    PUBMED: 24127788; DOI: 10.1111/bdi.12125

  • Replication of bipolar disorder susceptibility alleles and identification of two novel genome-wide significant associations in a new bipolar disorder case-control sample.

    Green EK, Hamshere M, Forty L, Gordon-Smith K, Fraser C, Russell E, Grozeva D, Kirov G, Holmans P, Moran JL et al.

    Molecular psychiatry 2013;18;12;1302-7

    PUBMED: 23070075; DOI: 10.1038/mp.2012.142

  • Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.

    McDonnell J, Dallman T, Atkin S, Turbitt DA, Connor TR, Grant KA, Thomson NR and Jenkins C

    Epidemiology and infection 2013;141;12;2568-75

    PUBMED: 23425681; DOI: 10.1017/S0950268813000137

  • Sociodemographic distribution of non-communicable disease risk factors in rural Uganda: a cross-sectional study.

    Murphy GA, Asiki G, Ekoru K, Nsubuga RN, Nakiyingi-Miiro J, Young EH, Seeley J, Sandhu MS and Kamali A

    International journal of epidemiology 2013;42;6;1740-53

    PUBMED: 24191304; PMC: 4234905; DOI: 10.1093/ije/dyt184

  • UBE2QL1 is disrupted by a constitutional translocation associated with renal tumor predisposition and is a novel candidate renal tumor suppressor gene.

    Wake NC, Ricketts CJ, Morris MR, Prigmore E, Gribble SM, Skytte AB, Brown M, Clarke N, Banks RE, Hodgson S et al.

    Human mutation 2013;34;12;1650-61

    PUBMED: 24000165; PMC: 4028990; DOI: 10.1002/humu.22433

  • Spindle assembly checkpoint of oocytes depends on a kinetochore structure determined by cohesin in meiosis I.

    Tachibana-Konwalski K, Godwin J, Borsos M, Rattani A, Adams DJ and Nasmyth K

    Current biology : CB 2013;23;24;2534-9

    PUBMED: 24291092; PMC: 3898714; DOI: 10.1016/j.cub.2013.10.052

  • The peculiar epidemiology of dracunculiasis in Chad.

    Eberhard ML, Ruiz-Tiben E, Hopkins DR, Farrell C, Toe F, Weiss A, Withers PC, Jenks MH, Thiele EA, Cotton JA et al.

    The American journal of tropical medicine and hygiene 2013;90;1;61-70

    PUBMED: 24277785; PMC: 3886430; DOI: 10.4269/ajtmh.13-0554

  • Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya.

    Borrmann S, Straimer J, Mwai L, Abdi A, Rippert A, Okombo J, Muriithi S, Sasi P, Kortok MM, Lowe B et al.

    Scientific reports 2013;3;3318

    PUBMED: 24270944; PMC: 3839035; DOI: 10.1038/srep03318

  • Policy challenges of clinical genome sequencing.

    Wright CF, Middleton A, Burton H, Cunningham F, Humphries SE, Hurst J, Birney E and Firth HV

    BMJ (Clinical research ed.) 2013;347;f6845

    PUBMED: 24270507; DOI: 10.1136/bmj.f6845

  • Amphotericin B increases influenza A virus infection by preventing IFITM3-mediated restriction.

    Lin TY, Chin CR, Everitt AR, Clare S, Perreira JM, Savidis G, Aker AM, John SP, Sarlah D, Carreira EM et al.

    Cell reports 2013;5;4;895-908

    PUBMED: 24268777; PMC: 3898084; DOI: 10.1016/j.celrep.2013.10.033

  • Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model.

    Everitt AR, Clare S, McDonald JU, Kane L, Harcourt K, Ahras M, Lall A, Hale C, Rodgers A, Young DB et al.

    PloS one 2013;8;11;e80723

    PUBMED: 24278312; PMC: 3836756; DOI: 10.1371/journal.pone.0080723

  • Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study.

    Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH, van Helden P, Pym A, Mahayiddin AA, Chuchottaworn C, Sanne IM et al.

    The Lancet. Respiratory medicine 2013;1;10;786-92

    PUBMED: 24461758; PMC: 3861685; DOI: 10.1016/S2213-2600(13)70231-5

  • Filling out the structural map of the NTF2-like superfamily.

    Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC and Aravind L

    BMC bioinformatics 2013;14;327

    PUBMED: 24246060; PMC: 3924330; DOI: 10.1186/1471-2105-14-327

  • Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus.

    Blue Mountains Eye Study (BMES) and Wellcome Trust Case Control Consortium 2 (WTCCC2)

    Human molecular genetics 2013;22;22;4653-60

    PUBMED: 23836780; PMC: 3904806; DOI: 10.1093/hmg/ddt293

  • Implementing a successful data-management framework: the UK10K managed access model.

    Muddyman D, Smee C, Griffin H and Kaye J

    Genome medicine 2013;5;11;100

    PUBMED: 24229443; PMC: 3978569; DOI: 10.1186/gm504

  • Phosphoinositide 3-kinase δ gene mutation predisposes to respiratory infection and airway damage.

    Angulo I, Vadas O, Garçon F, Banham-Hall E, Plagnol V, Leahy TR, Baxendale H, Coulter T, Curtis J, Wu C et al.

    Science (New York, N.Y.) 2013;342;6160;866-71

    PUBMED: 24136356; PMC: 3930011; DOI: 10.1126/science.1243292

  • Handbook of Proteolytic Enzymes

    Rawlings,N.D. and Salvesen,G.;

    Handbook of Proteolytic Enzymes 2013

    URL: https://www.sciencedirect.com/scien...ce/book/9780123822192

  • Near in place linear time minimum redundancy coding

    Kärkkäinen,J. and TISCHLER,G.

    Data Compression Conference Proceedings 2013;Art. No.: 6543077

    DOI: 10.1109/DCC.2013.49; URL: https://ieeexplore.ieee.org/xpl/ar...ticleDetails.jsp?arnumber=6543077

  • Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia.

    Dawson MA, Gudgin EJ, Horton SJ, Giotopoulos G, Meduri E, Robson S, Cannizzaro E, Osaki H, Wiese M, Putwain S et al.

    Leukemia 2013;28;2;311-20

    PUBMED: 24220271; PMC: 3918873; DOI: 10.1038/leu.2013.338

  • CCL3L1 copy number, HIV load, and immune reconstitution in sub-Saharan Africans.

    Aklillu E, Odenthal-Hesse L, Bowdrey J, Habtewold A, Ngaimisi E, Yimer G, Amogne W, Mugusi S, Minzi O, Makonnen E et al.

    BMC infectious diseases 2013;13;536

    PUBMED: 24219137; PMC: 3829100; DOI: 10.1186/1471-2334-13-536

  • Current status and new features of the Consensus Coding Sequence database.

    Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B et al.

    Nucleic acids research 2013;42;Database issue;D865-72

    PUBMED: 24217909; PMC: 3965069; DOI: 10.1093/nar/gkt1059

  • Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma.

    van Rooij N, van Buuren MM, Philips D, Velds A, Toebes M, Heemskerk B, van Dijk LJ, Behjati S, Hilkmann H, El Atmioui D et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2013;31;32;e439-42

    PUBMED: 24043743; PMC: 3836220; DOI: 10.1200/JCO.2012.47.7521

  • ADAM15 Peptidase

    Rawlings, N.

    Handbook of Proteolytic Enzymes 2013;1;253;1122-5

    DOI: 10.1016/B978-0-12-382219-2.00253-2; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192002532

  • Antarease

    Rawlings, N

    Handbook of Proteolytic Enzymes 2013;1;246;1079-81

    DOI: 10.1016/B978-0-12-382219-2.00246-5; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192002465

  • Bacteriophage T4 Prohead Endopeptidase

    Rawlings, N

    Handbook of Proteolytic Enzymes 2013;3;789;3560-2

    DOI: 10.1016/B978-0-12-382219-2.00789-4; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192007894

  • Dynamic image-based modelling of kidney branching morphogenesis

    Adivarahan,S.;, Menshykau,D.;, MICHOS,O.; and Iber,D.

    Lecture Notes in Computer Science 2013;8130 LNBI;106-19

    DOI: 10.1007/978-3-642-40708-6_9; URL: https://link.springer.com/chapter.../10.1007%2F978-3-642-40708-6_9

  • Genome-wide association study for osteoarthritis

    PANOUTSOPOULOU,K.;, SOUTHAM,L.; and ZEGGINI,E.;

    The Lancet 2013;381;9864;373

    DOI: 10.1016/S0140-6736(13)60168-3; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0140673613601683

  • Insect Gut Carboxypeptidase 3

    Vendrell,J.;, Avilés,F.X.; and BAYÉS,A.;

    Handbook of Proteolytic Enzymes 2013;1;3;1370-5

    DOI: 10.1016/B978-0-12-382219-2.00307-0; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192003070

  • Introduction: Aspartic and Glutamic Peptidases and Their Clans

    Rawlings, N; and Barrett, A

    Handbook of Proteolytic Enzymes 2013;1;1;3-19

    DOI: 10.1016/B978-0-12-382219-2.00001-6; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192000016

  • Introduction: Clan PB Containing N-terminal Nucleophile Peptidases

    Rawlings, N. and Barrett, A

    Handbook of Proteolytic Enzymes 2013;3;808;3648-53

    DOI: 10.1016/B978-0-12-382219-2.00808-5; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192008085

  • Introduction: Metallopeptidases and Their Clans

    Rawlings, N. and Barrett, A.

    Handbook of Proteolytic Enzymes 2013;1;77;325-70

    DOI: 10.1016/B978-0-12-382219-2.00077-6; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192000776

  • Introduction: Peptidases of Unknown Catalytic Type

    Rawlings, N and Barrett, A

    Handbook of Proteolytic Enzymes 2013;3;827;3747-9

    DOI: 10.1016/B978-0-12-382219-2.00827-9; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192008279

  • Introduction: Serine Peptidases and Their Clans

    Rawlings, N and Barrett, A

    Handbook of Proteolytic Enzymes 2013;3;559;2491-523

    DOI: 10.1016/B978-0-12-382219-2.00559-7; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192005597

  • Introduction: The Clans and Families of Cysteine Peptidases

    Rawlings, N. and Barrett, A.

    Handbook of Proteolytic Enzymes 2013;2;404;1743-73

    DOI: 10.1016/B978-0-12-382219-2.00404-X; URL: https://www.sciencedirect.com/scien...ce/article/pii/B978012382219200404X

  • Using Varying Negative Examples to Improve Computational Predictions of Transcription Factor Binding Sites

    Rezwan,F.;, Sun,Y.;, Davey,N.;, Adams,R.;, RUST,A.G.; and Robinson,M.

    Communications in Computer and Information Science 2013;311;234-43

    DOI: 10.1007/978-3-642-32909-8_24; URL: https://link.springer.com/chapter.../10.1007%2F978-3-642-32909-8_24

  • AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation.

    Aldridge S, Watt S, Quail MA, Rayner T, Lukk M, Bimson MF, Gaffney D and Odom DT

    Genome biology 2013;14;11;R124

    PUBMED: 24200198; PMC: 4053851; DOI: 10.1186/gb-2013-14-11-r124

  • De Novo Loss-of-Function Mutations in CHD2 Cause a Fever-Sensitive Myoclonic Epileptic Encephalopathy Sharing Features with Dravet Syndrome.

    Suls A, Jaehn JA, Kecskés A, Weber Y, Weckhuysen S, Craiu DC, Siekierska A, Djémié T, Afrikanova T, Gormley P et al.

    American journal of human genetics 2013;93;5;967-75

    PUBMED: 24207121; PMC: 3824114; DOI: 10.1016/j.ajhg.2013.09.017

  • Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

    Seth-Smith HM, Harris SR, Scott P, Parmar S, Marsh P, Unemo M, Clarke IN, Parkhill J and Thomson NR

    Nature protocols 2013;8;12;2404-12

    PUBMED: 24202554; DOI: 10.1038/nprot.2013.147

  • KSR2 mutations are associated with obesity, insulin resistance, and impaired cellular fuel oxidation.

    Pearce LR, Atanassova N, Banton MC, Bottomley B, van der Klaauw AA, Revelli JP, Hendricks A, Keogh JM, Henning E, Doree D et al.

    Cell 2013;155;4;765-77

    PUBMED: 24209692; PMC: 3898740; DOI: 10.1016/j.cell.2013.09.058

  • Mutations in the Gene Encoding IFT Dynein Complex Component WDR34 Cause Jeune Asphyxiating Thoracic Dystrophy.

    Schmidts M, Vodopiutz J, Christou-Savina S, Cortés CR, McInerney-Leo AM, Emes RD, Arts HH, Tüysüz B, D'Silva J, Leo PJ et al.

    American journal of human genetics 2013;93;5;932-44

    PUBMED: 24183451; PMC: 3824113; DOI: 10.1016/j.ajhg.2013.10.003

  • Rapid conversion of EUCOMM/KOMP-CSD alleles in mouse embryos using a cell-permeable Cre recombinase.

    Ryder E, Doe B, Gleeson D, Houghton R, Dalvi P, Grau E, Habib B, Miklejewska E, Newman S, Sethi D et al.

    Transgenic research 2013;23;1;177-85

    PUBMED: 24197666; PMC: 3890051; DOI: 10.1007/s11248-013-9764-x

  • Animal Legumain

    BARRETT,A.J. and Chen,J.-M.

    Handbook of Proteolytic Enzymes 2013;2;518;2309-14

    DOI: 10.1016/B978-0-12-382219-2.00516-0; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192005160

  • Cytosol Alanyl Aminopeptidase

    BARRETT,A.J.

    Handbook of Proteolytic Enzymes 2013;1;431-4

    DOI: 10.1016/B978-0-12-382219-2.00086-7; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192000867

  • Introduction: Unsequenced Serine Peptidases

    BARRETT,A.J

    Handbook of Proteolytic Enzymes 2013;3;824;3737

    DOI: 10.1016/B978-0-12-382219-2.00824-3; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192008243

  • Metridin

    BARRETT,A.J.

    Handbook of Proteolytic Enzymes 2013;3;581;2624-5

    DOI: 10.1016/B978-0-12-382219-2.00581-0; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192005810

  • Neurolysin

    Barrett, A.J.

    Handbook of Proteolytic Enzymes 2013;1;509-13

    DOI: 10.1016/B978-0-12-382219-2.00102-2;; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192001022

  • Peptidyl-Dipeptidase B

    BARRETT,A.J

    Handbook of Proteolytic Enzymes 2013;2;392;1710-11

    DOI: 10.1016/B978-0-12-382219-2.00392-6; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123822192003926

  • The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

    Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A et al.

    Nucleic acids research 2013;42;Database issue;D802-9

    PUBMED: 24194600; PMC: 3964955; DOI: 10.1093/nar/gkt977

  • Autologous antibody capture to enrich immunogenic viruses for viral discovery.

    Oude Munnink BB, Jazaeri Farsani SM, Deijs M, Jonkers J, Verhoeven JT, Ieven M, Goossens H, de Jong MD, Berkhout B, Loens K et al.

    PloS one 2013;8;11;e78454

    PUBMED: 24223808; PMC: 3817278; DOI: 10.1371/journal.pone.0078454

  • WormBase 2014: new views of curated biology.

    Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K et al.

    Nucleic acids research 2013;42;Database issue;D789-93

    PUBMED: 24194605; PMC: 3965043; DOI: 10.1093/nar/gkt1063

  • Assessment of transcript reconstruction methods for RNA-seq.

    Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J and Bertone P

    Nature methods 2013;10;12;1177-84

    PUBMED: 24185837; PMC: 3851240; DOI: 10.1038/nmeth.2714

  • Systematic evaluation of spliced alignment programs for RNA-seq data.

    Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R et al.

    Nature methods 2013;10;12;1185-91

    PUBMED: 24185836; PMC: 4018468; DOI: 10.1038/nmeth.2722

  • Advances in osteoarthritis genetics.

    Panoutsopoulou K and Zeggini E

    Journal of medical genetics 2013;50;11;715-24

    PUBMED: 23868913; PMC: 3812881; DOI: 10.1136/jmedgenet-2013-101754

  • Cereal killers.

    Otto TD and Reid AJ

    Nature reviews. Microbiology 2013;11;11;744

    PUBMED: 24129509; DOI: 10.1038/nrmicro3144

  • Mosaic copy number variation in human neurons.

    McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM and Gage FH

    Science (New York, N.Y.) 2013;342;6158;632-7

    PUBMED: 24179226; PMC: 3975283; DOI: 10.1126/science.1243472

  • Persistence of HIV-1 transmitted drug resistance mutations.

    Castro H, Pillay D, Cane P, Asboe D, Cambiano V, Phillips A, Dunn DT and UK Collaborative Group on HIV Drug Resistance

    The Journal of infectious diseases 2013;208;9;1459-63

    PUBMED: 23904291; PMC: 3789571; DOI: 10.1093/infdis/jit345

  • Piliation of invasive Streptococcus pneumoniae isolates in the era before pneumococcal conjugate vaccine introduction in Malawi.

    Kulohoma BW, Gray K, Kamng'ona A, Cornick J, Bentley SD, Heyderman RS and Everett DB

    Clinical and vaccine immunology : CVI 2013;20;11;1729-35

    PUBMED: 24027261; PMC: 3837777; DOI: 10.1128/CVI.00403-13

  • Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements.

    Grundberg E, Meduri E, Sandling JK, Hedman AK, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M et al.

    American journal of human genetics 2013;93;5;876-90

    PUBMED: 24183450; PMC: 3824131; DOI: 10.1016/j.ajhg.2013.10.004

  • Functional transcriptomics in the post-ENCODE era.

    Mudge JM, Frankish A and Harrow J

    Genome research 2013;23;12;1961-73

    PUBMED: 24172201; PMC: 3847767; DOI: 10.1101/gr.161315.113

  • Selecting antagonistic antibodies that control differentiation through inducible expression in embryonic stem cells.

    Melidoni AN, Dyson MR, Wormald S and McCafferty J

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;44;17802-7

    PUBMED: 24082130; PMC: 3816485; DOI: 10.1073/pnas.1312062110

  • Sleeping Beauty mutagenesis in a mouse medulloblastoma model defines networks that discriminate between human molecular subgroups.

    Genovesi LA, Ng CG, Davis MJ, Remke M, Taylor MD, Adams DJ, Rust AG, Ward JM, Ban KH, Jenkins NA et al.

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;46;E4325-34

    PUBMED: 24167280; PMC: 3832011; DOI: 10.1073/pnas.1318639110

  • Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone.

    Behjati S, Tarpey PS, Presneau N, Scheipl S, Pillay N, Van Loo P, Wedge DC, Cooke SL, Gundem G, Davies H et al.

    Nature genetics 2013;45;12;1479-82

    PUBMED: 24162739; PMC: 3839851; DOI: 10.1038/ng.2814

  • Ensembl Genomes 2013: scaling up access to genome-wide data.

    Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J et al.

    Nucleic acids research 2013;42;Database issue;D546-52

    PUBMED: 24163254; PMC: 3965094; DOI: 10.1093/nar/gkt979

  • Improved exome prioritization of disease genes through cross-species phenotype comparison.

    Robinson PN, Köhler S, Oellrich A, Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D et al.

    Genome research 2013;24;2;340-8

    PUBMED: 24162188; PMC: 3912424; DOI: 10.1101/gr.160325.113

  • MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.

    Rawlings ND, Waller M, Barrett AJ and Bateman A

    Nucleic acids research 2013;42;Database issue;D503-9

    PUBMED: 24157837; PMC: 3964991; DOI: 10.1093/nar/gkt953

  • DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation.

    Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP and Swaminathan GJ

    Nucleic acids research 2013;42;Database issue;D993-D1000

    PUBMED: 24150940; PMC: 3965078; DOI: 10.1093/nar/gkt937

  • Tracking the establishment of local endemic populations of an emergent enteric pathogen.

    Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, Campbell JI, Hoang NV, Vinh NT, Minh PV et al.

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;43;17522-7

    PUBMED: 24082120; PMC: 3808646; DOI: 10.1073/pnas.1308632110

  • Ectopic expression of activated notch or SOX2 reveals similar and unique roles in the development of the sensory cell progenitors in the mammalian inner ear.

    Pan W, Jin Y, Chen J, Rottier RJ, Steel KP and Kiernan AE

    The Journal of neuroscience : the official journal of the Society for Neuroscience 2013;33;41;16146-57

    PUBMED: 24107947; PMC: 3792456; DOI: 10.1523/JNEUROSCI.3150-12.2013

  • Discovery and refinement of loci associated with lipid levels.

    Willer CJ, Schmidt EM, Sengupta S, Peloso GM, Gustafsson S, Kanoni S, Ganna A, Chen J, Buchkovich ML, Mora S et al.

    Nature genetics 2013;45;11;1274-1283

    PUBMED: 24097068; PMC: 3838666; DOI: 10.1038/ng.2797

  • Integrative annotation of variants from 1092 humans: application to cancer genomics.

    Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A et al.

    Science (New York, N.Y.) 2013;342;6154;1235587

    PUBMED: 24092746; PMC: 3947637; DOI: 10.1126/science.1235587

  • Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.

    Poultney CS, Goldberg AP, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, De Rubeis S, Durand S, Stevens C, Rehnström K et al.

    American journal of human genetics 2013;93;4;607-19

    PUBMED: 24094742; PMC: 3791269; DOI: 10.1016/j.ajhg.2013.09.001

  • The association between circulating lipoprotein(a) and type 2 diabetes: is it causal?

    Ye Z, Haycock PC, Gurdasani D, Pomilla C, Boekholdt SM, Tsimikas S, Khaw KT, Wareham NJ, Sandhu MS and Forouhi NG

    Diabetes 2013;63;1;332-342

    PUBMED: 24089516; PMC: 4246060; DOI: 10.2337/db13-1144

  • The anatomy of successful computational biology software.

    Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J and Trapnell C

    Nature biotechnology 2013;31;10;894-7

    PUBMED: 24104757; PMC: 4166496; DOI: 10.1038/nbt.2721

  • DeNovoGear: de novo indel and point mutation discovery and phasing.

    Ramu A, Noordam MJ, Schwartz RS, Wuster A, Hurles ME, Cartwright RA and Conrad DF

    Nature methods 2013;10;10;985-7

    PUBMED: 23975140; PMC: 4003501; DOI: 10.1038/nmeth.2611

  • JAK2V617F leads to intrinsic changes in platelet formation and reactivity in a knock-in mouse model of essential thrombocythemia.

    Hobbs CM, Manning H, Bennett C, Vasquez L, Severin S, Brain L, Mazharian A, Guerrero JA, Li J, Soranzo N et al.

    Blood 2013;122;23;3787-97

    PUBMED: 24085768; PMC: 3843237; DOI: 10.1182/blood-2013-06-501452

  • Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.

    Booth MJ, Ost TW, Beraldi D, Bell NM, Branco MR, Reik W and Balasubramanian S

    Nature protocols 2013;8;10;1841-51

    PUBMED: 24008380; PMC: 3919000; DOI: 10.1038/nprot.2013.115

  • Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

    Lindsay B, Pop M, Antonio M, Walker AW, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine MM et al.

    Journal of clinical microbiology 2013;51;10;3263-9

    PUBMED: 23884998; PMC: 3811648; DOI: 10.1128/JCM.01342-13

  • Systematic identification of trans eQTLs as putative drivers of known disease associations.

    Westra HJ, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, Christiansen MW, Fairfax BP, Schramm K, Powell JE et al.

    Nature genetics 2013;45;10;1238-43

    PUBMED: 24013639; PMC: 3991562; DOI: 10.1038/ng.2756

  • Transcriptional regulation of Culex pipiens mosquitoes by Wolbachia influences cytoplasmic incompatibility.

    Pinto SB, Stainton K, Harris S, Kambris Z, Sutton ER, Bonsall MB, Parkhill J and Sinkins SP

    PLoS pathogens 2013;9;10;e1003647

    PUBMED: 24204251; PMC: 3814344; DOI: 10.1371/journal.ppat.1003647

  • Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation.

    Lemieux JE, Kyes SA, Otto TD, Feller AI, Eastman RT, Pinches RA, Berriman M, Su XZ and Newbold CI

    Molecular microbiology 2013;90;3;519-37

    PUBMED: 23980881; PMC: 3894959; DOI: 10.1111/mmi.12381

  • Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis.

    International Multiple Sclerosis Genetics Consortium (IMSGC), Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D et al.

    Nature genetics 2013;45;11;1353-60

    PUBMED: 24076602; PMC: 3832895; DOI: 10.1038/ng.2770

  • Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii.

    Hamidian M, Wynn M, Holt KE, Pickard D, Dougan G and Hall RM

    The Journal of antimicrobial chemotherapy 2013;69;2;557-8

    PUBMED: 24080502; PMC: 3886933; DOI: 10.1093/jac/dkt379

  • The cell-cycle state of stem cells determines cell fate propensity.

    Pauklin S and Vallier L

    Cell 2013;155;1;135-47

    PUBMED: 24074866; PMC: 3898746; DOI: 10.1016/j.cell.2013.08.031

  • Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway.

    Lee JC, Espéli M, Anderson CA, Linterman MA, Pocock JM, Williams NJ, Roberts R, Viatte S, Fu B, Peshu N et al.

    Cell 2013;155;1;57-69

    PUBMED: 24035192; PMC: 3790457; DOI: 10.1016/j.cell.2013.08.034

  • Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon.

    Yusa K

    Nature protocols 2013;8;10;2061-78

    PUBMED: 24071911; DOI: 10.1038/nprot.2013.126

  • Chicken interferon-inducible transmembrane protein 3 restricts influenza viruses and lyssaviruses in vitro.

    Smith SE, Gibson MS, Wash RS, Ferrara F, Wright E, Temperton N, Kellam P and Fife M

    Journal of virology 2013;87;23;12957-66

    PUBMED: 24067955; PMC: 3838109; DOI: 10.1128/JVI.01443-13

  • Murine models to study Clostridium difficile infection and transmission.

    Lawley TD and Young VB

    Anaerobe 2013;24;94-7

    PUBMED: 24076318; PMC: 4089867; DOI: 10.1016/j.anaerobe.2013.09.008

  • Single-cell mutational profiling and clonal phylogeny in cancer.

    Potter NE, Ermini L, Papaemmanuil E, Cazzaniga G, Vijayaraghavan G, Titley I, Ford A, Campbell P, Kearney L and Greaves M

    Genome research 2013;23;12;2115-25

    PUBMED: 24056532; PMC: 3847780; DOI: 10.1101/gr.159913.113

  • Cerebral organoids model human brain development and microcephaly.

    Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP and Knoblich JA

    Nature 2013;501;7467;373-9

    PUBMED: 23995685; PMC: 3817409; DOI: 10.1038/nature12517

  • A variant in LDLR is associated with abdominal aortic aneurysm.

    Bradley DT, Hughes AE, Badger SA, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Grétarsdóttir S, Burnand K et al.

    Circulation. Cardiovascular genetics 2013;6;5;498-504

    PUBMED: 24046328; DOI: 10.1161/CIRCGENETICS.113.000165

  • Pitpnm1 is expressed in hair cells during development but is not required for hearing.

    Carlisle FA, Pearson S, Steel KP and Lewis MA

    Neuroscience 2013;248;620-5

    PUBMED: 23820044; PMC: 3748349; DOI: 10.1016/j.neuroscience.2013.06.045

  • A library of functional recombinant cell-surface and secreted P. falciparum merozoite proteins.

    Crosnier C, Wanaguru M, McDade B, Osier FH, Marsh K, Rayner JC and Wright GJ

    Molecular & cellular proteomics : MCP 2013;12;12;3976-86

    PUBMED: 24043421; PMC: 3861738; DOI: 10.1074/mcp.O113.028357

  • Biochemical analysis of the Plasmodium falciparum erythrocyte-binding antigen-175 (EBA175)-glycophorin-A interaction: implications for vaccine design.

    Wanaguru M, Crosnier C, Johnson S, Rayner JC and Wright GJ

    The Journal of biological chemistry 2013;288;45;32106-17

    PUBMED: 24043627; PMC: 3820850; DOI: 10.1074/jbc.M113.484840

  • A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease.

    Lin YF, A DR, Guan S, Mamanova L and McDowall KJ

    BMC genomics 2013;14;620

    PUBMED: 24034785; PMC: 3848588; DOI: 10.1186/1471-2164-14-620

  • High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.

    Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J et al.

    Genetics 2013;195;3;1141-55

    PUBMED: 24037264; PMC: 3813843; DOI: 10.1534/genetics.113.155515

  • Clinical and biological implications of driver mutations in myelodysplastic syndromes.

    Papaemmanuil E, Gerstung M, Malcovati L, Tauro S, Gundem G, Van Loo P, Yoon CJ, Ellis P, Wedge DC, Pellagatti A et al.

    Blood 2013;122;22;3616-27; quiz 3699

    PUBMED: 24030381; PMC: 3837510; DOI: 10.1182/blood-2013-08-518886

  • Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

    Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW et al.

    Science (New York, N.Y.) 2013;341;6153;1514-7

    PUBMED: 24030491; PMC: 4012302; DOI: 10.1126/science.1240578

  • GATA1-mutant clones are frequent and often unsuspected in babies with Down syndrome: identification of a population at risk of leukemia.

    Roberts I, Alford K, Hall G, Juban G, Richmond H, Norton A, Vallance G, Perkins K, Marchi E, McGowan S et al.

    Blood 2013;122;24;3908-17

    PUBMED: 24021668; PMC: 3995281; DOI: 10.1182/blood-2013-07-515148

  • Microbiology. Fighting obesity with bacteria.

    Walker AW and Parkhill J

    Science (New York, N.Y.) 2013;341;6150;1069-70

    PUBMED: 24009379; DOI: 10.1126/science.1243787

  • Platelet Genomics

    Bray,P.F., Jones,C.I., SORANZO,N. and Ouwehand,W.H.

    Platelets 2013

    DOI: 10.1016/B978-0-12-387837-3.00004-3; URL: https://dx.doi.org/10.1016/B9...78-0-12-387837-3.00004-3

  • Determinants of invasiveness beneath the capsule of the pneumococcus.

    Klugman KP, Bentley SD and McGee L

    The Journal of infectious diseases 2013;209;3;321-2

    PUBMED: 24009157; PMC: 5739876; DOI: 10.1093/infdis/jit483

  • Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum.

    Balu B, Campbell C, Sedillo J, Maher S, Singh N, Thomas P, Zhang M, Pance A, Otto TD, Rayner JC and Adams JH

    Eukaryotic cell 2013;12;9;1171-8

    PUBMED: 23813392; PMC: 3811562; DOI: 10.1128/EC.00028-13

  • Back to the future!

    Dordel J and Reuter S

    Nature reviews. Microbiology 2013;11;9;600

    PUBMED: 23949601; DOI: 10.1038/nrmicro3099

  • Best practices in bioinformatics training for life scientists.

    Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C et al.

    Briefings in bioinformatics 2013;14;5;528-37

    PUBMED: 23803301; PMC: 3771230; DOI: 10.1093/bib/bbt043

  • Cardiometabolic risk in a rural Ugandan population.

    Murphy GA, Asiki G, Young EH, Seeley J, Nsubuga RN, Sandhu MS and Kamali A

    Diabetes care 2013;36;9;e143

    PUBMED: 23970722; PMC: 3747938; DOI: 10.2337/dc13-0739

  • Community-associated MRSA from the Indian subcontinent.

    Tong SY and Kearns AM

    The Lancet. Infectious diseases 2013;13;9;734-5

    PUBMED: 23969208; DOI: 10.1016/S1473-3099(13)70231-7

  • Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase.

    Yamanishi A, Yusa K, Horie K, Tokunaga M, Kusano K, Kokubu C and Takeda J

    Genome research 2013;23;9;1462-73

    PUBMED: 23908384; PMC: 3759722; DOI: 10.1101/gr.152744.112

  • Genetic risk prediction and a 2-stage risk screening strategy for coronary heart disease.

    Tikkanen E, Havulinna AS, Palotie A, Salomaa V and Ripatti S

    Arteriosclerosis, thrombosis, and vascular biology 2013;33;9;2261-6

    PUBMED: 23599444; PMC: 4210840; DOI: 10.1161/ATVBAHA.112.301120

  • Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification.

    Pham Thanh D, Tran Vu Thieu N, Tran Thuy C, Lodén M, Tuin K, Campbell JI, Van Minh Hoang N, Voong Vinh P, Farrar JJ, Holt KE et al.

    Journal of clinical microbiology 2013;51;9;2950-8

    PUBMED: 23824765; PMC: 3754622; DOI: 10.1128/JCM.01010-13

  • Independent specialization of the human and mouse X chromosomes for the male germ line.

    Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Graves T, Auger K, Warren WC, Wilson RK and Page DC

    Nature genetics 2013;45;9;1083-7

    PUBMED: 23872635; PMC: 3758364; DOI: 10.1038/ng.2705

  • Modeling the association of space, time, and host species with variation of the HA, NA, and NS genes of H5N1 highly pathogenic avian influenza viruses isolated from birds in Romania in 2005-2007.

    Alkhamis M, Perez A, Batey N, Howard W, Baillie G, Watson S, Franz S, Focosi-Snyman R, Onita I, Cioranu R et al.

    Avian diseases 2013;57;3;612-21

    PUBMED: 24283126; PMC: 3980047; DOI: 10.1637/10494-011713-Reg.1

  • μ-Opioid receptor gene (OPRM1) polymorphism A118G: lack of association in Finnish populations with alcohol dependence or alcohol consumption.

    Rouvinen-Lagerström N, Lahti J, Alho H, Kovanen L, Aalto M, Partonen T, Silander K, Sinclair D, Räikkönen K, Eriksson JG et al.

    Alcohol and alcoholism (Oxford, Oxfordshire) 2013;48;5;519-25

    PUBMED: 23729673; PMC: 4296254; DOI: 10.1093/alcalc/agt050

  • Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

    Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G et al.

    Nature genetics 2013;45;10;1176-82

    PUBMED: 23995134; PMC: 3800747; DOI: 10.1038/ng.2744

  • Nuclear Wave1 is required for reprogramming transcription in oocytes and for normal development.

    Miyamoto K, Teperek M, Yusa K, Allen GE, Bradshaw CR and Gurdon JB

    Science (New York, N.Y.) 2013;341;6149;1002-5

    PUBMED: 23990560; PMC: 3824084; DOI: 10.1126/science.1240376

  • A meta-analysis of genome-wide association studies identifies novel variants associated with osteoarthritis of the hip.

    Evangelou E, Kerkhof HJ, Styrkarsdottir U, Ntzani EE, Bos SD, Esko T, Evans DS, Metrustry S, Panoutsopoulou K, Ramos YF et al.

    Annals of the rheumatic diseases 2013;73;12;2130-6

    PUBMED: 23989986; PMC: 4251181; DOI: 10.1136/annrheumdis-2012-203114

  • Richness of human gut microbiome correlates with metabolic markers.

    Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S et al.

    Nature 2013;500;7464;541-6

    PUBMED: 23985870; DOI: 10.1038/nature12506

  • The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.

    Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C et al.

    Genome biology 2013;14;8;R88

    PUBMED: 23985316; PMC: 4054779; DOI: 10.1186/gb-2013-14-8-r88

  • Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.

    Cross-Disorder Group of the Psychiatric Genomics Consortium, Lee SH, Ripke S, Neale BM, Faraone SV, Purcell SM, Perlis RH, Mowry BJ, Thapar A, Goddard ME et al.

    Nature genetics 2013;45;9;984-94

    PUBMED: 23933821; DOI: 10.1038/ng.2711

  • What has high-throughput sequencing ever done for us?

    Parkhill J

    Nature reviews. Microbiology 2013;11;10;664-5

    PUBMED: 23979431; DOI: 10.1038/nrmicro3112

  • Genome-wide association analysis identifies 13 new risk loci for schizophrenia.

    Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M et al.

    Nature genetics 2013;45;10;1150-9

    PUBMED: 23974872; PMC: 3827979; DOI: 10.1038/ng.2742

  • Mutational genomics for cancer pathway discovery

    De Ridder,J., Kool,J, Uren,A.G., Bot,J., De Jong,J., RUST,A.G., Berns,A., Van Lohuizen,M., ADAMS,D.J., Wessels,L. and Reinders,M.;

    Lecture Notes in Computer Science  2013;7986;35-46

    DOI: 10.1007/978-3-642-39159-0_4; URL: https://link.springer.com/chapter.../10.1007/978-3-642-39159-0_4

  • A genome-wide association study and biological pathway analysis of epilepsy prognosis in a prospective cohort of newly treated epilepsy.

    Speed D, Hoggart C, Petrovski S, Tachmazidou I, Coffey A, Jorgensen A, Eleftherohorinou H, De Iorio M, Todaro M, De T et al.

    Human molecular genetics 2013;23;1;247-58

    PUBMED: 23962720; PMC: 3857947; DOI: 10.1093/hmg/ddt403

  • MiR-210 is induced by Oct-2, regulates B cells, and inhibits autoantibody production.

    Mok Y, Schwierzeck V, Thomas DC, Vigorito E, Rayner TF, Jarvis LB, Prosser HM, Bradley A, Withers DR, Mårtensson IL et al.

    Journal of immunology (Baltimore, Md. : 1950) 2013;191;6;3037-3048

    PUBMED: 23960236; PMC: 4162006; DOI: 10.4049/jimmunol.1301289

  • Preimplantation genetic diagnosis guided by single-cell genomics.

    Van der Aa N, Zamani Esteki M, Vermeesch JR and Voet T

    Genome medicine 2013;5;8;71

    PUBMED: 23998893; PMC: 3979122; DOI: 10.1186/gm475

  • Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos.

    Armant O, März M, Schmidt R, Ferg M, Diotel N, Ertzer R, Bryne JC, Yang L, Baader I, Reischl M et al.

    Developmental biology 2013;380;2;351-62

    PUBMED: 23684812; PMC: 4351915; DOI: 10.1016/j.ydbio.2013.05.006

  • Signatures of mutational processes in human cancer.

    Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, Bignell GR, Bolli N, Borg A, Børresen-Dale AL et al.

    Nature 2013;500;7463;415-21

    PUBMED: 23945592; PMC: 3776390; DOI: 10.1038/nature12477

  • Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.

    Reuter S, Ellington MJ, Cartwright EJ, Köser CU, Török ME, Gouliouris T, Harris SR, Brown NM, Holden MT, Quail M et al.

    JAMA internal medicine 2013;173;15;1397-404

    PUBMED: 23857503; PMC: 4001082; DOI: 10.1001/jamainternmed.2013.7734

  • Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.

    Hamilton-Williams EE, Rainbow DB, Cheung J, Christensen M, Lyons PA, Peterson LB, Steward CA, Sherman LA and Wicker LS

    Mammalian genome : official journal of the International Mammalian Genome Society 2013;24;9-10;358-75

    PUBMED: 23934554; PMC: 3824839; DOI: 10.1007/s00335-013-9466-y

  • Transmission of M abscessus in patients with cystic fibrosis - Authors' reply.

    Bryant JM, Grogono DM, Parkhill J and Floto RA

    Lancet (London, England) 2013;382;9891;504

    PUBMED: 23931921; DOI: 10.1016/S0140-6736(13)61709-2

  • Cancer gene discovery: exploiting insertional mutagenesis.

    Ranzani M, Annunziato S, Adams DJ and Montini E

    Molecular cancer research : MCR 2013;11;10;1141-58

    PUBMED: 23928056; PMC: 3836224; DOI: 10.1158/1541-7786.MCR-13-0244

  • Global analysis of the sporulation pathway of Clostridium difficile.

    Fimlaid KA, Bond JP, Schutz KC, Putnam EE, Leung JM, Lawley TD and Shen A

    PLoS genetics 2013;9;8;e1003660

    PUBMED: 23950727; PMC: 3738446; DOI: 10.1371/journal.pgen.1003660

  • TM4SF20 ancestral deletion and susceptibility to a pediatric disorder of early language delay and cerebral white matter hyperintensities.

    Wiszniewski W, Hunter JV, Hanchard NA, Willer JR, Shaw C, Tian Q, Illner A, Wang X, Cheung SW, Patel A et al.

    American journal of human genetics 2013;93;2;197-210

    PUBMED: 23810381; PMC: 3738832; DOI: 10.1016/j.ajhg.2013.05.027

  • Genome-wide mutational signatures of aristolochic acid and its application as a screening tool.

    Poon SL, Pang ST, McPherson JR, Yu W, Huang KK, Guan P, Weng WH, Siew EY, Liu Y, Heng HL et al.

    Science translational medicine 2013;5;197;197ra101

    PUBMED: 23926199; DOI: 10.1126/scitranslmed.3006086

  • The effect of FTO variation on increased osteoarthritis risk is mediated through body mass index: a Mendelian randomisation study.

    Panoutsopoulou K, Metrustry S, Doherty SA, Laslett LL, Maciewicz RA, Hart DJ, Zhang W, Muir KR, Wheeler M, Cooper C et al.

    Annals of the rheumatic diseases 2013;73;12;2082-6

    PUBMED: 23921993; PMC: 4251538; DOI: 10.1136/annrheumdis-2013-203772

  • Adaptive changes of the Insig1/SREBP1/SCD1 set point help adipose tissue to cope with increased storage demands of obesity.

    Carobbio S, Hagen RM, Lelliott CJ, Slawik M, Medina-Gomez G, Tan CY, Sicard A, Atherton HJ, Barbarroja N, Bjursell M et al.

    Diabetes 2013;62;11;3697-708

    PUBMED: 23919961; PMC: 3806615; DOI: 10.2337/db12-1748

  • In search of low-frequency and rare variants affecting complex traits.

    Panoutsopoulou K, Tachmazidou I and Zeggini E

    Human molecular genetics 2013;22;R1;R16-21

    PUBMED: 23922232; PMC: 3782074; DOI: 10.1093/hmg/ddt376

  • Deletion of TOP3β, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders.

    Stoll G, Pietiläinen OPH, Linder B, Suvisaari J, Brosi C, Hennah W, Leppä V, Torniainen M, Ripatti S, Ala-Mello S et al.

    Nature neuroscience 2013;16;9;1228-1237

    PUBMED: 23912948; PMC: 3986889; DOI: 10.1038/nn.3484

  • Molecular characterization of mutant mouse strains generated from the EUCOMM/KOMP-CSD ES cell resource.

    Ryder E, Gleeson D, Sethi D, Vyas S, Miklejewska E, Dalvi P, Habib B, Cook R, Hardy M, Jhaveri K et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2013;24;7-8;286-94

    PUBMED: 23912999; PMC: 3745610; DOI: 10.1007/s00335-013-9467-x

  • The COMBREX Project: Design, Methodology, and Initial Results.

    Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A et al.

    PLoS biology 2013;11;8;e1001638

    PUBMED: 24013487; PMC: 3754883; DOI: 10.1371/journal.pbio.1001638

  • An elephantine viral problem.

    Gall A and Palser A

    Nature reviews. Microbiology 2013;11;8;512

    PUBMED: 23832239; DOI: 10.1038/nrmicro3075

  • Computational approaches to identify functional genetic variants in cancer genomes.

    Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV et al.

    Nature methods 2013;10;8;723-9

    PUBMED: 23900255; PMC: 3919555; DOI: 10.1038/nmeth.2562

  • Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

    Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC et al.

    Cell 2013;154;3;530-40

    PUBMED: 23911320; PMC: 3732390; DOI: 10.1016/j.cell.2013.07.007

  • Diversity among human non-typhoidal salmonellae isolates from Zimbabwe.

    Paglietti B, Falchi G, Mason P, Chitsatso O, Nair S, Gwanzura L, Uzzau S, Cappuccinelli P, Wain J and Rubino S

    Transactions of the Royal Society of Tropical Medicine and Hygiene 2013;107;8;487-92

    PUBMED: 23843558; DOI: 10.1093/trstmh/trt046

  • iAnn: an event sharing platform for the life sciences.

    Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J et al.

    Bioinformatics (Oxford, England) 2013;29;15;1919-21

    PUBMED: 23742982; PMC: 3712218; DOI: 10.1093/bioinformatics/btt306

  • Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chickens.

    Crooks L, Carlborg Ö, Marklund S and Johansson AM

    G3 (Bethesda, Md.) 2013;3;8;1253-60

    PUBMED: 23708300; PMC: 3737165; DOI: 10.1534/g3.113.006643

  • Metabolomic markers reveal novel pathways of ageing and early development in human populations.

    Menni C, Kastenmüller G, Petersen AK, Bell JT, Psatha M, Tsai PC, Gieger C, Schulz H, Erte I, John S et al.

    International journal of epidemiology 2013;42;4;1111-9

    PUBMED: 23838602; PMC: 3781000; DOI: 10.1093/ije/dyt094

  • Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing.

    Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, Parkhill J, Dingle KE, Bowler IC, Jolley KA and Maiden MC

    Journal of clinical microbiology 2013;51;8;2526-34

    PUBMED: 23698529; PMC: 3719633; DOI: 10.1128/JCM.00066-13

  • Use of Vitek 2 antimicrobial susceptibility profile to identify mecC in methicillin-resistant Staphylococcus aureus.

    Cartwright EJ, Paterson GK, Raven KE, Harrison EM, Gouliouris T, Kearns A, Pichon B, Edwards G, Skov RL, Larsen AR et al.

    Journal of clinical microbiology 2013;51;8;2732-4

    PUBMED: 23720794; PMC: 3719650; DOI: 10.1128/JCM.00847-13

  • A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.

    Simon MM, Greenaway S, White JK, Fuchs H, Gailus-Durner V, Wells S, Sorg T, Wong K, Bedu E, Cartwright EJ et al.

    Genome biology 2013;14;7;R82

    PUBMED: 23902802; PMC: 4053787; DOI: 10.1186/gb-2013-14-7-r82

  • A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair.

    Britton S, Coates J and Jackson SP

    The Journal of cell biology 2013;202;3;579-95

    PUBMED: 23897892; PMC: 3734090; DOI: 10.1083/jcb.201303073

  • Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat.

    Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC et al.

    Cell 2013;154;3;691-703

    PUBMED: 23890820; PMC: 3732391; DOI: 10.1016/j.cell.2013.06.040

  • Biomarkers for type 2 diabetes and impaired fasting glucose using a nontargeted metabolomics approach.

    Menni C, Fauman E, Erte I, Perry JR, Kastenmüller G, Shin SY, Petersen AK, Hyde C, Psatha M, Ward KJ et al.

    Diabetes 2013;62;12;4270-6

    PUBMED: 23884885; PMC: 3837024; DOI: 10.2337/db13-0570

  • Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974.

    Wyres KL, van Tonder A, Lambertsen LM, Hakenbeck R, Parkhill J, Bentley SD and Brueggemann AB

    BMC genomics 2013;14;500

    PUBMED: 23879707; PMC: 3726389; DOI: 10.1186/1471-2164-14-500

  • Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS).

    Luan SL, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford PR, Rycroft A, Wren BW et al.

    Veterinary microbiology 2013;166;3-4;558-66

    PUBMED: 23928120; DOI: 10.1016/j.vetmic.2013.07.008

  • Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

    White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C et al.

    Cell 2013;154;2;452-64

    PUBMED: 23870131; PMC: 3717207; DOI: 10.1016/j.cell.2013.06.022

  • Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.

    Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP and Peacock SJ

    The New England journal of medicine 2013;369;3;290-2

    PUBMED: 23863072; PMC: 3836233; DOI: 10.1056/NEJMc1215305

  • A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.

    Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium 2, Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, Su Z, Band G et al.

    Biological psychiatry 2013;75;5;386-97

    PUBMED: 23871474; PMC: 3923972; DOI: 10.1016/j.biopsych.2013.03.033

  • A sequence variant associated with sortilin-1 (SORT1) on 1p13.3 is independently associated with abdominal aortic aneurysm.

    Jones GT, Bown MJ, Gretarsdottir S, Romaine SP, Helgadottir A, Yu G, Tromp G, Norman PE, Jin C, Baas AF et al.

    Human molecular genetics 2013;22;14;2941-7

    PUBMED: 23535823; PMC: 3690970; DOI: 10.1093/hmg/ddt141

  • Bacteriotherapy for the treatment of intestinal dysbiosis caused by Clostridium difficile infection.

    Adamu BO and Lawley TD

    Current opinion in microbiology 2013;16;5;596-601

    PUBMED: 23866975; PMC: 3840269; DOI: 10.1016/j.mib.2013.06.009

  • The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.

    Hall Z, Hernández H, Marsh JA, Teichmann SA and Robinson CV

    Structure (London, England : 1993) 2013;21;8;1325-37

    PUBMED: 23850452; PMC: 3737473; DOI: 10.1016/j.str.2013.06.004

  • FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency.

    Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D, Paul YL, Walter J et al.

    Cell stem cell 2013;13;3;351-9

    PUBMED: 23850245; PMC: 3765959; DOI: 10.1016/j.stem.2013.06.004

  • Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan.

    Carss KJ, Stevens E, Foley AR, Cirak S, Riemersma M, Torelli S, Hoischen A, Willer T, van Scherpenzeel M, Moore SA et al.

    American journal of human genetics 2013;93;1;29-41

    PUBMED: 23768512; PMC: 3710768; DOI: 10.1016/j.ajhg.2013.05.009

  • Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers.

    Gao X, Yang J, Tsang JC, Ooi J, Wu D and Liu P

    Stem cell reports 2013;1;2;183-97

    PUBMED: 24052952; PMC: 3757749; DOI: 10.1016/j.stemcr.2013.06.002

  • A genetic progression model of Braf(V600E)-induced intestinal tumorigenesis reveals targets for therapeutic intervention.

    Rad R, Cadiñanos J, Rad L, Varela I, Strong A, Kriegl L, Constantino-Casas F, Eser S, Hieber M, Seidler B et al.

    Cancer cell 2013;24;1;15-29

    PUBMED: 23845441; PMC: 3706745; DOI: 10.1016/j.ccr.2013.05.014

  • Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease.

    Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C and Kehrer-Sawatzki H

    Human genetics 2013;132;10;1077-130

    PUBMED: 23820649; PMC: 3778950; DOI: 10.1007/s00439-013-1331-2

  • The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.

    Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J et al.

    Nature genetics 2013;45;7;776-83

    PUBMED: 23749191; DOI: 10.1038/ng.2657

  • Consequences of whiB7 (Rv3197A) mutations in Beijing genotype isolates of the Mycobacterium tuberculosis complex.

    Köser CU, Bryant JM, Parkhill J and Peacock SJ

    Antimicrobial agents and chemotherapy 2013;57;7;3461

    PUBMED: 23761426; PMC: 3697354; DOI: 10.1128/AAC.00626-13

  • Culture-free club.

    Bryant JM

    Nature reviews. Microbiology 2013;11;7;434

    PUBMED: 23748338; DOI: 10.1038/nrmicro3052

  • Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.

    Cousminer DL, Berry DJ, Timpson NJ, Ang W, Thiering E, Byrne EM, Taal HR, Huikari V, Bradfield JP, Kerkhof M et al.

    Human molecular genetics 2013;22;13;2735-47

    PUBMED: 23449627; PMC: 3674797; DOI: 10.1093/hmg/ddt104

  • Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter.

    Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MC, Parkhill J and Falush D

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;29;11923-7

    PUBMED: 23818615; PMC: 3718156; DOI: 10.1073/pnas.1305559110

  • Identification of the zebrafish maternal and paternal transcriptomes.

    Harvey SA, Sealy I, Kettleborough R, Fenyes F, White R, Stemple D and Smith JC

    Development (Cambridge, England) 2013;140;13;2703-10

    PUBMED: 23720042; PMC: 3678340; DOI: 10.1242/dev.095091

  • Molecular Analysis of an Outbreak of Lethal Postpartum Sepsis Caused by Streptococcus pyogenes.

    Turner CE, Dryden M, Holden MT, Davies FJ, Lawrenson RA, Farzaneh L, Bentley SD, Efstratiou A and Sriskandan S

    Journal of clinical microbiology 2013;51;7;2089-95

    PUBMED: 23616448; PMC: 3697669; DOI: 10.1128/JCM.00679-13

  • Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks.

    Harris SR, Török ME, Cartwright EJ, Quail MA, Peacock SJ and Parkhill J

    Nature biotechnology 2013;31;7;592-4

    PUBMED: 23839141; PMC: 4335133; DOI: 10.1038/nbt.2616

  • Special focus: bioinformatics.

    Nawrocki EP and Burge SW

    RNA biology 2013;10;7;1160

    PUBMED: 23948768; PMC: 3849163; DOI: 10.4161/rna.25606

  • Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

    Gonzàlez-Porta M, Frankish A, Rung J, Harrow J and Brazma A

    Genome biology 2013;14;7;R70

    PUBMED: 23815980; PMC: 4053754; DOI: 10.1186/gb-2013-14-7-r70

  • Empirical research on the ethics of genomic research.

    Middleton A, Parker M, Wright CF, Bragin E, Hurles ME and DDD Study

    American journal of medical genetics. Part A 2013;161A;8;2099-101

    PUBMED: 23813698; PMC: 3884757; DOI: 10.1002/ajmg.a.36067

  • NDUFA4 mutations underlie dysfunction of a cytochrome c oxidase subunit linked to human neurological disease.

    Pitceathly RD, Rahman S, Wedatilake Y, Polke JM, Cirak S, Foley AR, Sailer A, Hurles ME, Stalker J, Hargreaves I et al.

    Cell reports 2013;3;6;1795-805

    PUBMED: 23746447; PMC: 3701321; DOI: 10.1016/j.celrep.2013.05.005

  • Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes.

    Rashid M, Robles-Espinoza CD, Rust AG and Adams DJ

    Bioinformatics (Oxford, England) 2013;29;17;2208-10

    PUBMED: 23803469; PMC: 3740632; DOI: 10.1093/bioinformatics/btt371

  • Genome-wide meta-analysis identifies new susceptibility loci for migraine.

    Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G et al.

    Nature genetics 2013;45;8;912-917

    PUBMED: 23793025; PMC: 4041123; DOI: 10.1038/ng.2676

  • The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.

    Li JW, Bolser D, Manske M, Giorgi FM, Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D and Schneider MV

    Briefings in bioinformatics 2013;14;5;548-55

    PUBMED: 23793381; PMC: 3771235; DOI: 10.1093/bib/bbt045

  • GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.

    Rietveld CA, Medland SE, Derringer J, Yang J, Esko T, Martin NW, Westra HJ, Shakhbazov K, Abdellaoui A, Agrawal A et al.

    Science (New York, N.Y.) 2013;340;6139;1467-71

    PUBMED: 23722424; PMC: 3751588; DOI: 10.1126/science.1235488

  • Hospital outbreak of Middle East respiratory syndrome coronavirus.

    Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, Cummings DA, Alabdullatif ZN, Assad M, Almulhim A, Makhdoom H et al.

    The New England journal of medicine 2013;369;5;407-16

    PUBMED: 23782161; PMC: 4029105; DOI: 10.1056/NEJMoa1306742

  • Rare variants in single-minded 1 (SIM1) are associated with severe obesity.

    Ramachandrappa S, Raimondo A, Cali AM, Keogh JM, Henning E, Saeed S, Thompson A, Garg S, Bochukova EG, Brage S et al.

    The Journal of clinical investigation 2013;123;7;3042-50

    PUBMED: 23778139; PMC: 3696558; DOI: 10.1172/JCI68016

  • Whole exome sequencing of adenoid cystic carcinoma.

    Stephens PJ, Davies HR, Mitani Y, Van Loo P, Shlien A, Tarpey PS, Papaemmanuil E, Cheverton A, Bignell GR, Butler AP et al.

    The Journal of clinical investigation 2013;123;7;2965-8

    PUBMED: 23778141; PMC: 3999050; DOI: 10.1172/JCI67201

  • Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma.

    Tarpey PS, Behjati S, Cooke SL, Van Loo P, Wedge DC, Pillay N, Marshall J, O'Meara S, Davies H, Nik-Zainal S et al.

    Nature genetics 2013;45;8;923-6

    PUBMED: 23770606; PMC: 3743157; DOI: 10.1038/ng.2668

  • The agr locus regulates virulence and colonization genes in Clostridium difficile 027.

    Martin MJ, Clare S, Goulding D, Faulds-Pain A, Barquist L, Browne HP, Pettit L, Dougan G, Lawley TD and Wren BW

    Journal of bacteriology 2013;195;16;3672-81

    PUBMED: 23772065; PMC: 3754575; DOI: 10.1128/JB.00473-13

  • A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping.

    Wei W, Ayub Q, Xue Y and Tyler-Smith C

    Forensic science international. Genetics 2013;7;6;568-572

    PUBMED: 23768990; PMC: 3820021; DOI: 10.1016/j.fsigen.2013.03.014

  • Negligible impact of rare autoimmune-locus coding-region variants on missing heritability.

    Hunt KA, Mistry V, Bockett NA, Ahmad T, Ban M, Barker JN, Barrett JC, Blackburn H, Brand O, Burren O et al.

    Nature 2013;498;7453;232-5

    PUBMED: 23698362; PMC: 3736321; DOI: 10.1038/nature12170

  • INMEX--a web-based tool for integrative meta-analysis of expression data.

    Xia J, Fjell CD, Mayer ML, Pena OM, Wishart DS and Hancock RE

    Nucleic acids research 2013;41;Web Server issue;W63-70

    PUBMED: 23766290; PMC: 3692077; DOI: 10.1093/nar/gkt338

  • Genome-wide association study on detailed profiles of smoking behavior and nicotine dependence in a twin sample.

    Loukola A, Wedenoja J, Keskitalo-Vuokko K, Broms U, Korhonen T, Ripatti S, Sarin AP, Pitkäniemi J, He L, Häppölä A et al.

    Molecular psychiatry 2013

    PUBMED: 23752247; DOI: 10.1038/mp.2013.72

  • Unusual features in organisation of capsular polysaccharide-related genes of C. jejuni strain X.

    Karlyshev AV, Quail MA, Parkhill J and Wren BW

    Gene 2013;522;1;37-45

    PUBMED: 23562723; DOI: 10.1016/j.gene.2013.03.087

  • Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system.

    Collins C, Keane TM, Turner DJ, O'Keeffe G, Fitzpatrick DA and Doyle S

    Journal of proteome research 2013;12;6;2552-70

    PUBMED: 23656496; PMC: 3679558; DOI: 10.1021/pr301131t

  • Detecting and characterizing genomic signatures of positive selection in global populations.

    Liu X, Ong RT, Pillai EN, Elzein AM, Small KS, Clark TG, Kwiatkowski DP and Teo YY

    American journal of human genetics 2013;92;6;866-81

    PUBMED: 23731540; PMC: 3675259; DOI: 10.1016/j.ajhg.2013.04.021

  • Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations.

    Bashford-Rogers RJ, Palser AL, Huntly BJ, Rance R, Vassiliou GS, Follows GA and Kellam P

    Genome research 2013;23;11;1874-84

    PUBMED: 23742949; PMC: 3814887; DOI: 10.1101/gr.154815.113

  • Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.

    Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, Kilpeläinen TO, Esko T, Mägi R, Li S et al.

    PLoS genetics 2013;9;6;e1003500

    PUBMED: 23754948; PMC: 3674993; DOI: 10.1371/journal.pgen.1003500

  • The sex-specific associations of the aromatase gene with Alzheimer's disease and its interaction with IL10 in the Epistasis Project.

    Medway C, Combarros O, Cortina-Borja M, Butler HT, Ibrahim-Verbaas CA, de Bruijn RF, Koudstaal PJ, van Duijn CM, Ikram MA, Mateo I et al.

    European journal of human genetics : EJHG 2013;22;2;216-20

    PUBMED: 23736221; PMC: 3895636; DOI: 10.1038/ejhg.2013.116

  • Genetic variants associated with warfarin dose in African-American individuals: a genome-wide association study.

    Perera MA, Cavallari LH, Limdi NA, Gamazon ER, Konkashbaev A, Daneshjou R, Pluzhnikov A, Crawford DC, Wang J, Liu N et al.

    Lancet (London, England) 2013;382;9894;790-6

    PUBMED: 23755828; PMC: 3759580; DOI: 10.1016/S0140-6736(13)60681-9

  • A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.

    Scally A, Yngvadottir B, Xue Y, Ayub Q, Durbin R and Tyler-Smith C

    PloS one 2013;8;6;e65066

    PUBMED: 23750230; PMC: 3672199; DOI: 10.1371/journal.pone.0065066

  • The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.

    Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D et al.

    Nature genetics 2013;45;6;701-6

    PUBMED: 23624526; PMC: 4000948; DOI: 10.1038/ng.2615

  • Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis.

    Hinks A, Cobb J, Marion MC, Prahalad S, Sudman M, Bowes J, Martin P, Comeau ME, Sajuthi S, Andrews R et al.

    Nature genetics 2013;45;6;664-9

    PUBMED: 23603761; PMC: 3673707; DOI: 10.1038/ng.2614

  • Evaluation of the genetic overlap between osteoarthritis with body mass index and height using genome-wide association scan data.

    Elliott KS, Chapman K, Day-Williams A, Panoutsopoulou K, Southam L, Lindgren CM, Arden N, Aslam N, Birrell F, Carluke I et al.

    Annals of the rheumatic diseases 2013;72;6;935-41

    PUBMED: 22956599; PMC: 3664369; DOI: 10.1136/annrheumdis-2012-202081

  • High-fat feeding rapidly induces obesity and lipid derangements in C57BL/6N mice.

    Podrini C, Cambridge EL, Lelliott CJ, Carragher DM, Estabel J, Gerdin AK, Karp NA, Scudamore CL, Sanger Mouse Genetics Project, Ramirez-Solis R and White JK

    Mammalian genome : official journal of the International Mammalian Genome Society 2013;24;5-6;240-51

    PUBMED: 23712496; PMC: 3685703; DOI: 10.1007/s00335-013-9456-0

  • Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity.

    Davies MR, Broadbent SE, Harris SR, Thomson NR and van der Woude MW

    PLoS genetics 2013;9;6;e1003568

    PUBMED: 23818865; PMC: 3688519; DOI: 10.1371/journal.pgen.1003568

  • Human melioidosis, Malawi, 2011.

    Katangwe T, Purcell J, Bar-Zeev N, Denis B, Montgomery J, Alaerts M, Heyderman RS, Dance DA, Kennedy N, Feasey N and Moxon CA

    Emerging infectious diseases 2013;19;6;981-4

    PUBMED: 23735189; PMC: 3713813; DOI: 10.3201/eid1906.120717

  • Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.

    den Hoed M, Eijgelsheim M, Esko T, Brundel BJ, Peal DS, Evans DM, Nolte IM, Segrè AV, Holm H, Handsaker RE et al.

    Nature genetics 2013;45;6;621-31

    PUBMED: 23583979; PMC: 3696959; DOI: 10.1038/ng.2610

  • Identification of nine new susceptibility loci for testicular cancer, including variants near DAZL and PRDM14.

    Ruark E, Seal S, McDonald H, Zhang F, Elliot A, Lau K, Perdeaux E, Rapley E, Eeles R, Peto J et al.

    Nature genetics 2013;45;6;686-9

    PUBMED: 23666240; PMC: 3680037; DOI: 10.1038/ng.2635

  • Meander: visually exploring the structural variome using space-filling curves.

    Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y and Aerts J

    Nucleic acids research 2013;41;11;e118

    PUBMED: 23605045; PMC: 3675473; DOI: 10.1093/nar/gkt254

  • Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee.

    Coscolla M, Lewin A, Metzger S, Maetz-Rennsing K, Calvignac-Spencer S, Nitsche A, Dabrowski PW, Radonic A, Niemann S, Parkhill J et al.

    Emerging infectious diseases 2013;19;6;969-76

    PUBMED: 23735084; PMC: 3713819; DOI: 10.3201/eid1906.121012

  • The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes.

    Steward CA, Gonzalez JM, Trevanion S, Sheppard D, Kerry G, Gilbert JG, Wicker LS, Rogers J and Harrow JL

    Database : the journal of biological databases and curation 2013;2013;bat032

    PUBMED: 23729657; PMC: 3668384; DOI: 10.1093/database/bat032

  • Global properties and functional complexity of human gene regulatory variation.

    Gaffney DJ

    PLoS genetics 2013;9;5;e1003501

    PUBMED: 23737752; PMC: 3667745; DOI: 10.1371/journal.pgen.1003501

  • Global analysis of apicomplexan protein S-acyl transferases reveals an enzyme essential for invasion.

    Frénal K, Tay CL, Mueller C, Bushell ES, Jia Y, Graindorge A, Billker O, Rayner JC and Soldati-Favre D

    Traffic (Copenhagen, Denmark) 2013;14;8;895-911

    PUBMED: 23638681; PMC: 3813974; DOI: 10.1111/tra.12081

  • Genomic triumph meets clinical reality.

    Ayub Q, Xue Y and Tyler-Smith C

    Genome biology 2013;14;5;307

    PUBMED: 23714135; PMC: 4054008; DOI: 10.1186/gb-2013-14-5-307

  • REAPR: a universal tool for genome assembly evaluation.

    Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M and Otto TD

    Genome biology 2013;14;5;R47

    PUBMED: 23710727; PMC: 3798757; DOI: 10.1186/gb-2013-14-5-r47

  • Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

    Rat Genome Sequencing and Mapping Consortium, Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M et al.

    Nature genetics 2013;45;7;767-75

    PUBMED: 23708188; PMC: 3821058; DOI: 10.1038/ng.2644

  • KAT5 tyrosine phosphorylation couples chromatin sensing to ATM signalling.

    Kaidi A and Jackson SP

    Nature 2013;498;7452;70-4

    PUBMED: 23708966; PMC: 3859897; DOI: 10.1038/nature12201

  • Genomic analysis of a novel spontaneous albino C57BL/6N mouse strain.

    Ryder E, Wong K, Gleeson D, Keane TM, Sethi D, Vyas S, Wardle-Jones H, Bussell JN, Houghton R, Salisbury J et al.

    Genesis (New York, N.Y. : 2000) 2013;51;7;523-8

    PUBMED: 23620107; PMC: 3799019; DOI: 10.1002/dvg.22398

  • Imputation-based meta-analysis of severe malaria in three African populations.

    Band G, Le QS, Jostins L, Pirinen M, Kivinen K, Jallow M, Sisay-Joof F, Bojang K, Pinder M, Sirugo G et al.

    PLoS genetics 2013;9;5;e1003509

    PUBMED: 23717212; PMC: 3662650; DOI: 10.1371/journal.pgen.1003509

  • Dnmt2-dependent methylomes lack defined DNA methylation patterns.

    Raddatz G, Guzzardo PM, Olova N, Fantappié MR, Rampp M, Schaefer M, Reik W, Hannon GJ and Lyko F

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;21;8627-31

    PUBMED: 23641003; PMC: 3666705; DOI: 10.1073/pnas.1306723110

  • Presynaptic maturation in auditory hair cells requires a critical period of sensory-independent spiking activity.

    Johnson SL, Kuhn S, Franz C, Ingham N, Furness DN, Knipper M, Steel KP, Adelman JP, Holley MC and Marcotti W

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;21;8720-5

    PUBMED: 23650376; PMC: 3666720; DOI: 10.1073/pnas.1219578110

  • Activation of the B cell antigen receptor triggers reactivation of latent Kaposi's sarcoma-associated herpesvirus in B cells.

    Kati S, Tsao EH, Günther T, Weidner-Glunde M, Rothämel T, Grundhoff A, Kellam P and Schulz TF

    Journal of virology 2013;87;14;8004-16

    PUBMED: 23678173; PMC: 3700181; DOI: 10.1128/JVI.00506-13

  • Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates.

    Ning J, Otto TD, Pfander C, Schwach F, Brochet M, Bushell E, Goulding D, Sanders M, Lefebvre PA, Pei J et al.

    Genes & development 2013;27;10;1198-215

    PUBMED: 23699412; PMC: 3672651; DOI: 10.1101/gad.212746.112

  • Structural and functional annotation of the porcine immunome.

    Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H, Mann KM, Sang Y, Zhang J, Carvalho-Silva D, Hunt T et al.

    BMC genomics 2013;14;332

    PUBMED: 23676093; PMC: 3658956; DOI: 10.1186/1471-2164-14-332

  • Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors.

    Klijn C, Koudijs MJ, Kool J, ten Hoeve J, Boer M, de Moes J, Akhtar W, van Miltenburg M, Vendel-Zwaagstra A, Reinders MJ et al.

    PloS one 2013;8;5;e62113

    PUBMED: 23690930; PMC: 3653918; DOI: 10.1371/journal.pone.0062113

  • Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses.

    Woods S, Coghlan A, Rivers D, Warnecke T, Jeffries SJ, Kwon T, Rogers A, Hurst LD and Ahringer J

    PLoS genetics 2013;9;5;e1003330

    PUBMED: 23675306; PMC: 3649981; DOI: 10.1371/journal.pgen.1003330

  • PhenoDigm: analyzing curated annotations to associate animal models with human diseases.

    Smedley D, Oellrich A, Köhler S, Ruef B, Sanger Mouse Genetics Project, Westerfield M, Robinson P, Lewis S and Mungall C

    Database : the journal of biological databases and curation 2013;2013;bat025

    PUBMED: 23660285; PMC: 3649640; DOI: 10.1093/database/bat025

  • The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication.

    John SP, Chin CR, Perreira JM, Feeley EM, Aker AM, Savidis G, Smith SE, Elia AE, Everitt AR, Vora M et al.

    Journal of virology 2013;87;14;7837-52

    PUBMED: 23658454; PMC: 3700195; DOI: 10.1128/JVI.00481-13

  • Population genomics of post-vaccine changes in pneumococcal epidemiology.

    Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP and Lipsitch M

    Nature genetics 2013;45;6;656-63

    PUBMED: 23644493; PMC: 3725542; DOI: 10.1038/ng.2625

  • Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses.

    Illingworth CJ, Parts L, Bergström A, Liti G and Mustonen V

    PloS one 2013;8;5;e62266

    PUBMED: 23658715; PMC: 3642125; DOI: 10.1371/journal.pone.0062266

  • A blood pressure genetic risk score is a significant predictor of incident cardiovascular events in 32,669 individuals.

    Havulinna AS, Kettunen J, Ukkola O, Osmond C, Eriksson JG, Kesäniemi YA, Jula A, Peltonen L, Kontula K, Salomaa V and Newton-Cheh C

    Hypertension 2013;61;5;987-94

    PUBMED: 23509078; PMC: 3648219; DOI: 10.1161/HYPERTENSIONAHA.111.00649

  • The intermediate filament protein, vimentin, is a regulator of NOD2 activity.

    Stevens C, Henderson P, Nimmo ER, Soares DC, Dogan B, Simpson KW, Barrett JC, International Inflammatory Bowel Disease Genetics Consortium, Wilson DC and Satsangi J

    Gut 2013;62;5;695-707

    PUBMED: 22684479; PMC: 4225453; DOI: 10.1136/gutjnl-2011-301775

  • The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

    Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS et al.

    Genome research 2013;23;5;749-61

    PUBMED: 23478400; PMC: 3638132; DOI: 10.1101/gr.148718.112

  • Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening.

    Adams D, Baldock R, Bhattacharya S, Copp AJ, Dickinson M, Greene ND, Henkelman M, Justice M, Mohun T, Murray SA et al.

    Disease models & mechanisms 2013;6;3;571-9

    PUBMED: 23519032; PMC: 3634642; DOI: 10.1242/dmm.011833

  • Cancer of mice and men: old twists and new tails.

    van der Weyden L and Adams DJ

    The Journal of pathology 2013;230;1;4-16

    PUBMED: 23436574; DOI: 10.1002/path.4184

  • Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.

    Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M, Naghra H, Cotton JA, Berriman M, Britton C and Gilleard JS

    International journal for parasitology 2013;43;6;465-75

    PUBMED: 23416426; DOI: 10.1016/j.ijpara.2012.12.011

  • Clonal analyses reveal associations of JAK2V617F homozygosity with hematologic features, age and gender in polycythemia vera and essential thrombocythemia.

    Godfrey AL, Chen E, Pagano F, Silber Y, Campbell PJ and Green AR

    Haematologica 2013;98;5;718-21

    PUBMED: 23633544; PMC: 3640115; DOI: 10.3324/haematol.2012.079129

  • Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney Disease.

    Schmidts M, Frank V, Eisenberger T, Al Turki S, Bizet AA, Antony D, Rix S, Decker C, Bachmann N, Bald M et al.

    Human mutation 2013;34;5;714-24

    PUBMED: 23418020; PMC: 4226634; DOI: 10.1002/humu.22294

  • Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.

    Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A, Guan Y, Pillay D et al.

    Emerging infectious diseases 2013;19;5;736-42B

    PUBMED: 23693015; PMC: 3647518; DOI: 10.3201/eid1905.130057

  • Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India.

    Saxena R, Saleheen D, Been LF, Garavito ML, Braun T, Bjonnes A, Young R, Ho WK, Rasheed A, Frossard P et al.

    Diabetes 2013;62;5;1746-55

    PUBMED: 23300278; PMC: 3636649; DOI: 10.2337/db12-1077

  • Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake.

    Tanaka T, Ngwa JS, van Rooij FJ, Zillikens MC, Wojczynski MK, Frazier-Wood AC, Houston DK, Kanoni S, Lemaitre RN, Luan J et al.

    The American journal of clinical nutrition 2013;97;6;1395-402

    PUBMED: 23636237; PMC: 3652928; DOI: 10.3945/ajcn.112.052183

  • Microbial genomes as cheat sheets.

    Bennett HM

    Nature reviews. Microbiology 2013;11;5;302

    PUBMED: 23563106; DOI: 10.1038/nrmicro3014

  • Non dominant-negative KCNJ2 gene mutations leading to Andersen-Tawil syndrome with an isolated cardiac phenotype.

    Limberg MM, Zumhagen S, Netter MF, Coffey AJ, Grace A, Rogers J, Böckelmann D, Rinné S, Stallmeyer B, Decher N and Schulze-Bahr E

    Basic research in cardiology 2013;108;3;353

    PUBMED: 23644778; DOI: 10.1007/s00395-013-0353-1

  • Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties.

    Menden MP, Iorio F, Garnett M, McDermott U, Benes CH, Ballester PJ and Saez-Rodriguez J

    PloS one 2013;8;4;e61318

    PUBMED: 23646105; PMC: 3640019; DOI: 10.1371/journal.pone.0061318

  • EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

    Fischer A, Illingworth CJ, Campbell PJ and Mustonen V

    Genome biology 2013;14;4;R39

    PUBMED: 23628380; PMC: 3663107; DOI: 10.1186/gb-2013-14-4-r39

  • Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.

    Casado P, Alcolea MP, Iorio F, Rodríguez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S and Cutillas PR

    Genome biology 2013;14;4;R37

    PUBMED: 23628362; PMC: 4054101; DOI: 10.1186/gb-2013-14-4-r37

  • Single-cell paired-end genome sequencing reveals structural variation per cell cycle.

    Voet T, Kumar P, Van Loo P, Cooke SL, Marshall J, Lin ML, Zamani Esteki M, Van der Aa N, Mateiu L, McBride DJ et al.

    Nucleic acids research 2013;41;12;6119-38

    PUBMED: 23630320; PMC: 3695511; DOI: 10.1093/nar/gkt345

  • Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.

    Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P, Suon S, Sreng S et al.

    Nature genetics 2013;45;6;648-55

    PUBMED: 23624527; PMC: 3807790; DOI: 10.1038/ng.2624

  • Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis.

    Liu JZ, Hov JR, Folseraas T, Ellinghaus E, Rushbrook SM, Doncheva NT, Andreassen OA, Weersma RK, Weismüller TJ, Eksteen B et al.

    Nature genetics 2013;45;6;670-5

    PUBMED: 23603763; PMC: 3667736; DOI: 10.1038/ng.2616

  • Olfaction and olfactory-mediated behaviour in psychiatric disease models.

    Huckins LM, Logan DW and Sánchez-Andrade G

    Cell and tissue research 2013;354;1;69-80

    PUBMED: 23604803; DOI: 10.1007/s00441-013-1617-7

  • The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains.

    Takada T, Ebata T, Noguchi H, Keane TM, Adams DJ, Narita T, Shin-I T, Fujisawa H, Toyoda A, Abe K et al.

    Genome research 2013;23;8;1329-38

    PUBMED: 23604024; PMC: 3730106; DOI: 10.1101/gr.156497.113

  • The African coelacanth genome provides insights into tetrapod evolution.

    Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N et al.

    Nature 2013;496;7445;311-6

    PUBMED: 23598338; PMC: 3633110; DOI: 10.1038/nature12027

  • Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture.

    Conte N, Varela I, Grove C, Manes N, Yusa K, Moreno T, Segonds-Pichon A, Bench A, Gudgin E, Herman B et al.

    Leukemia 2013;27;9;1820-5

    PUBMED: 23702683; PMC: 3768109; DOI: 10.1038/leu.2013.117

  • FOXP2 targets show evidence of positive selection in European populations.

    Ayub Q, Yngvadottir B, Chen Y, Xue Y, Hu M, Vernes SC, Fisher SE and Tyler-Smith C

    American journal of human genetics 2013;92;5;696-706

    PUBMED: 23602712; PMC: 3644635; DOI: 10.1016/j.ajhg.2013.03.019

  • A systematic genome-wide analysis of zebrafish protein-coding gene function.

    Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ et al.

    Nature 2013;496;7446;494-7

    PUBMED: 23594742; PMC: 3743023; DOI: 10.1038/nature11992

  • DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis.

    Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K, Campbell PJ, Rada C, Stratton MR and Neuberger MS

    eLife 2013;2;e00534

    PUBMED: 23599896; PMC: 3628087; DOI: 10.7554/eLife.00534

  • Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    Wilming LG, Hart EA, Coggill PC, Horton R, Gilbert JG, Clee C, Jones M, Lloyd C, Palmer S, Sims S et al.

    Database : the journal of biological databases and curation 2013;2013;bat011

    PUBMED: 23589541; PMC: 3626023; DOI: 10.1093/database/bat011

  • Imputation of rare variants in next-generation association studies.

    Asimit JL and Zeggini E

    Human heredity 2013;74;3-4;196-204

    PUBMED: 23594497; PMC: 3954458; DOI: 10.1159/000345602

  • Rare variant association testing for next-generation sequencing data via hierarchical clustering.

    Tachmazidou I, Morris A and Zeggini E

    Human heredity 2013;74;3-4;165-71

    PUBMED: 23594494; PMC: 3668801; DOI: 10.1159/000346022

  • Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.

    Paul DS, Albers CA, Rendon A, Voss K, Stephens J, HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH and Deloukas P

    Genome research 2013;23;7;1130-41

    PUBMED: 23570689; PMC: 3698506; DOI: 10.1101/gr.155127.113

  • Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria.

    Sundararaman SA, Liu W, Keele BF, Learn GH, Bittinger K, Mouacha F, Ahuka-Mundeke S, Manske M, Sherrill-Mix S, Li Y et al.

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;17;7020-5

    PUBMED: 23569255; PMC: 3637760; DOI: 10.1073/pnas.1305201110

  • Tailoring the models of transcription.

    Pance A

    International journal of molecular sciences 2013;14;4;7583-97

    PUBMED: 23567272; PMC: 3645704; DOI: 10.3390/ijms14047583

  • Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.

    Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR et al.

    Nature genetics 2013;45;5;501-12

    PUBMED: 23563607; PMC: 3973018; DOI: 10.1038/ng.2606

  • Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity.

    Wheeler E, Huang N, Bochukova EG, Keogh JM, Lindsay S, Garg S, Henning E, Blackburn H, Loos RJ, Wareham NJ et al.

    Nature genetics 2013;45;5;513-7

    PUBMED: 23563609; PMC: 4106235; DOI: 10.1038/ng.2607

  • SMIM1 underlies the Vel blood group and influences red blood cell traits.

    Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S et al.

    Nature genetics 2013;45;5;542-545

    PUBMED: 23563608; PMC: 4179282; DOI: 10.1038/ng.2603

  • Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus.

    Baker KS, Leggett RM, Bexfield NH, Alston M, Daly G, Todd S, Tachedjian M, Holmes CE, Crameri S, Wang LF et al.

    Virology 2013;441;2;95-106

    PUBMED: 23562481; PMC: 3667569; DOI: 10.1016/j.virol.2013.03.014

  • A genome-wide association study of depressive symptoms.

    Hek K, Demirkan A, Lahti J, Terracciano A, Teumer A, Cornelis MC, Amin N, Bakshis E, Baumert J, Ding J et al.

    Biological psychiatry 2013;73;7;667-78

    PUBMED: 23290196; PMC: 3845085; DOI: 10.1016/j.biopsych.2012.09.033

  • Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals.

    Chaudhuri RR, Morgan E, Peters SE, Pleasance SJ, Hudson DL, Davies HM, Wang J, van Diemen PM, Buckley AM, Bowen AJ et al.

    PLoS genetics 2013;9;4;e1003456

    PUBMED: 23637626; PMC: 3630085; DOI: 10.1371/journal.pgen.1003456

  • Cooperativity of imprinted genes inactivated by acquired chromosome 20q deletions.

    Aziz A, Baxter EJ, Edwards C, Cheong CY, Ito M, Bench A, Kelley R, Silber Y, Beer PA, Chng K et al.

    The Journal of clinical investigation 2013;123;5;2169-82

    PUBMED: 23543057; PMC: 3635733; DOI: 10.1172/JCI66113

  • Identification of seven loci affecting mean telomere length and their association with disease.

    Codd V, Nelson CP, Albrecht E, Mangino M, Deelen J, Buxton JL, Hottenga JJ, Fischer K, Esko T, Surakka I et al.

    Nature genetics 2013;45;4;422-7, 427e1-2

    PUBMED: 23535734; PMC: 4006270; DOI: 10.1038/ng.2528

  • Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study.

    Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reacher M, Haworth CS, Curran MD, Harris SR et al.

    Lancet (London, England) 2013;381;9877;1551-60

    PUBMED: 23541540; PMC: 3664974; DOI: 10.1016/S0140-6736(13)60632-7

  • Automatic event detection within thrombus formation based on integer programming

    Peter,L., Pauly,O., Jansen,S.B.G., Smethurst,P.A., Ouwehand,W.H. and Navab,N.

    Lecture Notes in Computer Science  2013;7766;215-24

    DOI: 10.1007/978-3-642-36620-8_21; URL: https://link.springer.com/chapter.../10.1007%2F978-3-642-36620-8_21

  • Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.

    Seth-Smith HM, Harris SR, Skilton RJ, Radebe FM, Golparian D, Shipitsyna E, Duy PT, Scott P, Cutcliffe LT, O'Neill C et al.

    Genome research 2013;23;5;855-66

    PUBMED: 23525359; PMC: 3638141; DOI: 10.1101/gr.150037.112

  • Bacterial genomes in epidemiology--present and future.

    Croucher NJ, Harris SR, Grad YH and Hanage WP

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120202

    PUBMED: 23382424; PMC: 3678326; DOI: 10.1098/rstb.2012.0202

  • Go retro and get a GRIP.

    Wong K, Adams DJ and Keane TM

    Genome biology 2013;14;3;108

    PUBMED: 23514103; PMC: 3663096; DOI: 10.1186/gb-2013-14-3-108

  • Deciphering the Mechanisms of Developmental Disorders (DMDD): a new programme for phenotyping embryonic lethal mice.

    Mohun T, Adams DJ, Baldock R, Bhattacharya S, Copp AJ, Hemberger M, Houart C, Hurles ME, Robertson E, Smith JC et al.

    Disease models & mechanisms 2013;6;3;562-6

    PUBMED: 23519034; PMC: 3634640; DOI: 10.1242/dmm.011957

  • The DOT1L rs12982744 polymorphism is associated with osteoarthritis of the hip with genome-wide statistical significance in males.

    Evangelou E, Valdes AM, Castano-Betancourt MC, Doherty M, Doherty S, Esko T, Ingvarsson T, Ioannidis JP, Kloppenburg M, Metspalu A et al.

    Annals of the rheumatic diseases 2013;72;7;1264-5

    PUBMED: 23505243; PMC: 3686326; DOI: 10.1136/annrheumdis-2012-203182

  • Comparative study of transcriptome profiles of mechanical- and skin-transformed Schistosoma mansoni schistosomula.

    Protasio AV, Dunne DW and Berriman M

    PLoS neglected tropical diseases 2013;7;3;e2091

    PUBMED: 23516644; PMC: 3597483; DOI: 10.1371/journal.pntd.0002091

  • The genomes of four tapeworm species reveal adaptations to parasitism.

    Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E et al.

    Nature 2013;496;7443;57-63

    PUBMED: 23485966; PMC: 3964345; DOI: 10.1038/nature12031

  • Mcph1-deficient mice reveal a role for MCPH1 in otitis media.

    Chen J, Ingham N, Clare S, Raisen C, Vancollie VE, Ismail O, McIntyre RE, Tsang SH, Mahajan VB, Dougan G et al.

    PloS one 2013;8;3;e58156

    PUBMED: 23516444; PMC: 3596415; DOI: 10.1371/journal.pone.0058156

  • A powerful molecular synergy between mutant Nucleophosmin and Flt3-ITD drives acute myeloid leukemia in mice.

    Mupo A, Celani L, Dovey O, Cooper JL, Grove C, Rad R, Sportoletti P, Falini B, Bradley A and Vassiliou GS

    Leukemia 2013;27;9;1917-20

    PUBMED: 23478666; PMC: 3768110; DOI: 10.1038/leu.2013.77

  • Mutations in B3GALNT2 cause congenital muscular dystrophy and hypoglycosylation of α-dystroglycan.

    Stevens E, Carss KJ, Cirak S, Foley AR, Torelli S, Willer T, Tambunan DE, Yau S, Brodd L, Sewry CA et al.

    American journal of human genetics 2013;92;3;354-65

    PUBMED: 23453667; PMC: 3591840; DOI: 10.1016/j.ajhg.2013.01.016

  • A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.

    Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J and Gardner PP

    Nucleic acids research 2013;41;8;4549-64

    PUBMED: 23470992; PMC: 3632133; DOI: 10.1093/nar/gkt148

  • The role of high-throughput technologies in clinical cancer genomics.

    Idris SF, Ahmad SS, Scott MA, Vassiliou GS and Hadfield J

    Expert review of molecular diagnostics 2013;13;2;167-81

    PUBMED: 23477557; DOI: 10.1586/erm.13.1

  • Examination of the relationship between variation at 17q21 and childhood wheeze phenotypes.

    Granell R, Henderson AJ, Timpson N, St Pourcain B, Kemp JP, Ring SM, Ho K, Montgomery SB, Dermitzakis ET, Evans DM and Sterne JA

    The Journal of allergy and clinical immunology 2013;131;3;685-94

    PUBMED: 23154084; PMC: 4427593; DOI: 10.1016/j.jaci.2012.09.021

  • Secretory meningiomas are defined by combined KLF4 K409Q and TRAF7 mutations.

    Reuss DE, Piro RM, Jones DT, Simon M, Ketter R, Kool M, Becker A, Sahm F, Pusch S, Meyer J et al.

    Acta neuropathologica 2013;125;3;351-8

    PUBMED: 23404370; DOI: 10.1007/s00401-013-1093-x

  • Sherlock Genomes - viral investigator.

    Smith SE and Wash RS

    Nature reviews. Microbiology 2013;11;3;150

    PUBMED: 23411861; PMC: 7097817; DOI: 10.1038/nrmicro2979

  • Therapeutic modulation of intestinal dysbiosis.

    Walker AW and Lawley TD

    Pharmacological research 2013;69;1;75-86

    PUBMED: 23017673; DOI: 10.1016/j.phrs.2012.09.008

  • Genome-wide diversity in the levant reveals recent structuring by culture.

    Haber M, Gauguier D, Youhanna S, Patterson N, Moorjani P, Botigué LR, Platt DE, Matisoo-Smith E, Soria-Hernanz DF, Wells RS et al.

    PLoS genetics 2013;9;2;e1003316

    PUBMED: 23468648; PMC: 3585000; DOI: 10.1371/journal.pgen.1003316

  • Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.

    Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SA, Siezen RJ, Borgdorff M et al.

    BMC infectious diseases 2013;13;110

    PUBMED: 23446317; PMC: 3599118; DOI: 10.1186/1471-2334-13-110

  • Targeting MYCN in neuroblastoma by BET bromodomain inhibition.

    Puissant A, Frumm SM, Alexe G, Bassil CF, Qi J, Chanthery YH, Nekritz EA, Zeid R, Gustafson WC, Greninger P et al.

    Cancer discovery 2013;3;3;308-23

    PUBMED: 23430699; PMC: 3672953; DOI: 10.1158/2159-8290.CD-12-0418

  • Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions.

    Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW, Haak W, Bradshaw CJ, Townsend G, Sołtysiak A, Alt KW et al.

    Nature genetics 2013;45;4;450-5, 455e1

    PUBMED: 23416520; PMC: 3996550; DOI: 10.1038/ng.2536

  • Evolution of equine influenza virus in vaccinated horses.

    Murcia PR, Baillie GJ, Stack JC, Jervis C, Elton D, Mumford JA, Daly J, Kellam P, Grenfell BT, Holmes EC and Wood JL

    Journal of virology 2013;87;8;4768-71

    PUBMED: 23388708; PMC: 3624384; DOI: 10.1128/JVI.03379-12

  • The evolutionary dynamics of influenza A virus adaptation to mammalian hosts.

    Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Guan Y, Wood JL, Brown IH, Kellam P et al.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120382

    PUBMED: 23382435; PMC: 3678336; DOI: 10.1098/rstb.2012.0382

  • Astroglial IFITM3 mediates neuronal impairments following neonatal immune challenge in mice.

    Ibi D, Nagai T, Nakajima A, Mizoguchi H, Kawase T, Tsuboi D, Kano S, Sato Y, Hayakawa M, Lange UC et al.

    Glia 2013;61;5;679-93

    PUBMED: 23382131; PMC: 7165731; DOI: 10.1002/glia.22461

  • Viral population analysis and minority-variant detection using short read next-generation sequencing.

    Watson SJ, Welkers MR, Depledge DP, Coulter E, Breuer JM, de Jong MD and Kellam P

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120205

    PUBMED: 23382427; PMC: 3678329; DOI: 10.1098/rstb.2012.0205

  • The 5q31 region in two African populations as a facet of natural selection by infectious diseases.

    Elhassan AA, Hussein AA, Mohamed HS, Rockett K, Kwiatkowski D, Elhassan AM and Ibrahim ME

    Genetika 2013;49;2;279-88

    PUBMED: 23668094; DOI: 10.7868/s0016675813020057

  • Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.

    O'Neill CE, Seth-Smith HMB, Van Der Pol B, Harris SR, Thomson NR, Cutcliffe LT and Clarke IN

    Microbiology (Reading, England) 2013;159;Pt 4;748-756

    PUBMED: 23378575; DOI: 10.1099/mic.0.065391-0

  • Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.

    Köttgen A, Albrecht E, Teumer A, Vitart V, Krumsiek J, Hundertmark C, Pistis G, Ruggiero D, O'Seaghdha CM, Haller T et al.

    Nature genetics 2013;45;2;145-54

    PUBMED: 23263486; PMC: 3663712; DOI: 10.1038/ng.2500

  • Progressive genome-wide introgression in agricultural Campylobacter coli.

    Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ et al.

    Molecular ecology 2013;22;4;1051-64

    PUBMED: 23279096; DOI: 10.1111/mec.12162

  • Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations.

    Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF et al.

    PloS one 2013;8;1;e54616

    PUBMED: 23382925; PMC: 3559847; DOI: 10.1371/journal.pone.0054616

  • Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains.

    Chen JW, Scaria J, Mao C, Sobral B, Zhang S, Lawley T and Chang YF

    Journal of proteome research 2013;12;3;1151-61

    PUBMED: 23298230; DOI: 10.1021/pr3007528

  • Current application and future perspectives of molecular typing methods to study Clostridium difficile infections.

    Knetsch CW, Lawley TD, Hensgens MP, Corver J, Wilcox MW and Kuijper EJ

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2013;18;4;20381

    PUBMED: 23369393; DOI: 10.2807/ese.18.04.20381-en

  • Genetic basis of Y-linked hearing impairment.

    Wang Q, Xue Y, Zhang Y, Long Q, Asan, Yang F, Turner DJ, Fitzgerald T, Ng BL, Zhao Y et al.

    American journal of human genetics 2013;92;2;301-6

    PUBMED: 23352258; PMC: 3567277; DOI: 10.1016/j.ajhg.2012.12.015

  • Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters.

    Gall A, Kaye S, Hué S, Bonsall D, Rance R, Baillie GJ, Fidler SJ, Weber JN, McClure MO, Kellam P and SPARTAC Trial Investigators

    Retrovirology 2013;10;8

    PUBMED: 23331949; PMC: 3605130; DOI: 10.1186/1742-4690-10-8

  • Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia.

    Diffner E, Beck D, Gudgin E, Thoms JA, Knezevic K, Pridans C, Foster S, Goode D, Lim WK, Boelen L et al.

    Blood 2013;121;12;2289-300

    PUBMED: 23327922; DOI: 10.1182/blood-2012-07-446120

  • Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer.

    Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, Rodrigues DN, Renwick A, Seal S, Ramsay E et al.

    Nature 2013;493;7432;406-10

    PUBMED: 23242139; PMC: 3759028; DOI: 10.1038/nature11725

  • Deciphering signatures of mutational processes operative in human cancer.

    Alexandrov LB, Nik-Zainal S, Wedge DC, Campbell PJ and Stratton MR

    Cell reports 2013;3;1;246-59

    PUBMED: 23318258; PMC: 3588146; DOI: 10.1016/j.celrep.2012.12.008

  • A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic.

    Holden MT, Hsu LY, Kurt K, Weinert LA, Mather AE, Harris SR, Strommenger B, Layer F, Witte W, de Lencastre H et al.

    Genome research 2013;23;4;653-64

    PUBMED: 23299977; PMC: 3613582; DOI: 10.1101/gr.147710.112

  • Mechanisms controlling the temporal degradation of Nek2A and Kif18A by the APC/C-Cdc20 complex.

    Sedgwick GG, Hayward DG, Di Fiore B, Pardo M, Yu L, Pines J and Nilsson J

    The EMBO journal 2013;32;2;303-14

    PUBMED: 23288039; PMC: 3553385; DOI: 10.1038/emboj.2012.335

  • SpoIVA and SipL are Clostridium difficile spore morphogenetic proteins.

    Putnam EE, Nock AM, Lawley TD and Shen A

    Journal of bacteriology 2013;195;6;1214-25

    PUBMED: 23292781; PMC: 3592010; DOI: 10.1128/JB.02181-12

  • Histone deacetylase 1 and 2 are essential for normal T-cell development and genomic stability in mice.

    Dovey OM, Foster CT, Conte N, Edwards SA, Edwards JM, Singh R, Vassiliou G, Bradley A and Cowley SM

    Blood 2013;121;8;1335-44

    PUBMED: 23287868; PMC: 3836254; DOI: 10.1182/blood-2012-07-441949

  • A common biological basis of obesity and nicotine addiction.

    Thorgeirsson TE, Gudbjartsson DF, Sulem P, Besenbacher S, Styrkarsdottir U, Thorleifsson G, Walters GB, TAG Consortium, Oxford-GSK Consortium, ENGAGE consortium et al.

    Translational psychiatry 2013;3;e308

    PUBMED: 24084939; PMC: 3818010; DOI: 10.1038/tp.2013.81

  • The distribution and 'in vivo' phase variation status of haemoglobin receptors in invasive meningococcal serogroup B disease: genotypic and phenotypic analysis.

    Lucidarme J, Findlow J, Chan H, Feavers IM, Gray SJ, Kaczmarski EB, Parkhill J, Bai X, Borrow R and Bayliss CD

    PloS one 2013;8;9;e76932

    PUBMED: 24098814; PMC: 3786947; DOI: 10.1371/journal.pone.0076932

  • The evolutionary path to extraintestinal pathogenic, drug-resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome.

    McNally A, Cheng L, Harris SR and Corander J

    Genome biology and evolution 2013;5;4;699-710

    PUBMED: 23493634; PMC: 3641635; DOI: 10.1093/gbe/evt038

  • The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.

    Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD and Rawlings ND

    F1000Research 2013;2;154

    PUBMED: 24555072; PMC: 3901451; DOI: 10.12688/f1000research.2-154.v2

  • The GenoChip: a new tool for genetic anthropology.

    Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L et al.

    Genome biology and evolution 2013;5;5;1021-31

    PUBMED: 23666864; PMC: 3673633; DOI: 10.1093/gbe/evt066

  • The malarial serine protease SUB1 plays an essential role in parasite liver stage development.

    Suarez C, Volkmann K, Gomes AR, Billker O and Blackman MJ

    PLoS pathogens 2013;9;12;e1003811

    PUBMED: 24348254; PMC: 3861531; DOI: 10.1371/journal.ppat.1003811

  • A member of the Plasmodium falciparum PHIST family binds to the erythrocyte cytoskeleton component band 4.1.

    Parish LA, Mai DW, Jones ML, Kitson EL and Rayner JC

    Malaria journal 2013;12;160

    PUBMED: 23663475; PMC: 3658886; DOI: 10.1186/1475-2875-12-160

  • A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.

    Feehery GR, Yigit E, Oyola SO, Langhorst BW, Schmidt VT, Stewart FJ, Dimalanta ET, Amaral-Zettler LA, Davis T, Quail MA and Pradhan S

    PloS one 2013;8;10;e76096

    PUBMED: 24204593; PMC: 3810253; DOI: 10.1371/journal.pone.0076096

  • A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates.

    Tachmazidou I, Dedoussis G, Southam L, Farmaki AE, Ritchie GR, Xifara DK, Matchan A, Hatzikotoulas K, Rayner NW, Chen Y et al.

    Nature communications 2013;4;2872

    PUBMED: 24343240; PMC: 3905724; DOI: 10.1038/ncomms3872

  • The relative timing of mutations in a breast cancer genome.

    Newman S, Howarth KD, Greenman CD, Bignell GR, Tavaré S and Edwards PA

    PloS one 2013;8;6;e64991

    PUBMED: 23762276; PMC: 3677865; DOI: 10.1371/journal.pone.0064991

  • The role of adiposity in cardiometabolic traits: a Mendelian randomization analysis.

    Fall T, Hägg S, Mägi R, Ploner A, Fischer K, Horikoshi M, Sarin AP, Thorleifsson G, Ladenvall C, Kals M et al.

    PLoS medicine 2013;10;6;e1001474

    PUBMED: 23824655; PMC: 3692470; DOI: 10.1371/journal.pmed.1001474

  • Association of cytokine and Toll-like receptor gene polymorphisms with severe malaria in three regions of Cameroon.

    Apinjoh TO, Anchang-Kimbi JK, Njua-Yafi C, Mugri RN, Ngwai AN, Rockett KA, Mbunwe E, Besingi RN, Clark TG, Kwiatkowski DP et al.

    PloS one 2013;8;11;e81071

    PUBMED: 24312262; PMC: 3842328; DOI: 10.1371/journal.pone.0081071

  • Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls.

    McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O et al.

    PLoS pathogens 2013;9;7;e1003515

    PUBMED: 23935489; PMC: 3723635; DOI: 10.1371/journal.ppat.1003515

  • Bcl11a controls Flt3 expression in early hematopoietic progenitors and is required for pDC development in vivo.

    Wu X, Satpathy AT, Kc W, Liu P, Murphy TL and Murphy KM

    PloS one 2013;8;5;e64800

    PUBMED: 23741395; PMC: 3669380; DOI: 10.1371/journal.pone.0064800

  • Burrows-Wheeler Transform for Terabases

    Siren J

    Data Compression Conference Proceedings 2013;211-20

    DOI: 10.1109/DCC.2016.17

  • Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

    Koohy H, Down TA and Hubbard TJ

    PloS one 2013;8;7;e69853

    PUBMED: 23922824; PMC: 3724795; DOI: 10.1371/journal.pone.0069853

  • Clinically relevant mutant DNA gyrase alters supercoiling, changes the transcriptome, and confers multidrug resistance.

    Webber MA, Ricci V, Whitehead R, Patel M, Fookes M, Ivens A and Piddock LJ

    mBio 2013;4;4

    PUBMED: 23882012; PMC: 3735185; DOI: 10.1128/mBio.00273-13

  • Clonal expansion analysis of transposon insertions by high-throughput sequencing identifies candidate cancer genes in a PiggyBac mutagenesis screen.

    Friedel RH, Friedel CC, Bonfert T, Shi R, Rad R and Soriano P

    PloS one 2013;8;8;e72338

    PUBMED: 23940809; PMC: 3733837; DOI: 10.1371/journal.pone.0072338

  • Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.

    Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT and Flicek P

    Genome biology 2013;14;12;R148

    PUBMED: 24380390; PMC: 4056453; DOI: 10.1186/gb-2013-14-12-r148

  • Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.

    Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE et al.

    F1000Research 2013;2

    PUBMED: 24358873; PMC: 3799545; DOI: 10.12688/f1000research.2-30.v1

  • Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses.

    Peel AJ, Sargan DR, Baker KS, Hayman DT, Barr JA, Crameri G, Suu-Ire R, Broder CC, Lembo T, Wang LF et al.

    Nature communications 2013;4;2770

    PUBMED: 24253424; PMC: 3836177; DOI: 10.1038/ncomms3770

  • Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.

    Beaudoin M, Goyette P, Boucher G, Lo KS, Rivas MA, Stevens C, Alikashani A, Ladouceur M, Ellinghaus D, Törkvist L et al.

    PLoS genetics 2013;9;9;e1003723

    PUBMED: 24068945; PMC: 3772057; DOI: 10.1371/journal.pgen.1003723

  • Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection.

    Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ et al.

    PLoS genetics 2013;9;10;e1003868

    PUBMED: 24130509; PMC: 3794909; DOI: 10.1371/journal.pgen.1003868

  • Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.

    Auburn S, Marfurt J, Maslen G, Campino S, Ruano Rubio V, Manske M, Machunter B, Kenangalem E, Noviyanti R, Trianty L et al.

    PloS one 2013;8;1;e53160

    PUBMED: 23308154; PMC: 3537768; DOI: 10.1371/journal.pone.0053160

  • Efficient knockin mouse generation by ssDNA oligonucleotides and zinc-finger nuclease assisted homologous recombination in zygotes.

    Shen B, Zhang X, Du Y, Wang J, Gong J, Zhang X, Tate PH, Li H, Huang X and Zhang W

    PloS one 2013;8;10;e77696

    PUBMED: 24167580; PMC: 3805579; DOI: 10.1371/journal.pone.0077696

  • Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing.

    Clark TG, Mallard K, Coll F, Preston M, Assefa S, Harris D, Ogwang S, Mumbowa F, Kirenga B, O'Sullivan DM et al.

    PloS one 2013;8;12;e83012

    PUBMED: 24349420; PMC: 3859632; DOI: 10.1371/journal.pone.0083012

  • Enhanced production of recombinant secretory proteins in Pichia pastoris by optimizing Kex2 P1' site.

    Yang S, Kuang Y, Li H, Liu Y, Hui X, Li P, Jiang Z, Zhou Y, Wang Y, Xu A et al.

    PloS one 2013;8;9;e75347

    PUBMED: 24069404; PMC: 3777899; DOI: 10.1371/journal.pone.0075347

  • Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

    Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML, Grützner F, Odom DT, Patient R, Ponting CP and Klose RJ

    eLife 2013;2;e00348

    PUBMED: 23467541; PMC: 3583005; DOI: 10.7554/eLife.00348

  • Etoposide induces nuclear re-localisation of AID.

    Lambert LJ, Walker S, Feltham J, Lee HJ, Reik W and Houseley J

    PloS one 2013;8;12;e82110

    PUBMED: 24324754; PMC: 3852760; DOI: 10.1371/journal.pone.0082110

  • Evolution of GluN2A/B cytoplasmic domains diversified vertebrate synaptic plasticity and behavior.

    Ryan TJ, Kopanitsa MV, Indersmitten T, Nithianantharajah J, Afinowi NO, Pettit C, Stanford LE, Sprengel R, Saksida LM, Bussey TJ et al.

    Nature neuroscience 2013;16;1;25-32

    PUBMED: 23201971; PMC: 3979286; DOI: 10.1038/nn.3277

  • Evolution of the thermopsin peptidase family (A5).

    Rawlings ND

    PloS one 2013;8;11;e78998

    PUBMED: 24312173; PMC: 3842238; DOI: 10.1371/journal.pone.0078998

  • Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007.

    Vodovnik M, Duncan SH, Reid MD, Cantlay L, Turner K, Parkhill J, Lamed R, Yeoman CJ, Miller ME, White BA et al.

    PloS one 2013;8;6;e65333

    PUBMED: 23750253; PMC: 3672088; DOI: 10.1371/journal.pone.0065333

  • Extensive diversity of Streptococcus pyogenes in a remote human population reflects global-scale transmission rather than localised diversification.

    Towers RJ, Carapetis JR, Currie BJ, Davies MR, Walker MJ, Dougan G and Giffard PM

    PloS one 2013;8;9;e73851

    PUBMED: 24066079; PMC: 3774777; DOI: 10.1371/journal.pone.0073851

  • Fine mapping of the pond snail left-right asymmetry (chirality) locus using RAD-Seq and fibre-FISH.

    Liu MM, Davey JW, Banerjee R, Han J, Yang F, Aboobaker A, Blaxter ML and Davison A

    PloS one 2013;8;8;e71067

    PUBMED: 23951082; PMC: 3741322; DOI: 10.1371/journal.pone.0071067

  • Gene expression changes with age in skin, adipose tissue, blood and brain.

    Glass D, Viñuela A, Davies MN, Ramasamy A, Parts L, Knowles D, Brown AA, Hedman AK, Small KS, Buil A et al.

    Genome biology 2013;14;7;R75

    PUBMED: 23889843; PMC: 4054017; DOI: 10.1186/gb-2013-14-7-r75

  • Genetic variants from lipid-related pathways and risk for incident myocardial infarction.

    Song C, Pedersen NL, Reynolds CA, Sabater-Lleal M, Kanoni S, Willenborg C, CARDIoGRAMplusC4D Consortium, Syvänen AC, Watkins H, Hamsten A et al.

    PloS one 2013;8;3;e60454

    PUBMED: 23555974; PMC: 3612051; DOI: 10.1371/journal.pone.0060454

  • Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar.

    Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S et al.

    mBio 2013;4;5;e00565-13

    PUBMED: 23982073; PMC: 3760250; DOI: 10.1128/mBio.00565-13

  • Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.

    Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR et al.

    Genome biology 2013;14;2;R11

    PUBMED: 23375108; PMC: 4053784; DOI: 10.1186/gb-2013-14-2-r11

  • Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans.

    Pistis G, Okonkwo SU, Traglia M, Sala C, Shin SY, Masciullo C, Buetti I, Massacane R, Mangino M, Thein SL et al.

    PloS one 2013;8;7;e69206

    PUBMED: 23935956; PMC: 3729833; DOI: 10.1371/journal.pone.0069206

  • Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum.

    Stringer SC, Carter AT, Webb MD, Wachnicka E, Crossman LC, Sebaihia M and Peck MW

    BMC genomics 2013;14;333

    PUBMED: 23679073; PMC: 3672017; DOI: 10.1186/1471-2164-14-333

  • Haploid genetic screens identify an essential role for PLP2 in the downregulation of novel plasma membrane targets by viral E3 ubiquitin ligases.

    Timms RT, Duncan LM, Tchasovnikarova IA, Antrobus R, Smith DL, Dougan G, Weekes MP and Lehner PJ

    PLoS pathogens 2013;9;11;e1003772

    PUBMED: 24278019; PMC: 3836740; DOI: 10.1371/journal.ppat.1003772

  • Harnessing the genome: development of a hierarchical typing scheme for meticillin-resistant Staphylococcus aureus.

    Stone MJ, Wain J, Ivens A, Feltwell T, Kearns AM and Bamford KB

    Journal of medical microbiology 2013;62;Pt 1;36-45

    PUBMED: 23002072; DOI: 10.1099/jmm.0.049957-0

  • Human candidate polymorphisms in sympatric ethnic groups differing in malaria susceptibility in Mali.

    Maiga B, Dolo A, Touré O, Dara V, Tapily A, Campino S, Sepulveda N, Risley P, Silva N, Silva N et al.

    PloS one 2013;8;10;e75675

    PUBMED: 24098393; PMC: 3788813; DOI: 10.1371/journal.pone.0075675

  • In Vitro Models of Brain Cancer

    RYAN,D.J. and Watts,C.

    Emerging Concepts in Neuro-Oncology 2013;75-86

    DOI: 10.1007/978-0-85729-458-6_5; URL: https://link.springer.com/chapter.../10.1007%2F978-0-85729-458-6_5

  • Incidence and characterisation of methicillin-resistant Staphylococcus aureus (MRSA) from nasal colonisation in participants attending a cattle veterinary conference in the UK.

    Paterson GK, Harrison EM, Craven EF, Petersen A, Larsen AR, Ellington MJ, Török ME, Peacock SJ, Parkhill J, Zadoks RN and Holmes MA

    PloS one 2013;8;7;e68463

    PUBMED: 23869220; PMC: 3711812; DOI: 10.1371/journal.pone.0068463

  • Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals.

    Zhang YH, Zhao Y, Li N, Peng YC, Giannoulatou E, Jin RH, Yan HP, Wu H, Liu JH, Liu N et al.

    Nature communications 2013;4;1418

    PUBMED: 23361009; PMC: 3562464; DOI: 10.1038/ncomms2433

  • Intestinal colonization resistance.

    Lawley TD and Walker AW

    Immunology 2013;138;1;1-11

    PUBMED: 23240815; PMC: 3533696; DOI: 10.1111/j.1365-2567.2012.03616.x

  • ISCB computational biology Wikipedia competition.

    Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P and Rost B

    PLoS computational biology 2013;9;9;e1003242

    PUBMED: 24068913; PMC: 3777890; DOI: 10.1371/journal.pcbi.1003242

  • Large scale variation in DNA copy number in chicken breeds.

    Crooijmans RP, Fife MS, Fitzgerald TW, Strickland S, Cheng HH, Kaiser P, Redon R and Groenen MA

    BMC genomics 2013;14;398

    PUBMED: 23763846; PMC: 3751642; DOI: 10.1186/1471-2164-14-398

  • Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking.

    Collier N, Tran MV, Le HQ, Ha QT, Oellrich A and Rebholz-Schuhmann D

    PloS one 2013;8;10;e72965

    PUBMED: 24155869; PMC: 3796529; DOI: 10.1371/journal.pone.0072965

  • LUD, a new protein domain associated with lactate utilization.

    Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY et al.

    BMC bioinformatics 2013;14;341

    PUBMED: 24274019; PMC: 3924224; DOI: 10.1186/1471-2105-14-341

  • Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations.

    O'Seaghdha CM, Wu H, Yang Q, Kapur K, Guessous I, Zuber AM, Köttgen A, Stoudmann C, Teumer A, Kutalik Z et al.

    PLoS genetics 2013;9;9;e1003796

    PUBMED: 24068962; PMC: 3778004; DOI: 10.1371/journal.pgen.1003796

  • Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans.

    Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Sarkissian CD, Ganslmeier R, Friederich S et al.

    Nature communications 2013;4;1764

    PUBMED: 23612305; PMC: 3978205; DOI: 10.1038/ncomms2656

  • Partial sleep restriction activates immune response-related gene expression pathways: experimental and epidemiological studies in humans.

    Aho V, Ollila HM, Rantanen V, Kronholm E, Surakka I, van Leeuwen WM, Lehto M, Matikainen S, Ripatti S, Härmä M et al.

    PloS one 2013;8;10;e77184

    PUBMED: 24194869; PMC: 3806729; DOI: 10.1371/journal.pone.0077184

  • Prelamin A causes progeria through cell-extrinsic mechanisms and prevents cancer invasion.

    de la Rosa J, Freije JM, Cabanillas R, Osorio FG, Fraga MF, Fernández-García MS, Rad R, Fanjul V, Ugalde AP, Liang Q et al.

    Nature communications 2013;4;2268

    PUBMED: 23917225; PMC: 3758871; DOI: 10.1038/ncomms3268

  • Quantifying single nucleotide variant detection sensitivity in exome sequencing.

    Meynert AM, Bicknell LS, Hurles ME, Jackson AP and Taylor MS

    BMC bioinformatics 2013;14;195

    PUBMED: 23773188; PMC: 3695811; DOI: 10.1186/1471-2105-14-195

  • Recombination-mediated genetic engineering of Plasmodium berghei DNA.

    Pfander C, Anar B, Brochet M, Rayner JC and Billker O

    Methods in molecular biology (Clifton, N.J.) 2013;923;127-38

    PUBMED: 22990774; DOI: 10.1007/978-1-62703-026-7_8

  • RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

    Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS et al.

    BMC genomics 2013;14;822

    PUBMED: 24267595; PMC: 4046660; DOI: 10.1186/1471-2164-14-822

  • RocA truncation underpins hyper-encapsulation, carriage longevity and transmissibility of serotype M18 group A streptococci.

    Lynskey NN, Goulding D, Gierula M, Turner CE, Dougan G, Edwards RJ and Sriskandan S

    PLoS pathogens 2013;9;12;e1003842

    PUBMED: 24367267; PMC: 3868526; DOI: 10.1371/journal.ppat.1003842

  • Serotonin: The Central Link between Bone Mass and Energy Metabolism

    Yadav,V.K.;

    Translational Endocrinology of Bone 2013;Chapter 5;51-62

    DOI: 10.1016/B978-0-12-415784-2.00005-1; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780124157842000051

  • So, you want to sequence a genome...

    Stemple DL

    Genome biology 2013;14;7;128

    PUBMED: 23906089; PMC: 4053694; DOI: 10.1186/gb-2013-14-7-128

  • Toward knowledge support for analysis and interpretation of complex traits.

    Collier N, Oellrich A and Groza T

    Genome biology 2013;14;9;214

    PUBMED: 24079802; PMC: 4053827; DOI: 10.1186/gb-2013-14-9-214

  • Tracking chromosome evolution in southern African gerbils using flow-sorted chromosome paints.

    Knight LI, Ng BL, Cheng W, Fu B, Yang F and Rambau RV

    Cytogenetic and genome research 2013;139;4;267-75

    PUBMED: 23652816; PMC: 3721133; DOI: 10.1159/000350696

  • Two new cytotypes reinforce that Micronycteris hirsuta Peters, 1869 does not represent a monotypic taxon.

    Ribas TF, Rodrigues LR, Nagamachi CY, Gomes AJ, Benathar TC, O'Brien PC, Yang F, Ferguson-Smith MA and Pieczarka JC

    BMC genetics 2013;14;119

    PUBMED: 24359225; PMC: 3878135; DOI: 10.1186/1471-2156-14-119

  • Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.

    Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L et al.

    BMC bioinformatics 2013;14;265

    PUBMED: 24004689; PMC: 3848476; DOI: 10.1186/1471-2105-14-265

  • Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.

    Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D et al.

    PloS one 2013;8;5;e65441

    PUBMED: 23734255; PMC: 3666984; DOI: 10.1371/journal.pone.0065441

  • Using genetic prediction from known complex disease Loci to guide the design of next-generation sequencing experiments.

    Jostins L, Levine AP and Barrett JC

    PloS one 2013;8;10;e76328

    PUBMED: 24204614; PMC: 3799779; DOI: 10.1371/journal.pone.0076328

2012

  • Genes involved in host-parasite interactions can be revealed by their correlated expression.

    Reid AJ and Berriman M

    Nucleic acids research 2012;41;3;1508-18

    PUBMED: 23275547; PMC: 3561955; DOI: 10.1093/nar/gks1340

  • Mcl-1 and FBW7 control a dominant survival pathway underlying HDAC and Bcl-2 inhibitor synergy in squamous cell carcinoma.

    He L, Torres-Lockhart K, Forster N, Ramakrishnan S, Greninger P, Garnett MJ, McDermott U, Rothenberg SM, Benes CH and Ellisen LW

    Cancer discovery 2012;3;3;324-37

    PUBMED: 23274910; PMC: 3595349; DOI: 10.1158/2159-8290.CD-12-0417

  • Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection.

    Illingworth CJ and Mustonen V

    PLoS pathogens 2012;8;12;e1003091

    PUBMED: 23300444; PMC: 3531508; DOI: 10.1371/journal.ppat.1003091

  • Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.

    Castillo-Ramírez S, Corander J, Marttinen P, Aldeljawi M, Hanage WP, Westh H, Boye K, Gulay Z, Bentley SD, Parkhill J et al.

    Genome biology 2012;13;12;R126

    PUBMED: 23270620; DOI: 10.1186/gb-2012-13-12-r126

  • VS-5584, a novel and highly selective PI3K/mTOR kinase inhibitor for the treatment of cancer.

    Hart S, Novotny-Diermayr V, Goh KC, Williams M, Tan YC, Ong LC, Cheong A, Ng BK, Amalini C, Madan B et al.

    Molecular cancer therapeutics 2012;12;2;151-61

    PUBMED: 23270925; PMC: 3588144; DOI: 10.1158/1535-7163.MCT-12-0466

  • Different patterns of Epstein-Barr virus latency in endemic Burkitt lymphoma (BL) lead to distinct variants within the BL-associated gene expression signature.

    Kelly GL, Stylianou J, Rasaiyaah J, Wei W, Thomas W, Croom-Carter D, Kohler C, Spang R, Woodman C, Kellam P et al.

    Journal of virology 2012;87;5;2882-94

    PUBMED: 23269792; PMC: 3571367; DOI: 10.1128/JVI.03003-12

  • A tetracycline-repressible transactivator system to study essential genes in malaria parasites.

    Pino P, Sebastian S, Kim EA, Bush E, Brochet M, Volkmann K, Kozlowski E, Llinás M, Billker O and Soldati-Favre D

    Cell host & microbe 2012;12;6;824-34

    PUBMED: 23245327; PMC: 3712325; DOI: 10.1016/j.chom.2012.10.016

  • Bcl11a is essential for lymphoid development and negatively regulates p53.

    Yu Y, Wang J, Khaled W, Burke S, Li P, Chen X, Yang W, Jenkins NA, Copeland NG, Zhang S and Liu P

    The Journal of experimental medicine 2012;209;13;2467-83

    PUBMED: 23230003; PMC: 3526365; DOI: 10.1084/jem.20121846

  • RetroSeq: transposable element discovery from next-generation sequencing data.

    Keane TM, Wong K and Adams DJ

    Bioinformatics (Oxford, England) 2012;29;3;389-90

    PUBMED: 23233656; PMC: 3562067; DOI: 10.1093/bioinformatics/bts697

  • Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

    He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB et al.

    Nature genetics 2012;45;1;109-13

    PUBMED: 23222960; PMC: 3605770; DOI: 10.1038/ng.2478

  • Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

    Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN et al.

    American journal of human genetics 2012;91;6;1022-32

    PUBMED: 23217326; PMC: 3516590; DOI: 10.1016/j.ajhg.2012.10.015

  • The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells.

    Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, Popp C, Thienpont B, Dean W and Reik W

    Molecular cell 2012;48;6;849-62

    PUBMED: 23219530; PMC: 3533687; DOI: 10.1016/j.molcel.2012.11.001

  • Efficient depletion of host DNA contamination in malaria clinical sequencing.

    Oyola SO, Gu Y, Manske M, Otto TD, O'Brien J, Alcock D, Macinnis B, Berriman M, Newbold CI, Kwiatkowski DP et al.

    Journal of clinical microbiology 2012;51;3;745-51

    PUBMED: 23224084; PMC: 3592063; DOI: 10.1128/JCM.02507-12

  • Seventy-five genetic loci influencing the human red blood cell.

    van der Harst P, Zhang W, Mateo Leach I, Rendon A, Verweij N, Sehmi J, Paul DS, Elling U, Allayee H, Li X et al.

    Nature 2012;492;7429;369-75

    PUBMED: 23222517; PMC: 3623669; DOI: 10.1038/nature11677

  • Large-scale association analysis identifies new risk loci for coronary artery disease.

    CARDIoGRAMplusC4D Consortium, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, Thompson JR, Ingelsson E, Saleheen D, Erdmann J et al.

    Nature genetics 2012;45;1;25-33

    PUBMED: 23202125; PMC: 3679547; DOI: 10.1038/ng.2480

  • A genome-wide association study of monozygotic twin-pairs suggests a locus related to variability of serum high-density lipoprotein cholesterol.

    Surakka I, Whitfield JB, Perola M, Visscher PM, Montgomery GW, Falchi M, Willemsen G, de Geus EJ, Magnusson PK, Christensen K et al.

    Twin research and human genetics : the official journal of the International Society for Twin Studies 2012;15;6;691-9

    PUBMED: 23031429; DOI: 10.1017/thg.2012.63

  • Bayesian refinement of association signals for 14 loci in 3 common diseases.

    Wellcome Trust Case Control Consortium, Maller JB, McVean G, Byrnes J, Vukcevic D, Palin K, Su Z, Howson JM, Auton A, Myers S et al.

    Nature genetics 2012;44;12;1294-301

    PUBMED: 23104008; PMC: 3791416; DOI: 10.1038/ng.2435

  • Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation.

    Coupland P, Chandra T, Quail M, Reik W and Swerdlow H

    BioTechniques 2012;53;6;365-72

    PUBMED: 23227987; PMC: 3808810; DOI: 10.2144/000113962

  • Generation of diversity by somatic mutation in the Camelus dromedarius T-cell receptor gamma variable domains.

    Vaccarelli G, Antonacci R, Tasco G, Yang F, Giordano L, El Ashmaoui HM, Hassanane MS, Massari S, Casadio R and Ciccarese S

    European journal of immunology 2012;42;12;3416-28

    PUBMED: 22961631; DOI: 10.1002/eji.201142176

  • Progressive cross-reactivity in IgE responses: an explanation for the slow development of human immunity to schistosomiasis?

    Fitzsimmons CM, Jones FM, Pinot de Moira A, Protasio AV, Khalife J, Dickinson HA, Tukahebwa EM and Dunne DW

    Infection and immunity 2012;80;12;4264-70

    PUBMED: 23006852; PMC: 3497412; DOI: 10.1128/IAI.00641-12

  • Ensembl 2013.

    Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S et al.

    Nucleic acids research 2012;41;Database issue;D48-55

    PUBMED: 23203987; PMC: 3531136; DOI: 10.1093/nar/gks1236

  • Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome.

    Basel-Vanagaite L, Dallapiccola B, Ramirez-Solis R, Segref A, Thiele H, Edwards A, Arends MJ, Miró X, White JK, Désir J et al.

    American journal of human genetics 2012;91;6;998-1010

    PUBMED: 23200864; PMC: 3516591; DOI: 10.1016/j.ajhg.2012.10.011

  • Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system.

    Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M et al.

    PloS one 2012;7;11;e50269

    PUBMED: 23209694; PMC: 3508930; DOI: 10.1371/journal.pone.0050269

  • Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia.

    Hilcenko C, Simpson PJ, Finch AJ, Bowler FR, Churcher MJ, Jin L, Packman LC, Shlien A, Campbell P, Kirwan M et al.

    Blood 2012;121;6;1028-38

    PUBMED: 23190533; DOI: 10.1182/blood-2012-10-461491

  • Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells.

    Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, Bindal N, Beare D, Smith JA, Thompson IR et al.

    Nucleic acids research 2012;41;Database issue;D955-61

    PUBMED: 23180760; PMC: 3531057; DOI: 10.1093/nar/gks1111

  • MED12 controls the response to multiple cancer drugs through regulation of TGF-β receptor signaling.

    Huang S, Hölzel M, Knijnenburg T, Schlicker A, Roepman P, McDermott U, Garnett M, Grernrum W, Sun C, Prahallad A et al.

    Cell 2012;151;5;937-50

    PUBMED: 23178117; PMC: 3672971; DOI: 10.1016/j.cell.2012.10.035

  • Human SH2B1 mutations are associated with maladaptive behaviors and obesity.

    Doche ME, Bochukova EG, Su HW, Pearce LR, Keogh JM, Henning E, Cline JM, Saeed S, Dale A, Cheetham T et al.

    The Journal of clinical investigation 2012;122;12;4732-6

    PUBMED: 23160192; PMC: 3533535; DOI: 10.1172/JCI62696

  • Analyses of pig genomes provide insight into porcine demography and evolution.

    Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ et al.

    Nature 2012;491;7424;393-8

    PUBMED: 23151582; PMC: 3566564; DOI: 10.1038/nature11622

  • Controls of nucleosome positioning in the human genome.

    Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y and Pritchard JK

    PLoS genetics 2012;8;11;e1003036

    PUBMED: 23166509; PMC: 3499251; DOI: 10.1371/journal.pgen.1003036

  • Disruption of mouse Cenpj, a regulator of centriole biogenesis, phenocopies Seckel syndrome.

    McIntyre RE, Lakshminarasimhan Chavali P, Ismail O, Carragher DM, Sanchez-Andrade G, Forment JV, Fu B, Del Castillo Velasco-Herrera M, Edwards A, van der Weyden L et al.

    PLoS genetics 2012;8;11;e1003022

    PUBMED: 23166506; PMC: 3499256; DOI: 10.1371/journal.pgen.1003022

  • Semaphorin-7A is an erythrocyte receptor for P. falciparum merozoite-specific TRAP homolog, MTRAP.

    Bartholdson SJ, Bustamante LY, Crosnier C, Johnson S, Lea S, Rayner JC and Wright GJ

    PLoS pathogens 2012;8;11;e1003031

    PUBMED: 23166499; PMC: 3499583; DOI: 10.1371/journal.ppat.1003031

  • Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.

    Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW et al.

    The Lancet. Infectious diseases 2012;13;2;137-46

    PUBMED: 23158499; PMC: 3556524; DOI: 10.1016/S1473-3099(12)70277-3

  • Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

    Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J and Peacock SJ

    The Lancet. Infectious diseases 2012;13;2;130-6

    PUBMED: 23158674; PMC: 3556525; DOI: 10.1016/S1473-3099(12)70268-2

  • Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation.

    Quail MA, Gu Y, Swerdlow H and Mayho M

    Electrophoresis 2012;33;23;3521-8

    PUBMED: 23147856; DOI: 10.1002/elps.201200128

  • High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.

    Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K et al.

    Nature genetics 2012;44;12;1336-40

    PUBMED: 23143596; PMC: 3605761; DOI: 10.1038/ng.2462

  • A full-length recombinant Plasmodium falciparum PfRH5 protein induces inhibitory antibodies that are effective across common PfRH5 genetic variants.

    Bustamante LY, Bartholdson SJ, Crosnier C, Campos MG, Wanaguru M, Nguon C, Kwiatkowski DP, Wright GJ and Rayner JC

    Vaccine 2012;31;2;373-9

    PUBMED: 23146673; PMC: 3538003; DOI: 10.1016/j.vaccine.2012.10.106

  • A common single-nucleotide variant in T is strongly associated with chordoma.

    Pillay N, Plagnol V, Tarpey PS, Lobo SB, Presneau N, Szuhai K, Halai D, Berisha F, Cannon SR, Mead S et al.

    Nature genetics 2012;44;11;1185-7

    PUBMED: 23064415; DOI: 10.1038/ng.2419

  • A dominantly acting murine allele of Mcm4 causes chromosomal abnormalities and promotes tumorigenesis.

    Bagley BN, Keane TM, Maklakova VI, Marshall JG, Lester RA, Cancel MM, Paulsen AR, Bendzick LE, Been RA, Kogan SC et al.

    PLoS genetics 2012;8;11;e1003034

    PUBMED: 23133403; PMC: 3486839; DOI: 10.1371/journal.pgen.1003034

  • An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.

    Nelson AC, Pillay N, Henderson S, Presneau N, Tirabosco R, Halai D, Berisha F, Flicek P, Stemple DL, Stern CD et al.

    The Journal of pathology 2012;228;3;274-85

    PUBMED: 22847733; PMC: 6089345; DOI: 10.1002/path.4082

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT and McVean GA

    Nature 2012;491;7422;56-65

    PUBMED: 23128226; PMC: 3498066; DOI: 10.1038/nature11632

  • Copy number variation of the APC gene is associated with regulation of bone mineral density.

    Chew S, Dastani Z, Brown SJ, Lewis JR, Dudbridge F, Soranzo N, Surdulescu GL, Richards JB, Spector TD and Wilson SG

    Bone 2012;51;5;939-43

    PUBMED: 22884971; PMC: 3918860; DOI: 10.1016/j.bone.2012.07.022

  • Finding NECA: zebrafish screen identifies key signalling pathway in β-cell regeneration.

    Seth A

    Disease models & mechanisms 2012;5;6;709-10

    PUBMED: 23115198; PMC: 3484851; DOI: 10.1242/dmm.010876

  • Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

    Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA et al.

    Nature 2012;491;7422;119-24

    PUBMED: 23128233; PMC: 3491803; DOI: 10.1038/nature11582

  • Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

    Amambua-Ngwa A, Tetteh KK, Manske M, Gomez-Escobar N, Stewart LB, Deerhake ME, Cheeseman IH, Newbold CI, Holder AA, Knuepfer E et al.

    PLoS genetics 2012;8;11;e1002992

    PUBMED: 23133397; PMC: 3486833; DOI: 10.1371/journal.pgen.1002992

  • Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.

    Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C et al.

    PLoS pathogens 2012;8;10;e1002995

    PUBMED: 23133377; PMC: 3486913; DOI: 10.1371/journal.ppat.1002995

  • Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

    Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J et al.

    Nature 2012;491;7424;399-405

    PUBMED: 23103869; PMC: 3530898; DOI: 10.1038/nature11547

  • The transcription factor T-bet regulates intestinal inflammation mediated by interleukin-7 receptor+ innate lymphoid cells.

    Powell N, Walker AW, Stolarczyk E, Canavan JB, Gökmen MR, Marks E, Jackson I, Hashim A, Curtis MA, Jenner RG et al.

    Immunity 2012;37;4;674-84

    PUBMED: 23063332; PMC: 3540260; DOI: 10.1016/j.immuni.2012.09.008

  • The B10 Idd9.3 locus mediates accumulation of functionally superior CD137(+) regulatory T cells in the nonobese diabetic type 1 diabetes model.

    Kachapati K, Adams DE, Wu Y, Steward CA, Rainbow DB, Wicker LS, Mittler RS and Ridgway WM

    Journal of immunology (Baltimore, Md. : 1950) 2012;189;10;5001-15

    PUBMED: 23066155; PMC: 3505683; DOI: 10.4049/jimmunol.1101013

  • Lipoprotein(a) and risk of coronary, cerebrovascular, and peripheral artery disease: the EPIC-Norfolk prospective population study.

    Gurdasani D, Sjouke B, Tsimikas S, Hovingh GK, Luben RN, Wainwright NW, Pomilla C, Wareham NJ, Khaw KT, Boekholdt SM and Sandhu MS

    Arteriosclerosis, thrombosis, and vascular biology 2012;32;12;3058-65

    PUBMED: 23065826; PMC: 4210842; DOI: 10.1161/ATVBAHA.112.255521

  • Metal binding in proteins: Machine learning complements X-ray absorption spectroscopy

    Lippi,M., Passerini,A., PUNTA,M. and Frasconi,P.

    Lecture Notes in Computer Science  2012;7524;854-857

    DOI: 10.1007/978-3-642-33486-3_63; URL: https://link.springer.com/chapter.../10.1007%2F978-3-642-33486-3_63

  • Olorin: combining gene flow with exome sequencing in large family studies of complex disease.

    Morris JA and Barrett JC

    Bioinformatics (Oxford, England) 2012;28;24;3320-1

    PUBMED: 23052039; PMC: 3519455; DOI: 10.1093/bioinformatics/bts609

  • Transposon mutagenesis identifies genes that transform neural stem cells into glioma-initiating cells.

    Koso H, Takeda H, Yew CC, Ward JM, Nariai N, Ueno K, Nagasaki M, Watanabe S, Rust AG, Adams DJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;44;E2998-3007

    PUBMED: 23045694; PMC: 3497753; DOI: 10.1073/pnas.1215899109

  • Recessive HYDIN mutations cause primary ciliary dyskinesia without randomization of left-right body asymmetry.

    Olbrich H, Schmidts M, Werner C, Onoufriadis A, Loges NT, Raidt J, Banki NF, Shoemark A, Burgoyne T, Al Turki S et al.

    American journal of human genetics 2012;91;4;672-84

    PUBMED: 23022101; PMC: 3484652; DOI: 10.1016/j.ajhg.2012.08.016

  • A calibrated human Y-chromosomal phylogeny based on resequencing.

    Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, Carbone I, Xue Y and Tyler-Smith C

    Genome research 2012;23;2;388-95

    PUBMED: 23038768; PMC: 3561879; DOI: 10.1101/gr.143198.112

  • Learned recognition of maternal signature odors mediates the first suckling episode in mice.

    Logan DW, Brunet LJ, Webb WR, Cutforth T, Ngai J and Stowers L

    Current biology : CB 2012;22;21;1998-2007

    PUBMED: 23041191; PMC: 3494771; DOI: 10.1016/j.cub.2012.08.041

  • TNiK is required for postsynaptic and nuclear signaling pathways and cognitive function.

    Coba MP, Komiyama NH, Nithianantharajah J, Kopanitsa MV, Indersmitten T, Skene NG, Tuck EJ, Fricker DG, Elsegood KA, Stanford LE et al.

    The Journal of neuroscience : the official journal of the Society for Neuroscience 2012;32;40;13987-99

    PUBMED: 23035106; PMC: 3978779; DOI: 10.1523/JNEUROSCI.2433-12.2012

  • A balanced translocation truncates Neurotrimin in a family with intracranial and thoracic aortic aneurysm.

    Luukkonen TM, Pöyhönen M, Palotie A, Ellonen P, Lagström S, Lee JH, Terwilliger JD, Salonen R and Varilo T

    Journal of medical genetics 2012;49;10;621-9

    PUBMED: 23054244; PMC: 4039200; DOI: 10.1136/jmedgenet-2012-100977

  • A suggested new bacteriophage genus: "Viunalikevirus".

    Adriaenssens EM, Ackermann HW, Anany H, Blasdel B, Connerton IF, Goulding D, Griffiths MW, Hooton SP, Kutter EM, Kropinski AM et al.

    Archives of virology 2012;157;10;2035-46

    PUBMED: 22707043; DOI: 10.1007/s00705-012-1360-5

  • Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.

    Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P and Skarnes WC

    Mammalian genome : official journal of the International Mammalian Genome Society 2012;23;9-10;641-52

    PUBMED: 22991088; PMC: 4106044; DOI: 10.1007/s00335-012-9428-9

  • Discovery by the Epistasis Project of an epistatic interaction between the GSTM3 gene and the HHEX/IDE/KIF11 locus in the risk of Alzheimer's disease.

    Bullock JM, Medway C, Cortina-Borja M, Turton JC, Prince JA, Ibrahim-Verbaas CA, Schuur M, Breteler MM, van Duijn CM, Kehoe PG et al.

    Neurobiology of aging 2012;34;4;1309.e1-7

    PUBMED: 23036584; DOI: 10.1016/j.neurobiolaging.2012.08.010

  • Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.

    Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM, Al-Mashhadani MN, Kariuki S, Msefula CL, Gordon MA, de Pinna E et al.

    Nature genetics 2012;44;11;1215-21

    PUBMED: 23023330; PMC: 3491877; DOI: 10.1038/ng.2423

  • The GENCODE pseudogene resource.

    Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M et al.

    Genome biology 2012;13;9;R51

    PUBMED: 22951037; PMC: 3491395; DOI: 10.1186/gb-2012-13-9-r51

  • Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.

    Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D and Kellam P

    Journal of clinical microbiology 2012;50;12;3838-44

    PUBMED: 22993180; PMC: 3502977; DOI: 10.1128/JCM.01516-12

  • Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation.

    Huang J, Sabater-Lleal M, Asselbergs FW, Tregouet D, Shin SY, Ding J, Baumert J, Oudot-Mellakh T, Folkersen L, Johnson AD et al.

    Blood 2012;120;24;4873-81

    PUBMED: 22990020; PMC: 3520624; DOI: 10.1182/blood-2012-06-436188

  • Comparative genomic analyses of the Taylorellae.

    Hauser H, Richter DC, van Tonder A, Clark L and Preston A

    Veterinary microbiology 2012;159;1-2;195-203

    PUBMED: 22541164; DOI: 10.1016/j.vetmic.2012.03.041

  • Genome mapping and genomics of caenorhabditis elegans

    Hodgkin,J., PAULINI,M. and TULI,M.A.

    Genome Mapping and Genomics in Animals 2012;4;17-30

    DOI: 10.1007/978-3-642-31316-5-2

  • A GWAS sequence variant for platelet volume marks an alternative DNM3 promoter in megakaryocytes near a MEIS1 binding site.

    Nürnberg ST, Rendon A, Smethurst PA, Paul DS, Voss K, Thon JN, Lloyd-Jones H, Sambrook JG, Tijssen MR, HaemGen Consortium et al.

    Blood 2012;120;24;4859-68

    PUBMED: 22972982; PMC: 3520622; DOI: 10.1182/blood-2012-01-401893

  • Estimating reassortment rates in co-circulating Eurasian swine influenza viruses.

    Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P, McCauley JW, Wood JLN, Brown IH, Pybus OG, Leigh Brown AJ and For The Combating Swine Influenza Initiative Cosi Consortium

    The Journal of general virology 2012;93;Pt 11;2326-2336

    PUBMED: 22971819; PMC: 3542128; DOI: 10.1099/vir.0.044503-0

  • Detection of cytoplasmic nucleophosmin expression by imaging flow cytometry.

    Grimwade L, Gudgin E, Bloxham D, Bottley G, Vassiliou G, Huntly B, Scott MA and Erber WN

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2012;81;10;896-900

    PUBMED: 22968966; DOI: 10.1002/cyto.a.22116

  • Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis.

    Liu JZ, Almarri MA, Gaffney DJ, Mells GF, Jostins L, Cordell HJ, Ducker SJ, Day DB, Heneghan MA, Neuberger JM et al.

    Nature genetics 2012;44;10;1137-41

    PUBMED: 22961000; PMC: 3459817; DOI: 10.1038/ng.2395

  • Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project.

    Ayadi A, Birling MC, Bottomley J, Bussell J, Fuchs H, Fray M, Gailus-Durner V, Greenaway S, Houghton R, Karp N et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2012;23;9-10;600-10

    PUBMED: 22961258; PMC: 3463797; DOI: 10.1007/s00335-012-9418-y

  • DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders.

    Swaminathan GJ, Bragin E, Chatzimichali EA, Corpas M, Bevan AP, Wright CF, Carter NP, Hurles ME and Firth HV

    Human molecular genetics 2012;21;R1;R37-44

    PUBMED: 22962312; PMC: 3459644; DOI: 10.1093/hmg/dds362

  • An integrated encyclopedia of DNA elements in the human genome.

    ENCODE Project Consortium

    Nature 2012;489;7414;57-74

    PUBMED: 22955616; PMC: 3439153; DOI: 10.1038/nature11247

  • Genomics: ENCODE explained.

    Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y and Segal E

    Nature 2012;489;7414;52-5

    PUBMED: 22955614; DOI: 10.1038/489052a

  • Landscape of transcription in human cells.

    Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al.

    Nature 2012;489;7414;101-8

    PUBMED: 22955620; PMC: 3684276; DOI: 10.1038/nature11233

  • Genome-wide association analysis of imputed rare variants: application to seven common complex diseases.

    Mägi R, Asimit JL, Day-Williams AG, Zeggini E and Morris AP

    Genetic epidemiology 2012;36;8;785-96

    PUBMED: 22951892; PMC: 3569874; DOI: 10.1002/gepi.21675

  • The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

    Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L et al.

    Molecular & cellular proteomics : MCP 2012;11;12;1682-9

    PUBMED: 22949509; PMC: 3518121; DOI: 10.1074/mcp.O112.021543

  • Mapping cis- and trans-regulatory effects across multiple tissues in twins.

    Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A et al.

    Nature genetics 2012;44;10;1084-9

    PUBMED: 22941192; PMC: 3784328; DOI: 10.1038/ng.2394

  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

    Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al.

    Genome research 2012;22;9;1775-89

    PUBMED: 22955988; PMC: 3431493; DOI: 10.1101/gr.132159.111

  • Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

    Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T et al.

    Genome research 2012;22;9;1698-710

    PUBMED: 22955982; PMC: 3431487; DOI: 10.1101/gr.134478.111

  • Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein.

    Collins J, van Pijkeren JP, Svensson L, Claesson MJ, Sturme M, Li Y, Cooney JC, van Sinderen D, Walker AW, Parkhill J et al.

    Molecular microbiology 2012;85;5;862-77

    PUBMED: 22724453; DOI: 10.1111/j.1365-2958.2012.08148.x

  • GENCODE: the reference human genome annotation for The ENCODE Project.

    Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al.

    Genome research 2012;22;9;1760-74

    PUBMED: 22955987; PMC: 3431492; DOI: 10.1101/gr.135350.111

  • Gene expression profiles in white blood cells of volunteers exposed to a 50 Hz electromagnetic field.

    Kirschenlohr H, Ellis P, Hesketh R and Metcalfe J

    Radiation research 2012;178;3;138-49

    PUBMED: 22856684; DOI: 10.1667/rr2859.1

  • Genetic markers for SSG resistance in Leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent.

    Vanaerschot M, Decuypere S, Downing T, Imamura H, Stark O, De Doncker S, Roy S, Ostyn B, Maes L, Khanal B et al.

    The Journal of infectious diseases 2012;206;5;752-5

    PUBMED: 22753945; PMC: 4125624; DOI: 10.1093/infdis/jis424

  • Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese.

    Dunstan SJ, Rockett KA, Quyen NT, Teo YY, Thai CQ, Hang NT, Jeffreys A, Clark TG, Small KS, Simmons CP et al.

    Genes and immunity 2012;13;6;503-8

    PUBMED: 22673309; PMC: 3758997; DOI: 10.1038/gene.2012.25

  • Generation of the Sotos syndrome deletion in mice.

    Migdalska AM, van der Weyden L, Ismail O, Sanger Mouse Genetics Project, Rust AG, Rashid M, White JK, Sánchez-Andrade G, Lupski JR, Logan DW et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2012;23;11-12;749-57

    PUBMED: 22926222; PMC: 3510424; DOI: 10.1007/s00335-012-9416-0

  • Automatic segmentation and tracking of thrombus formation within in vitro microscopic video sequences

    Peter,L., Brieu,N, Jansen,S., Smethurst,P.A., OUWEHAND,W.H. and Navab,N.

    Proceedings - International Symposium on Biomedical Imaging 2012;1635-7

    DOI: 10.1109/ISBI.2012.6235890

  • Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

    Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT and Marioni JC

    Genome research 2012;22;12;2376-84

    PUBMED: 22919075; PMC: 3514667; DOI: 10.1101/gr.142281.112

  • Sequencing and characterization of the FVB/NJ mouse genome.

    Wong K, Bumpstead S, Van Der Weyden L, Reinholdt LG, Wilming LG, Adams DJ and Keane TM

    Genome biology 2012;13;8;R72

    PUBMED: 22916792; PMC: 3491372; DOI: 10.1186/gb-2012-13-8-r72

  • Genomic variation in the vomeronasal receptor gene repertoires of inbred mice.

    Wynn EH, Sánchez-Andrade G, Carss KJ and Logan DW

    BMC genomics 2012;13;415

    PUBMED: 22908939; PMC: 3460788; DOI: 10.1186/1471-2164-13-415

  • Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis.

    Jones ML, Collins MO, Goulding D, Choudhary JS and Rayner JC

    Cell host & microbe 2012;12;2;246-58

    PUBMED: 22901544; PMC: 3501726; DOI: 10.1016/j.chom.2012.06.005

  • JAK2V617F homozygosity arises commonly and recurrently in PV and ET, but PV is characterized by expansion of a dominant homozygous subclone.

    Godfrey AL, Chen E, Pagano F, Ortmann CA, Silber Y, Bellosillo B, Guglielmelli P, Harrison CN, Reilly JT, Stegelmann F et al.

    Blood 2012;120;13;2704-7

    PUBMED: 22898600; PMC: 3672970; DOI: 10.1182/blood-2012-05-431791

  • LRP1B deletion in high-grade serous ovarian cancers is associated with acquired chemotherapy resistance to liposomal doxorubicin.

    Cowin PA, George J, Fereday S, Loehrer E, Van Loo P, Cullinane C, Etemadmoghadam D, Ftouni S, Galletta L, Anglesio MS et al.

    Cancer research 2012;72;16;4060-73

    PUBMED: 22896685; DOI: 10.1158/0008-5472.CAN-12-0203

  • Design and implementation of ProteinWorldDB

    Lifschitz,S., Viana,C.J.M., Tristão,C., Catanho,M., Degrave,W.M., De Miranda,A.B., Bezerra,M. and OTTO,T.D.

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)  2012;7409;144-55

    DOI: 10.1007/978-3-642-31927-3_13

  • Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

    Scott RA, Lagou V, Welch RP, Wheeler E, Montasser ME, Luan J, Mägi R, Strawbridge RJ, Rehnberg E, Gustafsson S et al.

    Nature genetics 2012;44;9;991-1005

    PUBMED: 22885924; PMC: 3433394; DOI: 10.1038/ng.2385

  • Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.

    Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A et al.

    Nature genetics 2012;44;9;981-90

    PUBMED: 22885922; PMC: 3442244; DOI: 10.1038/ng.2383

  • Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study.

    Voight BF, Peloso GM, Orho-Melander M, Frikke-Schmidt R, Barbalic M, Jensen MK, Hindy G, Hólm H, Ding EL, Johnson T et al.

    Lancet (London, England) 2012;380;9841;572-80

    PUBMED: 22607825; PMC: 3419820; DOI: 10.1016/S0140-6736(12)60312-2

  • Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.

    Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A, Yu J, Sangal V, Brown DJ, Coia JE, Kim DW et al.

    Nature genetics 2012;44;9;1056-9

    PUBMED: 22863732; PMC: 3442231; DOI: 10.1038/ng.2369

  • 'Sifting the significance from the data' - the impact of high-throughput genomic technologies on human genetics and health care.

    Clarke AJ, Cooper DN, Krawczak M, Tyler-Smith C, Wallace HM, Wilkie AO, Raymond FL, Chadwick R, Craddock N, John R et al.

    Human genomics 2012;6;11

    PUBMED: 23244462; PMC: 3500243; DOI: 10.1186/1479-7364-6-11

  • Rapid-throughput skeletal phenotyping of 100 knockout mice identifies 9 new genes that determine bone strength.

    Bassett JH, Gogakos A, White JK, Evans H, Jacques RM, van der Spek AH, Sanger Mouse Genetics Project, Ramirez-Solis R, Ryder E, Sunter D et al.

    PLoS genetics 2012;8;8;e1002858

    PUBMED: 22876197; PMC: 3410859; DOI: 10.1371/journal.pgen.1002858

  • Molecular characterization of the 2011 Hong Kong scarlet fever outbreak.

    Tse H, Bao JY, Davies MR, Maamary P, Tsoi HW, Tong AH, Ho TC, Lin CH, Gillen CM, Barnett TC et al.

    The Journal of infectious diseases 2012;206;3;341-51

    PUBMED: 22615319; PMC: 4125623; DOI: 10.1093/infdis/jis362

  • Biochemical and functional analysis of two Plasmodium falciparum blood-stage 6-cys proteins: P12 and P41.

    Taechalertpaisarn T, Crosnier C, Bartholdson SJ, Hodder AN, Thompson J, Bustamante LY, Wilson DW, Sanders PR, Wright GJ, Rayner JC et al.

    PloS one 2012;7;7;e41937

    PUBMED: 22848665; PMC: 3407074; DOI: 10.1371/journal.pone.0041937

  • Genome-wide meta-analysis of common variant differences between men and women.

    Boraska V, Jerončić A, Colonna V, Southam L, Nyholt DR, Rayner NW, Perry JR, Toniolo D, Albrecht E, Ang W et al.

    Human molecular genetics 2012;21;21;4805-15

    PUBMED: 22843499; PMC: 3471397; DOI: 10.1093/hmg/dds304

  • Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus.

    Rinaldi G, Eckert SE, Tsai IJ, Suttiprapa S, Kines KJ, Tort JF, Mann VH, Turner DJ, Berriman M and Brindley PJ

    PLoS pathogens 2012;8;7;e1002820

    PUBMED: 22911241; PMC: 3406096; DOI: 10.1371/journal.ppat.1002820

  • Rapid turnover of long noncoding RNAs and the evolution of gene expression.

    Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT and Marques AC

    PLoS genetics 2012;8;7;e1002841

    PUBMED: 22844254; PMC: 3406015; DOI: 10.1371/journal.pgen.1002841

  • A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

    Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP and Gu Y

    BMC genomics 2012;13;341

    PUBMED: 22827831; PMC: 3431227; DOI: 10.1186/1471-2164-13-341

  • A familial case with interstitial 2q36 deletion: variable phenotypic expression in full and mosaic state.

    Freitas ÉL, Gribble SM, Simioni M, Vieira TP, Prigmore E, Krepischi AC, Rosenberg C, Pearson PL, Melo DG and Gil-da-Silva-Lopes VL

    European journal of medical genetics 2012;55;11;660-5

    PUBMED: 22820457; DOI: 10.1016/j.ejmg.2012.06.015

  • A Plasmodium calcium-dependent protein kinase controls zygote development and transmission by translationally activating repressed mRNAs.

    Sebastian S, Brochet M, Collins MO, Schwach F, Jones ML, Goulding D, Rayner JC, Choudhary JS and Billker O

    Cell host & microbe 2012;12;1;9-19

    PUBMED: 22817984; PMC: 3414820; DOI: 10.1016/j.chom.2012.05.014

  • Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.

    Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I et al.

    Nature 2012;487;7407;375-9

    PUBMED: 22722859; PMC: 3738909; DOI: 10.1038/nature11174

  • Genetically distinct subsets within ANCA-associated vasculitis.

    Lyons PA, Rayner TF, Trivedi S, Holle JU, Watts RA, Jayne DR, Baslund B, Brenchley P, Bruchfeld A, Chaudhry AN et al.

    The New England journal of medicine 2012;367;3;214-23

    PUBMED: 22808956; DOI: 10.1056/NEJMoa1108735

  • Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network.

    Serra-Musach J, Aguilar H, Iorio F, Comellas F, Berenguer A, Brunet J, Saez-Rodriguez J and Pujana MA

    Integrative biology : quantitative biosciences from nano to macro 2012;4;9;1038-48

    PUBMED: 22806580; PMC: 4699251; DOI: 10.1039/c2ib20052j

  • Permissive and restricted virus infection of murine embryonic stem cells.

    Wash R, Calabressi S, Franz S, Griffiths SJ, Goulding D, Tan EP, Wise H, Digard P, Haas J, Efstathiou S and Kellam P

    The Journal of general virology 2012;93;Pt 10;2118-2130

    PUBMED: 22815272; PMC: 3541792; DOI: 10.1099/vir.0.043406-0

  • Next-generation sequencing of experimental mouse strains.

    Yalcin B, Adams DJ, Flint J and Keane TM

    Mammalian genome : official journal of the International Mammalian Genome Society 2012;23;9-10;490-8

    PUBMED: 22772437; PMC: 3463794; DOI: 10.1007/s00335-012-9402-6

  • Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.

    arcOGEN Consortium, arcOGEN Collaborators, Zeggini E, Panoutsopoulou K, Southam L, Rayner NW, Day-Williams AG, Lopes MC, Boraska V, Esko T et al.

    Lancet (London, England) 2012;380;9844;815-23

    PUBMED: 22763110; PMC: 3443899; DOI: 10.1016/S0140-6736(12)60681-3

  • The fallacy of ratio correction to address confounding factors.

    Karp NA, Segonds-Pichon A, Gerdin AK, Ramírez-Solis R and White JK

    Laboratory animals 2012;46;3;245-52

    PUBMED: 22829707; PMC: 4152922; DOI: 10.1258/la.2012.012003

  • Predisposition gene identification in common cancers by exome sequencing: insights from familial breast cancer.

    Snape K, Ruark E, Tarpey P, Renwick A, Turnbull C, Seal S, Murray A, Hanks S, Douglas J, Stratton MR and Rahman N

    Breast cancer research and treatment 2012;134;1;429-33

    PUBMED: 22527104; DOI: 10.1007/s10549-012-2057-x

  • Ubiquitous Hepatocystis infections, but no evidence of Plasmodium falciparum-like malaria parasites in wild greater spot-nosed monkeys (Cercopithecus nictitans).

    Ayouba A, Mouacha F, Learn GH, Mpoudi-Ngole E, Rayner JC, Sharp PM, Hahn BH, Delaporte E and Peeters M

    International journal for parasitology 2012;42;8;709-13

    PUBMED: 22691606; DOI: 10.1016/j.ijpara.2012.05.004

  • Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA.

    Lindhurst MJ, Parker VE, Payne F, Sapp JC, Rudge S, Harris J, Witkowski AM, Zhang Q, Groeneveld MP, Scott CE et al.

    Nature genetics 2012;44;8;928-33

    PUBMED: 22729222; PMC: 3461408; DOI: 10.1038/ng.2332

  • Impact of restricted marital practices on genetic variation in an endogamous Gujarati group.

    Pemberton TJ, Li FY, Hanson EK, Mehta NU, Choi S, Ballantyne J, Belmont JW, Rosenberg NA, Tyler-Smith C and Patel PI

    American journal of physical anthropology 2012;149;1;92-103

    PUBMED: 22729696; PMC: 3436606; DOI: 10.1002/ajpa.22101

  • Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory--pipe dream or reality?

    Török ME and Peacock SJ

    The Journal of antimicrobial chemotherapy 2012;67;10;2307-8

    PUBMED: 22729921; DOI: 10.1093/jac/dks247

  • Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool.

    Pagani L, Kivisild T, Tarekegn A, Ekong R, Plaster C, Gallego Romero I, Ayub Q, Mehdi SQ, Thomas MG, Luiselli D et al.

    American journal of human genetics 2012;91;1;83-96

    PUBMED: 22726845; PMC: 3397267; DOI: 10.1016/j.ajhg.2012.05.015

  • Small effective population size and genetic homogeneity in the Val Borbera isolate.

    Colonna V, Pistis G, Bomba L, Mona S, Matullo G, Boano R, Sala C, Viganò F, Torroni A, Achilli A et al.

    European journal of human genetics : EJHG 2012;21;1;89-94

    PUBMED: 22713810; PMC: 3522197; DOI: 10.1038/ejhg.2012.113

  • Loss of RASSF1A synergizes with deregulated RUNX2 signaling in tumorigenesis.

    van der Weyden L, Papaspyropoulos A, Poulogiannis G, Rust AG, Rashid M, Adams DJ, Arends MJ and O'Neill E

    Cancer research 2012;72;15;3817-3827

    PUBMED: 22710434; PMC: 4067151; DOI: 10.1158/0008-5472.CAN-11-3343

  • The genomic landscape shaped by selection on transposable elements across 18 mouse strains.

    Nellåker C, Keane TM, Yalcin B, Wong K, Agam A, Belgard TG, Flint J, Adams DJ, Frankel WN and Ponting CP

    Genome biology 2012;13;6;R45

    PUBMED: 22703977; PMC: 3446317; DOI: 10.1186/gb-2012-13-6-r45

  • Finding a needle in a haystack. Microbial metatranscriptomes.

    Chappell L

    Nature reviews. Microbiology 2012;10;7;446

    PUBMED: 22699963; DOI: 10.1038/nrmicro2821

  • Impact of common variation in bone-related genes on type 2 diabetes and related traits.

    Billings LK, Hsu YH, Ackerman RJ, Dupuis J, Voight BF, Rasmussen-Torvik LJ, Hercberg S, Lathrop M, Barnes D, Langenberg C et al.

    Diabetes 2012;61;8;2176-86

    PUBMED: 22698912; PMC: 3402303; DOI: 10.2337/db11-1515

  • SynGAP isoforms exert opposing effects on synaptic strength.

    McMahon AC, Barnett MW, O'Leary TS, Stoney PN, Collins MO, Papadia S, Choudhary JS, Komiyama NH, Grant SG, Hardingham GE et al.

    Nature communications 2012;3;900

    PUBMED: 22692543; PMC: 3621422; DOI: 10.1038/ncomms1900

  • Genome-wide association analysis identifies susceptibility loci for migraine without aura.

    Freilinger T, Anttila V, de Vries B, Malik R, Kallela M, Terwindt GM, Pozo-Rosich P, Winsvold B, Nyholt DR, van Oosterhout WP et al.

    Nature genetics 2012;44;7;777-82

    PUBMED: 22683712; PMC: 3773912; DOI: 10.1038/ng.2307

  • A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

    Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M and Otto TD

    Nature protocols 2012;7;7;1260-84

    PUBMED: 22678431; PMC: 3648784; DOI: 10.1038/nprot.2012.068

  • The role of sphingosine-1-phosphate transporter Spns2 in immune system function.

    Nijnik A, Clare S, Hale C, Chen J, Raisen C, Mottram L, Lucas M, Estabel J, Ryder E, Adissu H et al.

    Journal of immunology (Baltimore, Md. : 1950) 2012;189;1;102-11

    PUBMED: 22664872; PMC: 3381845; DOI: 10.4049/jimmunol.1200282

  • Novel mutations consolidate KCTD7 as a progressive myoclonus epilepsy gene.

    Kousi M, Anttila V, Schulz A, Calafato S, Jakkula E, Riesch E, Myllykangas L, Kalimo H, Topçu M, Gökben S et al.

    Journal of medical genetics 2012;49;6;391-9

    PUBMED: 22693283; DOI: 10.1136/jmedgenet-2012-100859

  • Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs.

    Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, Ormond D, Oliver K, Elton D, Mumford JA et al.

    PLoS pathogens 2012;8;5;e1002730

    PUBMED: 22693449; PMC: 3364949; DOI: 10.1371/journal.ppat.1002730

  • The tomato genome sequence provides insights into fleshy fruit evolution.

    Tomato Genome Consortium

    Nature 2012;485;7400;635-41

    PUBMED: 22660326; PMC: 3378239; DOI: 10.1038/nature11119

  • The Clostridium difficile spo0A gene is a persistence and transmission factor.

    Deakin LJ, Clare S, Fagan RP, Dawson LF, Pickard DJ, West MR, Wren BW, Fairweather NF, Dougan G and Lawley TD

    Infection and immunity 2012;80;8;2704-11

    PUBMED: 22615253; PMC: 3434595; DOI: 10.1128/IAI.00147-12

  • The life history of 21 breast cancers.

    Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, Raine K, Jones D, Marshall J, Ramakrishna M et al.

    Cell 2012;149;5;994-1007

    PUBMED: 22608083; PMC: 3428864; DOI: 10.1016/j.cell.2012.04.023

  • Mutational processes molding the genomes of 21 breast cancers.

    Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, Jones D, Hinton J, Marshall J, Stebbings LA et al.

    Cell 2012;149;5;979-93

    PUBMED: 22608084; PMC: 3414841; DOI: 10.1016/j.cell.2012.04.024

  • The landscape of cancer genes and mutational processes in breast cancer.

    Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR et al.

    Nature 2012;486;7403;400-4

    PUBMED: 22722201; PMC: 3428862; DOI: 10.1038/nature11017

  • A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.

    Manning AK, Hivert MF, Scott RA, Grimsby JL, Bouatia-Naji N, Chen H, Rybin D, Liu CT, Bielak LF, Prokopenko I et al.

    Nature genetics 2012;44;6;659-69

    PUBMED: 22581228; PMC: 3613127; DOI: 10.1038/ng.2274

  • Sibling rivalry among paralogs promotes evolution of the human brain.

    Tyler-Smith C and Xue Y

    Cell 2012;149;4;737-9

    PUBMED: 22579279; PMC: 3477634; DOI: 10.1016/j.cell.2012.04.020

  • Transmission of malaria to mosquitoes blocked by bumped kinase inhibitors.

    Ojo KK, Pfander C, Mueller NR, Burstroem C, Larson ET, Bryan CM, Fox AM, Reid MC, Johnson SM, Murphy RC et al.

    The Journal of clinical investigation 2012;122;6;2301-5

    PUBMED: 22565309; PMC: 3366411; DOI: 10.1172/JCI61822

  • Exome sequencing of liver fluke-associated cholangiocarcinoma.

    Ong CK, Subimerb C, Pairojkul C, Wongkham S, Cutcutache I, Yu W, McPherson JR, Allen GE, Ng CC, Wong BH et al.

    Nature genetics 2012;44;6;690-3

    PUBMED: 22561520; DOI: 10.1038/ng.2273

  • Increased tumorigenesis associated with loss of the tumor suppressor gene Cadm1.

    van der Weyden L, Arends MJ, Rust AG, Poulogiannis G, McIntyre RE and Adams DJ

    Molecular cancer 2012;11;29

    PUBMED: 22553910; PMC: 3489691; DOI: 10.1186/1476-4598-11-29

  • The 1000 Genomes Project: data management and community access.

    Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M et al.

    Nature methods 2012;9;5;459-62

    PUBMED: 22543379; PMC: 3340611; DOI: 10.1038/nmeth.1974

  • A genome-wide association meta-analysis identifies new childhood obesity loci.

    Bradfield JP, Taal HR, Timpson NJ, Scherag A, Lecoeur C, Warrington NM, Hypponen E, Holst C, Valcarcel B, Thiering E et al.

    Nature genetics 2012;44;5;526-31

    PUBMED: 22484627; PMC: 3370100; DOI: 10.1038/ng.2247

  • Bcl11a is required for neuronal morphogenesis and sensory circuit formation in dorsal spinal cord development.

    John A, Brylka H, Wiegreffe C, Simon R, Liu P, Jüttner R, Crenshaw EB, Luyten FP, Jenkins NA, Copeland NG et al.

    Development (Cambridge, England) 2012;139;10;1831-41

    PUBMED: 22491945; PMC: 4067532; DOI: 10.1242/dev.072850

  • Changes in HDL cholesterol and cardiovascular outcomes after lipid modification therapy.

    Ray K, Wainwright NW, Visser L, Witteman J, Breteler M, Ambegaonkar B, Hofman A, Stricker B, Wareham N, Khaw KT and Sandhu M

    Heart (British Cardiac Society) 2012;98;10;780-5

    PUBMED: 22447463; DOI: 10.1136/heartjnl-2011-301405

  • Common variants at 12q15 and 12q24 are associated with infant head circumference.

    Taal HR, St Pourcain B, Thiering E, Das S, Mook-Kanamori DO, Warrington NM, Kaakinen M, Kreiner-Møller E, Bradfield JP, Freathy RM et al.

    Nature genetics 2012;44;5;532-8

    PUBMED: 22504419; PMC: 3773913; DOI: 10.1038/ng.2238

  • Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes.

    Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, Rajasegaran V, Heng HL, Deng N, Gan A et al.

    Nature genetics 2012;44;5;570-4

    PUBMED: 22484628; DOI: 10.1038/ng.2246

  • Image-based characterization of thrombus formation in time-lapse DIC microscopy.

    Brieu N, Navab N, Serbanovic-Canic J, Ouwehand WH, Stemple DL, Cvejic A and Groher M

    Medical image analysis 2012;16;4;915-31

    PUBMED: 22482997; PMC: 3740235; DOI: 10.1016/j.media.2012.02.002

  • Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of α-dystroglycan.

    Roscioli T, Kamsteeg EJ, Buysse K, Maystadt I, van Reeuwijk J, van den Elzen C, van Beusekom E, Riemersma M, Pfundt R, Vissers LE et al.

    Nature genetics 2012;44;5;581-5

    PUBMED: 22522421; PMC: 3378661; DOI: 10.1038/ng.2253

  • The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma.

    Pérez-Mancera PA, Rust AG, van der Weyden L, Kristiansen G, Li A, Sarver AL, Silverstein KA, Grützmann R, Aust D, Rümmele P et al.

    Nature 2012;486;7402;266-70

    PUBMED: 22699621; PMC: 3376394; DOI: 10.1038/nature11114

  • The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

    Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;20;E1277-86

    PUBMED: 22538806; PMC: 3356629; DOI: 10.1073/pnas.1201061109

  • High levels of RNA-editing site conservation amongst 15 laboratory mouse strains.

    Danecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S, Ponting CP, Flint J, Durbin R, Keane TM and Adams DJ

    Genome biology 2012;13;4;26

    PUBMED: 22524474; PMC: 3446300; DOI: 10.1186/gb-2012-13-4-r26

  • Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population.

    Bell JT, Tsai PC, Yang TP, Pidsley R, Nisbet J, Glass D, Mangino M, Zhai G, Zhang F, Valdes A et al.

    PLoS genetics 2012;8;4;e1002629

    PUBMED: 22532803; PMC: 3330116; DOI: 10.1371/journal.pgen.1002629

  • Patterns of cis regulatory variation in diverse human populations.

    Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M et al.

    PLoS genetics 2012;8;4;e1002639

    PUBMED: 22532805; PMC: 3330104; DOI: 10.1371/journal.pgen.1002639

  • Nuclear receptor binding protein 1 regulates intestinal progenitor cell homeostasis and tumour formation.

    Wilson CH, Crombie C, van der Weyden L, Poulogiannis G, Rust AG, Pardo M, Gracia T, Yu L, Choudhary J, Poulin GB et al.

    The EMBO journal 2012;31;11;2486-97

    PUBMED: 22510880; PMC: 3365428; DOI: 10.1038/emboj.2012.91

  • Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma.

    Persson M, Andrén Y, Moskaluk CA, Frierson HF, Cooke SL, Futreal PA, Kling T, Nelander S, Nordkvist A, Persson F and Stenman G

    Genes, chromosomes & cancer 2012;51;8;805-17

    PUBMED: 22505352; DOI: 10.1002/gcc.21965

  • Misuse of hierarchical linear models overstates the significance of a reported association between OXTR and prosociality.

    Jostins L, Pickrell JK, MacArthur DG and Barrett JC

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;18;E1048

    PUBMED: 22499788; PMC: 3344973; DOI: 10.1073/pnas.1202539109

  • optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.

    Shah TS, Liu JZ, Floyd JA, Morris JA, Wirth N, Barrett JC and Anderson CA

    Bioinformatics (Oxford, England) 2012;28;12;1598-603

    PUBMED: 22500001; PMC: 3371828; DOI: 10.1093/bioinformatics/bts180

  • Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.

    Wright JC, Collins MO, Yu L, Käll L, Brosch M and Choudhary JS

    Molecular & cellular proteomics : MCP 2012;11;8;478-91

    PUBMED: 22493177; PMC: 3412976; DOI: 10.1074/mcp.O111.014522

  • Generation of multipotent lung and airway progenitors from mouse ESCs and patient-specific cystic fibrosis iPSCs.

    Mou H, Zhao R, Sherwood R, Ahfeldt T, Lapey A, Wain J, Sicilian L, Izvolsky K, Musunuru K, Cowan C and Rajagopal J

    Cell stem cell 2012;10;4;385-97

    PUBMED: 22482504; PMC: 3474327; DOI: 10.1016/j.stem.2012.01.018

  • Analysis of context-dependent errors for illumina sequencing.

    Abnizova I, Leonard S, Skelly T, Brown A, Jackson D, Gourtovaia M, Qi G, Te Boekhorst R, Faruque N, Lewis K and Cox T

    Journal of bioinformatics and computational biology 2012;10;2;1241005

    PUBMED: 22809341; DOI: 10.1142/S0219720012410053

  • Interaction of insulin and PPAR-α genes in Alzheimer's disease: the Epistasis Project.

    Kölsch H, Lehmann DJ, Ibrahim-Verbaas CA, Combarros O, van Duijn CM, Hammond N, Belbin O, Cortina-Borja M, Lehmann MG, Aulchenko YS et al.

    Journal of neural transmission (Vienna, Austria : 1996) 2012;119;4;473-9

    PUBMED: 22065208; DOI: 10.1007/s00702-011-0732-4

  • Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).

    Lawton J, Brugat T, Yan YX, Reid AJ, Böhme U, Otto TD, Pain A, Jackson A, Berriman M, Cunningham D et al.

    BMC genomics 2012;13;125

    PUBMED: 22458863; PMC: 3384456; DOI: 10.1186/1471-2164-13-125

  • Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.

    Dastani Z, Hivert MF, Timpson N, Perry JR, Yuan X, Scott RA, Henneman P, Heid IM, Kizer JR, Lyytikäinen LP et al.

    PLoS genetics 2012;8;3;e1002607

    PUBMED: 22479202; PMC: 3315470; DOI: 10.1371/journal.pgen.1002607

  • Afghanistan's ethnic groups share a Y-chromosomal heritage structured by historical events.

    Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martínez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M et al.

    PloS one 2012;7;3;e34288

    PUBMED: 22470552; PMC: 3314501; DOI: 10.1371/journal.pone.0034288

  • Systematic identification of genomic markers of drug sensitivity in cancer cells.

    Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J et al.

    Nature 2012;483;7391;570-5

    PUBMED: 22460902; PMC: 3349233; DOI: 10.1038/nature11005

  • Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis.

    Stahl EA, Wegmann D, Trynka G, Gutierrez-Achury J, Do R, Voight BF, Kraft P, Chen R, Kallberg HJ, Kurreeman FA et al.

    Nature genetics 2012;44;5;483-9

    PUBMED: 22446960; PMC: 6560362; DOI: 10.1038/ng.2232

  • IFITM3 restricts the morbidity and mortality associated with influenza.

    Everitt AR, Clare S, Pertel T, John SP, Wash RS, Smith SE, Chin CR, Feeley EM, Sims JS, Adams DJ et al.

    Nature 2012;484;7395;519-23

    PUBMED: 22446628; PMC: 3648786; DOI: 10.1038/nature10921

  • Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

    Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A and Robertson DL

    BMC bioinformatics 2012;13;47

    PUBMED: 22443413; PMC: 3359224; DOI: 10.1186/1471-2105-13-47

  • ARIEL and AMELIA: testing for an accumulation of rare variants using next-generation sequencing data.

    Asimit JL, Day-Williams AG, Morris AP and Zeggini E

    Human heredity 2012;73;2;84-94

    PUBMED: 22441326; PMC: 3477640; DOI: 10.1159/000336982

  • Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy.

    Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham SM, Mourier T, Norton R, Quail MA et al.

    PLoS pathogens 2012;8;3;e1002567

    PUBMED: 22457617; PMC: 3310773; DOI: 10.1371/journal.ppat.1002567

  • Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

    Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A and Tress ML

    Molecular biology and evolution 2012;29;9;2265-83

    PUBMED: 22446687; PMC: 3424414; DOI: 10.1093/molbev/mss100

  • The importance of identifying alternative splicing in vertebrate genome annotation.

    Frankish A, Mudge JM, Thomas M and Harrow J

    Database : the journal of biological databases and curation 2012;2012;bas014

    PUBMED: 22434846; PMC: 3308168; DOI: 10.1093/database/bas014

  • Community gene annotation in practice.

    Loveland JE, Gilbert JG, Griffiths E and Harrow JL

    Database : the journal of biological databases and curation 2012;2012;bas009

    PUBMED: 22434843; PMC: 3308165; DOI: 10.1093/database/bas009

  • Tracking and coordinating an international curation effort for the CCDS Project.

    Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S et al.

    Database : the journal of biological databases and curation 2012;2012;bas008

    PUBMED: 22434842; PMC: 3308164; DOI: 10.1093/database/bas008

  • An insertional mutagenesis screen identifies genes that cooperate with Mll-AF9 in a murine leukemogenesis model.

    Bergerson RJ, Collier LS, Sarver AL, Been RA, Lugthart S, Diers MD, Zuber J, Rappaport AR, Nixon MJ, Silverstein KA et al.

    Blood 2012;119;19;4512-23

    PUBMED: 22427200; PMC: 3362364; DOI: 10.1182/blood-2010-04-281428

  • Detailed metabolic and genetic characterization reveals new associations for 30 known lipid loci.

    Tukiainen T, Kettunen J, Kangas AJ, Lyytikäinen LP, Soininen P, Sarin AP, Tikkanen E, O'Reilly PF, Savolainen MJ, Kaski K et al.

    Human molecular genetics 2012;21;6;1444-55

    PUBMED: 22156771; DOI: 10.1093/hmg/ddr581

  • Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma.

    Mann KM, Ward JM, Yew CC, Kovochich A, Dawson DW, Black MA, Brett BT, Sheetz TE, Dupuy AJ, Australian Pancreatic Cancer Genome Initiative et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;16;5934-41

    PUBMED: 22421440; PMC: 3341075; DOI: 10.1073/pnas.1202490109

  • No interactions between previously associated 2-hour glucose gene variants and physical activity or BMI on 2-hour glucose levels.

    Scott RA, Chu AY, Grarup N, Manning AK, Hivert MF, Shungin D, Tönjes A, Yesupriya A, Barnes D, Bouatia-Naji N et al.

    Diabetes 2012;61;5;1291-6

    PUBMED: 22415877; PMC: 3331745; DOI: 10.2337/db11-0973

  • Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.

    Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT, Marsh P, Skilton RJ, Holland MJ, Mabey D, Peeling RW et al.

    Nature genetics 2012;44;4;413-9, S1

    PUBMED: 22406642; PMC: 3378690; DOI: 10.1038/ng.2214

  • Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

    Gerlinger M, Rowan AJ, Horswell S, Math M, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A et al.

    The New England journal of medicine 2012;366;10;883-892

    PUBMED: 22397650; PMC: 4878653; DOI: 10.1056/NEJMoa1113205

  • BLUEPRINT to decode the epigenetic signature written in blood.

    Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A et al.

    Nature biotechnology 2012;30;3;224-6

    PUBMED: 22398613; DOI: 10.1038/nbt.2153

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T et al.

    Nature 2012;483;7388;169-75

    PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842

  • The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella.

    Ricci V, Loman N, Pallen M, Ivens A, Fookes M, Langridge GC, Wain J and Piddock LJ

    The Journal of antimicrobial chemotherapy 2012;67;3;589-99

    PUBMED: 22186876; PMC: 4125622; DOI: 10.1093/jac/dkr515

  • Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius.

    Strouts FR, Power P, Croucher NJ, Corton N, van Tonder A, Quail MA, Langford PR, Hudson MJ, Parkhill J, Kroll JS and Bentley SD

    Emerging infectious diseases 2012;18;3;449-57

    PUBMED: 22377449; PMC: 3309571; DOI: 10.3201/eid1803.110728

  • Meta-analysis of genome-wide association studies for personality.

    de Moor MH, Costa PT, Terracciano A, Krueger RF, de Geus EJ, Toshiko T, Penninx BW, Esko T, Madden PA, Derringer J et al.

    Molecular psychiatry 2012;17;3;337-49

    PUBMED: 21173776; DOI: 10.1038/mp.2010.128

  • Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.

    Auburn S, Campino S, Miotto O, Djimde AA, Zongo I, Manske M, Maslen G, Mangano V, Alcock D, MacInnis B et al.

    PloS one 2012;7;2;e32891

    PUBMED: 22393456; PMC: 3290604; DOI: 10.1371/journal.pone.0032891

  • The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex.

    Bentley SD, Comas I, Bryant JM, Walker D, Smith NH, Harris SR, Thurston S, Gagneux S, Wood J, Antonio M et al.

    PLoS neglected tropical diseases 2012;6;2;e1552

    PUBMED: 22389744; PMC: 3289620; DOI: 10.1371/journal.pntd.0001552

  • From HLA association to function.

    Barrett JC

    Nature genetics 2012;44;3;235-6

    PUBMED: 22366857; DOI: 10.1038/ng.2207

  • Jdp2 downregulates Trp53 transcription to promote leukaemogenesis in the context of Trp53 heterozygosity.

    van der Weyden L, Rust AG, McIntyre RE, Robles-Espinoza CD, del Castillo Velasco-Herrera M, Strogantsev R, Ferguson-Smith AC, McCarthy S, Keane TM, Arends MJ and Adams DJ

    Oncogene 2012;32;3;397-402

    PUBMED: 22370638; PMC: 3550594; DOI: 10.1038/onc.2012.56

  • Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome.

    Albers CA, Paul DS, Schulze H, Freson K, Stephens JC, Smethurst PA, Jolley JD, Cvejic A, Kostadima M, Bertone P et al.

    Nature genetics 2012;44;4;435-9, S1-2

    PUBMED: 22366785; PMC: 3428915; DOI: 10.1038/ng.1083

  • Evolutionary genetics of the human Rh blood group system.

    Perry GH, Xue Y, Smith RS, Meyer WK, Calışkan M, Yanez-Cuna O, Lee AS, Gutiérrez-Arcelus M, Ober C, Hollox EJ et al.

    Human genetics 2012;131;7;1205-16

    PUBMED: 22367406; PMC: 3378649; DOI: 10.1007/s00439-012-1147-5

  • A benchmarked protein microarray-based platform for the identification of novel low-affinity extracellular protein interactions.

    Sun Y, Gallagher-Jones M, Barker C and Wright GJ

    Analytical biochemistry 2012;424;1;45-53

    PUBMED: 22342946; PMC: 3325482; DOI: 10.1016/j.ab.2012.01.034

  • A systematic survey of loss-of-function variants in human protein-coding genes.

    MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB et al.

    Science (New York, N.Y.) 2012;335;6070;823-8

    PUBMED: 22344438; PMC: 3299548; DOI: 10.1126/science.1215040

  • Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

    Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C et al.

    Cell 2012;148;4;780-91

    PUBMED: 22341448; PMC: 3281993; DOI: 10.1016/j.cell.2011.11.065

  • Gene-gene interactions in breast cancer susceptibility.

    Turnbull C, Seal S, Renwick A, Warren-Perry M, Hughes D, Elliott A, Pernet D, Peock S, Adlard JW, Barwell J et al.

    Human molecular genetics 2012;21;4;958-62

    PUBMED: 22072393; PMC: 4125627; DOI: 10.1093/hmg/ddr525

  • Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.

    Jackson AP, Berry A, Aslett M, Allison HC, Burton P, Vavrova-Anderson J, Brown R, Browne H, Corton N, Hauser H et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;9;3416-21

    PUBMED: 22331916; PMC: 3295286; DOI: 10.1073/pnas.1117313109

  • Assignment of protein interactions from affinity purification/mass spectrometry data.

    Pardo M and Choudhary JS

    Journal of proteome research 2012;11;3;1462-74

    PUBMED: 22283744; DOI: 10.1021/pr2011632

  • An evaluation of different meta-analysis approaches in the presence of allelic heterogeneity.

    Asimit J, Day-Williams A, Zgaga L, Rudan I, Boraska V and Zeggini E

    European journal of human genetics : EJHG 2012;20;6;709-12

    PUBMED: 22293689; PMC: 3355266; DOI: 10.1038/ejhg.2011.274

  • Cestode genomics - progress and prospects for advancing basic and applied aspects of flatworm biology.

    Olson PD, Zarowiecki M, Kiss F and Brehm K

    Parasite immunology 2012;34;2-3;130-50

    PUBMED: 21793855; DOI: 10.1111/j.1365-3024.2011.01319.x

  • Expression of chemosensory proteins in the tsetse fly Glossina morsitans morsitans is related to female host-seeking behaviour.

    Liu R, He X, Lehane S, Lehane M, Hertz-Fowler C, Berriman M, Field LM and Zhou JJ

    Insect molecular biology 2012;21;1;41-8

    PUBMED: 22074189; PMC: 3664020; DOI: 10.1111/j.1365-2583.2011.01114.x

  • Dissecting the regulatory architecture of gene expression QTLs.

    Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y and Pritchard JK

    Genome biology 2012;13;1;R7

    PUBMED: 22293038; PMC: 3334587; DOI: 10.1186/gb-2012-13-1-r7

  • Genome-wide association study identifies multiple loci influencing human serum metabolite levels.

    Kettunen J, Tukiainen T, Sarin AP, Ortega-Alonso A, Tikkanen E, Lyytikäinen LP, Kangas AJ, Soininen P, Würtz P, Silander K et al.

    Nature genetics 2012;44;3;269-76

    PUBMED: 22286219; PMC: 3605033; DOI: 10.1038/ng.1073

  • Rare MTNR1B variants impairing melatonin receptor 1B function contribute to type 2 diabetes.

    Bonnefond A, Clément N, Fawcett K, Yengo L, Vaillant E, Guillaume JL, Dechaume A, Payne F, Roussel R, Czernichow S et al.

    Nature genetics 2012;44;3;297-301

    PUBMED: 22286214; PMC: 3773908; DOI: 10.1038/ng.1053

  • High-throughput decoding of antitrypanosomal drug efficacy and resistance.

    Alsford S, Eckert S, Baker N, Glover L, Sanchez-Flores A, Leung KF, Turner DJ, Field MC, Berriman M and Horn D

    Nature 2012;482;7384;232-6

    PUBMED: 22278056; PMC: 3303116; DOI: 10.1038/nature10771

  • Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile.

    Mullany P, Williams R, Langridge GC, Turner DJ, Whalan R, Clayton C, Lawley T, Hussain H, McCurrie K, Morden N et al.

    Applied and environmental microbiology 2012;78;7;2147-53

    PUBMED: 22267673; PMC: 3302608; DOI: 10.1128/AEM.06193-11

  • Cancer gene discovery in the mouse.

    McIntyre RE, van der Weyden L and Adams DJ

    Current opinion in genetics & development 2012;22;1;14-20

    PUBMED: 22265936; DOI: 10.1016/j.gde.2011.12.003

  • Modeling partial monosomy for human chromosome 21q11.2-q21.1 reveals haploinsufficient genes influencing behavior and fat deposition.

    Migdalska AM, van der Weyden L, Ismail O, White JK, Sanger Mouse Genetics Project, Sánchez-Andrade G, Logan DW, Arends MJ and Adams DJ

    PloS one 2012;7;1;e29681

    PUBMED: 22276124; PMC: 3262805; DOI: 10.1371/journal.pone.0029681

  • A combined functional annotation score for non-synonymous variants.

    Lopes MC, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J and Zeggini E

    Human heredity 2012;73;1;47-51

    PUBMED: 22261837; PMC: 3390741; DOI: 10.1159/000334984

  • Shared loci for migraine and epilepsy on chromosomes 14q12-q23 and 12q24.2-q24.3.

    Polvi A, Siren A, Kallela M, Rantala H, Artto V, Sobel EM, Palotie A, Lehesjoki AE and Wessman M

    Neurology 2012;78;3;202-9

    PUBMED: 22218271; PMC: 3653199; DOI: 10.1212/WNL.0b013e31823fcd87

  • Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.

    Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P and Odom DT

    Cell 2012;148;1-2;335-48

    PUBMED: 22244452; PMC: 3368268; DOI: 10.1016/j.cell.2011.11.058

  • A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.

    Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M, Aslett MA, De Silva N, Velarde GS, Anderson TJ, Clark RC et al.

    PLoS neglected tropical diseases 2012;6;1;e1455

    PUBMED: 22253936; PMC: 3254664; DOI: 10.1371/journal.pntd.0001455

  • Communication about DTC testing: commentary on a 'family experience of personal genomics'.

    Middleton A

    Journal of genetic counseling 2012;21;3;392-8

    PUBMED: 22223062; DOI: 10.1007/s10897-011-9472-8

  • A method to infer positive selection from marker dynamics in an asexual population.

    Illingworth CJ and Mustonen V

    Bioinformatics (Oxford, England) 2012;28;6;831-7

    PUBMED: 22223745; PMC: 3307107; DOI: 10.1093/bioinformatics/btr722

  • A genome-wide association search for type 2 diabetes genes in African Americans.

    Palmer ND, McDonough CW, Hicks PJ, Roh BH, Wing MR, An SS, Hester JM, Cooke JN, Bostrom MA, Rudock ME et al.

    PloS one 2012;7;1;e29202

    PUBMED: 22238593; PMC: 3251563; DOI: 10.1371/journal.pone.0029202

  • Evidence for transcript networks composed of chimeric RNAs in human cells.

    Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al.

    PloS one 2012;7;1;e28213

    PUBMED: 22238572; PMC: 3251577; DOI: 10.1371/journal.pone.0028213

  • Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

    Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP and Quail MA

    BMC genomics 2012;13;1

    PUBMED: 22214261; PMC: 3312816; DOI: 10.1186/1471-2164-13-1

  • The alveolin IMC1h is required for normal ookinete and sporozoite motility behaviour and host colonisation in Plasmodium berghei.

    Volkmann K, Pfander C, Burstroem C, Ahras M, Goulding D, Rayner JC, Frischknecht F, Billker O and Brochet M

    PloS one 2012;7;7;e41409

    PUBMED: 22844474; PMC: 3402405; DOI: 10.1371/journal.pone.0041409

  • An atypical facial appearance and growth pattern in a child with Cornelia de Lange Syndrome: an intragenic deletion predicting loss of the N-terminal region of NIPBL.

    Murray JE, Walayat M, Gillett P, Sharkey FH, Rajan D, Carter NP and FitzPatrick DR

    Clinical dysmorphology 2012;21;1;22-3

    PUBMED: 21934607; DOI: 10.1097/MCD.0b013e32834c4afc

  • The battle of the SNPs.

    Downing T

    Nature reviews. Microbiology 2012;10;1;6

    PUBMED: 22138960; DOI: 10.1038/nrmicro2716

  • The fine-scale architecture of structural variants in 17 mouse genomes.

    Yalcin B, Wong K, Bhomra A, Goodson M, Keane TM, Adams DJ and Flint J

    Genome biology 2012;13;3;R18

    PUBMED: 22439878; PMC: 3439969; DOI: 10.1186/gb-2012-13-3-r18

  • An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS.

    Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G, Manske M, Imwong M, Dondorp AM, Kwiatkowski DP et al.

    The open genomics journal 2012;5

    PUBMED: 24273626; PMC: 3837216; DOI: 10.2174/1875693X01205010018

  • The Pfam protein families database.

    Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al.

    Nucleic acids research 2012;40;Database issue;D290-301

    PUBMED: 22127870; PMC: 3245129; DOI: 10.1093/nar/gkr1065

  • A robust clustering algorithm for identifying problematic samples in genome-wide association studies.

    Bellenguez C, Strange A, Freeman C, Wellcome Trust Case Control Consortium, Donnelly P and Spencer CC

    Bioinformatics (Oxford, England) 2012;28;1;134-5

    PUBMED: 22057162; PMC: 3244763; DOI: 10.1093/bioinformatics/btr599

  • The role of variation at AβPP, PSEN1, PSEN2, and MAPT in late onset Alzheimer's disease.

    Gerrish A, Russo G, Richards A, Moskvina V, Ivanov D, Harold D, Sims R, Abraham R, Hollingworth P, Chapman J et al.

    Journal of Alzheimer's disease : JAD 2012;28;2;377-87

    PUBMED: 22027014; PMC: 4118466; DOI: 10.3233/JAD-2011-110824

  • Discovery of new treatments in the context of delivering personalized medicine

    Holgate ST, PALOTIE A

    Personalized Medicine. 2012;9;101-4

  • Improving transcription factor binding site predictions by using randomised negative examples

    Rezwan F, Sun Y, Davey N, Adams R, RUST AG, Robinson M

    Lecture Notes in Computer Science 2012;7223;225-37

  • The rocky road to personalized medicine: Computational and statistical challenges

    Corander J, Aittokallio T, RIPATTI S, Kaski S

    Personalized Medicine. 2012;9;109-14

  • Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study.

    Le Quesne Stabej P, Saihan Z, Rangesh N, Steele-Stallard HB, Ambrose J, Coffey A, Emmerson J, Haralambous E, Hughes Y, Steel KP et al.

    Journal of medical genetics 2012;49;1;27-36

    PUBMED: 22135276; PMC: 3678402; DOI: 10.1136/jmedgenet-2011-100468

  • Direct-to-Consumer Genetic Testing; Molecular Genetics and Personalized Medicine

    WRIGHT,C. F. and MACARTHUR,D. G.

    Molecular and Translational Medicine 2012;215-36

    DOI: 10.1007/978-1-61779-530-5_10

  • FiRePat - Finding Regulatory Patterns between sRNAs and Genes

    Mohorianu,I., Lopez-Gomollon,S., SCHWACH,F., Dalmay,T. and Moulton,V.

    Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery 2012;2;3;273-84

    DOI: 10.1002/widm.1053

  • First detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in bulk tank milk in the United Kingdom, January to July 2012.

    Paterson GK, Larsen J, Harrison EM, Larsen AR, Morgan FJ, Peacock SJ, Parkhill J, Zadoks RN and Holmes MA

    Euro surveillance : bulletin Européen sur les maladies transmissibles = European communicable disease bulletin 2012;17;50

    PUBMED: 23241232

  • Genetic analysis of Xenopus tropicalis.

    Geach TJ, Stemple DL and Zimmerman LB

    Methods in molecular biology (Clifton, N.J.) 2012;917;69-110

    PUBMED: 22956083; DOI: 10.1007/978-1-61779-992-1_5

  • Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach.

    Everett DB, Cornick J, Denis B, Chewapreecha C, Croucher N, Harris S, Parkhill J, Gordon S, Carrol ED, French N et al.

    PloS one 2012;7;9;e44250

    PUBMED: 22970189; PMC: 3438182; DOI: 10.1371/journal.pone.0044250

  • Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.

    Demirkan A, van Duijn CM, Ugocsai P, Isaacs A, Pramstaller PP, Liebisch G, Wilson JF, Johansson Å, Rudan I, Aulchenko YS et al.

    PLoS genetics 2012;8;2;e1002490

    PUBMED: 22359512; PMC: 3280968; DOI: 10.1371/journal.pgen.1002490

  • Genome-wide association study to identify common variants associated with brachial circumference: a meta-analysis of 14 cohorts.

    Boraska V, Day-Williams A, Franklin CS, Elliott KS, Panoutsopoulou K, Tachmazidou I, Albrecht E, Bandinelli S, Beilin LJ, Bochud M et al.

    PloS one 2012;7;3;e31369

    PUBMED: 22479309; PMC: 3315559; DOI: 10.1371/journal.pone.0031369

  • Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex.

    Downing T, Stark O, Vanaerschot M, Imamura H, Sanders M, Decuypere S, de Doncker S, Maes I, Rijal S, Sundar S et al.

    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2012;12;1;149-59

    PUBMED: 22119748; PMC: 3315668; DOI: 10.1016/j.meegid.2011.11.005

  • Pluripotency and its layers of complexity.

    Ooi J and Liu P

    Cell regeneration (London, England) 2012;1;1;7

    PUBMED: 25408870; PMC: 4230502; DOI: 10.1186/2045-9769-1-7

  • Transferrin and HFE genes interact in Alzheimer's disease risk: the Epistasis Project.

    Lehmann DJ, Schuur M, Warden DR, Hammond N, Belbin O, Kölsch H, Lehmann MG, Wilcock GK, Brown K, Kehoe PG et al.

    Neurobiology of aging 2012;33;1;202.e1-13

    PUBMED: 20817350; DOI: 10.1016/j.neurobiolaging.2010.07.018

  • Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples.

    Venkatesan M, Amaratunga C, Campino S, Auburn S, Koch O, Lim P, Uk S, Socheat D, Kwiatkowski DP, Fairhurst RM and Plowe CV

    Malaria journal 2012;11;41

    PUBMED: 22321373; PMC: 3295709; DOI: 10.1186/1475-2875-11-41

  • Using mouse models to study function of transcriptional factors in T cell development.

    Li P, Xiao Y, Liu Z and Liu P

    Cell regeneration (London, England) 2012;1;1;8

    PUBMED: 25408871; PMC: 4230505; DOI: 10.1186/2045-9769-1-8

  • WormBase: Annotating many nematode genomes.

    Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P and Sternberg PW

    Worm 2012;1;1;15-21

    PUBMED: 24058818; PMC: 3670165; DOI: 10.4161/worm.19574

  • Zebrafish breeding in the laboratory environment.

    Nasiadka A and Clark MD

    ILAR journal / National Research Council, Institute of Laboratory Animal Resources 2012;53;2;161-8

    PUBMED: 23382347; DOI: 10.1093/ilar.53.2.161

2011

  • Genomics in 2011: challenges and opportunities.

    Adams DJ, Berger B, Harismendy O, Huttenhower C, Liu XS, Myers CL, Oshlack A, Rinn JL and Walhout AJ

    Genome biology 2011;12;12;137

    PUBMED: 22204305; PMC: 3334607; DOI: 10.1186/gb-2011-12-12-137

  • Optimal enzymes for amplifying sequencing libraries.

    Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF, McQuillan JA, Swerdlow HP and Oyola SO

    Nature methods 2011;9;1;10-1

    PUBMED: 22205512; DOI: 10.1038/nmeth.1814

  • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

    Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA

    Bioinformatics (Oxford, England) 2011;28;4;464-9

    PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703

  • A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing.

    Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, Kellam P, Drou N, Caccamo M, Tiley L et al.

    PloS one 2011;6;12;e28879

    PUBMED: 22216131; PMC: 3244418; DOI: 10.1371/journal.pone.0028879

  • The critical role of histone H2A-deubiquitinase Mysm1 in hematopoiesis and lymphocyte differentiation.

    Nijnik A, Clare S, Hale C, Raisen C, McIntyre RE, Yusa K, Everitt AR, Mottram L, Podrini C, Lucas M et al.

    Blood 2011;119;6;1370-9

    PUBMED: 22184403; DOI: 10.1182/blood-2011-05-352666

  • Coordinating cell cycle progression via cyclin specificity.

    Pagliuca FW, Collins MO and Choudhary JS

    Cell cycle (Georgetown, Tex.) 2011;10;24;4195-6

    PUBMED: 22156915; DOI: 10.4161/cc.10.24.18395

  • Jamb and jamc are essential for vertebrate myocyte fusion.

    Powell GT and Wright GJ

    PLoS biology 2011;9;12;e1001216

    PUBMED: 22180726; PMC: 3236736; DOI: 10.1371/journal.pbio.1001216

  • Blood pressure loci identified with a gene-centric array.

    Johnson T, Gaunt TR, Newhouse SJ, Padmanabhan S, Tomaszewski M, Kumari M, Morris RW, Tzoulaki I, O'Brien ET, Poulter NR et al.

    American journal of human genetics 2011;89;6;688-700

    PUBMED: 22100073; PMC: 3234370; DOI: 10.1016/j.ajhg.2011.10.013

  • A homozygous mutant embryonic stem cell bank applicable for phenotype-driven genetic screening.

    Horie K, Kokubu C, Yoshida J, Akagi K, Isotani A, Oshitani A, Yusa K, Ikeda R, Huang Y, Bradley A and Takeda J

    Nature methods 2011;8;12;1071-7

    PUBMED: 22020066; DOI: 10.1038/nmeth.1739

  • Animals learn new tricks from microorganisms.

    Zarowiecki M

    Nature reviews. Microbiology 2011;9;12;836

    PUBMED: 22085859; DOI: 10.1038/nrmicro2694

  • Association of known loci with lipid levels among children and prediction of dyslipidemia in adults.

    Tikkanen E, Tuovinen T, Widén E, Lehtimäki T, Viikari J, Kähönen M, Peltonen L, Raitakari OT and Ripatti S

    Circulation. Cardiovascular genetics 2011;4;6;673-80

    PUBMED: 21984478; DOI: 10.1161/CIRCGENETICS.111.960369

  • Common variants on 8p12 and 1q24.2 confer risk of schizophrenia.

    Shi Y, Li Z, Xu Q, Wang T, Li T, Shen J, Zhang F, Chen J, Zhou G, Ji W et al.

    Nature genetics 2011;43;12;1224-7

    PUBMED: 22037555; DOI: 10.1038/ng.980

  • Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing.

    de Gruijter JM, Lao O, Vermeulen M, Xue Y, Woodwark C, Gillson CJ, Coffey AJ, Ayub Q, Mehdi SQ, Kayser M and Tyler-Smith C

    Investigative genetics 2011;2;1;24

    PUBMED: 22133426; PMC: 3287149; DOI: 10.1186/2041-2223-2-24

  • Defining the power limits of genome-wide association scan meta-analyses.

    Chapman K, Ferreira T, Morris A, Asimit J and Zeggini E

    Genetic epidemiology 2011;35;8;781-9

    PUBMED: 21922540; PMC: 3428938; DOI: 10.1002/gepi.20627

  • Diabetes does not influence activation of coagulation, fibrinolysis or anticoagulant pathways in Gram-negative sepsis (melioidosis).

    Koh GC, Meijers JC, Maude RR, Limmathurotsakul D, Day NP, Peacock SJ, van der Poll T and Wiersinga WJ

    Thrombosis and haemostasis 2011;106;6;1139-48

    PUBMED: 21979378; DOI: 10.1160/TH11-07-0504

  • New gene functions in megakaryopoiesis and platelet formation.

    Gieger C, Radhakrishnan A, Cvejic A, Tang W, Porcu E, Pistis G, Serbanovic-Canic J, Elling U, Goodall AH, Labrune Y et al.

    Nature 2011;480;7376;201-8

    PUBMED: 22139419; PMC: 3335296; DOI: 10.1038/nature10659

  • Quantifying selection acting on a complex trait using allele frequency time series data.

    Illingworth CJ, Parts L, Schiffels S, Liti G and Mustonen V

    Molecular biology and evolution 2011;29;4;1187-97

    PUBMED: 22114362; PMC: 3731369; DOI: 10.1093/molbev/msr289

  • Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

    Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J et al.

    Briefings in bioinformatics 2011;13;3;383-9

    PUBMED: 22110242; PMC: 3357490; DOI: 10.1093/bib/bbr064

  • A world in a grain of sand: human history from genetic data.

    Colonna V, Pagani L, Xue Y and Tyler-Smith C

    Genome biology 2011;12;11;234

    PUBMED: 22104725; PMC: 3334592; DOI: 10.1186/gb-2011-12-11-234

  • Specific capture and whole-genome sequencing of viruses from clinical samples.

    Depledge DP, Palser AL, Watson SJ, Lai IY, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P and Breuer J

    PloS one 2011;6;11;e27805

    PUBMED: 22125625; PMC: 3220689; DOI: 10.1371/journal.pone.0027805

  • Marked endotheliotropism of highly pathogenic avian influenza virus H5N1 following intestinal inoculation in cats.

    Reperant LA, van de Bildt MW, van Amerongen G, Leijten LM, Watson S, Palser A, Kellam P, Eissens AC, Frijlink HW, Osterhaus AD and Kuiken T

    Journal of virology 2011;86;2;1158-65

    PUBMED: 22090101; PMC: 3255817; DOI: 10.1128/JVI.06375-11

  • De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

    Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M, Ruderfer D, Moran J, Chambert K, Toncheva D, Georgieva L et al.

    Molecular psychiatry 2011;17;2;142-53

    PUBMED: 22083728; PMC: 3603134; DOI: 10.1038/mp.2011.154

  • Ensembl 2012.

    Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S et al.

    Nucleic acids research 2011;40;Database issue;D84-90

    PUBMED: 22086963; PMC: 3245178; DOI: 10.1093/nar/gkr991

  • Acquired bleeding disorders

    Perry,D.J and GROVE,C.

    Blood and Bone Marrow Pathology 2011;565-82

    URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780702031472000353

  • Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1.

    Bown MJ, Jones GT, Harrison SC, Wright BJ, Bumpstead S, Baas AF, Gretarsdottir S, Badger SA, Bradley DT, Burnand K et al.

    American journal of human genetics 2011;89;5;619-27

    PUBMED: 22055160; PMC: 3213391; DOI: 10.1016/j.ajhg.2011.10.002

  • Basigin is a receptor essential for erythrocyte invasion by Plasmodium falciparum.

    Crosnier C, Bustamante LY, Bartholdson SJ, Bei AK, Theron M, Uchikawa M, Mboup S, Ndir O, Kwiatkowski DP, Duraisingh MT et al.

    Nature 2011;480;7378;534-7

    PUBMED: 22080952; PMC: 3245779; DOI: 10.1038/nature10606

  • Replication of the association of a MET variant with autism in a Chinese Han population.

    Zhou X, Xu Y, Wang J, Zhou H, Liu X, Ayub Q, Wang X, Tyler-Smith C, Wu L and Xue Y

    PloS one 2011;6;11;e27428

    PUBMED: 22110649; PMC: 3217055; DOI: 10.1371/journal.pone.0027428

  • WormBase 2012: more genomes, more data, new website.

    Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R et al.

    Nucleic acids research 2011;40;Database issue;D735-41

    PUBMED: 22067452; PMC: 3245152; DOI: 10.1093/nar/gkr954

  • Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.

    Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, Szperl A, Bakker SF, Bardella MT, Bhaw-Rosun L, Castillejo G et al.

    Nature genetics 2011;43;12;1193-201

    PUBMED: 22057235; PMC: 3242065; DOI: 10.1038/ng.998

  • Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis.

    March HN, Rust AG, Wright NA, ten Hoeve J, de Ridder J, Eldridge M, van der Weyden L, Berns A, Gadiot J, Uren A et al.

    Nature genetics 2011;43;12;1202-9

    PUBMED: 22057237; PMC: 3233530; DOI: 10.1038/ng.990

  • Ollier disease and Maffucci syndrome are caused by somatic mosaic mutations of IDH1 and IDH2.

    Amary MF, Damato S, Halai D, Eskandarpour M, Berisha F, Bonar F, McCarthy S, Fantin VR, Straley KS, Lobo S et al.

    Nature genetics 2011;43;12;1262-5

    PUBMED: 22057236; DOI: 10.1038/ng.994

  • Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.

    Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X et al.

    Human genetics 2011;131;5;665-74

    PUBMED: 22057783; PMC: 3325425; DOI: 10.1007/s00439-011-1111-9

  • Silencing of RhoA nucleotide exchange factor, ARHGEF3, reveals its unexpected role in iron uptake.

    Serbanovic-Canic J, Cvejic A, Soranzo N, Stemple DL, Ouwehand WH and Freson K

    Blood 2011;118;18;4967-76

    PUBMED: 21715309; PMC: 3208301; DOI: 10.1182/blood-2011-02-337295

  • Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania.

    Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, Harris D, Her Y, Herzyk P, Imamura H et al.

    Genome research 2011;21;12;2129-42

    PUBMED: 22038252; PMC: 3227102; DOI: 10.1101/gr.122945.111

  • Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.

    Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH, Cotton JA, Hilley JD, de Doncker S, Maes I, Mottram JC et al.

    Genome research 2011;21;12;2143-56

    PUBMED: 22038251; PMC: 3227103; DOI: 10.1101/gr.123430.111

  • Mendelian randomization study of B-type natriuretic peptide and type 2 diabetes: evidence of causal association from population studies.

    Pfister R, Sharp S, Luben R, Welsh P, Barroso I, Salomaa V, Meirhaeghe A, Khaw KT, Sattar N, Langenberg C and Wareham NJ

    PLoS medicine 2011;8;10;e1001112

    PUBMED: 22039354; PMC: 3201934; DOI: 10.1371/journal.pmed.1001112

  • Bacterial epidemiology and biology--lessons from genome sequencing.

    Parkhill J and Wren BW

    Genome biology 2011;12;10;230

    PUBMED: 22027015; PMC: 3333767; DOI: 10.1186/gb-2011-12-10-230

  • A scalable pipeline for highly effective genetic modification of a malaria parasite.

    Pfander C, Anar B, Schwach F, Otto TD, Brochet M, Volkmann K, Quail MA, Pain A, Rosen B, Skarnes W et al.

    Nature methods 2011;8;12;1078-82

    PUBMED: 22020067; PMC: 3431185; DOI: 10.1038/nmeth.1742

  • A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol.

    Surakka I, Isaacs A, Karssen LC, Laurila PP, Middelberg RP, Tikkanen E, Ried JS, Lamina C, Mangino M, Igl W et al.

    PLoS genetics 2011;7;10;e1002333

    PUBMED: 22028671; PMC: 3197672; DOI: 10.1371/journal.pgen.1002333

  • Low-bias, strand-specific transcriptome Illumina sequencing by on-flowcell reverse transcription (FRT-seq).

    Mamanova L and Turner DJ

    Nature protocols 2011;6;11;1736-47

    PUBMED: 22015844; DOI: 10.1038/nprot.2011.399

  • Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis.

    Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, Palser AL, Watson SJ, Hedge J, Underwood A et al.

    Journal of virology 2011;86;1;11-8

    PUBMED: 22013031; PMC: 3255882; DOI: 10.1128/JVI.05347-11

  • Identity-by-descent-based phasing and imputation in founder populations using graphical models.

    Palin K, Campbell H, Wright AF, Wilson JF and Durbin R

    Genetic epidemiology 2011;35;8;853-60

    PUBMED: 22006673; PMC: 3368215; DOI: 10.1002/gepi.20635

  • Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.

    Chambers JC, Zhang W, Sehmi J, Li X, Wass MN, Van der Harst P, Holm H, Sanna S, Kavousi M, Baumeister SE et al.

    Nature genetics 2011;43;11;1131-8

    PUBMED: 22001757; PMC: 3482372; DOI: 10.1038/ng.970

  • In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma.

    Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA et al.

    Cell 2011;147;2;382-95

    PUBMED: 22000016; PMC: 3236086; DOI: 10.1016/j.cell.2011.09.032

  • Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells.

    Yusa K, Rashid ST, Strick-Marchand H, Varela I, Liu PQ, Paschon DE, Miranda E, Ordóñez A, Hannan NR, Rouhani FJ et al.

    Nature 2011;478;7369;391-4

    PUBMED: 21993621; PMC: 3198846; DOI: 10.1038/nature10424

  • Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor gamma and liver receptor homolog 1.

    Wang W, Yang J, Liu H, Lu D, Chen X, Zenonos Z, Campos LS, Rad R, Guo G, Zhang S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2011;108;45;18283-8

    PUBMED: 21990348; PMC: 3215025; DOI: 10.1073/pnas.1100893108

  • An activating mutation of AKT2 and human hypoglycemia.

    Hussain K, Challis B, Rocha N, Payne F, Minic M, Thompson A, Daly A, Scott C, Harris J, Smillie BJ et al.

    Science (New York, N.Y.) 2011;334;6055;474

    PUBMED: 21979934; PMC: 3204221; DOI: 10.1126/science.1210878

  • Male lineages in the Himalayan foothills: a commentary on Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India.

    Ayub Q

    Journal of human genetics 2011;56;12;813-4

    PUBMED: 21975650; DOI: 10.1038/jhg.2011.114

  • Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.

    Kooner JS, Saleheen D, Sim X, Sehmi J, Zhang W, Frossard P, Been LF, Chia KS, Dimas AS, Hassanali N et al.

    Nature genetics 2011;43;10;984-9

    PUBMED: 21874001; DOI: 10.1038/ng.921

  • Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque.

    Bis JC, Kavousi M, Franceschini N, Isaacs A, Abecasis GR, Schminke U, Post WS, Smith AV, Cupples LA, Markus HS et al.

    Nature genetics 2011;43;10;940-7

    PUBMED: 21909108; PMC: 3257519; DOI: 10.1038/ng.920

  • The Lin28/let-7 axis regulates glucose metabolism.

    Zhu H, Shyh-Chang N, Segrè AV, Shinoda G, Shah SP, Einhorn WS, Takeuchi A, Engreitz JM, Hagan JP, Kharas MG et al.

    Cell 2011;147;1;81-94

    PUBMED: 21962509; PMC: 3353524; DOI: 10.1016/j.cell.2011.08.033

  • Comprehensive comparison of three commercial human whole-exome capture platforms.

    Asan, Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, Wang J, Wu M, Liu X, Tian G et al.

    Genome biology 2011;12;9;R95

    PUBMED: 21955857; PMC: 3308058; DOI: 10.1186/gb-2011-12-9-r95

  • Developing and implementing an institute-wide data sharing policy.

    Dyke SO and Hubbard TJ

    Genome medicine 2011;3;9;60

    PUBMED: 21955348; PMC: 3239235; DOI: 10.1186/gm276

  • Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts.

    Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C et al.

    The New England journal of medicine 2011;365;15;1384-95

    PUBMED: 21995386; PMC: 3322589; DOI: 10.1056/NEJMoa1103283

  • Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.

    Soler Artigas M, Loth DW, Wain LV, Gharib SA, Obeidat M, Tang W, Zhai G, Zhao JH, Smith AV, Huffman JE et al.

    Nature genetics 2011;43;11;1082-90

    PUBMED: 21946350; PMC: 3267376; DOI: 10.1038/ng.941

  • Mobilization of giant piggyBac transposons in the mouse genome.

    Li MA, Turner DJ, Ning Z, Yusa K, Liang Q, Eckert S, Rad L, Fitzgerald TW, Craig NL and Bradley A

    Nucleic acids research 2011;39;22;e148

    PUBMED: 21948799; PMC: 3239208; DOI: 10.1093/nar/gkr764

  • RNAcentral: A vision for an international database of RNA sequences.

    Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP et al.

    RNA (New York, N.Y.) 2011;17;11;1941-6

    PUBMED: 21940779; PMC: 3198587; DOI: 10.1261/rna.2750811

  • Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.

    Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ and Steel KP

    Genome biology 2011;12;9;R90

    PUBMED: 21936904; PMC: 3308053; DOI: 10.1186/gb-2011-12-9-r90

  • APC15 drives the turnover of MCC-CDC20 to make the spindle assembly checkpoint responsive to kinetochore attachment.

    Mansfeld J, Collin P, Collins MO, Choudhary JS and Pines J

    Nature cell biology 2011;13;10;1234-43

    PUBMED: 21926987; PMC: 3188299; DOI: 10.1038/ncb2347

  • Emergent neutrality in adaptive asexual evolution.

    Schiffels S, Szöllosi GJ, Mustonen V and Lässig M

    Genetics 2011;189;4;1361-75

    PUBMED: 21926305; PMC: 3241435; DOI: 10.1534/genetics.111.132027

  • Expressions of individuality.

    Chappell L

    Nature reviews. Microbiology 2011;9;10;701

    PUBMED: 21921932; DOI: 10.1038/nrmicro2662

  • Mouse genomic variation and its effect on phenotypes and gene regulation.

    Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M et al.

    Nature 2011;477;7364;289-94

    PUBMED: 21921910; PMC: 3276836; DOI: 10.1038/nature10413

  • Sequence-based characterization of structural variation in the mouse genome.

    Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A et al.

    Nature 2011;477;7364;326-9

    PUBMED: 21921916; PMC: 3428933; DOI: 10.1038/nature10432

  • Dlg3 trafficking and apical tight junction formation is regulated by nedd4 and nedd4-2 e3 ubiquitin ligases.

    Van Campenhout CA, Eitelhuber A, Gloeckner CJ, Giallonardo P, Gegg M, Oller H, Grant SG, Krappmann D, Ueffing M and Lickert H

    Developmental cell 2011;21;3;479-91

    PUBMED: 21920314; DOI: 10.1016/j.devcel.2011.08.003

  • Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.

    International Consortium for Blood Pressure Genome-Wide Association Studies, Ehret GB, Munroe PB, Rice KM, Bochud M, Johnson AD, Chasman DI, Smith AV, Tobin MD, Verwoert GC et al.

    Nature 2011;478;7367;103-9

    PUBMED: 21909115; PMC: 3340926; DOI: 10.1038/nature10405

  • Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

    Wain LV, Verwoert GC, O'Reilly PF, Shi G, Johnson T, Johnson AD, Bochud M, Rice KM, Henneman P, Smith AV et al.

    Nature genetics 2011;43;10;1005-11

    PUBMED: 21909110; PMC: 3445021; DOI: 10.1038/ng.922

  • High altitude adaptation in Daghestani populations from the Caucasus.

    Pagani L, Ayub Q, MacArthur DG, Xue Y, Baillie JK, Chen Y, Kozarewa I, Turner DJ, Tofanelli S, Bulayeva K et al.

    Human genetics 2011;131;3;423-33

    PUBMED: 21904933; PMC: 3312735; DOI: 10.1007/s00439-011-1084-8

  • Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.

    Illingworth CJ and Mustonen V

    Genetics 2011;189;3;989-1000

    PUBMED: 21900272; PMC: 3213378; DOI: 10.1534/genetics.111.133975

  • Candidate gene association study for diabetic retinopathy in persons with type 2 diabetes: the Candidate gene Association Resource (CARe).

    Sobrin L, Green T, Sim X, Jensen RA, Tai ES, Tay WT, Wang JJ, Mitchell P, Sandholm N, Liu Y et al.

    Investigative ophthalmology & visual science 2011;52;10;7593-602

    PUBMED: 21873659; PMC: 3183981; DOI: 10.1167/iovs.11-7510

  • Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

    Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ et al.

    PLoS pathogens 2011;7;9;e1002219

    PUBMED: 21909270; PMC: 3164644; DOI: 10.1371/journal.ppat.1002219

  • Large-scale gene-centric analysis identifies novel variants for coronary artery disease.

    IBC 50K CAD Consortium

    PLoS genetics 2011;7;9;e1002260

    PUBMED: 21966275; PMC: 3178591; DOI: 10.1371/journal.pgen.1002260

  • Q8IYL2 is a candidate gene for the familial epilepsy syndrome of Partial Epilepsy with Pericentral Spikes (PEPS).

    Leschziner GD, Coffey AJ, Andrew T, Gregorio SP, Dias-Neto E, Calafato M, Bentley DR, Kinton L, Sander JW and Johnson MR

    Epilepsy research 2011;96;1-2;109-15

    PUBMED: 21658913; DOI: 10.1016/j.eplepsyres.2011.05.010

  • Total zinc intake may modify the glucose-raising effect of a zinc transporter (SLC30A8) variant: a 14-cohort meta-analysis.

    Kanoni S, Nettleton JA, Hivert MF, Ye Z, van Rooij FJ, Shungin D, Sonestedt E, Ngwa JS, Wojczynski MK, Lemaitre RN et al.

    Diabetes 2011;60;9;2407-16

    PUBMED: 21810599; PMC: 3161318; DOI: 10.2337/db11-0176

  • TSIDER1, a short and non-autonomous Salivarian trypanosome-specific retroposon related to the ingi6 subclade.

    Bringaud F, Berriman M and Hertz-Fowler C

    Molecular and biochemical parasitology 2011;179;1;30-6

    PUBMED: 21664383; DOI: 10.1016/j.molbiopara.2011.05.007

  • Two covariance models for iron-responsive elements.

    Stevens SG, Gardner PP and Brown C

    RNA biology 2011;8;5;792-801

    PUBMED: 21881407; DOI: 10.4161/rna.8.5.16037

  • Human metabolic individuality in biomedical and pharmaceutical research.

    Suhre K, Shin SY, Petersen AK, Mohney RP, Meredith D, Wägele B, Altmaier E, CARDIoGRAM, Deloukas P, Erdmann J et al.

    Nature 2011;477;7362;54-60

    PUBMED: 21886157; PMC: 3832838; DOI: 10.1038/nature10354

  • Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

    Strawbridge RJ, Dupuis J, Prokopenko I, Barker A, Ahlqvist E, Rybin D, Petrie JR, Travers ME, Bouatia-Naji N, Dimas AS et al.

    Diabetes 2011;60;10;2624-34

    PUBMED: 21873549; PMC: 3178302; DOI: 10.2337/db11-0415

  • A variant in MCF2L is associated with osteoarthritis.

    Day-Williams AG, Southam L, Panoutsopoulou K, Rayner NW, Esko T, Estrada K, Helgadottir HT, Hofman A, Ingvarsson T, Jonsson H et al.

    American journal of human genetics 2011;89;3;446-50

    PUBMED: 21871595; PMC: 3169824; DOI: 10.1016/j.ajhg.2011.08.001

  • Genetic risk prediction in complex disease.

    Jostins L and Barrett JC

    Human molecular genetics 2011;20;R2;R182-8

    PUBMED: 21873261; PMC: 3179379; DOI: 10.1093/hmg/ddr378

  • Determinants of bluetongue virus virulence in murine models of disease.

    Caporale M, Wash R, Pini A, Savini G, Franchi P, Golder M, Patterson-Kane J, Mertens P, Di Gialleonardo L, Armillotta G et al.

    Journal of virology 2011;85;21;11479-89

    PUBMED: 21865388; PMC: 3194974; DOI: 10.1128/JVI.05226-11

  • Evidence for several waves of global transmission in the seventh cholera pandemic.

    Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH, Kariuki S, Croucher NJ, Choi SY, Harris SR, Lebens M et al.

    Nature 2011;477;7365;462-5

    PUBMED: 21866102; PMC: 3736323; DOI: 10.1038/nature10392

  • The tammar wallaby major histocompatibility complex shows evidence of past genomic instability.

    Siddle HV, Deakin JE, Coggill P, Whilming LG, Harrow J, Kaufman J, Beck S and Belov K

    BMC genomics 2011;12;421

    PUBMED: 21854592; PMC: 3179965; DOI: 10.1186/1471-2164-12-421

  • Sequencing skippy: the genome sequence of an Australian kangaroo, Macropus eugenii.

    Murchison EP and Adams DJ

    Genome biology 2011;12;8;123

    PUBMED: 21861852; PMC: 3245606; DOI: 10.1186/gb-2011-12-8-123

  • High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors.

    Koudijs MJ, Klijn C, van der Weyden L, Kool J, ten Hoeve J, Sie D, Prasetyanti PR, Schut E, Kas S, Whipp T et al.

    Genome research 2011;21;12;2181-9

    PUBMED: 21852388; PMC: 3227106; DOI: 10.1101/gr.112763.110

  • Salmonella bongori provides insights into the evolution of the Salmonellae.

    Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C, Connor TR, Seth-Smith H, Vernikos GS, Robinson KS, Sanders M et al.

    PLoS pathogens 2011;7;8;e1002191

    PUBMED: 21876672; PMC: 3158058; DOI: 10.1371/journal.ppat.1002191

  • Phylogenetic analysis of murine leukemia virus sequences from longitudinally sampled chronic fatigue syndrome patients suggests PCR contamination rather than viral evolution.

    Katzourakis A, Hué S, Kellam P and Towers GJ

    Journal of virology 2011;85;20;10909-13

    PUBMED: 21849443; PMC: 3187511; DOI: 10.1128/JVI.00827-11

  • Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry.

    Joron M, Frezal L, Jones RT, Chamberlain NL, Lee SF, Haag CR, Whibley A, Becuwe M, Baxter SW, Ferguson L et al.

    Nature 2011;477;7363;203-6

    PUBMED: 21841803; PMC: 3717454; DOI: 10.1038/nature10341

  • Real-time sequencing.

    Otto TD

    Nature reviews. Microbiology 2011;9;9;633

    PUBMED: 21836624; DOI: 10.1038/nrmicro2638

  • Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients.

    Robinson T, Campino SG, Auburn S, Assefa SA, Polley SD, Manske M, MacInnis B, Rockett KA, Maslen GL, Sanders M et al.

    PloS one 2011;6;8;e23204

    PUBMED: 21853089; PMC: 3154926; DOI: 10.1371/journal.pone.0023204

  • A British approach to sampling.

    Tyler-Smith C and Xue Y

    European journal of human genetics : EJHG 2011;20;2;129-30

    PUBMED: 21829226; PMC: 3260911; DOI: 10.1038/ejhg.2011.153

  • A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation.

    Seitan VC, Hao B, Tachibana-Konwalski K, Lavagnolli T, Mira-Bontenbal H, Brown KE, Teng G, Carroll T, Terry A, Horan K et al.

    Nature 2011;476;7361;467-71

    PUBMED: 21832993; PMC: 3179485; DOI: 10.1038/nature10312

  • A resource of vectors and ES cells for targeted deletion of microRNAs in mice.

    Prosser HM, Koike-Yusa H, Cooper JD, Law FC and Bradley A

    Nature biotechnology 2011;29;9;840-5

    PUBMED: 21822254; PMC: 3242032; DOI: 10.1038/nbt.1929

  • Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery.

    Pagliuca FW, Collins MO, Lichawska A, Zegerman P, Choudhary JS and Pines J

    Molecular cell 2011;43;3;406-17

    PUBMED: 21816347; PMC: 3332305; DOI: 10.1016/j.molcel.2011.05.031

  • Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome.

    Chaudhuri RR, Yu L, Kanji A, Perkins TT, Gardner PP, Choudhary J, Maskell DJ and Grant AJ

    Microbiology (Reading, England) 2011;157;Pt 10;2922-2932

    PUBMED: 21816880; PMC: 3353397; DOI: 10.1099/mic.0.050278-0

  • A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.

    Holt DC, Holden MT, Tong SY, Castillo-Ramirez S, Clarke L, Quail MA, Currie BJ, Parkhill J, Bentley SD, Feil EJ and Giffard PM

    Genome biology and evolution 2011;3;881-95

    PUBMED: 21813488; PMC: 3175761; DOI: 10.1093/gbe/evr078

  • Genome watch: Honey, I shrunk the mimiviral genome.

    Tsai IJ

    Nature reviews. Microbiology 2011;9;8;563

    PUBMED: 21747393; DOI: 10.1038/nrmicro2623

  • Meta analysis of candidate gene variants outside the LPA locus with Lp(a) plasma levels in 14,500 participants of six White European cohorts.

    Zabaneh D, Kumari M, Sandhu M, Wareham N, Wainwright N, Papamarkou T, Hopewell J, Clarke R, Li K, Palmen J et al.

    Atherosclerosis 2011;217;2;447-51

    PUBMED: 21592478; DOI: 10.1016/j.atherosclerosis.2011.04.015

  • Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study.

    García-Álvarez L, Holden MT, Lindsay H, Webb CR, Brown DF, Curran MD, Walpole E, Brooks K, Pickard DJ, Teale C et al.

    The Lancet. Infectious diseases 2011;11;8;595-603

    PUBMED: 21641281; PMC: 3829197; DOI: 10.1016/S1473-3099(11)70126-8

  • RNIE: genome-wide prediction of bacterial intrinsic terminators.

    Gardner PP, Barquist L, Bateman A, Nawrocki EP and Weinberg Z

    Nucleic acids research 2011;39;14;5845-52

    PUBMED: 21478170; PMC: 3152330; DOI: 10.1093/nar/gkr168

  • Stella-Cre mice are highly efficient Cre deleters.

    Liu H, Wang W, Chew SK, Lee SC, Li J, Vassiliou GS, Green T, Futreal PA, Bradley A, Zhang S and Liu P

    Genesis (New York, N.Y. : 2000) 2011;49;8;689-95

    PUBMED: 21786403; PMC: 3674523; DOI: 10.1002/dvg.20741

  • CCR4-associated factor 1 coordinates the expression of Plasmodium falciparum egress and invasion proteins.

    Balu B, Maher SP, Pance A, Chauhan C, Naumov AV, Andrews RM, Ellis PD, Khan SM, Lin JW, Janse CJ et al.

    Eukaryotic cell 2011;10;9;1257-63

    PUBMED: 21803864; PMC: 3187058; DOI: 10.1128/EC.05099-11

  • An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing.

    Auburn S, Campino S, Clark TG, Djimde AA, Zongo I, Pinches R, Manske M, Mangano V, Alcock D, Anastasi E et al.

    PloS one 2011;6;7;e22213

    PUBMED: 21789235; PMC: 3138765; DOI: 10.1371/journal.pone.0022213

  • Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome.

    Albers CA, Cvejic A, Favier R, Bouwmans EE, Alessi MC, Bertone P, Jordan G, Kettleborough RN, Kiddle G, Kostadima M et al.

    Nature genetics 2011;43;8;735-7

    PUBMED: 21765411; PMC: 3428934; DOI: 10.1038/ng.885

  • The impact of recombination on dN/dS within recently emerged bacterial clones.

    Castillo-Ramírez S, Harris SR, Holden MT, He M, Parkhill J, Bentley SD and Feil EJ

    PLoS pathogens 2011;7;7;e1002129

    PUBMED: 21779170; PMC: 3136474; DOI: 10.1371/journal.ppat.1002129

  • Inference of human population history from individual whole-genome sequences.

    Li H and Durbin R

    Nature 2011;475;7357;493-6

    PUBMED: 21753753; PMC: 3154645; DOI: 10.1038/nature10231

  • Indian Siddis: African descendants with Indian admixture.

    Shah AM, Tamang R, Moorjani P, Rani DS, Govindaraj P, Kulkarni G, Bhattacharya T, Mustak MS, Bhaskar LV, Reddy AG et al.

    American journal of human genetics 2011;89;1;154-61

    PUBMED: 21741027; PMC: 3135801; DOI: 10.1016/j.ajhg.2011.05.030

  • Modernizing reference genome assemblies.

    Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR et al.

    PLoS biology 2011;9;7;e1001091

    PUBMED: 21750661; PMC: 3130012; DOI: 10.1371/journal.pbio.1001091

  • Linkage analysis without defined pedigrees.

    Day-Williams AG, Blangero J, Dyer TD, Lange K and Sobel EM

    Genetic epidemiology 2011;35;5;360-70

    PUBMED: 21465549; PMC: 3290352; DOI: 10.1002/gepi.20584

  • Design and cohort description of the InterAct Project: an examination of the interaction of genetic and lifestyle factors on the incidence of type 2 diabetes in the EPIC Study.

    InterAct Consortium, Langenberg C, Sharp S, Forouhi NG, Franks PW, Schulze MB, Kerrison N, Ekelund U, Barroso I, Panico S et al.

    Diabetologia 2011;54;9;2272-82

    PUBMED: 21717116; PMC: 4222062; DOI: 10.1007/s00125-011-2182-9

  • Maps of open chromatin guide the functional follow-up of genome-wide association signals: application to hematological traits.

    Paul DS, Nisbet JP, Yang TP, Meacham S, Rendon A, Hautaviita K, Tallila J, White J, Tijssen MR, Sivapalaratnam S et al.

    PLoS genetics 2011;7;6;e1002139

    PUBMED: 21738486; PMC: 3128100; DOI: 10.1371/journal.pgen.1002139

  • Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.

    Kilpeläinen TO, Zillikens MC, Stančákova A, Finucane FM, Ried JS, Langenberg C, Zhang W, Beckmann JS, Luan J, Vandenput L et al.

    Nature genetics 2011;43;8;753-60

    PUBMED: 21706003; PMC: 3262230; DOI: 10.1038/ng.866

  • The mouse genetics toolkit: revealing function and mechanism.

    van der Weyden L, White JK, Adams DJ and Logan DW

    Genome biology 2011;12;6;224

    PUBMED: 21722353; PMC: 3218837; DOI: 10.1186/gb-2011-12-6-224

  • The Deciphering Developmental Disorders (DDD) study.

    Firth HV, Wright CF and DDD Study

    Developmental medicine and child neurology 2011;53;8;702-3

    PUBMED: 21679367; DOI: 10.1111/j.1469-8749.2011.04032.x

  • A conditional knockout resource for the genome-wide study of mouse gene function.

    Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T et al.

    Nature 2011;474;7351;337-42

    PUBMED: 21677750; PMC: 3572410; DOI: 10.1038/nature10163

  • Genome-wide association study reveals three susceptibility loci for common migraine in the general population.

    Chasman DI, Schürks M, Anttila V, de Vries B, Schminke U, Launer LJ, Terwindt GM, van den Maagdenberg AM, Fendrich K, Völzke H et al.

    Nature genetics 2011;43;7;695-8

    PUBMED: 21666692; PMC: 3125402; DOI: 10.1038/ng.856

  • Variation in genome-wide mutation rates within and between human families.

    Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV et al.

    Nature genetics 2011;43;7;712-4

    PUBMED: 21666693; PMC: 3322360; DOI: 10.1038/ng.862

  • Computational identification of insertional mutagenesis targets for cancer gene discovery.

    de Jong J, de Ridder J, van der Weyden L, Sun N, van Uitert M, Berns A, van Lohuizen M, Jonkers J, Adams DJ and Wessels LF

    Nucleic acids research 2011;39;15;e105

    PUBMED: 21652642; PMC: 3159484; DOI: 10.1093/nar/gkr447

  • Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay.

    Campino S, Auburn S, Kivinen K, Zongo I, Ouedraogo JB, Mangano V, Djimde A, Doumbo OK, Kiara SM, Nzila A et al.

    PloS one 2011;6;6;e20251

    PUBMED: 21673999; PMC: 3108946; DOI: 10.1371/journal.pone.0020251

  • The Genomic Standards Consortium.

    Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Glöckner FO, Hirschman L, Karsch-Mizrachi I et al.

    PLoS biology 2011;9;6;e1001088

    PUBMED: 21713030; PMC: 3119656; DOI: 10.1371/journal.pbio.1001088

  • Differential protein expression throughout the life cycle of Trypanosoma congolense, a major parasite of cattle in Africa.

    Eyford BA, Sakurai T, Smith D, Loveless B, Hertz-Fowler C, Donelson JE, Inoue N and Pearson TW

    Molecular and biochemical parasitology 2011;177;2;116-25

    PUBMED: 21354217; DOI: 10.1016/j.molbiopara.2011.02.009

  • Does a short breastfeeding period protect from FTO-induced adiposity in children?

    Dedoussis GV, Yannakoulia M, Timpson NJ, Manios Y, Kanoni S, Scott RA, Papoutsakis C, Deloukas P, Pitsiladis YP, Davey-Smith G et al.

    International journal of pediatric obesity : IJPO : an official journal of the International Association for the Study of Obesity 2011;6;2-2;e326-35

    PUBMED: 20863147; DOI: 10.3109/17477166.2010.490269

  • Examining the overlap between genome-wide rare variant association signals and linkage peaks in rheumatoid arthritis.

    Eyre S, Ke X, Lawrence R, Bowes J, Panoutsopoulou K, Barton A, Thomson W, Worthington J and Zeggini E

    Arthritis and rheumatism 2011;63;6;1522-6

    PUBMED: 21370227; PMC: 3428937; DOI: 10.1002/art.30315

  • Genome sequencing gets func-y.

    Reid AJ

    Nature reviews. Microbiology 2011;9;6;401

    PUBMED: 21572456; DOI: 10.1038/nrmicro2583

  • Impact of temperament on depression and anxiety symptoms and depressive disorder in a population-based birth cohort.

    Nyman E, Miettunen J, Freimer N, Joukamaa M, Mäki P, Ekelund J, Peltonen L, Järvelin MR, Veijola J and Paunio T

    Journal of affective disorders 2011;131;1-3;393-7

    PUBMED: 21570580; DOI: 10.1016/j.jad.2010.12.008

  • Messenger RNA and microRNA profiling during early mouse EB formation.

    Tripathi R, Saini HK, Rad R, Abreu-Goodger C, van Dongen S and Enright AJ

    Gene expression patterns : GEP 2011;11;5-6;334-44

    PUBMED: 21440681; DOI: 10.1016/j.gep.2011.03.004

  • Cell type-specific DNA methylation at intragenic CpG islands in the immune system.

    Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R and Bird A

    Genome research 2011;21;7;1074-86

    PUBMED: 21628449; PMC: 3129250; DOI: 10.1101/gr.118703.110

  • Modeling the evolution of ETV6-RUNX1-induced B-cell precursor acute lymphoblastic leukemia in mice.

    van der Weyden L, Giotopoulos G, Rust AG, Matheson LS, van Delft FW, Kong J, Corcoran AE, Greaves MF, Mullighan CG, Huntly BJ and Adams DJ

    Blood 2011;118;4;1041-51

    PUBMED: 21628403; PMC: 3622520; DOI: 10.1182/blood-2011-02-338848

  • Evidence that Cd101 is an autoimmune diabetes gene in nonobese diabetic mice.

    Rainbow DB, Moule C, Fraser HI, Clark J, Howlett SK, Burren O, Christensen M, Moody V, Steward CA, Mohammed JP et al.

    Journal of immunology (Baltimore, Md. : 1950) 2011;187;1;325-36

    PUBMED: 21613616; PMC: 3128927; DOI: 10.4049/jimmunol.1003523

  • A comprehensive evaluation of potential lung function associated genes in the SpiroMeta general population sample.

    Obeidat M, Wain LV, Shrine N, Kalsheker N, Soler Artigas M, Repapi E, Burton PR, Johnson T, Ramasamy A, Zhao JH et al.

    PloS one 2011;6;5;e19382

    PUBMED: 21625484; PMC: 3098839; DOI: 10.1371/journal.pone.0019382

  • IDH1 and IDH2 mutations are frequent events in central chondrosarcoma and central and periosteal chondromas but not in other mesenchymal tumours.

    Amary MF, Bacsi K, Maggiani F, Damato S, Halai D, Berisha F, Pollock R, O'Donnell P, Grigoriadis A, Diss T et al.

    The Journal of pathology 2011;224;3;334-43

    PUBMED: 21598255; DOI: 10.1002/path.2913

  • ATMIN is required for maintenance of genomic stability and suppression of B cell lymphoma.

    Loizou JI, Sancho R, Kanu N, Bolland DJ, Yang F, Rada C, Corcoran AE and Behrens A

    Cancer cell 2011;19;5;587-600

    PUBMED: 21575860; PMC: 4452547; DOI: 10.1016/j.ccr.2011.03.022

  • Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators.

    Tijssen MR, Cvejic A, Joshi A, Hannah RL, Ferreira R, Forrai A, Bellissimo DC, Oram SH, Smethurst PA, Wilson NK et al.

    Developmental cell 2011;20;5;597-609

    PUBMED: 21571218; PMC: 3145975; DOI: 10.1016/j.devcel.2011.04.008

  • FoSTeS, MMBIR and NAHR at the human proximal Xp region and the mechanisms of human Xq isochromosome formation.

    Koumbaris G, Hatzisevastou-Loukidou H, Alexandrou A, Ioannides M, Christodoulou C, Fitzgerald T, Rajan D, Clayton S, Kitsiou-Tzeli S, Vermeesch JR et al.

    Human molecular genetics 2011;20;10;1925-36

    PUBMED: 21349920; PMC: 3428953; DOI: 10.1093/hmg/ddr074

  • Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes.

    Small KS, Hedman AK, Grundberg E, Nica AC, Thorleifsson G, Kong A, Thorsteindottir U, Shin SY, Richards HB, GIANT Consortium et al.

    Nature genetics 2011;43;6;561-4

    PUBMED: 21572415; PMC: 3192952; DOI: 10.1038/ng.833

  • Cutting edge: the membrane attack complex of complement is required for the development of murine experimental cerebral malaria.

    Ramos TN, Darley MM, Hu X, Billker O, Rayner JC, Ahras M, Wohler JE and Barnum SR

    Journal of immunology (Baltimore, Md. : 1950) 2011;186;12;6657-60

    PUBMED: 21572031; PMC: 3110530; DOI: 10.4049/jimmunol.1100603

  • Parallel evolution of genes and languages in the Caucasus region.

    Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W et al.

    Molecular biology and evolution 2011;28;10;2905-20

    PUBMED: 21571925; PMC: 3355373; DOI: 10.1093/molbev/msr126

  • The origins, evolution, and functional potential of alternative splicing in vertebrates.

    Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T and Harrow J

    Molecular biology and evolution 2011;28;10;2949-59

    PUBMED: 21551269; PMC: 3176834; DOI: 10.1093/molbev/msr127

  • A worldwide analysis of beta-defensin copy number variation suggests recent selection of a high-expressing DEFB103 gene copy in East Asia.

    Hardwick RJ, Machado LR, Zuccherato LW, Antolinos S, Xue Y, Shawa N, Gilman RH, Cabrera L, Berg DE, Tyler-Smith C et al.

    Human mutation 2011;32;7;743-50

    PUBMED: 21387465; PMC: 3263423; DOI: 10.1002/humu.21491

  • The effect of next-generation sequencing technology on complex trait research.

    Day-Williams AG and Zeggini E

    European journal of clinical investigation 2011;41;5;561-7

    PUBMED: 21155765; PMC: 3107422; DOI: 10.1111/j.1365-2362.2010.02437.x

  • Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio.

    Gomes-Santos CS, Braks J, Prudêncio M, Carret C, Gomes AR, Pain A, Feltwell T, Khan S, Waters A, Janse C et al.

    PLoS pathogens 2011;7;5;e1002046

    PUBMED: 21625527; PMC: 3098293; DOI: 10.1371/journal.ppat.1002046

  • Enterotypes of the human gut microbiome.

    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM et al.

    Nature 2011;473;7346;174-80

    PUBMED: 21508958; PMC: 3728647; DOI: 10.1038/nature09944

  • A user's guide to the encyclopedia of DNA elements (ENCODE).

    ENCODE Project Consortium

    PLoS biology 2011;9;4;e1001046

    PUBMED: 21526222; PMC: 3079585; DOI: 10.1371/journal.pbio.1001046

  • An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations.

    Tan JC, Miller BA, Tan A, Patel JJ, Cheeseman IH, Anderson TJ, Manske M, Maslen G, Kwiatkowski DP and Ferdig MT

    Genome biology 2011;12;4;R35

    PUBMED: 21477297; PMC: 3218861; DOI: 10.1186/gb-2011-12-4-r35

  • Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

    Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL, Fookes M, Roberts K, Monson R, Nair S, Kingsley RA et al.

    PLoS pathogens 2011;7;4;e1002018

    PUBMED: 21490962; PMC: 3072379; DOI: 10.1371/journal.ppat.1002018

  • Assessing the complex architecture of polygenic traits in diverged yeast populations.

    Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ and Liti G

    Molecular ecology 2011;20;7;1401-13

    PUBMED: 21261765; DOI: 10.1111/j.1365-294X.2011.05005.x

  • Genetic screens using the piggyBac transposon.

    Chew SK, Rad R, Futreal PA, Bradley A and Liu P

    Methods (San Diego, Calif.) 2011;53;4;366-71

    PUBMED: 21185377; PMC: 3650578; DOI: 10.1016/j.ymeth.2010.12.022

  • Phase I trial of a selective c-MET inhibitor ARQ 197 incorporating proof of mechanism pharmacodynamic studies.

    Yap TA, Olmos D, Brunetto AT, Tunariu N, Barriuso J, Riisnaes R, Pope L, Clark J, Futreal A, Germuska M et al.

    Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2011;29;10;1271-9

    PUBMED: 21383285; DOI: 10.1200/JCO.2010.31.0367

  • Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

    Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS and Hubbard T

    Genome research 2011;21;5;756-67

    PUBMED: 21460061; PMC: 3083093; DOI: 10.1101/gr.114272.110

  • Assessment of a 44 gene classifier for the evaluation of chronic fatigue syndrome from peripheral blood mononuclear cell gene expression.

    Frampton D, Kerr J, Harrison TJ and Kellam P

    PloS one 2011;6;3;e16872

    PUBMED: 21479222; PMC: 3068152; DOI: 10.1371/journal.pone.0016872

  • Early Diagnosis of Werner's Syndrome Using Exome-Wide Sequencing in a Single, Atypical Patient.

    Raffan E, Hurst LA, Turki SA, Carpenter G, Scott C, Daly A, Coffey A, Bhaskar S, Howard E, Khan N et al.

    Frontiers in endocrinology 2011;2;8

    PUBMED: 22654791; PMC: 3356119; DOI: 10.3389/fendo.2011.00008

  • Next-generation association studies for complex traits.

    Zeggini E

    Nature genetics 2011;43;4;287-8

    PUBMED: 21445070; PMC: 3435533; DOI: 10.1038/ng0411-287

  • Mutant nucleophosmin and cooperating pathways drive leukemia initiation and progression in mice.

    Vassiliou GS, Cooper JL, Rad R, Li J, Rice S, Uren A, Rad L, Ellis P, Andrews R, Banerjee R et al.

    Nature genetics 2011;43;5;470-5

    PUBMED: 21441929; PMC: 3084174; DOI: 10.1038/ng.796

  • Germline fitness-based scoring of cancer mutations.

    Fischer A, Greenman C and Mustonen V

    Genetics 2011;188;2;383-93

    PUBMED: 21441214; PMC: 3122307; DOI: 10.1534/genetics.111.127480

  • HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans.

    McCormack M, Alfirevic A, Bourgeois S, Farrell JJ, Kasperavičiūtė D, Carrington M, Sills GJ, Marson T, Jia X, de Bakker PI et al.

    The New England journal of medicine 2011;364;12;1134-43

    PUBMED: 21428769; PMC: 3113609; DOI: 10.1056/NEJMoa1013297

  • No evidence of XMRV or related retroviruses in a London HIV-1-positive patient cohort.

    Gray ER, Garson JA, Breuer J, Edwards S, Kellam P, Pillay D and Towers GJ

    PloS one 2011;6;3;e18096

    PUBMED: 21448291; PMC: 3063244; DOI: 10.1371/journal.pone.0018096

  • Ethical issues in human genomics research in developing countries.

    de Vries J, Bull SJ, Doumbo O, Ibrahim M, Mercereau-Puijalon O, Kwiatkowski D and Parker M

    BMC medical ethics 2011;12;5

    PUBMED: 21418562; PMC: 3076260; DOI: 10.1186/1472-6939-12-5

  • Comparative whole genome sequence analysis of the carcinogenic bacterial model pathogen Helicobacter felis.

    Arnold IC, Zigova Z, Holden M, Lawley TD, Rad R, Dougan G, Falkow S, Bentley SD and Müller A

    Genome biology and evolution 2011;3;302-8

    PUBMED: 21402865; PMC: 4197744; DOI: 10.1093/gbe/evr022

  • Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.

    Mells GF, Floyd JA, Morley KI, Cordell HJ, Franklin CS, Shin SY, Heneghan MA, Neuberger JM, Donaldson PT, Day DB et al.

    Nature genetics 2011;43;4;329-32

    PUBMED: 21399635; PMC: 3071550; DOI: 10.1038/ng.789

  • Acute sensitivity of the oral mucosa to oncogenic K-ras.

    van der Weyden L, Alcolea MP, Jones PH, Rust AG, Arends MJ and Adams DJ

    The Journal of pathology 2011;224;1;22-32

    PUBMED: 21381032; PMC: 3627303; DOI: 10.1002/path.2853

  • Tumor-specific diagnostic marker for transmissible facial tumors of Tasmanian devils: immunohistochemistry studies.

    Tovar C, Obendorf D, Murchison EP, Papenfuss AT, Kreiss A and Woods GM

    Veterinary pathology 2011;48;6;1195-203

    PUBMED: 21383118; DOI: 10.1177/0300985811400447

  • A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.

    Coronary Artery Disease (C4D) Genetics Consortium

    Nature genetics 2011;43;4;339-44

    PUBMED: 21378988; DOI: 10.1038/ng.782

  • Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21.

    Papageorgiou EA, Karagrigoriou A, Tsaliki E, Velissariou V, Carter NP and Patsalis PC

    Nature medicine 2011;17;4;510-3

    PUBMED: 21378977; PMC: 3977039; DOI: 10.1038/nm.2312

  • Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.

    Schunkert H, König IR, Kathiresan S, Reilly MP, Assimes TL, Holm H, Preuss M, Stewart AF, Barbalic M, Gieger C et al.

    Nature genetics 2011;43;4;333-8

    PUBMED: 21378990; PMC: 3119261; DOI: 10.1038/ng.784

  • Activation of K-RAS by co-mutation of codons 19 and 20 is transforming.

    Naguib A, Wilson CH, Adams DJ and Arends MJ

    Journal of molecular signaling 2011;6;2

    PUBMED: 21371307; PMC: 3056876; DOI: 10.1186/1750-2187-6-2

  • The GENCODE exome: sequencing the complete human exome.

    Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S et al.

    European journal of human genetics : EJHG 2011;19;7;827-31

    PUBMED: 21364695; PMC: 3137498; DOI: 10.1038/ejhg.2011.28

  • Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets.

    Jostins L, Morley KI and Barrett JC

    European journal of human genetics : EJHG 2011;19;6;662-6

    PUBMED: 21364697; PMC: 3110048; DOI: 10.1038/ejhg.2011.10

  • The clinical and molecular genetic features of idiopathic infantile periodic alternating nystagmus.

    Thomas MG, Crosier M, Lindsay S, Kumar A, Thomas S, Araki M, Talbot CJ, McLean RJ, Surendran M, Taylor K et al.

    Brain : a journal of neurology 2011;134;Pt 3;892-902

    PUBMED: 21303855; PMC: 4125620; DOI: 10.1093/brain/awq373

  • Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.

    Speliotes EK, Yerges-Armstrong LM, Wu J, Hernaez R, Kim LJ, Palmer CD, Gudnason V, Eiriksdottir G, Garcia ME, Launer LJ et al.

    PLoS genetics 2011;7;3;e1001324

    PUBMED: 21423719; PMC: 3053321; DOI: 10.1371/journal.pgen.1001324

  • Genome-wide association studies and type 2 diabetes.

    Wheeler E and Barroso I

    Briefings in functional genomics 2011;10;2;52-60

    PUBMED: 21436302; DOI: 10.1093/bfgp/elr008

  • A plethora of Plasmodium species in wild apes: a source of human infection?

    Rayner JC, Liu W, Peeters M, Sharp PM and Hahn BH

    Trends in parasitology 2011;27;5;222-9

    PUBMED: 21354860; PMC: 3087880; DOI: 10.1016/j.pt.2011.01.006

  • aCGH.Spline--an R package for aCGH dye bias normalization.

    Fitzgerald TW, Larcombe LD, Le Scouarnec S, Clayton S, Rajan D, Carter NP and Redon R

    Bioinformatics (Oxford, England) 2011;27;9;1195-200

    PUBMED: 21357574; PMC: 3077069; DOI: 10.1093/bioinformatics/btr107

  • Analysis of XMRV integration sites from human prostate cancer tissues suggests PCR contamination rather than genuine human infection.

    Garson JA, Kellam P and Towers GJ

    Retrovirology 2011;8;13

    PUBMED: 21352548; PMC: 3050814; DOI: 10.1186/1742-4690-8-13

  • Perilipin deficiency and autosomal dominant partial lipodystrophy.

    Gandotra S, Le Dour C, Bottomley W, Cervera P, Giral P, Reznik Y, Charpentier G, Auclair M, Delépine M, Barroso I et al.

    The New England journal of medicine 2011;364;8;740-8

    PUBMED: 21345103; PMC: 3773916; DOI: 10.1056/NEJMoa1007487

  • Founder effect in the Horn of Africa for an insulin receptor mutation that may impair receptor recycling.

    Raffan E, Soos MA, Rocha N, Tuthill A, Thomsen AR, Hyden CS, Gregory JW, Hindmarsh P, Dattani M, Cochran E et al.

    Diabetologia 2011;54;5;1057-65

    PUBMED: 21318406; PMC: 3071941; DOI: 10.1007/s00125-011-2066-z

  • Zebrafish Fukutin family proteins link the unfolded protein response with dystroglycanopathies.

    Lin YY, White RJ, Torelli S, Cirak S, Muntoni F and Stemple DL

    Human molecular genetics 2011;20;9;1763-75

    PUBMED: 21317159; PMC: 3071672; DOI: 10.1093/hmg/ddr059

  • RATT: Rapid Annotation Transfer Tool.

    Otto TD, Dillon GP, Degrave WS and Berriman M

    Nucleic acids research 2011;39;9;e57

    PUBMED: 21306991; PMC: 3089447; DOI: 10.1093/nar/gkq1268

  • A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.

    Méndez-Lago M, Bergman CM, de Pablos B, Tracey A, Whitehead SL and Villasante A

    Molecular biology and evolution 2011;28;7;1967-71

    PUBMED: 21297157; PMC: 4202384; DOI: 10.1093/molbev/msr034

  • Glyburide is anti-inflammatory and associated with reduced mortality in melioidosis.

    Koh GC, Maude RR, Schreiber MF, Limmathurotsakul D, Wiersinga WJ, Wuthiekanun V, Lee SJ, Mahavanakul W, Chaowagul W, Chierakul W et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2011;52;6;717-25

    PUBMED: 21293047; PMC: 3049341; DOI: 10.1093/cid/ciq192

  • Dominant and diet-responsive groups of bacteria within the human colonic microbiota.

    Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A et al.

    The ISME journal 2011;5;2;220-30

    PUBMED: 20686513; PMC: 3105703; DOI: 10.1038/ismej.2010.118

  • Meta-analysis of genome-wide association studies confirms a susceptibility locus for knee osteoarthritis on chromosome 7q22.

    Evangelou E, Valdes AM, Kerkhof HJ, Styrkarsdottir U, Zhu Y, Meulenbelt I, Lories RJ, Karassa FB, Tylzanowski P, Bos SD et al.

    Annals of the rheumatic diseases 2011;70;2;349-55

    PUBMED: 21068099; PMC: 3615180; DOI: 10.1136/ard.2010.132787

  • High incidence of recurrent copy number variants in patients with isolated and syndromic Müllerian aplasia.

    Nik-Zainal S, Strick R, Storer M, Huang N, Rad R, Willatt L, Fitzgerald T, Martin V, Sandford R, Carter NP et al.

    Journal of medical genetics 2011;48;3;197-204

    PUBMED: 21278390; PMC: 3322361; DOI: 10.1136/jmg.2010.082412

  • Rapid pneumococcal evolution in response to clinical interventions.

    Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS et al.

    Science (New York, N.Y.) 2011;331;6016;430-4

    PUBMED: 21273480; PMC: 3648787; DOI: 10.1126/science.1198545

  • Comparative and demographic analysis of orang-utan genomes.

    Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P et al.

    Nature 2011;469;7331;529-33

    PUBMED: 21270892; PMC: 3060778; DOI: 10.1038/nature09687

  • The effect of genome-wide association scan quality control on imputation outcome for common variants.

    Southam L, Panoutsopoulou K, Rayner NW, Chapman K, Durrant C, Ferreira T, Arden N, Carr A, Deloukas P, Doherty M et al.

    European journal of human genetics : EJHG 2011;19;5;610-4

    PUBMED: 21267008; PMC: 3083623; DOI: 10.1038/ejhg.2010.242

  • A research agenda for malaria eradication: basic science and enabling technologies.

    malERA Consultative Group on Basic Science and Enabling Technologies

    PLoS medicine 2011;8;1;e1000399

    PUBMED: 21311584; PMC: 3026698; DOI: 10.1371/journal.pmed.1000399

  • Joint genetic analysis of gene expression data with inferred cellular phenotypes.

    Parts L, Stegle O, Winn J and Durbin R

    PLoS genetics 2011;7;1;e1001276

    PUBMED: 21283789; PMC: 3024309; DOI: 10.1371/journal.pgen.1001276

  • Dalliance: interactive genome viewing on the web.

    Down TA, Piipari M and Hubbard TJ

    Bioinformatics (Oxford, England) 2011;27;6;889-90

    PUBMED: 21252075; PMC: 3051325; DOI: 10.1093/bioinformatics/btr020

  • Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.

    Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J et al.

    Nature 2011;469;7331;539-42

    PUBMED: 21248752; PMC: 3030920; DOI: 10.1038/nature09639

  • miR-96 regulates the progression of differentiation in mammalian cochlear inner and outer hair cells.

    Kuhn S, Johnson SL, Furness DN, Chen J, Ingham N, Hilton JM, Steffes G, Lewis MA, Zampini V, Hackney CM et al.

    Proceedings of the National Academy of Sciences of the United States of America 2011;108;6;2355-60

    PUBMED: 21245307; PMC: 3038748; DOI: 10.1073/pnas.1016646108

  • Synthetic associations are unlikely to account for many common disease genome-wide association signals.

    Anderson CA, Soranzo N, Zeggini E and Barrett JC

    PLoS biology 2011;9;1;e1000580

    PUBMED: 21267062; PMC: 3022527; DOI: 10.1371/journal.pbio.1000580

  • Troponin T is essential for sarcomere assembly in zebrafish skeletal muscle.

    Ferrante MI, Kiff RM, Goulding DA and Stemple DL

    Journal of cell science 2011;124;Pt 4;565-77

    PUBMED: 21245197; PMC: 3031369; DOI: 10.1242/jcs.071274

  • Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia.

    Crossan GP, van der Weyden L, Rosado IV, Langevin F, Gaillard PHL, McIntyre RE, Sanger Mouse Genetics Project, Gallagher F, Kettunen MI, Lewis DY et al.

    Nature genetics 2011;43;2;147-52

    PUBMED: 21240276; PMC: 3624090; DOI: 10.1038/ng.752

  • An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes.

    Xue Y and Tyler-Smith C

    Genes 2011;2;1;36-47

    PUBMED: 24710137; PMC: 3924835; DOI: 10.3390/genes2010036

  • Massive genomic rearrangement acquired in a single catastrophic event during cancer development.

    Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA et al.

    Cell 2011;144;1;27-40

    PUBMED: 21215367; PMC: 3065307; DOI: 10.1016/j.cell.2010.11.055

  • PoolHap: inferring haplotype frequencies from pooled samples by next generation sequencing.

    Long Q, Jeffares DC, Zhang Q, Ye K, Nizhynska V, Ning Z, Tyler-Smith C and Nordborg M

    PloS one 2011;6;1;e15292

    PUBMED: 21264334; PMC: 3016441; DOI: 10.1371/journal.pone.0015292

  • A hyperactive piggyBac transposase for mammalian applications.

    Yusa K, Zhou L, Li MA, Bradley A and Craig NL

    Proceedings of the National Academy of Sciences of the United States of America 2011;108;4;1531-6

    PUBMED: 21205896; PMC: 3029773; DOI: 10.1073/pnas.1008322108

  • An evaluation of different target enrichment methods in pooled sequencing designs for complex disease association studies.

    Day-Williams AG, McLay K, Drury E, Edkins S, Coffey AJ, Palotie A and Zeggini E

    PloS one 2011;6;11;e26279

    PUBMED: 22069447; PMC: 3206031; DOI: 10.1371/journal.pone.0026279

  • An evaluation of power to detect low-frequency variant associations using allele-matching tests that account for uncertainty.

    Zeggini E and Asimit JL

    Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2011;100-5

    PUBMED: 21121037; PMC: 3337640

  • A modified vaccinia Ankara virus (MVA) vaccine expressing African horse sickness virus (AHSV) VP2 protects against AHSV challenge in an IFNAR -/- mouse model.

    Castillo-Olivares J, Calvo-Pinilla E, Casanova I, Bachanek-Bankowska K, Chiam R, Maan S, Nieto JM, Ortego J and Mertens PP

    PloS one 2011;6;1;e16503

    PUBMED: 21298069; PMC: 3027694; DOI: 10.1371/journal.pone.0016503

  • 96-plex molecular barcoding for the Illumina Genome Analyzer.

    Kozarewa I and Turner DJ

    Methods in molecular biology (Clifton, N.J.) 2011;733;279-98

    PUBMED: 21431778; DOI: 10.1007/978-1-61779-089-8_20

  • A call for papers for the second special issue of SIGS from the genomic standards consortium

    Field D, STERK P, Kottmann R

    Standards in Genomic Sciences 2011;4;111-2

  • ADAM-15 disintegrin-like domain structure and function

    LU D, Scully M, Kakkar V, Lu X

    Toxins. 2011;2;2411-27

  • An exceptional gene: Evolution of the TSPY gene family in humans and other great apes

    XUE Y, TYLER-SMITH C

    Genes. 2011;2;36-47

  • Effect of using varying negative examples in transcription factor binding site predictions

    Rezwan F, Sun Y, Davey N, Adams R, RUST AG, Robinson M

    Lecture Notes in Computer Science 2011;6623 LNCS;1-12

  • Essential thrombocythemia: seeing the wood for the trees Response

    Beer PA, Erber WN, CAMPBELL PJ, Green AR

    Blood. 2011;118;1180-1

  • Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21

    Papageorgiou EA, Karagrigoriou A, Tsaliki E, Velissariou V, CARTER NP, Patsalis PC

    Obstetrical and Gynecological Survey 2011;66;419

  • Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

    Harrison A, Lemey P, HURLES ME, Moyes C, Horn S, Pryor J, Malani J, Supuri M, Masta A, Teriboriki B et al.

    Viruses-Basel. 2011;3;83-101

  • Kino: A generic document management system for biologists using SA-REST and faceted search

    Ranabahu A, Parikh P, Panahiazar M, Sheth A, LOGAN-KLUMPLER F

    Proceedings - 5th IEEE International Conference on Semantic Computing, ICSC 2011;205-8

  • Live vaccines and their role in modern vaccinology

    DOUGAN G, GOULDING D, Hall LJ

    Replicating Vaccines. 2011;Part 1;3-14

  • Reply: Ileal pouch microbial diversity

    McLaughlin SD, Walker AW, CHURCHER C, CLARK SK, Tekkis PP, Johnson MW, PARKHILL J, CICLITIRA PJ, DOUGAN G, Nicholls RJ et al.

    Annals of Surgery. 2011;254;669-70

  • Amplification-free library preparation for paired-end Illumina sequencing.

    Kozarewa I and Turner DJ

    Methods in molecular biology (Clifton, N.J.) 2011;733;257-66

    PUBMED: 21431776; DOI: 10.1007/978-1-61779-089-8_18

  • Analysis of complex disease association studies

    ZEGGINI,E. and Morris,A.

    Analysis of complex disease association studies 2011

    URL: https://www.sciencedirect.com/scien...ce/book/9780123751423

  • Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.

    Laing R, Hunt M, Protasio AV, Saunders G, Mungall K, Laing S, Jackson F, Quail M, Beech R, Berriman M and Gilleard JS

    PloS one 2011;6;8;e23216

    PUBMED: 21858033; PMC: 3156134; DOI: 10.1371/journal.pone.0023216

  • Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder.

    Frank RA, McRae AF, Pocklington AJ, van de Lagemaat LN, Navarro P, Croning MD, Komiyama NH, Bradley SJ, Challiss RA, Armstrong JD et al.

    PloS one 2011;6;4;e19011

    PUBMED: 21559497; PMC: 3084736; DOI: 10.1371/journal.pone.0019011

  • Gene inactivation and its implications for annotation in the era of personal genomics.

    Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J and Gerstein M

    Genes & development 2011;25;1;1-10

    PUBMED: 21205862; PMC: 3012931; DOI: 10.1101/gad.1968411

  • Genetic and structural variation in the gastric cancer kinome revealed through targeted deep sequencing.

    Zang ZJ, Ong CK, Cutcutache I, Yu W, Zhang SL, Huang D, Ler LD, Dykema K, Gan A, Tao J et al.

    Cancer research 2011;71;1;29-39

    PUBMED: 21097718; PMC: 3719377; DOI: 10.1158/0008-5472.CAN-10-1749

  • Genetic risk reclassification for type 2 diabetes by age below or above 50 years using 40 type 2 diabetes risk single nucleotide polymorphisms.

    de Miguel-Yanes JM, Shrader P, Pencina MJ, Fox CS, Manning AK, Grant RW, Dupuis J, Florez JC, D'Agostino RB, Cupples LA et al.

    Diabetes care 2011;34;1;121-5

    PUBMED: 20889853; PMC: 3005447; DOI: 10.2337/dc10-1265

  • Genomic libraries: I. Construction and screening of fosmid genomic libraries.

    Quail MA, Matthews L, Sims S, Lloyd C, Beasley H and Baxter SW

    Methods in molecular biology (Clifton, N.J.) 2011;772;37-58

    PUBMED: 22065431; DOI: 10.1007/978-1-61779-228-1_3

  • Genomic libraries: II. Subcloning, sequencing, and assembling large-insert genomic DNA clones.

    Quail MA, Matthews L, Sims S, Lloyd C, Beasley H and Baxter SW

    Methods in molecular biology (Clifton, N.J.) 2011;772;59-81

    PUBMED: 22065432; DOI: 10.1007/978-1-61779-228-1_4

  • Genotype Calling

    Inouye,M. and Teo,Y.Y.

    Analysis of Complex Disease Association Studies 2011;Chapter 5;69-86

    DOI: I10.1016/B978-0-12-375142-3.10005-7; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123751423100057

  • High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease.

    Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G and Petrovska L

    BMC microbiology 2011;11;7

    PUBMED: 21219646; PMC: 3032643; DOI: 10.1186/1471-2180-11-7

  • Interpreting Association Signals

    Soranzo,N and Dudbridge,F.;

    Analysis of Complex Disease Association Studies 2011;Chapter 16;261-76

    DOI: 10.1016/B978-0-12-375142-3.10016-1; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123751423100161

  • Introducing the Human Brain Project

    Markram,H., Meier,K., Lippert,T., Grillner,S., Frackowiak,R., Dehaene,S., Knoll,A., Sompolinsky,H., Verstreken,K., DeFelipe,J. et al.

    Procedia Computer Science 2011;7;39-42

    DOI: 10.1016/j.procs.2011.12.015

  • ITFoM - The IT future of medicine

    Lehrach,H., Subrak,R., Boyle,P., Pasterk,M., Zatloukal,K., Muller, H., HUBBARD,T., Brand,A., Girolami,M. et al.

    Procedia Computer Science 2011;7;26-9

    DOI: 10.1016/j.procs.2011.12.012; URL: https://dx.doi.org/10.1016/j.procs.2011.12.012

2010

  • Common variants near ATM are associated with glycemic response to metformin in type 2 diabetes.

    GoDARTS and UKPDS Diabetes Pharmacogenetics Study Group, Wellcome Trust Case Control Consortium 2, Zhou K, Bellenguez C, Spencer CC, Bennett AJ, Coleman RL, Tavendale R, Hawley SA, Donnelly LA et al.

    Nature genetics 2010;43;2;117-20

    PUBMED: 21186350; PMC: 3030919; DOI: 10.1038/ng.735

  • Insights into the genetic architecture of osteoarthritis from stage 1 of the arcOGEN study.

    Panoutsopoulou K, Southam L, Elliott KS, Wrayner N, Zhai G, Beazley C, Thorleifsson G, Arden NK, Carr A, Chapman K et al.

    Annals of the rheumatic diseases 2010;70;5;864-7

    PUBMED: 21177295; PMC: 3070286; DOI: 10.1136/ard.2010.141473

  • Disease-associated XMRV sequences are consistent with laboratory contamination.

    Hué S, Gray ER, Gall A, Katzourakis A, Tan CP, Houldcroft CJ, McLaren S, Pillay D, Futreal A, Garson JA et al.

    Retrovirology 2010;7;1;111

    PUBMED: 21171979; PMC: 3018392; DOI: 10.1186/1742-4690-7-111

  • Characterization of the proteome, diseases and evolution of the human postsynaptic density.

    Bayés A, van de Lagemaat LN, Collins MO, Croning MD, Whittle IR, Choudhary JS and Grant SG

    Nature neuroscience 2010;14;1;19-21

    PUBMED: 21170055; PMC: 3040565; DOI: 10.1038/nn.2719

  • Metagenomics and the molecular identification of novel viruses.

    Bexfield N and Kellam P

    Veterinary journal (London, England : 1997) 2010;190;2;191-198

    PUBMED: 21111643; PMC: 7110547; DOI: 10.1016/j.tvjl.2010.10.014

  • Prmt5 is essential for early mouse development and acts in the cytoplasm to maintain ES cell pluripotency.

    Tee WW, Pardo M, Theunissen TW, Yu L, Choudhary JS, Hajkova P and Surani MA

    Genes & development 2010;24;24;2772-7

    PUBMED: 21159818; PMC: 3003195; DOI: 10.1101/gad.606110

  • Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis.

    Painter JN, Anderson CA, Nyholt DR, Macgregor S, Lin J, Lee SH, Lambert A, Zhao ZZ, Roseman F, Guo Q et al.

    Nature genetics 2010;43;1;51-4

    PUBMED: 21151130; PMC: 3019124; DOI: 10.1038/ng.731

  • Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.

    Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W et al.

    Science (New York, N.Y.) 2010;330;6010;1549-51

    PUBMED: 21148394; DOI: 10.1126/science.1195203

  • Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities.

    van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, Carroll MP, Parkhill J and Bruce KD

    The ISME journal 2010;5;5;780-91

    PUBMED: 21151003; PMC: 3105771; DOI: 10.1038/ismej.2010.175

  • CEP152 is a genome maintenance protein disrupted in Seckel syndrome.

    Kalay E, Yigit G, Aslan Y, Brown KE, Pohl E, Bicknell LS, Kayserili H, Li Y, Tüysüz B, Nürnberg G et al.

    Nature genetics 2010;43;1;23-6

    PUBMED: 21131973; PMC: 3430850; DOI: 10.1038/ng.725

  • EpiChIP: gene-by-gene quantification of epigenetic modification levels.

    Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P and Teichmann SA

    Nucleic acids research 2010;39;5;e27

    PUBMED: 21131282; PMC: 3061070; DOI: 10.1093/nar/gkq1226

  • Family history of premature coronary heart disease and risk prediction in the EPIC-Norfolk prospective population study.

    Sivapalaratnam S, Boekholdt SM, Trip MD, Sandhu MS, Luben R, Kastelein JJ, Wareham NJ and Khaw KT

    Heart (British Cardiac Society) 2010;96;24;1985-9

    PUBMED: 20962344; DOI: 10.1136/hrt.2010.210740

  • Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.

    Franke A, McGovern DP, Barrett JC, Wang K, Radford-Smith GL, Ahmad T, Lees CW, Balschun T, Lee J, Roberts R et al.

    Nature genetics 2010;42;12;1118-25

    PUBMED: 21102463; PMC: 3299551; DOI: 10.1038/ng.717

  • Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon.

    Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A et al.

    European journal of human genetics : EJHG 2010;19;3;334-40

    PUBMED: 21119711; PMC: 3062011; DOI: 10.1038/ejhg.2010.177

  • Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis.

    Bowes J, Lawrence R, Eyre S, Panoutsopoulou K, Orozco G, Elliott KS, Ke X, Morris AP, UKRAG, Thomson W et al.

    Human genetics 2010;128;6;627-33

    PUBMED: 20852893; PMC: 2978888; DOI: 10.1007/s00439-010-0889-1

  • Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.

    Elks CE, Perry JR, Sulem P, Chasman DI, Franceschini N, He C, Lunetta KL, Visser JA, Byrne EM, Cousminer DL et al.

    Nature genetics 2010;42;12;1077-85

    PUBMED: 21102462; PMC: 3140055; DOI: 10.1038/ng.714

  • Beyond the Genome: genomics research ten years after the human genome sequence.

    Casto AM and Amid C

    Genome biology 2010;11;11;309

    PUBMED: 21122162; PMC: 3156947; DOI: 10.1186/gb-2010-11-11-309

  • Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06.

    Bennett JS, Bentley SD, Vernikos GS, Quail MA, Cherevach I, White B, Parkhill J and Maiden MC

    BMC genomics 2010;11;652

    PUBMED: 21092259; PMC: 3091772; DOI: 10.1186/1471-2164-11-652

  • The Molecular Basis of Leukaemia and Lymphoma

    Vassiliou,G.S. and Green,A.R.;

    Postgraduate Haematology 2010;Chapter 21;380-94

    DOI: 10.1002/9781444323160.ch21; URL: https://onlinelibrary.wiley.com/doi/...10.1002/9781444323160.ch21/summary

  • The role of vitamin D receptor gene polymorphisms in the bone mineral density of Greek postmenopausal women with low calcium intake.

    Stathopoulou MG, Dedoussis GV, Trovas G, Theodoraki EV, Katsalira A, Dontas IA, Hammond N, Deloukas P and Lyritis GP

    The Journal of nutritional biochemistry 2010;22;8;752-7

    PUBMED: 21115334; DOI: 10.1016/j.jnutbio.2010.06.007

  • Ensembl 2011.

    Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S et al.

    Nucleic acids research 2010;39;Database issue;D800-6

    PUBMED: 21045057; PMC: 3013672; DOI: 10.1093/nar/gkq1064

  • An adaptable two-color flow cytometric assay to quantitate the invasion of erythrocytes by Plasmodium falciparum parasites.

    Theron M, Hesketh RL, Subramanian S and Rayner JC

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2010;77;11;1067-74

    PUBMED: 20872885; PMC: 3047707; DOI: 10.1002/cyto.a.20972

  • A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1.

    Genetic Analysis of Psoriasis Consortium &amp; the Wellcome Trust Case Control Consortium 2, Strange A, Capon F, Spencer CC, Knight J, Weale ME, Allen MH, Barton A, Band G, Bellenguez C et al.

    Nature genetics 2010;42;11;985-90

    PUBMED: 20953190; DOI: 10.1038/ng.694

  • Common variants in the ATP2B1 gene are associated with susceptibility to hypertension: the Japanese Millennium Genome Project.

    Tabara Y, Kohara K, Kita Y, Hirawa N, Katsuya T, Ohkubo T, Hiura Y, Tajima A, Morisaki T, Miyata T et al.

    Hypertension 2010;56;5;973-80

    PUBMED: 20921432; DOI: 10.1161/HYPERTENSIONAHA.110.153429

  • Natural history of Christianson syndrome.

    Schroer RJ, Holden KR, Tarpey PS, Matheus MG, Griesemer DA, Friez MJ, Fan JZ, Simensen RJ, Strømme P, Stevenson RE et al.

    American journal of medical genetics. Part A 2010;152A;11;2775-83

    PUBMED: 20949524; DOI: 10.1002/ajmg.a.33093

  • A map of human genome variation from population-scale sequencing.

    1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME and McVean GA

    Nature 2010;467;7319;1061-73

    PUBMED: 20981092; PMC: 3042601; DOI: 10.1038/nature09534

  • The patterns and dynamics of genomic instability in metastatic pancreatic cancer.

    Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, Stebbings LA, Morsberger LA, Latimer C, McLaren S, Lin ML et al.

    Nature 2010;467;7319;1109-13

    PUBMED: 20981101; PMC: 3137369; DOI: 10.1038/nature09460

  • Y-chromosome R-M343 African lineages and sickle cell disease reveal structured assimilation in Lebanon.

    Haber M, Platt DE, Khoury S, Badro DA, Abboud M, Tyler-Smith C and Zalloua PA

    Journal of human genetics 2010;56;1;29-33

    PUBMED: 20981037; PMC: 3312574; DOI: 10.1038/jhg.2010.131

  • Dindel: accurate indel calls from short-read data.

    Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH and Durbin R

    Genome research 2010;21;6;961-73

    PUBMED: 20980555; PMC: 3106329; DOI: 10.1101/gr.112326.110

  • X-box binding protein 1 induces the expression of the lytic cycle transactivator of Kaposi's sarcoma-associated herpesvirus but not Epstein-Barr virus in co-infected primary effusion lymphoma.

    Lai IY, Farrell PJ and Kellam P

    The Journal of general virology 2010;92;Pt 2;421-31

    PUBMED: 20980528; PMC: 3081082; DOI: 10.1099/vir.0.025494-0

  • Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture.

    Chaubey G, Metspalu M, Choi Y, Mägi R, Romero IG, Soares P, van Oven M, Behar DM, Rootsi S, Hudjashov G et al.

    Molecular biology and evolution 2010;28;2;1013-24

    PUBMED: 20978040; PMC: 3355372; DOI: 10.1093/molbev/msq288

  • A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses.

    Ripatti S, Tikkanen E, Orho-Melander M, Havulinna AS, Silander K, Sharma A, Guiducci C, Perola M, Jula A, Sinisalo J et al.

    Lancet (London, England) 2010;376;9750;1393-400

    PUBMED: 20971364; PMC: 2965351; DOI: 10.1016/S0140-6736(10)61267-6

  • Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes.

    Tachibana-Konwalski K, Godwin J, van der Weyden L, Champion L, Kudo NR, Adams DJ and Nasmyth K

    Genes & development 2010;24;22;2505-16

    PUBMED: 20971813; PMC: 2975927; DOI: 10.1101/gad.605910

  • The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission.

    Tewari R, Straschil U, Bateman A, Böhme U, Cherevach I, Gong P, Pain A and Billker O

    Cell host & microbe 2010;8;4;377-87

    PUBMED: 20951971; PMC: 2977076; DOI: 10.1016/j.chom.2010.09.006

  • CCRaVAT and QuTie-enabling analysis of rare variants in large-scale case control and quantitative trait association studies.

    Lawrence R, Day-Williams AG, Elliott KS, Morris AP and Zeggini E

    BMC bioinformatics 2010;11;527

    PUBMED: 20964851; PMC: 2973964; DOI: 10.1186/1471-2105-11-527

  • Dual RMCE for efficient re-engineering of mouse mutant alleles.

    Osterwalder M, Galli A, Rosen B, Skarnes WC, Zeller R and Lopez-Rios J

    Nature methods 2010;7;11;893-5

    PUBMED: 20953177; PMC: 3576631; DOI: 10.1038/nmeth.1521

  • Characterising and predicting haploinsufficiency in the human genome.

    Huang N, Lee I, Marcotte EM and Hurles ME

    PLoS genetics 2010;6;10;e1001154

    PUBMED: 20976243; PMC: 2954820; DOI: 10.1371/journal.pgen.1001154

  • PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice.

    Rad R, Rad L, Wang W, Cadinanos J, Vassiliou G, Rice S, Campos LS, Yusa K, Banerjee R, Li MA et al.

    Science (New York, N.Y.) 2010;330;6007;1104-7

    PUBMED: 20947725; PMC: 3719098; DOI: 10.1126/science.1193004

  • Somatic structural rearrangements in genetically engineered mouse mammary tumors.

    Varela I, Klijn C, Stephens PJ, Mudie LJ, Stebbings L, Galappaththige D, van der Gulden H, Schut E, Klarenbeek S, Campbell PJ et al.

    Genome biology 2010;11;10;R100

    PUBMED: 20942901; PMC: 3218656; DOI: 10.1186/gb-2010-11-10-r100

  • Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.

    Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Lango Allen H, Lindgren CM, Luan J, Mägi R et al.

    Nature genetics 2010;42;11;937-48

    PUBMED: 20935630; PMC: 3014648; DOI: 10.1038/ng.686

  • Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.

    Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, Steinthorsdottir V, Thorleifsson G, Zillikens MC, Speliotes EK, Mägi R et al.

    Nature genetics 2010;42;11;949-60

    PUBMED: 20935629; PMC: 3000924; DOI: 10.1038/ng.685

  • The impact of gene expression regulation on evolution of extracellular signaling pathways.

    Charoensawan V, Adryan B, Martin S, Söllner C, Thisse B, Thisse C, Wright GJ and Teichmann SA

    Molecular & cellular proteomics : MCP 2010;9;12;2666-77

    PUBMED: 20935258; PMC: 3101855; DOI: 10.1074/mcp.M110.003020

  • The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.

    Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S et al.

    Nucleic acids research 2010;39;Database issue;D849-55

    PUBMED: 20929875; PMC: 3013768; DOI: 10.1093/nar/gkq879

  • AnnoTrack--a tracking system for genome annotation.

    Kokocinski F, Harrow J and Hubbard T

    BMC genomics 2010;11;538

    PUBMED: 20923551; PMC: 3091687; DOI: 10.1186/1471-2164-11-538

  • Being more realistic about the public health impact of genomic medicine.

    Hall WD, Mathews R and Morley KI

    PLoS medicine 2010;7;10

    PUBMED: 20967240; PMC: 2953533; DOI: 10.1371/journal.pmed.1000347

  • DUFs: families in search of function.

    Bateman A, Coggill P and Finn RD

    Acta crystallographica. Section F, Structural biology and crystallization communications 2010;66;Pt 10;1148-52

    PUBMED: 20944204; PMC: 2954198; DOI: 10.1107/S1744309110001685

  • Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging.

    Surakka I, Kristiansson K, Anttila V, Inouye M, Barnes C, Moutsianas L, Salomaa V, Daly M, Palotie A, Peltonen L and Ripatti S

    Genome research 2010;20;10;1344-51

    PUBMED: 20810666; PMC: 2945183; DOI: 10.1101/gr.106534.110

  • Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.

    Ikram MK, Sim X, Xueling S, Jensen RA, Cotch MF, Hewitt AW, Ikram MA, Wang JJ, Klein R, Klein BE et al.

    PLoS genetics 2010;6;10;e1001184

    PUBMED: 21060863; PMC: 2965750; DOI: 10.1371/journal.pgen.1001184

  • The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.

    Letek M, González P, Macarthur I, Rodríguez H, Freeman TC, Valero-Rello A, Blanco M, Buckley T, Cherevach I, Fahey R et al.

    PLoS genetics 2010;6;9;e1001145

    PUBMED: 20941392; PMC: 2947987; DOI: 10.1371/journal.pgen.1001145

  • Ten simple rules for editing Wikipedia.

    Logan DW, Sandal M, Gardner PP, Manske M and Bateman A

    PLoS computational biology 2010;6;9

    PUBMED: 20941386; PMC: 2947980; DOI: 10.1371/journal.pcbi.1000941

  • Hundreds of variants clustered in genomic loci and biological pathways affect human height.

    Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S et al.

    Nature 2010;467;7317;832-8

    PUBMED: 20881960; PMC: 2955183; DOI: 10.1038/nature09410

  • Single genome amplification and direct amplicon sequencing of Plasmodium spp. DNA from ape fecal specimens.

    Liu W, Li Y, Peeters M, Rayner J, Sharp P, Shaw G and Hahn B

    Protocol exchange 2010;2010

    PUBMED: 25221670; PMC: 4161957; DOI: 10.1038/nprot.2010.156

  • Genetic predisposition to long-term nondiabetic deteriorations in glucose homeostasis: Ten-year follow-up of the GLACIER study.

    Renström F, Shungin D, Johansson I, MAGIC Investigators, Florez JC, Hallmans G, Hu FB and Franks PW

    Diabetes 2010;60;1;345-54

    PUBMED: 20870969; PMC: 3012192; DOI: 10.2337/db10-0933

  • Genetic variants influencing circulating lipid levels and risk of coronary artery disease.

    Waterworth DM, Ricketts SL, Song K, Chen L, Zhao JH, Ripatti S, Aulchenko YS, Zhang W, Yuan X, Lim N et al.

    Arteriosclerosis, thrombosis, and vascular biology 2010;30;11;2264-76

    PUBMED: 20864672; PMC: 3891568; DOI: 10.1161/ATVBAHA.109.201020

  • Origin of the human malaria parasite Plasmodium falciparum in gorillas.

    Liu W, Li Y, Learn GH, Rudicell RS, Robertson JD, Keele BF, Ndjango JB, Sanz CM, Morgan DB, Locatelli S et al.

    Nature 2010;467;7314;420-5

    PUBMED: 20864995; PMC: 2997044; DOI: 10.1038/nature09442

  • Orphan CpG islands identify numerous conserved promoters in the mammalian genome.

    Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R and Bird AP

    PLoS genetics 2010;6;9;e1001134

    PUBMED: 20885785; PMC: 2944787; DOI: 10.1371/journal.pgen.1001134

  • Common variants at 10 genomic loci influence hemoglobin A₁(C) levels via glycemic and nonglycemic pathways.

    Soranzo N, Sanna S, Wheeler E, Gieger C, Radke D, Dupuis J, Bouatia-Naji N, Langenberg C, Prokopenko I, Stolerman E et al.

    Diabetes 2010;59;12;3229-39

    PUBMED: 20858683; PMC: 2992787; DOI: 10.2337/db10-0502

  • Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites.

    Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D, Loewe L, Fawcett R, Kumar S et al.

    BMC genomics 2010;11;499

    PUBMED: 20846421; PMC: 2996995; DOI: 10.1186/1471-2164-11-499

  • Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the "N4-like viruses".

    Ceyssens PJ, Brabban A, Rogge L, Lewis MS, Pickard D, Goulding D, Dougan G, Noben JP, Kropinski A, Kutter E and Lavigne R

    Virology 2010;405;1;26-30

    PUBMED: 20619867; PMC: 3715699; DOI: 10.1016/j.virol.2010.06.011

  • Legionella pneumophila strain 130b possesses a unique combination of type IV secretion systems and novel Dot/Icm secretion system effector proteins.

    Schroeder GN, Petty NK, Mousnier A, Harding CR, Vogrin AJ, Wee B, Fry NK, Harrison TG, Newton HJ, Thomson NR et al.

    Journal of bacteriology 2010;192;22;6001-16

    PUBMED: 20833813; PMC: 2976443; DOI: 10.1128/JB.00778-10

  • Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function.

    Goodall AH, Burns P, Salles I, Macaulay IC, Jones CI, Ardissino D, de Bono B, Bray SL, Deckmyn H, Dudbridge F et al.

    Blood 2010;116;22;4646-56

    PUBMED: 20833976; PMC: 2996120; DOI: 10.1182/blood-2010-04-280925

  • An immune response network associated with blood lipid levels.

    Inouye M, Silander K, Hamalainen E, Salomaa V, Harald K, Jousilahti P, Männistö S, Eriksson JG, Saarela J, Ripatti S et al.

    PLoS genetics 2010;6;9;e1001113

    PUBMED: 20844574; PMC: 2936545; DOI: 10.1371/journal.pgen.1001113

  • Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.

    Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C et al.

    Microbiology (Reading, England) 2010;156;Pt 11;3255-3269

    PUBMED: 20829291; PMC: 3090145; DOI: 10.1099/mic.0.042978-0

  • A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

    Heinig M, Petretto E, Wallace C, Bottolo L, Rotival M, Lu H, Li Y, Sarwar R, Langley SR, Bauerfeind A et al.

    Nature 2010;467;7314;460-4

    PUBMED: 20827270; PMC: 3657719; DOI: 10.1038/nature09386

  • A conserved acetyl esterase domain targets diverse bacteriophages to the Vi capsular receptor of Salmonella enterica serovar Typhi.

    Pickard D, Toribio AL, Petty NK, van Tonder A, Yu L, Goulding D, Barrell B, Rance R, Harris D, Wetter M et al.

    Journal of bacteriology 2010;192;21;5746-54

    PUBMED: 20817773; PMC: 2953684; DOI: 10.1128/JB.00659-10

  • Commercially available outbred mice for genome-wide association studies.

    Yalcin B, Nicod J, Bhomra A, Davidson S, Cleak J, Farinelli L, Østerås M, Whitley A, Yuan W, Gan X et al.

    PLoS genetics 2010;6;9;e1001085

    PUBMED: 20838427; PMC: 2932682; DOI: 10.1371/journal.pgen.1001085

  • Integrating common and rare genetic variation in diverse human populations.

    International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F et al.

    Nature 2010;467;7311;52-8

    PUBMED: 20811451; PMC: 3173859; DOI: 10.1038/nature09298

  • MicroRNAs in mouse development and disease.

    Lewis MA and Steel KP

    Seminars in cell & developmental biology 2010;21;7;774-80

    PUBMED: 20152923; PMC: 2938480; DOI: 10.1016/j.semcdb.2010.02.004

  • Loss-of-function variants in the genomes of healthy humans.

    MacArthur DG and Tyler-Smith C

    Human molecular genetics 2010;19;R2;R125-30

    PUBMED: 20805107; PMC: 2953739; DOI: 10.1093/hmg/ddq365

  • Racial/ethnic differences in association of fasting glucose-associated genomic loci with fasting glucose, HOMA-B, and impaired fasting glucose in the U.S. adult population.

    Yang Q, Liu T, Shrader P, Yesupriya A, Chang MH, Dowling NF, Ned RM, Dupuis J, Florez JC, Khoury MJ et al.

    Diabetes care 2010;33;11;2370-7

    PUBMED: 20805255; PMC: 2963497; DOI: 10.2337/dc10-0898

  • Synthetic associations in the context of genome-wide association scan signals.

    Orozco G, Barrett JC and Zeggini E

    Human molecular genetics 2010;19;R2;R137-44

    PUBMED: 20805105; PMC: 2953742; DOI: 10.1093/hmg/ddq368

  • Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1.

    Anttila V, Stefansson H, Kallela M, Todt U, Terwindt GM, Calafato MS, Nyholt DR, Dimas AS, Freilinger T, Müller-Myhsok B et al.

    Nature genetics 2010;42;10;869-73

    PUBMED: 20802479; PMC: 2948563; DOI: 10.1038/ng.652

  • A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.

    Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL et al.

    Journal of bacteriology 2010;192;21;5822-31

    PUBMED: 20802035; PMC: 2953697; DOI: 10.1128/JB.00710-10

  • Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling.

    Martin S, Söllner C, Charoensawan V, Adryan B, Thisse B, Thisse C, Teichmann S and Wright GJ

    Molecular & cellular proteomics : MCP 2010;9;12;2654-65

    PUBMED: 20802085; PMC: 3101854; DOI: 10.1074/mcp.M110.004119

  • Use of purified Clostridium difficile spores to facilitate evaluation of health care disinfection regimens.

    Lawley TD, Clare S, Deakin LJ, Goulding D, Yen JL, Raisen C, Brandt C, Lovell J, Cooke F, Clark TG and Dougan G

    Applied and environmental microbiology 2010;76;20;6895-900

    PUBMED: 20802075; PMC: 2953018; DOI: 10.1128/AEM.00718-10

  • Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits.

    Segrè AV, DIAGRAM Consortium, MAGIC investigators, Groop L, Mootha VK, Daly MJ and Altshuler D

    PLoS genetics 2010;6;8

    PUBMED: 20714348; PMC: 2920848; DOI: 10.1371/journal.pgen.1001058

  • Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.

    Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P and Dermitzakis ET

    Bioinformatics (Oxford, England) 2010;26;19;2474-6

    PUBMED: 20702402; PMC: 2944204; DOI: 10.1093/bioinformatics/btq452

  • PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice.

    Poulogiannis G, McIntyre RE, Dimitriadi M, Apps JR, Wilson CH, Ichimura K, Luo F, Cantley LC, Wyllie AH, Adams DJ and Arends MJ

    Proceedings of the National Academy of Sciences of the United States of America 2010;107;34;15145-50

    PUBMED: 20696900; PMC: 2930574; DOI: 10.1073/pnas.1009941107

  • Interactions of dietary whole-grain intake with fasting glucose- and insulin-related genetic loci in individuals of European descent: a meta-analysis of 14 cohort studies.

    Nettleton JA, McKeown NM, Kanoni S, Lemaitre RN, Hivert MF, Ngwa J, van Rooij FJ, Sonestedt E, Wojczynski MK, Ye Z et al.

    Diabetes care 2010;33;12;2684-91

    PUBMED: 20693352; PMC: 2992213; DOI: 10.2337/dc10-1150

  • Biological, clinical and population relevance of 95 loci for blood lipids.

    Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Ripatti S, Chasman DI, Willer CJ et al.

    Nature 2010;466;7307;707-13

    PUBMED: 20686565; PMC: 3039276; DOI: 10.1038/nature09270

  • Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels.

    Meyer TE, Verwoert GC, Hwang SJ, Glazer NL, Smith AV, van Rooij FJ, Ehret GB, Boerwinkle E, Felix JF, Leak TS et al.

    PLoS genetics 2010;6;8

    PUBMED: 20700443; PMC: 2916845; DOI: 10.1371/journal.pgen.1001045

  • Slingshot: a PiggyBac based transposon system for tamoxifen-inducible 'self-inactivating' insertional mutagenesis.

    Kong J, Wang F, Brenton JD and Adams DJ

    Nucleic acids research 2010;38;18;e173

    PUBMED: 20688953; PMC: 2952874; DOI: 10.1093/nar/gkq658

  • Genetic determinants of major blood lipids in Pakistanis compared with Europeans.

    Saleheen D, Soranzo N, Rasheed A, Scharnagl H, Gwilliam R, Alexander M, Inouye M, Zaidi M, Potter S, Haycock P et al.

    Circulation. Cardiovascular genetics 2010;3;4;348-57

    PUBMED: 20570915; DOI: 10.1161/CIRCGENETICS.109.906180

  • An investigation of clinical and immunological events following repeated aerodigestive tract challenge infections with live Mycobacterium bovis Bacille Calmette Guérin.

    Schreiber F, Huo Z, Giemza R, Woodrow M, Fenner N, Stephens Z, Dougan G, Prideaux S, Castello-Branco LR and Lewis DJ

    Vaccine 2010;28;33;5427-31

    PUBMED: 20558246; PMC: 3764428; DOI: 10.1016/j.vaccine.2010.06.005

  • CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.

    Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T et al.

    PLoS genetics 2010;6;7;e1001023

    PUBMED: 20657823; PMC: 2904778; DOI: 10.1371/journal.pgen.1001023

  • Quantifying the mechanisms of domain gain in animal proteins.

    Buljan M, Frankish A and Bateman A

    Genome biology 2010;11;7;R74

    PUBMED: 20633280; PMC: 2926785; DOI: 10.1186/gb-2010-11-7-r74

  • Methods for Improving Genome Annotation

    Mudge,J. and Harrow,J.

    Knowledge-Based Bioinformatics: From Analysis to Interpretation 2010;Chapter 9;209-32

    DOI: 10.1002/9780470669716.ch9; URL: https://onlinelibrary.wiley.com/doi/...10.1002/9780470669716.ch9/summary

  • Association of the 9p21.3 locus with risk of first-ever myocardial infarction in Pakistanis: case-control study in South Asia and updated meta-analysis of Europeans.

    Saleheen D, Alexander M, Rasheed A, Wormser D, Soranzo N, Hammond N, Butterworth A, Zaidi M, Haycock P, Bumpstead S et al.

    Arteriosclerosis, thrombosis, and vascular biology 2010;30;7;1467-73

    PUBMED: 20395598; DOI: 10.1161/ATVBAHA.109.197210

  • Chemokine ligand 2 genetic variants, serum monocyte chemoattractant protein-1 levels, and the risk of coronary artery disease.

    van Wijk DF, van Leuven SI, Sandhu MS, Tanck MW, Hutten BA, Wareham NJ, Kastelein JJ, Stroes ES, Khaw KT and Boekholdt SM

    Arteriosclerosis, thrombosis, and vascular biology 2010;30;7;1460-6

    PUBMED: 20431065; DOI: 10.1161/ATVBAHA.110.205526

  • Low-density lipoprotein receptor-related protein 5 polymorphisms are associated with bone mineral density in Greek postmenopausal women: an interaction with calcium intake.

    Stathopoulou MG, Dedoussis GV, Trovas G, Katsalira A, Hammond N, Deloukas P and Lyritis GP

    Journal of the American Dietetic Association 2010;110;7;1078-83

    PUBMED: 20630166; DOI: 10.1016/j.jada.2010.04.007

  • Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.

    Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G et al.

    Nature genetics 2010;42;7;579-89

    PUBMED: 20581827; PMC: 3080658; DOI: 10.1038/ng.609

  • Variants in ACAD10 are associated with type 2 diabetes, insulin resistance and lipid oxidation in Pima Indians.

    Bian L, Hanson RL, Muller YL, Ma L, MAGIC Investigators, Kobes S, Knowler WC, Bogardus C and Baier LJ

    Diabetologia 2010;53;7;1349-53

    PUBMED: 20390405; PMC: 2947857; DOI: 10.1007/s00125-010-1695-y

  • Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer.

    Turnbull C, Rapley EA, Seal S, Pernet D, Renwick A, Hughes D, Ricketts M, Linger R, Nsengimana J, Deloukas P et al.

    Nature genetics 2010;42;7;604-7

    PUBMED: 20543847; DOI: 10.1038/ng.607

  • Visualizing chromosome mosaicism and detecting ethnic outliers by the method of "rare" heterozygotes and homozygotes (RHH).

    McGinnis RE, Deloukas P, McLaren WM and Inouye M

    Human molecular genetics 2010;19;13;2539-53

    PUBMED: 20211853; PMC: 2883336; DOI: 10.1093/hmg/ddq102

  • Genomic architecture characterizes tumor progression paths and fate in breast cancer patients.

    Russnes HG, Vollan HK, Lingjaerde OC, Krasnitz A, Lundin P, Naume B, Sørlie T, Borgen E, Rye IH, Langerød A et al.

    Science translational medicine 2010;2;38;38ra47

    PUBMED: 20592421; DOI: 10.1126/scitranslmed.3000611

  • Metamotifs--a generative model for building families of nucleotide position weight matrices.

    Piipari M, Down TA and Hubbard TJ

    BMC bioinformatics 2010;11;348

    PUBMED: 20579334; PMC: 2906491; DOI: 10.1186/1471-2105-11-348

  • Evaluating the discriminative power of multi-trait genetic risk scores for type 2 diabetes in a northern Swedish population.

    Fontaine-Bisson B, Renström F, Rolandsson O, MAGIC, Payne F, Hallmans G, Barroso I and Franks PW

    Diabetologia 2010;53;10;2155-62

    PUBMED: 20571754; PMC: 2931645; DOI: 10.1007/s00125-010-1792-y

  • Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

    McLaren W, Pritchard B, Rios D, Chen Y, Flicek P and Cunningham F

    Bioinformatics (Oxford, England) 2010;26;16;2069-70

    PUBMED: 20562413; PMC: 2916720; DOI: 10.1093/bioinformatics/btq330

  • Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

    Otto TD, Sanders M, Berriman M and Newbold C

    Bioinformatics (Oxford, England) 2010;26;14;1704-7

    PUBMED: 20562415; PMC: 2894513; DOI: 10.1093/bioinformatics/btq269

  • Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion.

    Li P, Burke S, Wang J, Chen X, Ortiz M, Lee SC, Lu D, Campos L, Goulding D, Ng BL et al.

    Science (New York, N.Y.) 2010;329;5987;85-9

    PUBMED: 20538915; PMC: 3628452; DOI: 10.1126/science.1188063

  • The activating mutation R201C in GNAS promotes intestinal tumourigenesis in Apc(Min/+) mice through activation of Wnt and ERK1/2 MAPK pathways.

    Wilson CH, McIntyre RE, Arends MJ and Adams DJ

    Oncogene 2010;29;32;4567-75

    PUBMED: 20531296; PMC: 2923080; DOI: 10.1038/onc.2010.202

  • A rapid and scalable method for selecting recombinant mouse monoclonal antibodies.

    Crosnier C, Staudt N and Wright GJ

    BMC biology 2010;8;76

    PUBMED: 20525357; PMC: 2898661; DOI: 10.1186/1741-7007-8-76

  • Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.

    Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, McKinley C, Egan P, Ross L, Hayward B et al.

    Nucleic acids research 2010;38;14;e151

    PUBMED: 20525786; PMC: 2919738; DOI: 10.1093/nar/gkq510

  • Loss of NPC1 function in a patient with a co-inherited novel insulin receptor mutation does not grossly modify the severity of the associated insulin resistance.

    Kirk J, Porter KM, Parker V, Barroso I, O'Rahilly S, Hendriksz C and Semple RK

    Journal of inherited metabolic disease 2010;33 Suppl 3;S227-32

    PUBMED: 20521171; PMC: 3757264; DOI: 10.1007/s10545-010-9107-5

  • A pharmacometric model describing the relationship between warfarin dose and INR response with respect to variations in CYP2C9, VKORC1, and age.

    Hamberg AK, Wadelius M, Lindh JD, Dahl ML, Padrini R, Deloukas P, Rane A and Jonsson EN

    Clinical pharmacology and therapeutics 2010;87;6;727-34

    PUBMED: 20410877; DOI: 10.1038/clpt.2010.37

  • Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

    Kim DU, Hayles J, Kim D, Wood V, Park HO, Won M, Yoo HS, Duhig T, Nam M, Palmer G et al.

    Nature biotechnology 2010;28;6;617-23

    PUBMED: 20473289; DOI: 10.1038/nbt.1628

  • CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion.

    Reid AJ, Ranea JA, Clegg AB and Orengo CA

    PloS one 2010;5;6;e10908

    PUBMED: 20532224; PMC: 2879367; DOI: 10.1371/journal.pone.0010908

  • Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae.

    Walsh F, Cooke NM, Smith SG, Moran GP, Cooke FJ, Ivens A, Wain J and Rogers TR

    International journal of antimicrobial agents 2010;35;6;593-8

    PUBMED: 20356716; DOI: 10.1016/j.ijantimicag.2010.02.011

  • Laser excitation power and the flow cytometric resolution of complex karyotypes.

    Ng BL and Carter NP

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2010;77;6;585-8

    PUBMED: 20506467; PMC: 4131141; DOI: 10.1002/cyto.a.20904

  • Evoker: a visualization tool for genotype intensity data.

    Morris JA, Randall JC, Maller JB and Barrett JC

    Bioinformatics (Oxford, England) 2010;26;14;1786-7

    PUBMED: 20507892; PMC: 3073232; DOI: 10.1093/bioinformatics/btq280

  • Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally.

    Sutherland CJ, Tanomsing N, Nolder D, Oguike M, Jennison C, Pukrittayakamee S, Dolecek C, Hien TT, do Rosário VE, Arez AP et al.

    The Journal of infectious diseases 2010;201;10;1544-50

    PUBMED: 20380562; DOI: 10.1086/652240

  • Ensembl variation resources.

    Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P et al.

    BMC genomics 2010;11;293

    PUBMED: 20459805; PMC: 2894800; DOI: 10.1186/1471-2164-11-293

  • Using caching and optimization techniques to improve performance of the Ensembl website.

    Parker A, Bragin E, Brent S, Pritchard B, Smith JA and Trevanion S

    BMC bioinformatics 2010;11;239

    PUBMED: 20459812; PMC: 3098060; DOI: 10.1186/1471-2105-11-239

  • 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers.

    Bouwman P, Aly A, Escandell JM, Pieterse M, Bartkova J, van der Gulden H, Hiddingh S, Thanasoula M, Kulkarni A, Yang Q et al.

    Nature structural & molecular biology 2010;17;6;688-95

    PUBMED: 20453858; PMC: 2912507; DOI: 10.1038/nsmb.1831

  • A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.

    Stegle O, Parts L, Durbin R and Winn J

    PLoS computational biology 2010;6;5;e1000770

    PUBMED: 20463871; PMC: 2865505; DOI: 10.1371/journal.pcbi.1000770

  • Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilms tumour susceptibility gene.

    Slade I, Stephens P, Douglas J, Barker K, Stebbings L, Abbaszadeh F, Pritchard-Jones K, FACT collaboration, Cole R, Pizer B et al.

    Journal of medical genetics 2010;47;5;342-7

    PUBMED: 19948536; DOI: 10.1136/jmg.2009.072983

  • Genetic loci influencing kidney function and chronic kidney disease.

    Chambers JC, Zhang W, Lord GM, van der Harst P, Lawlor DA, Sehmi JS, Gale DP, Wass MN, Ahmadi KR, Bakker SJ et al.

    Nature genetics 2010;42;5;373-5

    PUBMED: 20383145; DOI: 10.1038/ng.566

  • Plasmodium falciparum ATP6 not under selection during introduction of artemisinin combination therapy in Peru.

    Woodrow CJ and Bustamante LY

    Antimicrobial agents and chemotherapy 2010;54;5;2280; author reply 2280-1

    PUBMED: 20404129; PMC: 2863640; DOI: 10.1128/AAC.01341-09

  • Variants at DGKB/TMEM195, ADRA2A, GLIS3 and C2CD4B loci are associated with reduced glucose-stimulated beta cell function in middle-aged Danish people.

    Boesgaard TW, Grarup N, Jørgensen T, Borch-Johnsen K, Meta-Analysis of Glucose and Insulin-Related Trait Consortium (MAGIC), Hansen T and Pedersen O

    Diabetologia 2010;53;8;1647-55

    PUBMED: 20419449; DOI: 10.1007/s00125-010-1753-5

  • Meta-analysis and imputation refines the association of 15q25 with smoking quantity.

    Liu JZ, Tozzi F, Waterworth DM, Pillai SG, Muglia P, Middleton L, Berrettini W, Knouff CW, Yuan X, Waeber G et al.

    Nature genetics 2010;42;5;436-40

    PUBMED: 20418889; PMC: 3612983; DOI: 10.1038/ng.572

  • Dysregulated humoral immunity to nontyphoidal Salmonella in HIV-infected African adults.

    MacLennan CA, Gilchrist JJ, Gordon MA, Cunningham AF, Cobbold M, Goodall M, Kingsley RA, van Oosterhout JJ, Msefula CL, Mandala WL et al.

    Science (New York, N.Y.) 2010;328;5977;508-12

    PUBMED: 20413503; DOI: 10.1126/science.1180346

  • Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes.

    Qi L, Cornelis MC, Kraft P, Stanya KJ, Linda Kao WH, Pankow JS, Dupuis J, Florez JC, Fox CS, Paré G et al.

    Human molecular genetics 2010;19;13;2706-15

    PUBMED: 20418489; PMC: 2883345; DOI: 10.1093/hmg/ddq156

  • Failure to validate association between 12p13 variants and ischemic stroke.

    International Stroke Genetics Consortium and Wellcome Trust Case-Control Consortium 2

    The New England journal of medicine 2010;362;16;1547-50

    PUBMED: 20410525; PMC: 2978046; DOI: 10.1056/NEJMc0910050

  • The RING-CH ligase K5 antagonizes restriction of KSHV and HIV-1 particle release by mediating ubiquitin-dependent endosomal degradation of tetherin.

    Pardieu C, Vigan R, Wilson SJ, Calvi A, Zang T, Bieniasz P, Kellam P, Towers GJ and Neil SJ

    PLoS pathogens 2010;6;4;e1000843

    PUBMED: 20419159; PMC: 2855335; DOI: 10.1371/journal.ppat.1000843

  • CpG islands influence chromatin structure via the CpG-binding protein Cfp1.

    Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr AR, Deaton A, Andrews R, James KD et al.

    Nature 2010;464;7291;1082-6

    PUBMED: 20393567; PMC: 3730110; DOI: 10.1038/nature08924

  • Distinct variants at LIN28B influence growth in height from birth to adulthood.

    Widén E, Ripatti S, Cousminer DL, Surakka I, Lappalainen T, Järvelin MR, Eriksson JG, Raitakari O, Salomaa V, Sovio U et al.

    American journal of human genetics 2010;86;5;773-82

    PUBMED: 20398887; PMC: 2869010; DOI: 10.1016/j.ajhg.2010.03.010

  • International network of cancer genome projects.

    International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I et al.

    Nature 2010;464;7291;993-8

    PUBMED: 20393554; PMC: 2902243; DOI: 10.1038/nature08987

  • Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia.

    Kariuki S, Revathi G, Kiiru J, Mengo DM, Mwituria J, Muyodi J, Munyalo A, Teo YY, Holt KE, Kingsley RA and Dougan G

    Journal of clinical microbiology 2010;48;6;2171-6

    PUBMED: 20392916; PMC: 2884483; DOI: 10.1128/JCM.01983-09

  • The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.

    Jackson AP, Sanders M, Berry A, McQuillan J, Aslett MA, Quail MA, Chukualim B, Capewell P, MacLeod A, Melville SE et al.

    PLoS neglected tropical diseases 2010;4;4;e658

    PUBMED: 20404998; PMC: 2854126; DOI: 10.1371/journal.pntd.0000658

  • A visual migraine aura locus maps to 9q21-q22.

    Tikka-Kleemola P, Artto V, Vepsäläinen S, Sobel EM, Räty S, Kaunisto MA, Anttila V, Hämäläinen E, Sumelahti ML, Ilmavirta M et al.

    Neurology 2010;74;15;1171-7

    PUBMED: 20385888; PMC: 2865729; DOI: 10.1212/WNL.0b013e3181d8ffcb

  • Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.

    Tsai IJ, Otto TD and Berriman M

    Genome biology 2010;11;4;R41

    PUBMED: 20388197; PMC: 2884544; DOI: 10.1186/gb-2010-11-4-r41

  • The genetics of obesity: FTO leads the way.

    Fawcett KA and Barroso I

    Trends in genetics : TIG 2010;26;6;266-74

    PUBMED: 20381893; PMC: 2906751; DOI: 10.1016/j.tig.2010.02.006

  • Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.

    Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S et al.

    Science (New York, N.Y.) 2010;328;5981;1036-40

    PUBMED: 20378774; PMC: 3008766; DOI: 10.1126/science.1186176

  • Ectodomains of the LDL receptor-related proteins LRP1b and LRP4 have anchorage independent functions in vivo.

    Dietrich MF, van der Weyden L, Prosser HM, Bradley A, Herz J and Adams DJ

    PloS one 2010;5;4;e9960

    PUBMED: 20383322; PMC: 2850915; DOI: 10.1371/journal.pone.0009960

  • Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight.

    Freathy RM, Mook-Kanamori DO, Sovio U, Prokopenko I, Timpson NJ, Berry DJ, Warrington NM, Widen E, Hottenga JJ, Kaakinen M et al.

    Nature genetics 2010;42;5;430-5

    PUBMED: 20372150; PMC: 2862164; DOI: 10.1038/ng.567

  • Evolutionary dynamics of Clostridium difficile over short and long time scales.

    He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R et al.

    Proceedings of the National Academy of Sciences of the United States of America 2010;107;16;7527-32

    PUBMED: 20368420; PMC: 2867753; DOI: 10.1073/pnas.0914322107

  • Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

    Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP et al.

    Nature genetics 2010;42;5;400-5

    PUBMED: 20364138; PMC: 3329635; DOI: 10.1038/ng.555

  • Mutation spectrum revealed by breakpoint sequencing of human germline CNVs.

    Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, Turner DJ and Hurles ME

    Nature genetics 2010;42;5;385-91

    PUBMED: 20364136; PMC: 3428939; DOI: 10.1038/ng.564

  • An expanded Oct4 interaction network: implications for stem cell biology, development, and disease.

    Pardo M, Lang B, Yu L, Prosser H, Bradley A, Babu MM and Choudhary J

    Cell stem cell 2010;6;4;382-395

    PUBMED: 20362542; PMC: 2860244; DOI: 10.1016/j.stem.2010.03.004

  • Nonobese diabetic congenic strain analysis of autoimmune diabetes reveals genetic complexity of the Idd18 locus and identifies Vav3 as a candidate gene.

    Fraser HI, Dendrou CA, Healy B, Rainbow DB, Howlett S, Smink LJ, Gregory S, Steward CA, Todd JA, Peterson LB and Wicker LS

    Journal of immunology (Baltimore, Md. : 1950) 2010;184;9;5075-84

    PUBMED: 20363978; PMC: 2886967; DOI: 10.4049/jimmunol.0903734

  • The genome of a songbird.

    Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S et al.

    Nature 2010;464;7289;757-62

    PUBMED: 20360741; PMC: 3187626; DOI: 10.1038/nature08819

  • Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.

    Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I and Dermitzakis ET

    PLoS genetics 2010;6;4;e1000895

    PUBMED: 20369022; PMC: 2848550; DOI: 10.1371/journal.pgen.1000895

  • Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

    Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF et al.

    Nature 2010;464;7289;713-20

    PUBMED: 20360734; PMC: 2892339; DOI: 10.1038/nature08979

  • Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.

    Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U et al.

    Nature 2010;464;7289;721-7

    PUBMED: 20360735; PMC: 3108885; DOI: 10.1038/nature08869

  • Phylogenetic analysis of gene structure and alternative splicing in alpha-actinins.

    Lek M, MacArthur DG, Yang N and North KN

    Molecular biology and evolution 2010;27;4;773-80

    PUBMED: 19897525; PMC: 4125621; DOI: 10.1093/molbev/msp268

  • Rare copy number variants: a point of rarity in genetic risk for bipolar disorder and schizophrenia.

    Grozeva D, Kirov G, Ivanov D, Jones IR, Jones L, Green EK, St Clair DM, Young AH, Ferrier N, Farmer AE et al.

    Archives of general psychiatry 2010;67;4;318-27

    PUBMED: 20368508; PMC: 4476027; DOI: 10.1001/archgenpsychiatry.2010.25

  • Systematic analysis of human protein complexes identifies chromosome segregation proteins.

    Hutchins JR, Toyoda Y, Hegemann B, Poser I, Hériché JK, Sykora MM, Augsburg M, Hudecz O, Buschhorn BA, Bulkescher J et al.

    Science (New York, N.Y.) 2010;328;5978;593-9

    PUBMED: 20360068; PMC: 2989461; DOI: 10.1126/science.1181348

  • Analysis of TBC1D4 in patients with severe insulin resistance.

    Dash S, Langenberg C, Fawcett KA, Semple RK, Romeo S, Sharp S, Sano H, Lienhard GE, Rochford JJ, Howlett T et al.

    Diabetologia 2010;53;6;1239-42

    PUBMED: 20349035; PMC: 2860565; DOI: 10.1007/s00125-010-1724-x

  • Tryptophan depletion and formation of alpha-aminoadipic and gamma-glutamic semialdehydes in porcine burger patties with added phenolic-rich fruit extracts.

    Ganhão R, Morcuende D and Estévez M

    Journal of agricultural and food chemistry 2010;58;6;3541-8

    PUBMED: 20170109; DOI: 10.1021/jf903356m

  • Curators of the world unite: the International Society of Biocuration.

    Bateman A

    Bioinformatics (Oxford, England) 2010;26;8;991

    PUBMED: 20305270; DOI: 10.1093/bioinformatics/btq101

  • European lactase persistence genotype shows evidence of association with increase in body mass index.

    Kettunen J, Silander K, Saarela O, Amin N, Müller M, Timpson N, Surakka I, Ripatti S, Laitinen J, Hartikainen AL et al.

    Human molecular genetics 2010;19;6;1129-36

    PUBMED: 20015952; PMC: 2830824; DOI: 10.1093/hmg/ddp561

  • iMotifs: an integrated sequence motif visualization and analysis environment.

    Piipari M, Down TA, Saini H, Enright A and Hubbard TJ

    Bioinformatics (Oxford, England) 2010;26;6;843-4

    PUBMED: 20106815; PMC: 2832821; DOI: 10.1093/bioinformatics/btq026

  • Antagonistic coevolution accelerates molecular evolution.

    Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B et al.

    Nature 2010;464;7286;275-8

    PUBMED: 20182425; PMC: 3717453; DOI: 10.1038/nature08798

  • Transcriptome genetics using second generation sequencing in a Caucasian population.

    Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R and Dermitzakis ET

    Nature 2010;464;7289;773-7

    PUBMED: 20220756; PMC: 3836232; DOI: 10.1038/nature08903

  • Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.

    Zhang ZD, Frankish A, Hunt T, Harrow J and Gerstein M

    Genome biology 2010;11;3;R26

    PUBMED: 20210993; PMC: 2864566; DOI: 10.1186/gb-2010-11-3-r26

  • A human gut microbial gene catalogue established by metagenomic sequencing.

    Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T et al.

    Nature 2010;464;7285;59-65

    PUBMED: 20203603; DOI: 10.1038/nature08821

  • Reverse engineering a gene network using an asynchronous parallel evolution strategy.

    Jostins L and Jaeger J

    BMC systems biology 2010;4;17

    PUBMED: 20196855; PMC: 2850326; DOI: 10.1186/1752-0509-4-17

  • Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans.

    Liu R, Lehane S, He X, Lehane M, Hertz-Fowler C, Berriman M, Pickett JA, Field LM and Zhou JJ

    Cellular and molecular life sciences : CMLS 2010;67;6;919-29

    PUBMED: 20012146; PMC: 4174292; DOI: 10.1007/s00018-009-0221-1

  • Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/Sb locus.

    Ferguson L, Lee SF, Chamberlain N, Nadeau N, Joron M, Baxter S, Wilkinson P, Papanicolaou A, Kumar S, Kee TJ et al.

    Molecular ecology 2010;19 Suppl 1;240-54

    PUBMED: 20331783; DOI: 10.1111/j.1365-294X.2009.04475.x

  • Common variants near TERC are associated with mean telomere length.

    Codd V, Mangino M, van der Harst P, Braund PS, Kaiser M, Beveridge AJ, Rafelt S, Moore J, Nelson C, Soranzo N et al.

    Nature genetics 2010;42;3;197-9

    PUBMED: 20139977; DOI: 10.1038/ng.532

  • Multiple common variants for celiac disease influencing immune gene expression.

    Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adány R, Aromaa A et al.

    Nature genetics 2010;42;4;295-302

    PUBMED: 20190752; PMC: 2847618; DOI: 10.1038/ng.543

  • Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state.

    Skene PJ, Illingworth RS, Webb S, Kerr AR, James KD, Turner DJ, Andrews R and Bird AP

    Molecular cell 2010;37;4;457-68

    PUBMED: 20188665; PMC: 4338610; DOI: 10.1016/j.molcel.2010.01.030

  • Detailed physiologic characterization reveals diverse mechanisms for novel genetic Loci regulating glucose and insulin metabolism in humans.

    Ingelsson E, Langenberg C, Hivert MF, Prokopenko I, Lyssenko V, Dupuis J, Mägi R, Sharp S, Jackson AU, Assimes TL et al.

    Diabetes 2010;59;5;1266-75

    PUBMED: 20185807; PMC: 2857908; DOI: 10.2337/db09-1568

  • Meeting report: a workshop on Best Practices in Genome Annotation.

    Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P and Hannick LI

    Database : the journal of biological databases and curation 2010;2010;baq001

    PUBMED: 20428316; PMC: 2860899; DOI: 10.1093/database/baq001

  • Signatures of mutation and selection in the cancer genome.

    Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C et al.

    Nature 2010;463;7283;893-8

    PUBMED: 20164919; PMC: 3145113; DOI: 10.1038/nature08768

  • Emx2 and early hair cell development in the mouse inner ear.

    Holley M, Rhodes C, Kneebone A, Herde MK, Fleming M and Steel KP

    Developmental biology 2010;340;2;547-56

    PUBMED: 20152827; PMC: 2877772; DOI: 10.1016/j.ydbio.2010.02.004

  • Microindel detection in short-read sequence data.

    Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S and Robinson PN

    Bioinformatics (Oxford, England) 2010;26;6;722-9

    PUBMED: 20144947; DOI: 10.1093/bioinformatics/btq027

  • New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

    Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M et al.

    Molecular microbiology 2010;76;1;12-24

    PUBMED: 20141604; PMC: 2859250; DOI: 10.1111/j.1365-2958.2009.07026.x

  • An evaluation of statistical approaches to rare variant analysis in genetic association studies.

    Morris AP and Zeggini E

    Genetic epidemiology 2010;34;2;188-93

    PUBMED: 19810025; PMC: 2962811; DOI: 10.1002/gepi.20450

  • Interleukin-8 mediates resistance to antiangiogenic agent sunitinib in renal cell carcinoma.

    Huang D, Ding Y, Zhou M, Rini BI, Petillo D, Qian CN, Kahnoski R, Futreal PA, Furge KA and Teh BT

    Cancer research 2010;70;3;1063-71

    PUBMED: 20103651; PMC: 3719378; DOI: 10.1158/0008-5472.CAN-09-3965

  • Methodological challenges of genome-wide association analysis in Africa.

    Teo YY, Small KS and Kwiatkowski DP

    Nature reviews. Genetics 2010;11;2;149-60

    PUBMED: 20084087; PMC: 3769612; DOI: 10.1038/nrg2731

  • Target-enrichment strategies for next-generation sequencing.

    Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J and Turner DJ

    Nature methods 2010;7;2;111-8

    PUBMED: 20111037; DOI: 10.1038/nmeth.1419

  • Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946.

    Sebaihia M, Bocsanczy AM, Biehl BS, Quail MA, Perna NT, Glasner JD, DeClerck GA, Cartinhour S, Schneider DJ, Bentley SD et al.

    Journal of bacteriology 2010;192;7;2020-1

    PUBMED: 20118253; PMC: 2838050; DOI: 10.1128/JB.00022-10

  • Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach.

    Mattison J, Kool J, Uren AG, de Ridder J, Wessels L, Jonkers J, Bignell GR, Butler A, Rust AG, Brosch M et al.

    Cancer research 2010;70;3;883-95

    PUBMED: 20103622; PMC: 2880710; DOI: 10.1158/0008-5472.CAN-09-1737

  • The ear

    Spiden,S.L. and Steel,K.P.;

    Embryos, Genes and Birth Defects 2010;Chapter 10;231-62

    DOI: 10.1002/9780470090121.ch10; URL: https://onlinelibrary.wiley.com/doi/...10.1002/9780470090121.ch10/summary

  • Evolution of MRSA during hospital transmission and intercontinental spread.

    Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA et al.

    Science (New York, N.Y.) 2010;327;5964;469-74

    PUBMED: 20093474; PMC: 2821690; DOI: 10.1126/science.1182395

  • Salmonella enterica serovar Typhimurium mutants completely lacking the F(0)F(1) ATPase are novel live attenuated vaccine strains.

    Northen H, Paterson GK, Constantino-Casas F, Bryant CE, Clare S, Mastroeni P, Peters SE and Maskell DJ

    Vaccine 2010;28;4;940-9

    PUBMED: 19925904; PMC: 3898827; DOI: 10.1016/j.vaccine.2009.10.146

  • The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization.

    Unemo M, Seth-Smith HMB, Cutcliffe LT, Skilton RJ, Barlow D, Goulding D, Persson K, Harris SR, Kelly A, Bjartling C et al.

    Microbiology (Reading, England) 2010;156;Pt 5;1394-1404

    PUBMED: 20093289; PMC: 3541825; DOI: 10.1099/mic.0.036830-0

  • Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.

    Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM et al.

    PloS one 2010;5;1;e8801

    PUBMED: 20098708; PMC: 2808357; DOI: 10.1371/journal.pone.0008801

  • A predominantly neolithic origin for European paternal lineages.

    Balaresque P, Bowden GR, Adams SM, Leung HY, King TE, Rosser ZH, Goodwin J, Moisan JP, Richard C, Millward A et al.

    PLoS biology 2010;8;1;e1000285

    PUBMED: 20087410; PMC: 2799514; DOI: 10.1371/journal.pbio.1000285

  • FRT-seq: amplification-free, strand-specific transcriptome sequencing.

    Mamanova L, Andrews RM, James KD, Sheridan EM, Ellis PD, Langford CF, Ost TW, Collins JE and Turner DJ

    Nature methods 2010;7;2;130-2

    PUBMED: 20081834; PMC: 2861772; DOI: 10.1038/nmeth.1417

  • Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge.

    Saxena R, Hivert MF, Langenberg C, Tanaka T, Pankow JS, Vollenweider P, Lyssenko V, Bouatia-Naji N, Dupuis J, Jackson AU et al.

    Nature genetics 2010;42;2;142-8

    PUBMED: 20081857; PMC: 2922003; DOI: 10.1038/ng.521

  • New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

    Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, Jackson AU, Wheeler E, Glazer NL, Bouatia-Naji N, Gloyn AL et al.

    Nature genetics 2010;42;2;105-16

    PUBMED: 20081858; PMC: 3018764; DOI: 10.1038/ng.520

  • KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.

    Hansen A, Henderson S, Lagos D, Nikitenko L, Coulter E, Roberts S, Gratrix F, Plaisance K, Renne R, Bower M et al.

    Genes & development 2010;24;2;195-205

    PUBMED: 20080955; PMC: 2807354; DOI: 10.1101/gad.553410

  • Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes.

    Kool J, Uren AG, Martins CP, Sie D, de Ridder J, Turner G, van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P et al.

    Cancer research 2010;70;2;520-31

    PUBMED: 20068150; PMC: 2875110; DOI: 10.1158/0008-5472.CAN-09-2736

  • Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes.

    Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, Latimer C et al.

    Nature 2010;463;7279;360-3

    PUBMED: 20054297; PMC: 2820242; DOI: 10.1038/nature08672

  • The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu.

    Karkey A, Arjyal A, Anders KL, Boni MF, Dongol S, Koirala S, My PV, Nga TV, Clements AC, Holt KE et al.

    PloS one 2010;5;11;e13988

    PUBMED: 21085575; PMC: 2981554; DOI: 10.1371/journal.pone.0013988

  • The dopamine β-hydroxylase -1021C/T polymorphism is associated with the risk of Alzheimer's disease in the Epistasis Project.

    Combarros O, Warden DR, Hammond N, Cortina-Borja M, Belbin O, Lehmann MG, Wilcock GK, Brown K, Kehoe PG, Barber R et al.

    BMC medical genetics 2010;11;162

    PUBMED: 21070631; PMC: 2994840; DOI: 10.1186/1471-2350-11-162

  • The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam.

    Nguyen NT, Ha V, Tran NV, Stabler R, Pham DT, Le TM, van Doorn HR, Cerdeño-Tárraga A, Thomson N, Campbell J et al.

    PLoS neglected tropical diseases 2010;4;6;e702

    PUBMED: 20544028; PMC: 2882334; DOI: 10.1371/journal.pntd.0000702

  • The use of DNA transposons for cancer gene discovery in mice.

    Vassiliou G, Rad R and Bradley A

    Methods in enzymology 2010;477;91-106

    PUBMED: 20699138; DOI: 10.1016/S0076-6879(10)77006-3

  • Computing behaviour in complex synapses

    Grant, S.G

    Biochemist. 2010;32;6-9

  • Data quality control in genetic case-control association studies

    ANDERSON CA, Pettersson FH, Clarke GM, Cardon LR, Morris AP, Zondervan KT

    Nature Protocols. 2010;5;1564-73

  • Leena Peltonen 1952-2010 Obituary

    STRATTON MR, Lander E

    Cell. 2010;141;208-9

  • Mouse welfare terms

    Gardiner M, Wells S, Trower C, SALISBURY J, Mallon AM, Beck T, MELVIN D, Bussell J

    Animal Technology and Welfare. 2010;9;175

  • Three authors reply

    Salanti G, ZEGGINI E, Ioannidis JPA

    American Journal of Epidemiology. 2010;171;1155-6

  • Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

    Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Le Mercier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D et al.

    Viruses-Basel. 2010;2;2258-68

  • Using randomised vectors in transcription factor binding site predictions

    Rezwan F, Sun Y, Davey N, Adams R, RUST AG, Robinson M

    Proceedings - 9th International Conference on Machine Learning and Applications, ICMLA 2010;5708880

  • Genetic evidence of multiple loci in dystocia--difficult labour.

    Algovik M, Kivinen K, Peterson H, Westgren M and Kere J

    BMC medical genetics 2010;11;105

    PUBMED: 20587075; PMC: 2914646; DOI: 10.1186/1471-2350-11-105

  • Hypokalemic periodic paralysis associated with thyrotoxicosis, renal tubular acidosis and nephrogenic diabetes insipidus.

    Im EJ, Lee JM, Kim JH, Chang SA, Moon SD, Ahn YB, Son HS, Cha BY, Lee KW and Son HY

    Endocrine journal 2010;57;4;347-50

    PUBMED: 20150720

  • Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach.

    Klijn C, Bot J, Adams DJ, Reinders M, Wessels L and Jonkers J

    PLoS computational biology 2010;6;1;e1000631

    PUBMED: 20052266; PMC: 2791203; DOI: 10.1371/journal.pcbi.1000631

  • Large-scale association analysis of TNF/LTA gene region polymorphisms in type 2 diabetes.

    Boraska V, Rayner NW, Groves CJ, Frayling TM, Diakite M, Rockett KA, Kwiatkowski DP, Day-Williams AG, McCarthy MI and Zeggini E

    BMC medical genetics 2010;11;69

    PUBMED: 20459604; PMC: 2873325; DOI: 10.1186/1471-2350-11-69

  • Leishmania-specific surface antigens show sub-genus sequence variation and immune recognition.

    Depledge DP, MacLean LM, Hodgkinson MR, Smith BA, Jackson AP, Ma S, Uliana SR and Smith DF

    PLoS neglected tropical diseases 2010;4;9;e829

    PUBMED: 20927190; PMC: 2946902; DOI: 10.1371/journal.pntd.0000829

  • Mass Spectrometry for Microbial Proteomics: Issues in Data Analysis with Electrophoretic or Mass Spectrometric Expression Proteomic Data

    Karp, N.

    Mass Spectrometry for Microbial Proteomics 2010;Chapter 18;423-40

    DOI: 10.1002/9780470665497.ch18; URL: https://onlinelibrary.wiley.com/doi/...10.1002/9780470665497.ch18/summary;jsessionid=C18EE48CEA80BB29BA75600B58FD5E7C.f02t03

  • Rare variant association analysis methods for complex traits.

    Asimit J and Zeggini E

    Annual review of genetics 2010;44;293-308

    PUBMED: 21047260; DOI: 10.1146/annurev-genet-102209-163421

  • Scoring and validation of tandem MS peptide identification methods.

    Brosch M and Choudhary J

    Methods in molecular biology (Clifton, N.J.) 2010;604;43-53

    PUBMED: 20013363; DOI: 10.1007/978-1-60761-444-9_4

  • Thioredoxin and glutathione systems differ in parasitic and free-living platyhelminths.

    Otero L, Bonilla M, Protasio AV, Fernández C, Gladyshev VN and Salinas G

    BMC genomics 2010;11;237

    PUBMED: 20385027; PMC: 2873472; DOI: 10.1186/1471-2164-11-237

2009

  • A genome-wide perspective of genetic variation in human metabolism.

    Illig T, Gieger C, Zhai G, Römisch-Margl W, Wang-Sattler R, Prehn C, Altmaier E, Kastenmüller G, Kato BS, Mewes HW et al.

    Nature genetics 2009;42;2;137-41

    PUBMED: 20037589; PMC: 3773904; DOI: 10.1038/ng.507

  • Detailed investigation of the role of common and low-frequency WFS1 variants in type 2 diabetes risk.

    Fawcett KA, Wheeler E, Morris AP, Ricketts SL, Hallmans G, Rolandsson O, Daly A, Wasson J, Permutt A, Hattersley AT et al.

    Diabetes 2009;59;3;741-6

    PUBMED: 20028947; PMC: 2828659; DOI: 10.2337/db09-0920

  • Copy number variant detection in inbred strains from short read sequence data.

    Simpson JT, McIntyre RE, Adams DJ and Durbin R

    Bioinformatics (Oxford, England) 2009;26;4;565-7

    PUBMED: 20022973; PMC: 2820678; DOI: 10.1093/bioinformatics/btp693

  • Parental origin of sequence variants associated with complex diseases.

    Kong A, Steinthorsdottir V, Masson G, Thorleifsson G, Sulem P, Besenbacher S, Jonasdottir A, Sigurdsson A, Kristinsson KT, Jonasdottir A et al.

    Nature 2009;462;7275;868-74

    PUBMED: 20016592; PMC: 3746295; DOI: 10.1038/nature08625

  • A comprehensive catalogue of somatic mutations from a human cancer genome.

    Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR et al.

    Nature 2009;463;7278;191-6

    PUBMED: 20016485; PMC: 3145108; DOI: 10.1038/nature08658

  • A small-cell lung cancer genome with complex signatures of tobacco exposure.

    Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C et al.

    Nature 2009;463;7278;184-90

    PUBMED: 20016488; PMC: 2880489; DOI: 10.1038/nature08629

  • A high-throughput pharmaceutical screen identifies compounds with specific toxicity against BRCA2-deficient tumors.

    Evers B, Schut E, van der Burg E, Braumuller TM, Egan DA, Holstege H, Edser P, Adams DJ, Wade-Martins R, Bouwman P and Jonkers J

    Clinical cancer research : an official journal of the American Association for Cancer Research 2009;16;1;99-108

    PUBMED: 20008842; PMC: 2802735; DOI: 10.1158/1078-0432.CCR-09-2434

  • Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

    Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE and Harrow JL

    BMC genomics 2009;10;606

    PUBMED: 20003482; PMC: 2807441; DOI: 10.1186/1471-2164-10-606

  • Genome-wide association study identifies five loci associated with lung function.

    Repapi E, Sayers I, Wain LV, Burton PR, Johnson T, Obeidat M, Zhao JH, Ramasamy A, Zhai G, Vitart V et al.

    Nature genetics 2009;42;1;36-44

    PUBMED: 20010834; PMC: 2862965; DOI: 10.1038/ng.501

  • Floxin, a resource for genetically engineering mouse ESCs.

    Singla V, Hunkapiller J, Santos N, Seol AD, Norman AR, Wakenight P, Skarnes WC and Reiter JF

    Nature methods 2009;7;1;50-2

    PUBMED: 19966808; PMC: 2895430; DOI: 10.1038/nmeth.1406

  • Large, rare chromosomal deletions associated with severe early-onset obesity.

    Bochukova EG, Huang N, Keogh J, Henning E, Purmann C, Blaszczyk K, Saeed S, Hamilton-Shield J, Clayton-Smith J, O'Rahilly S et al.

    Nature 2009;463;7281;666-70

    PUBMED: 19966786; PMC: 3108883; DOI: 10.1038/nature08689

  • A general basis for cognition in the evolution of synapse signaling complexes.

    Grant SG

    Cold Spring Harbor symposia on quantitative biology 2009;74;249-57

    PUBMED: 19955255; DOI: 10.1101/sqb.2009.74.033

  • The T3SS effector EspT defines a new category of invasive enteropathogenic E. coli (EPEC) which form intracellular actin pedestals.

    Bulgin R, Arbeloa A, Goulding D, Dougan G, Crepin VF, Raymond B and Frankel G

    PLoS pathogens 2009;5;12;e1000683

    PUBMED: 20011125; PMC: 2782363; DOI: 10.1371/journal.ppat.1000683

  • Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease.

    McCarroll SA, Bradner JE, Turpeinen H, Volin L, Martin PJ, Chilewski SD, Antin JH, Lee SJ, Ruutu T, Storer B et al.

    Nature genetics 2009;41;12;1341-4

    PUBMED: 19935662; PMC: 2804745; DOI: 10.1038/ng.490

  • Reduced TFAP2A function causes variable optic fissure closure and retinal defects and sensitizes eye development to mutations in other morphogenetic regulators.

    Gestri G, Osborne RJ, Wyatt AW, Gerrelli D, Gribble S, Stewart H, Fryer A, Bunyan DJ, Prescott K, Collin JR et al.

    Human genetics 2009;126;6;791-803

    PUBMED: 19685247; PMC: 3083835; DOI: 10.1007/s00439-009-0730-x

  • Signal initiation in biological systems: the properties and detection of transient extracellular protein interactions.

    Wright GJ

    Molecular bioSystems 2009;5;12;1405-12

    PUBMED: 19593473; PMC: 2898632; DOI: 10.1039/B903580J

  • Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW).

    Holden MT, Lindsay JA, Corton C, Quail MA, Cockfield JD, Pathak S, Batra R, Parkhill J, Bentley SD and Edgeworth JD

    Journal of bacteriology 2009;192;3;888-92

    PUBMED: 19948800; PMC: 2812470; DOI: 10.1128/JB.01255-09

  • Ethical data release in genome-wide association studies in developing countries.

    Parker M, Bull SJ, de Vries J, Agbenyega T, Doumbo OK and Kwiatkowski DP

    PLoS medicine 2009;6;11;e1000143

    PUBMED: 19956792; PMC: 2771895; DOI: 10.1371/journal.pmed.1000143

  • Genetic evidence that raised sex hormone binding globulin (SHBG) levels reduce the risk of type 2 diabetes.

    Perry JR, Weedon MN, Langenberg C, Jackson AU, Lyssenko V, Sparsø T, Thorleifsson G, Grallert H, Ferrucci L, Maggio M et al.

    Human molecular genetics 2009;19;3;535-44

    PUBMED: 19933169; PMC: 2798726; DOI: 10.1093/hmg/ddp522

  • Pooled analysis indicates that the GSTT1 deletion, GSTM1 deletion, and GSTP1 Ile105Val polymorphisms do not modify breast cancer risk in BRCA1 and BRCA2 mutation carriers.

    Spurdle AB, Fahey P, Chen X, McGuffog L, kConFab, Easton D, Peock S, Cook M, EMBRACE, Simard J et al.

    Breast cancer research and treatment 2009;122;1;281-5

    PUBMED: 19921428; PMC: 3074275; DOI: 10.1007/s10549-009-0601-0

  • Regulation of the Epstein-Barr virus Zp promoter in B lymphocytes during reactivation from latency.

    McDonald C, Karstegl CE, Kellam P and Farrell PJ

    The Journal of general virology 2009;91;Pt 3;622-9

    PUBMED: 19923262; DOI: 10.1099/vir.0.017277-0

  • The Pfam protein families database.

    Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K et al.

    Nucleic acids research 2009;38;Database issue;D211-22

    PUBMED: 19920124; PMC: 2808889; DOI: 10.1093/nar/gkp985

  • Common variants at five new loci associated with early-onset inflammatory bowel disease.

    Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P et al.

    Nature genetics 2009;41;12;1335-40

    PUBMED: 19915574; PMC: 3267927; DOI: 10.1038/ng.489

  • COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

    Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, Cole C, Kok CY, Jia M, Ewing R, Menzies A et al.

    Nucleic acids research 2009;38;Database issue;D652-7

    PUBMED: 19906727; PMC: 2808858; DOI: 10.1093/nar/gkp995

  • Ensembl's 10th year.

    Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S et al.

    Nucleic acids research 2009;38;Database issue;D557-62

    PUBMED: 19906699; PMC: 2808936; DOI: 10.1093/nar/gkp972

  • Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

    Steward CA, Humphray S, Plumb B, Jones MC, Quail MA, Rice S, Cox T, Davies R, Bonfield J, Keane TM et al.

    Genomics 2009;95;2;105-10

    PUBMED: 19909804; PMC: 2824108; DOI: 10.1016/j.ygeno.2009.10.004

  • The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.

    Petty NK, Bulgin R, Crepin VF, Cerdeño-Tárraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A, Clark L et al.

    Journal of bacteriology 2009;192;2;525-38

    PUBMED: 19897651; PMC: 2805327; DOI: 10.1128/JB.01144-09

  • MEROPS: the peptidase database.

    Rawlings ND, Barrett AJ and Bateman A

    Nucleic acids research 2009;38;Database issue;D227-33

    PUBMED: 19892822; PMC: 2808883; DOI: 10.1093/nar/gkp971

  • Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a.

    Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, King RJ, Lin AA, Chow CE, Semino O, Battaglia V et al.

    European journal of human genetics : EJHG 2009;18;4;479-84

    PUBMED: 19888303; PMC: 2987245; DOI: 10.1038/ejhg.2009.194

  • CARM1 is required in embryonic stem cells to maintain pluripotency and resist differentiation.

    Wu Q, Bruce AW, Jedrusik A, Ellis PD, Andrews RM, Langford CF, Glover DM and Zernicka-Goetz M

    Stem cells (Dayton, Ohio) 2009;27;11;2637-45

    PUBMED: 19544422; PMC: 4135545; DOI: 10.1002/stem.131

  • Effects of calcium signaling on Plasmodium falciparum erythrocyte invasion and post-translational modification of gliding-associated protein 45 (PfGAP45).

    Jones ML, Cottingham C and Rayner JC

    Molecular and biochemical parasitology 2009;168;1;55-62

    PUBMED: 19576251; PMC: 2754074; DOI: 10.1016/j.molbiopara.2009.06.007

  • GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs.

    Lawrence R, Day-Williams AG, Mott R, Broxholme J, Cardon LR and Zeggini E

    BMC bioinformatics 2009;10;367

    PUBMED: 19878600; PMC: 2777181; DOI: 10.1186/1471-2105-10-367

  • A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose.

    Paterson AD, Waggott D, Boright AP, Hosseini SM, Shen E, Sylvestre MP, Wong I, Bharaj B, Cleary PA, Lachin JM et al.

    Diabetes 2009;59;2;539-49

    PUBMED: 19875614; PMC: 2809960; DOI: 10.2337/db09-0653

  • Microduplications of 16p11.2 are associated with schizophrenia.

    McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, Yoon S, Perkins DO, Dickel DE, Kusenda M, Krastoshevsky O et al.

    Nature genetics 2009;41;11;1223-7

    PUBMED: 19855392; PMC: 2951180; DOI: 10.1038/ng.474

  • A novel system of polymorphic and diverse NK cell receptors in primates.

    Averdam A, Petersen B, Rosner C, Neff J, Roos C, Eberle M, Aujard F, Münch C, Schempp W, Carrington M et al.

    PLoS genetics 2009;5;10;e1000688

    PUBMED: 19834558; PMC: 2757895; DOI: 10.1371/journal.pgen.1000688

  • Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels.

    Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD et al.

    Genome biology 2009;10;10;R112

    PUBMED: 19825173; PMC: 2784327; DOI: 10.1186/gb-2009-10-10-r112

  • A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations.

    Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, de Knijff P, Kayser M, Xue Y and Tyler-Smith C

    Molecular biology and evolution 2009;27;2;385-93

    PUBMED: 19822636; PMC: 2806244; DOI: 10.1093/molbev/msp243

  • Origins and functional impact of copy number variation in the human genome.

    Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P et al.

    Nature 2009;464;7289;704-12

    PUBMED: 19812545; PMC: 3330748; DOI: 10.1038/nature08516

  • Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations.

    Eaaswarkhanth M, Haque I, Ravesh Z, Romero IG, Meganathan PR, Dubey B, Khan FA, Chaubey G, Kivisild T, Tyler-Smith C et al.

    European journal of human genetics : EJHG 2009;18;3;354-63

    PUBMED: 19809480; PMC: 2859343; DOI: 10.1038/ejhg.2009.168

  • Epilepsy and mental retardation limited to females with PCDH19 mutations can present de novo or in single generation families.

    Hynes K, Tarpey P, Dibbens LM, Bayly MA, Berkovic SF, Smith R, Raisi ZA, Turner SJ, Brown NJ, Desai TD et al.

    Journal of medical genetics 2009;47;3;211-6

    PUBMED: 19752159; DOI: 10.1136/jmg.2009.068817

  • From small reads do mighty genomes grow.

    Croucher NJ

    Nature reviews. Microbiology 2009;7;9;621

    PUBMED: 19680245; DOI: 10.1038/nrmicro2211

  • Genome-wide microarray-based comparative genomic hybridization analysis of lymphoplasmacytic lymphomas reveals heterogeneous aberrations.

    Buckley PG, Walsh SH, Laurell A, Sundström C, Roos G, Langford CF, Dumanski JP and Rosenquist R

    Leukemia & lymphoma 2009;50;9;1528-34

    PUBMED: 19672776; DOI: 10.1080/10428190903131763

  • Neuroproteomics: understanding the molecular organization and complexity of the brain.

    Bayés A and Grant SG

    Nature reviews. Neuroscience 2009;10;9;635-46

    PUBMED: 19693028; DOI: 10.1038/nrn2701

  • Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

    Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, Skuce C, Taylor R, Abdellah Z, Zhao Y et al.

    Current biology : CB 2009;19;17;1453-7

    PUBMED: 19716302; PMC: 2748900; DOI: 10.1016/j.cub.2009.07.032

  • SnoopCGH: software for visualizing comparative genomic hybridization data.

    Almagro-Garcia J, Manske M, Carret C, Campino S, Auburn S, Macinnis BL, Maslen G, Pain A, Newbold CI, Kwiatkowski DP and Clark TG

    Bioinformatics (Oxford, England) 2009;25;20;2732-3

    PUBMED: 19687029; PMC: 2759554; DOI: 10.1093/bioinformatics/btp488

  • LookSeq: a browser-based viewer for deep sequencing data.

    Manske HM and Kwiatkowski DP

    Genome research 2009;19;11;2125-32

    PUBMED: 19679872; PMC: 2775587; DOI: 10.1101/gr.093443.109

  • Common variants conferring risk of schizophrenia.

    Stefansson H, Ophoff RA, Steinberg S, Andreassen OA, Cichon S, Rujescu D, Werge T, Pietiläinen OP, Mors O, Mortensen PB et al.

    Nature 2009;460;7256;744-7

    PUBMED: 19571808; PMC: 3077530; DOI: 10.1038/nature08186

  • Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi.

    Falchi M, Bataille V, Hayward NK, Duffy DL, Bishop JA, Pastinen T, Cervino A, Zhao ZZ, Deloukas P, Soranzo N et al.

    Nature genetics 2009;41;8;915-9

    PUBMED: 19578365; PMC: 3080738; DOI: 10.1038/ng.410

  • Partial lipodystrophy and insulin resistant diabetes in a patient with a homozygous nonsense mutation in CIDEC.

    Rubio-Cabezas O, Puri V, Murano I, Saudek V, Semple RK, Dash S, Hyden CS, Bottomley W, Vigouroux C, Magré J et al.

    EMBO molecular medicine 2009;1;5;280-7

    PUBMED: 20049731; PMC: 2891108; DOI: 10.1002/emmm.200900037

  • Testing the water: marine metagenomics.

    Langridge G

    Nature reviews. Microbiology 2009;7;8;552

    PUBMED: 19609255; DOI: 10.1038/nrmicro2188

  • Common regulatory variation impacts gene expression in a cell type-dependent manner.

    Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M et al.

    Science (New York, N.Y.) 2009;325;5945;1246-50

    PUBMED: 19644074; PMC: 2867218; DOI: 10.1126/science.1174148

  • Genetic structure of nomadic Bedouin from Kuwait.

    Mohammad T, Xue Y, Evison M and Tyler-Smith C

    Heredity 2009;103;5;425-33

    PUBMED: 19639002; PMC: 2869035; DOI: 10.1038/hdy.2009.72

  • De novo apparently balanced translocations in man are predominantly paternal in origin and associated with a significant increase in paternal age.

    Thomas NS, Morris JK, Baptista J, Ng BL, Crolla JA and Jacobs PA

    Journal of medical genetics 2009;47;2;112-5

    PUBMED: 19638350; DOI: 10.1136/jmg.2009.069716

  • A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

    Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ et al.

    PLoS genetics 2009;5;7;e1000569

    PUBMED: 19609351; PMC: 2704369; DOI: 10.1371/journal.pgen.1000569

  • The genome of the blood fluke Schistosoma mansoni.

    Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD et al.

    Nature 2009;460;7253;352-8

    PUBMED: 19606141; PMC: 2756445; DOI: 10.1038/nature08160

  • The Schistosoma japonicum genome reveals features of host-parasite interplay.

    Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium

    Nature 2009;460;7253;345-51

    PUBMED: 19606140; PMC: 3747554; DOI: 10.1038/nature08140

  • Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis.

    Holden MT, Hauser H, Sanders M, Ngo TH, Cherevach I, Cronin A, Goodhead I, Mungall K, Quail MA, Price C et al.

    PloS one 2009;4;7;e6072

    PUBMED: 19603075; PMC: 2705793; DOI: 10.1371/journal.pone.0006072

  • Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies.

    Nolte IM, Wallace C, Newhouse SJ, Waggott D, Fu J, Soranzo N, Gwilliam R, Deloukas P, Savelieva I, Zheng D et al.

    PloS one 2009;4;7;e6138

    PUBMED: 19587794; PMC: 2704957; DOI: 10.1371/journal.pone.0006138

  • Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens.

    Wilkinson P, Waterfield NR, Crossman L, Corton C, Sanchez-Contreras M, Vlisidou I, Barron A, Bignell A, Clark L, Ormond D et al.

    BMC genomics 2009;10;302

    PUBMED: 19583835; PMC: 2717986; DOI: 10.1186/1471-2164-10-302

  • SNP-o-matic.

    Manske HM and Kwiatkowski DP

    Bioinformatics (Oxford, England) 2009;25;18;2434-5

    PUBMED: 19574284; PMC: 2735664; DOI: 10.1093/bioinformatics/btp403

  • The versatility and adaptation of bacteria from the genus Stenotrophomonas.

    Ryan RP, Monchy S, Cardinale M, Taghavi S, Crossman L, Avison MB, Berg G, van der Lelie D and Dow JM

    Nature reviews. Microbiology 2009;7;7;514-25

    PUBMED: 19528958; DOI: 10.1038/nrmicro2163

  • CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo.

    Wang Z, Tollervey J, Briese M, Turner D and Ule J

    Methods (San Diego, Calif.) 2009;48;3;287-93

    PUBMED: 19272451; DOI: 10.1016/j.ymeth.2009.02.021

  • Genetic utility of broadly defined bipolar schizoaffective disorder as a diagnostic concept.

    Hamshere ML, Green EK, Jones IR, Jones L, Moskvina V, Kirov G, Grozeva D, Nikolov I, Vukcevic D, Caesar S et al.

    The British journal of psychiatry : the journal of mental science 2009;195;1;23-9

    PUBMED: 19567891; PMC: 2802523; DOI: 10.1192/bjp.bp.108.061424

  • HI: haplotype improver using paired-end short reads.

    Long Q, MacArthur D, Ning Z and Tyler-Smith C

    Bioinformatics (Oxford, England) 2009;25;18;2436-7

    PUBMED: 19570807; PMC: 2735667; DOI: 10.1093/bioinformatics/btp412

  • Improved protocols for the illumina genome analyzer sequencing system.

    Quail MA, Swerdlow H and Turner DJ

    Current protocols in human genetics 2009;Chapter 18;Unit 18.2

    PUBMED: 19582764; PMC: 3849550; DOI: 10.1002/0471142905.hg1802s62

  • Milk and two oligosaccharides.

    Walker A

    Nature reviews. Microbiology 2009;7;7;483

    PUBMED: 19528955; DOI: 10.1038/nrmicro2169

  • Neonates harbour highly active gammadelta T cells with selective impairments in preterm infants.

    Gibbons DL, Haque SF, Silberzahn T, Hamilton K, Langford C, Ellis P, Carr R and Hayday AC

    European journal of immunology 2009;39;7;1794-806

    PUBMED: 19544311; DOI: 10.1002/eji.200939222

  • Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts.

    Lawley TD, Clare S, Walker AW, Goulding D, Stabler RA, Croucher N, Mastroeni P, Scott P, Raisen C, Mottram L et al.

    Infection and immunity 2009;77;9;3661-9

    PUBMED: 19564382; PMC: 2737984; DOI: 10.1128/IAI.00558-09

  • Abnormal behavior in a chromosome-engineered mouse model for human 15q11-13 duplication seen in autism.

    Nakatani J, Tamada K, Hatanaka F, Ise S, Ohta H, Inoue K, Tomonaga S, Watanabe Y, Chung YJ, Banerjee R et al.

    Cell 2009;137;7;1235-46

    PUBMED: 19563756; PMC: 3710970; DOI: 10.1016/j.cell.2009.04.024

  • Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

    Lindgren CM, Heid IM, Randall JC, Lamina C, Steinthorsdottir V, Qi L, Speliotes EK, Thorleifsson G, Willer CJ, Herrera BM et al.

    PLoS genetics 2009;5;6;e1000508

    PUBMED: 19557161; PMC: 2695778; DOI: 10.1371/journal.pgen.1000508

  • Genome flexibility in Neisseria meningitidis.

    Schoen C, Tettelin H, Parkhill J and Frosch M

    Vaccine 2009;27 Suppl 2;B103-11

    PUBMED: 19477564; PMC: 3898611; DOI: 10.1016/j.vaccine.2009.04.064

  • Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores.

    Lawley TD, Croucher NJ, Yu L, Clare S, Sebaihia M, Goulding D, Pickard DJ, Parkhill J, Choudhary J and Dougan G

    Journal of bacteriology 2009;191;17;5377-86

    PUBMED: 19542279; PMC: 2725610; DOI: 10.1128/JB.00597-09

  • Calcium-dependent signaling and kinases in apicomplexan parasites.

    Billker O, Lourido S and Sibley LD

    Cell host & microbe 2009;5;6;612-22

    PUBMED: 19527888; PMC: 2718762; DOI: 10.1016/j.chom.2009.05.017

  • Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder.

    Holmans P, Green EK, Pahwa JS, Ferreira MA, Purcell SM, Sklar P, Wellcome Trust Case-Control Consortium, Owen MJ, O'Donovan MC and Craddock N

    American journal of human genetics 2009;85;1;13-24

    PUBMED: 19539887; PMC: 2706963; DOI: 10.1016/j.ajhg.2009.05.011

  • Agouti C57BL/6N embryonic stem cells for mouse genetic resources.

    Pettitt SJ, Liang Q, Rairdan XY, Moran JL, Prosser HM, Beier DR, Lloyd KC, Bradley A and Skarnes WC

    Nature methods 2009;6;7;493-5

    PUBMED: 19525957; PMC: 3555078; DOI: 10.1038/nmeth.1342

  • Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants?

    Southam L, Soranzo N, Montgomery SB, Frayling TM, McCarthy MI, Barroso I and Zeggini E

    Diabetologia 2009;52;9;1846-51

    PUBMED: 19526209; PMC: 2723682; DOI: 10.1007/s00125-009-1419-3

  • Biology of Genomes: making sense of sequence.

    Macarthur DG

    Genome medicine 2009;1;6;61

    PUBMED: 19566913; PMC: 2703870; DOI: 10.1186/gm61

  • Ectopic recombination of a malaria var gene during mitosis associated with an altered var switch rate.

    Duffy MF, Byrne TJ, Carret C, Ivens A and Brown GV

    Journal of molecular biology 2009;389;3;453-69

    PUBMED: 19389407; PMC: 3898907; DOI: 10.1016/j.jmb.2009.04.032

  • The Sequence Alignment/Map format and SAMtools.

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R and 1000 Genome Project Data Processing Subgroup

    Bioinformatics (Oxford, England) 2009;25;16;2078-9

    PUBMED: 19505943; PMC: 2723002; DOI: 10.1093/bioinformatics/btp352

  • Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages.

    Romero P, Croucher NJ, Hiller NL, Hu FZ, Ehrlich GD, Bentley SD, García E and Mitchell TJ

    Journal of bacteriology 2009;191;15;4854-62

    PUBMED: 19502408; PMC: 2715734; DOI: 10.1128/JB.01272-08

  • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

    Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al.

    Genome research 2009;19;7;1316-23

    PUBMED: 19498102; PMC: 2704439; DOI: 10.1101/gr.080531.108

  • Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

    Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL et al.

    Nature 2009;459;7247;657-62

    PUBMED: 19465905; PMC: 2834264; DOI: 10.1038/nature08064

  • Genomic and genic deletions of the FOX gene cluster on 16q24.1 and inactivating mutations of FOXF1 cause alveolar capillary dysplasia and other malformations.

    Stankiewicz P, Sen P, Bhatt SS, Storer M, Xia Z, Bejjani BA, Ou Z, Wiszniewska J, Driscoll DJ, Maisenbacher MK et al.

    American journal of human genetics 2009;84;6;780-91

    PUBMED: 19500772; PMC: 2694971; DOI: 10.1016/j.ajhg.2009.05.005

  • ABACAS: algorithm-based automatic contiguation of assembled sequences.

    Assefa S, Keane TM, Otto TD, Newbold C and Berriman M

    Bioinformatics (Oxford, England) 2009;25;15;1968-9

    PUBMED: 19497936; PMC: 2712343; DOI: 10.1093/bioinformatics/btp347

  • Accurate and sensitive peptide identification with Mascot Percolator.

    Brosch M, Yu L, Hubbard T and Choudhary J

    Journal of proteome research 2009;8;6;3176-81

    PUBMED: 19338334; PMC: 2734080; DOI: 10.1021/pr800982s

  • Chromosomal mobilization and reintegration of Sleeping Beauty and PiggyBac transposons.

    Liang Q, Kong J, Stalker J and Bradley A

    Genesis (New York, N.Y. : 2000) 2009;47;6;404-8

    PUBMED: 19391106; DOI: 10.1002/dvg.20508

  • Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

    Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM and Vetrie D

    Genome research 2009;19;6;994-1005

    PUBMED: 19401398; PMC: 2694481; DOI: 10.1101/gr.089086.108

  • Genetic diversity amongst isolates of Neospora caninum, and the development of a multiplex assay for the detection of distinct strains.

    Al-Qassab S, Reichel MP, Ivens A and Ellis JT

    Molecular and cellular probes 2009;23;3-4;132-9

    PUBMED: 19496247

  • Genome watch: What a scorcher!

    Cerdeño-Tárraga AM

    Nature reviews. Microbiology 2009;7;6;408-9

    PUBMED: 19444245; DOI: 10.1038/nrmicro2154

  • Loci at chromosomes 13, 19 and 20 influence age at natural menopause.

    Stolk L, Zhai G, van Meurs JB, Verbiest MM, Visser JA, Estrada K, Rivadeneira F, Williams FM, Cherkas L, Deloukas P et al.

    Nature genetics 2009;41;6;645-7

    PUBMED: 19448619; PMC: 3000545; DOI: 10.1038/ng.387

  • Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations.

    Kolz M, Johnson T, Sanna S, Teumer A, Vitart V, Perola M, Mangino M, Albrecht E, Wallace C, Farrall M et al.

    PLoS genetics 2009;5;6;e1000504

    PUBMED: 19503597; PMC: 2683940; DOI: 10.1371/journal.pgen.1000504

  • Meta-analysis of genome-wide association data identifies two loci influencing age at menarche.

    Perry JR, Stolk L, Franceschini N, Lunetta KL, Zhai G, McArdle PF, Smith AV, Aspelund T, Bandinelli S, Boerwinkle E et al.

    Nature genetics 2009;41;6;648-50

    PUBMED: 19448620; PMC: 2942986; DOI: 10.1038/ng.386

  • Single domain antibodies against the collagen signalling receptor glycoprotein VI are inhibitors of collagen induced thrombus formation.

    Walker A, Pugh N, Garner SF, Stephens J, Maddox B, Ouwehand WH, Farndale RW, Steward M and Bloodomics Consortium

    Platelets 2009;20;4;268-76

    PUBMED: 19459133; DOI: 10.1080/09537100902893792

  • Transposon-mediated genome manipulation in vertebrates.

    Ivics Z, Li MA, Mátés L, Boeke JD, Nagy A, Bradley A and Izsvák Z

    Nature methods 2009;6;6;415-22

    PUBMED: 19478801; PMC: 2867038; DOI: 10.1038/nmeth.1332

  • A genome-wide association study of testicular germ cell tumor.

    Rapley EA, Turnbull C, Al Olama AA, Dermitzakis ET, Linger R, Huddart RA, Renwick A, Hughes D, Hines S, Seal S et al.

    Nature genetics 2009;41;7;807-10

    PUBMED: 19483681; PMC: 2871592; DOI: 10.1038/ng.394

  • Lineage-specific biology revealed by a finished genome assembly of the mouse.

    Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M et al.

    PLoS biology 2009;7;5;e1000112

    PUBMED: 19468303; PMC: 2680341; DOI: 10.1371/journal.pbio.1000112

  • Genome-wide and fine-resolution association analysis of malaria in West Africa.

    Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M et al.

    Nature genetics 2009;41;6;657-65

    PUBMED: 19465909; PMC: 2889040; DOI: 10.1038/ng.388

  • A truncation mutation in TBC1D4 in a family with acanthosis nigricans and postprandial hyperinsulinemia.

    Dash S, Sano H, Rochford JJ, Semple RK, Yeo G, Hyden CS, Soos MA, Clark J, Rodin A, Langenberg C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2009;106;23;9350-5

    PUBMED: 19470471; PMC: 2695078; DOI: 10.1073/pnas.0900909106

  • Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain.

    Seth-Smith HM, Harris SR, Persson K, Marsh P, Barron A, Bignell A, Bjartling C, Clark L, Cutcliffe LT, Lambden PR et al.

    BMC genomics 2009;10;239

    PUBMED: 19460133; PMC: 2693142; DOI: 10.1186/1471-2164-10-239

  • Common genetic variation in the melatonin receptor 1B gene (MTNR1B) is associated with decreased early-phase insulin response.

    Langenberg C, Pascoe L, Mari A, Tura A, Laakso M, Frayling TM, Barroso I, Loos RJ, Wareham NJ, Walker M and RISC Consortium

    Diabetologia 2009;52;8;1537-42

    PUBMED: 19455304; PMC: 2709880; DOI: 10.1007/s00125-009-1392-x

  • Next-generation sequencing of vertebrate experimental organisms.

    Turner DJ, Keane TM, Sudbery I and Adams DJ

    Mammalian genome : official journal of the International Mammalian Genome Society 2009;20;6;327-38

    PUBMED: 19452216; PMC: 2714443; DOI: 10.1007/s00335-009-9187-4

  • Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins.

    Fernández E, Collins MO, Uren RT, Kopanitsa MV, Komiyama NH, Croning MD, Zografos L, Armstrong JD, Choudhary JS and Grant SG

    Molecular systems biology 2009;5;269

    PUBMED: 19455133; PMC: 2694677; DOI: 10.1038/msb.2009.27

  • Genetic variation in LIN28B is associated with the timing of puberty.

    Ong KK, Elks CE, Li S, Zhao JH, Luan J, Andersen LB, Bingham SA, Brage S, Smith GD, Ekelund U et al.

    Nature genetics 2009;41;6;729-33

    PUBMED: 19448623; PMC: 3000552; DOI: 10.1038/ng.382

  • Gene body methylation of the dimethylarginine dimethylamino-hydrolase 2 (Ddah2) gene is an epigenetic biomarker for neural stem cell differentiation.

    Bäckdahl L, Herberth M, Wilson G, Tate P, Campos LS, Cortese R, Eckhardt F and Beck S

    Epigenetics 2009;4;4;248-54

    PUBMED: 19535899; DOI: 10.4161/epi.9093

  • Public health. The cholera crisis in Africa.

    Bhattacharya S, Black R, Bourgeois L, Clemens J, Cravioto A, Deen JL, Dougan G, Glass R, Grais RF, Greco M et al.

    Science (New York, N.Y.) 2009;324;5929;885

    PUBMED: 19443768; DOI: 10.1126/science.1173890

  • Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.

    Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA et al.

    Genome biology 2009;10;5;R51

    PUBMED: 19432983; PMC: 2718517; DOI: 10.1186/gb-2009-10-5-r51

  • Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.

    Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C et al.

    Nature genetics 2009;41;6;703-7

    PUBMED: 19430480; PMC: 2889014; DOI: 10.1038/ng.381

  • Genome-wide association study identifies eight loci associated with blood pressure.

    Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath SC, Eyheramendy S et al.

    Nature genetics 2009;41;6;666-76

    PUBMED: 19430483; PMC: 2891673; DOI: 10.1038/ng.361

  • Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

    O'Connor MN, Salles II, Cvejic A, Watkins NA, Walker A, Garner SF, Jones CI, Macaulay IC, Steward M, Zwaginga JJ et al.

    Blood 2009;113;19;4754-62

    PUBMED: 19109564; PMC: 2680375; DOI: 10.1182/blood-2008-06-162693

  • Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23.

    Orozco G, Hinks A, Eyre S, Ke X, Gibbons LJ, Bowes J, Flynn E, Martin P, Wellcome Trust Case Control Consortium, YEAR consortium et al.

    Human molecular genetics 2009;18;14;2693-9

    PUBMED: 19417005; PMC: 2701332; DOI: 10.1093/hmg/ddp193

  • Genome watch: breaking the ICE.

    Seth-Smith H and Croucher NJ

    Nature reviews. Microbiology 2009;7;5;328-9

    PUBMED: 19369947; DOI: 10.1038/nrmicro2137

  • Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2.

    Ahmed S, Thomas G, Ghoussaini M, Healey CS, Humphreys MK, Platte R, Morrison J, Maranian M, Pooley KA, Luben R et al.

    Nature genetics 2009;41;5;585-90

    PUBMED: 19330027; PMC: 2748125; DOI: 10.1038/ng.354

  • A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites.

    Uren AG, Mikkers H, Kool J, van der Weyden L, Lund AH, Wilson CH, Rance R, Jonkers J, van Lohuizen M, Berns A and Adams DJ

    Nature protocols 2009;4;5;789-98

    PUBMED: 19528954; PMC: 3627465; DOI: 10.1038/nprot.2009.64

  • X-box binding protein 1 contributes to induction of the Kaposi's sarcoma-associated herpesvirus lytic cycle under hypoxic conditions.

    Dalton-Griffin L, Wilson SJ and Kellam P

    Journal of virology 2009;83;14;7202-9

    PUBMED: 19403667; PMC: 2704782; DOI: 10.1128/JVI.00076-09

  • Neurotransmitters drive combinatorial multistate postsynaptic density networks.

    Coba MP, Pocklington AJ, Collins MO, Kopanitsa MV, Uren RT, Swamy S, Croning MD, Choudhary JS and Grant SG

    Science signaling 2009;2;68;ra19

    PUBMED: 19401593; PMC: 3280897; DOI: 10.1126/scisignal.2000102

  • The genome sequence of taurine cattle: a window to ruminant biology and evolution.

    Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L et al.

    Science (New York, N.Y.) 2009;324;5926;522-8

    PUBMED: 19390049; PMC: 2943200; DOI: 10.1126/science.1169588

  • Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

    Bovine HapMap Consortium, Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM et al.

    Science (New York, N.Y.) 2009;324;5926;528-32

    PUBMED: 19390050; PMC: 2735092; DOI: 10.1126/science.1167936

  • A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation.

    Tarpey PS, Smith R, Pleasance E, Whibley A, Edkins S, Hardy C, O'Meara S, Latimer C, Dicks E, Menzies A et al.

    Nature genetics 2009;41;5;535-43

    PUBMED: 19377476; PMC: 2872007; DOI: 10.1038/ng.367

  • IRS2 variants and syndromes of severe insulin resistance.

    Bottomley WE, Soos MA, Adams C, Guran T, Howlett TA, Mackie A, Miell J, Monson JP, Temple R, Tenenbaum-Rakover Y et al.

    Diabetologia 2009;52;6;1208-11

    PUBMED: 19377890; PMC: 2680062; DOI: 10.1007/s00125-009-1345-4

  • An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.

    Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N et al.

    Nature genetics 2009;41;5;614-8

    PUBMED: 19363478; PMC: 2705913; DOI: 10.1038/ng.369

  • Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss.

    Mencía A, Modamio-Høybjør S, Redshaw N, Morín M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T et al.

    Nature genetics 2009;41;5;609-13

    PUBMED: 19363479; DOI: 10.1038/ng.355

  • The cancer genome.

    Stratton MR, Campbell PJ and Futreal PA

    Nature 2009;458;7239;719-24

    PUBMED: 19360079; PMC: 2821689; DOI: 10.1038/nature07943

  • Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.

    Soranzo N, Rivadeneira F, Chinappen-Horsley U, Malkina I, Richards JB, Hammond N, Stolk L, Nica A, Inouye M, Hofman A et al.

    PLoS genetics 2009;5;4;e1000445

    PUBMED: 19343178; PMC: 2661236; DOI: 10.1371/journal.pgen.1000445

  • DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.

    Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM and Carter NP

    American journal of human genetics 2009;84;4;524-33

    PUBMED: 19344873; PMC: 2667985; DOI: 10.1016/j.ajhg.2009.03.010

  • Megaoesophagus in Rassf1a-null mice.

    van der Weyden L, Happerfield L, Arends MJ and Adams DJ

    International journal of experimental pathology 2009;90;2;101-8

    PUBMED: 19335548; PMC: 2676702; DOI: 10.1111/j.1365-2613.2008.00635.x

  • Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.

    Motallebipour M, Enroth S, Punga T, Ameur A, Koch C, Dunham I, Komorowski J, Ericsson J and Wadelius C

    The FEBS journal 2009;276;7;1878-90

    PUBMED: 19292868; DOI: 10.1111/j.1742-4658.2009.06914.x

  • Somatic and germline genetics at the JAK2 locus.

    Campbell PJ

    Nature genetics 2009;41;4;385-6

    PUBMED: 19338077; DOI: 10.1038/ng0409-385

  • Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon.

    Yusa K, Rad R, Takeda J and Bradley A

    Nature methods 2009;6;5;363-9

    PUBMED: 19337237; PMC: 2677165; DOI: 10.1038/nmeth.1323

  • Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer.

    van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, Edkins S, Hardy C, O'Meara S, Teague J et al.

    Nature genetics 2009;41;5;521-3

    PUBMED: 19330029; PMC: 2873835; DOI: 10.1038/ng.349

  • Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens.

    Holden MT, Heather Z, Paillot R, Steward KF, Webb K, Ainslie F, Jourdan T, Bason NC, Holroyd NE, Mungall K et al.

    PLoS pathogens 2009;5;3;e1000346

    PUBMED: 19325880; PMC: 2654543; DOI: 10.1371/journal.ppat.1000346

  • Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor.

    Ban M, Goris A, Lorentzen AR, Baker A, Mihalova T, Ingram G, Booth DR, Heard RN, Stewart GJ, Bogaert E et al.

    European journal of human genetics : EJHG 2009;17;10;1309-13

    PUBMED: 19293837; PMC: 2782567; DOI: 10.1038/ejhg.2009.41

  • TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression.

    Campino S, Forton J, Auburn S, Fry A, Diakite M, Richardson A, Hull J, Jallow M, Sisay-Joof F, Pinder M et al.

    Malaria journal 2009;8;44

    PUBMED: 19284650; PMC: 2660361; DOI: 10.1186/1475-2875-8-44

  • Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: proposed guidelines for improving data collection, distribution, and integration.

    Olivier M, Petitjean A, Teague J, Forbes S, Dunnick JK, den Dunnen JT, Langerød A, Wilkinson JM, Vihinen M, Cotton RG et al.

    Human mutation 2009;30;3;275-82

    PUBMED: 19006239; DOI: 10.1002/humu.20832

  • Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms.

    Vermeulen M, Wollstein A, van der Gaag K, Lao O, Xue Y, Wang Q, Roewer L, Knoblauch H, Tyler-Smith C, de Knijff P and Kayser M

    Forensic science international. Genetics 2009;3;4;205-13

    PUBMED: 19647704; PMC: 3312386; DOI: 10.1016/j.fsigen.2009.01.009

  • Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations.

    Clark TG, Diakite M, Auburn S, Campino S, Fry AE, Green A, Richardson A, Small K, Teo YY, Wilson J et al.

    The Journal of infectious diseases 2009;199;4;569-75

    PUBMED: 19281305; PMC: 2742199; DOI: 10.1086/596320

  • Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease.

    Trégouët DA, König IR, Erdmann J, Munteanu A, Braund PS, Hall AS, Grosshennig A, Linsel-Nitschke P, Perret C, DeSuremain M et al.

    Nature genetics 2009;41;3;283-5

    PUBMED: 19198611; DOI: 10.1038/ng.314

  • Support for the involvement of large copy number variants in the pathogenesis of schizophrenia.

    Kirov G, Grozeva D, Norton N, Ivanov D, Mantripragada KK, Holmans P, International Schizophrenia Consortium, Wellcome Trust Case Control Consortium, Craddock N, Owen MJ and O'Donovan MC

    Human molecular genetics 2009;18;8;1497-503

    PUBMED: 19181681; PMC: 2664144; DOI: 10.1093/hmg/ddp043

  • Large scale association analysis of novel genetic loci for coronary artery disease.

    Coronary Artery Disease Consortium, Samani NJ, Deloukas P, Erdmann J, Hengstenberg C, Kuulasmaa K, McGinnis R, Schunkert H, Soranzo N, Thompson J et al.

    Arteriosclerosis, thrombosis, and vascular biology 2009;29;5;774-80

    PUBMED: 19164808; PMC: 3315048; DOI: 10.1161/ATVBAHA.108.181388

  • Replication and extension of genome-wide association study results for obesity in 4923 adults from northern Sweden.

    Renström F, Payne F, Nordström A, Brito EC, Rolandsson O, Hallmans G, Barroso I, Nordström P, Franks PW and GIANT Consortium

    Human molecular genetics 2009;18;8;1489-96

    PUBMED: 19164386; PMC: 2664142; DOI: 10.1093/hmg/ddp041

  • A home for RNA families at RNA Biology

    Gardner, P. P, Bateman, A. G.

    Rna Biology 2009;6;2-4

  • Generation of Paint Probes by Flow-Sorted and Mocrodissected Chromosomes

    Yang, F, Trifonov, V.A, Ng, B. L., Kosyakova, N, Carter, N. P.

    Fluorescence In Situ Hybridization (FISH) - Application Guide. 2009;35-52

  • Human Molecular Genetics

    Sudbery, P., Sudbery, I.

    3rd Edition;Pearson Educational;ISBN978-0132051576 2009

  • Influenza-specific amino acid substitution model

    Cuong DC, Vinh LS, Quang LS

    KSE 2009 - The 1st International Conference on Knowledge and Systems Engineering. 2009;5361735;19-25

  • Neuroproteomics

    Collins MO, Grant SGN

    Encyclopedia of Neuroscience 2009;971-81

  • The discovery of genes implicated in myocardial infarction

    Ouwehand WH, Bloodomics-Cardiogenics-Consortia

    Journal of Thrombosis and Haemostasis; 22nd Congress of the International-Society-on-Thrombosis-and-Haemostasis. 2009;7;305-7

  • Identification of MAMDC1 as a candidate susceptibility gene for systemic lupus erythematosus (SLE).

    Hellquist A, Zucchelli M, Lindgren CM, Saarialho-Kere U, Järvinen TM, Koskenmies S, Julkunen H, Onkamo P, Skoog T, Panelius J et al.

    PloS one 2009;4;12;e8037

    PUBMED: 19997561; PMC: 2785483; DOI: 10.1371/journal.pone.0008037

  • Induction of antibody responses to African horse sickness virus (AHSV) in ponies after vaccination with recombinant modified vaccinia Ankara (MVA).

    Chiam R, Sharp E, Maan S, Rao S, Mertens P, Blacklaws B, Davis-Poynter N, Wood J and Castillo-Olivares J

    PloS one 2009;4;6;e5997

    PUBMED: 19543394; PMC: 2694985; DOI: 10.1371/journal.pone.0005997

  • Influence of genetic background on tumor karyotypes: evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma.

    Thomas R, Wang HJ, Tsai PC, Langford CF, Fosmire SP, Jubala CM, Getzy DM, Cutter GR, Modiano JF and Breen M

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2009;17;3;365-77

    PUBMED: 19337847; DOI: 10.1007/s10577-009-9028-z

  • Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas.

    Thomas R, Valli VE, Ellis P, Bell J, Karlsson EK, Cullen J, Lindblad-Toh K, Langford CF and Breen M

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2009;17;8;987-1000

    PUBMED: 19941159; DOI: 10.1007/s10577-009-9096-0

  • Preparation of bacteriophage lysates and pure DNA.

    Pickard DJ

    Methods in molecular biology (Clifton, N.J.) 2009;502;3-9

    PUBMED: 19082547; DOI: 10.1007/978-1-60327-565-1_1

  • Testing for rare variant associations in complex diseases.

    Asimit J and Zeggini E

    Genome medicine 2009;1;11;24

    PUBMED: 21542888; PMC: 3129640; DOI: 10.1186/gm238

  • Typhoid Fever

    Kingsley,R.A. and Dougan,G.;

    Vaccines for Biodefense and Emerging and Neglected Diseases 2009;Chapter 57;1147–1161

    DOI: 10.1016/B978-0-12-369408-9.00057-3; URL: https://www.sciencedirect.com/scien...ce/article/pii/B9780123694089000573

2008

  • The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.

    Hjerde E, Lorentzen MS, Holden MT, Seeger K, Paulsen S, Bason N, Churcher C, Harris D, Norbertczak H, Quail MA et al.

    BMC genomics 2008;9;616

    PUBMED: 19099551; PMC: 2627896; DOI: 10.1186/1471-2164-9-616

  • Inferring selection on amino acid preference in protein domains.

    Moses AM and Durbin R

    Molecular biology and evolution 2008;26;3;527-36

    PUBMED: 19095755; PMC: 2716081; DOI: 10.1093/molbev/msn286

  • Gene-wide analyses of genome-wide association data sets: evidence for multiple common risk alleles for schizophrenia and bipolar disorder and for overlap in genetic risk.

    Moskvina V, Craddock N, Holmans P, Nikolov I, Pahwa JS, Green E, Wellcome Trust Case Control Consortium, Owen MJ and O'Donovan MC

    Molecular psychiatry 2008;14;3;252-60

    PUBMED: 19065143; PMC: 3970088; DOI: 10.1038/mp.2008.133

  • A DNA transposon-based approach to validate oncogenic mutations in the mouse.

    Su Q, Prosser HM, Campos LS, Ortiz M, Nakamura T, Warren M, Dupuy AJ, Jenkins NA, Copeland NG, Bradley A and Liu P

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;50;19904-9

    PUBMED: 19064922; PMC: 2597691; DOI: 10.1073/pnas.0807785105

  • Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.

    Sabatti C, Service SK, Hartikainen AL, Pouta A, Ripatti S, Brodsky J, Jones CG, Zaitlen NA, Varilo T, Kaakinen M et al.

    Nature genetics 2008;41;1;35-46

    PUBMED: 19060910; PMC: 2687077; DOI: 10.1038/ng.271

  • Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.

    Aulchenko YS, Ripatti S, Lindqvist I, Boomsma D, Heid IM, Pramstaller PP, Penninx BW, Janssens AC, Wilson JF, Spector T et al.

    Nature genetics 2008;41;1;47-55

    PUBMED: 19060911; PMC: 2687074; DOI: 10.1038/ng.269

  • Variants in MTNR1B influence fasting glucose levels.

    Prokopenko I, Langenberg C, Florez JC, Saxena R, Soranzo N, Thorleifsson G, Loos RJ, Manning AK, Jackson AU, Aulchenko Y et al.

    Nature genetics 2008;41;1;77-81

    PUBMED: 19060907; PMC: 2682768; DOI: 10.1038/ng.290

  • The genome-wide patterns of variation expose significant substructure in a founder population.

    Jakkula E, Rehnström K, Varilo T, Pietiläinen OP, Paunio T, Pedersen NL, deFaire U, Järvelin MR, Saharinen J, Freimer N et al.

    American journal of human genetics 2008;83;6;787-94

    PUBMED: 19061986; PMC: 2668058; DOI: 10.1016/j.ajhg.2008.11.005

  • A large genome center's improvements to the Illumina sequencing system.

    Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H and Turner DJ

    Nature methods 2008;5;12;1005-10

    PUBMED: 19034268; PMC: 2610436; DOI: 10.1038/nmeth.1270

  • A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

    Behar DM, Blue-Smith J, Soria-Hernanz DF, Tzur S, Hadid Y, Bormans C, Moen A, Tyler-Smith C, Quintana-Murci L, Wells RS and Genographic Consortium

    Human mutation 2008;29;12;1387-91

    PUBMED: 18629826; PMC: 2697596; DOI: 10.1002/humu.20835

  • A novel streptococcal integrative conjugative element involved in iron acquisition.

    Heather Z, Holden MT, Steward KF, Parkhill J, Song L, Challis GL, Robinson C, Davis-Poynter N and Waller AS

    Molecular microbiology 2008;70;5;1274-92

    PUBMED: 18990191; DOI: 10.1111/j.1365-2958.2008.06481.x

  • Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors.

    Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A and Söding J

    Bioinformatics (Oxford, England) 2008;25;2;159-62

    PUBMED: 19010806; PMC: 2639001; DOI: 10.1093/bioinformatics/btn595

  • Susceptibility loci for intracranial aneurysm in European and Japanese populations.

    Bilguvar K, Yasuno K, Niemelä M, Ruigrok YM, von Und Zu Fraunberg M, van Duijn CM, van den Berg LH, Mane S, Mason CE, Choi M et al.

    Nature genetics 2008;40;12;1472-7

    PUBMED: 18997786; PMC: 2682433; DOI: 10.1038/ng.240

  • EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa.

    Abd El-Aziz MM, Barragan I, O'Driscoll CA, Goodstadt L, Prigmore E, Borrego S, Mena M, Pieras JI, El-Ashry MF, Safieh LA et al.

    Nature genetics 2008;40;11;1285-7

    PUBMED: 18836446; PMC: 2719291; DOI: 10.1038/ng.241

  • Male-pattern baldness susceptibility locus at 20p11.

    Richards JB, Yuan X, Geller F, Waterworth D, Bataille V, Glass D, Song K, Waeber G, Vollenweider P, Aben KK et al.

    Nature genetics 2008;40;11;1282-4

    PUBMED: 18849991; PMC: 2672151; DOI: 10.1038/ng.255

  • Population-specific risk of type 2 diabetes conferred by HNF4A P2 promoter variants: a lesson for replication studies.

    Barroso I, Luan J, Wheeler E, Whittaker P, Wasson J, Zeggini E, Weedon MN, Hunt S, Venkatesh R, Frayling TM et al.

    Diabetes 2008;57;11;3161-5

    PUBMED: 18728231; PMC: 2570416; DOI: 10.2337/db08-0719

  • Post-genomic challenges for collaborative research in infectious diseases.

    Okeke IN and Wain J

    Nature reviews. Microbiology 2008;6;11;858-64

    PUBMED: 18711428; DOI: 10.1038/nrmicro1989

  • Sequence data swell for nematodes.

    Hertz-Fowler C and Pain A

    Nature reviews. Microbiology 2008;6;11;800-1

    PUBMED: 18923407; DOI: 10.1038/nrmicro2021

  • The novel mouse mutation Oblivion inactivates the PMCA2 pump and causes progressive hearing loss.

    Spiden SL, Bortolozzi M, Di Leva F, de Angelis MH, Fuchs H, Lim D, Ortolano S, Ingham NJ, Brini M, Carafoli E et al.

    PLoS genetics 2008;4;10;e1000238

    PUBMED: 18974863; PMC: 2568954; DOI: 10.1371/journal.pgen.1000238

  • iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.

    Kong J, Zhu F, Stalker J and Adams DJ

    Bioinformatics (Oxford, England) 2008;24;24;2923-5

    PUBMED: 18974167; PMC: 2639305; DOI: 10.1093/bioinformatics/btn541

  • Telomeric expression sites are highly conserved in Trypanosoma brucei.

    Hertz-Fowler C, Figueiredo LM, Quail MA, Becker M, Jackson A, Bason N, Brooks K, Churcher C, Fahkro S, Goodhead I et al.

    PloS one 2008;3;10;e3527

    PUBMED: 18953401; PMC: 2567434; DOI: 10.1371/journal.pone.0003527

  • Rfam: updates to the RNA families database.

    Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR and Bateman A

    Nucleic acids research 2008;37;Database issue;D136-40

    PUBMED: 18953034; PMC: 2686503; DOI: 10.1093/nar/gkn766

  • Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69.

    Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P et al.

    Journal of bacteriology 2008;191;1;347-54

    PUBMED: 18952797; PMC: 2612414; DOI: 10.1128/JB.01238-08

  • The RNA WikiProject: community annotation of RNA families.

    Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S and Bateman A

    RNA (New York, N.Y.) 2008;14;12;2462-4

    PUBMED: 18945806; PMC: 2590952; DOI: 10.1261/rna.1200508

  • The Protein Feature Ontology: a tool for the unification of protein feature annotations.

    Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ et al.

    Bioinformatics (Oxford, England) 2008;24;23;2767-72

    PUBMED: 18936051; PMC: 2912506; DOI: 10.1093/bioinformatics/btn528

  • The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.

    Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S et al.

    Journal of bacteriology 2008;191;1;261-77

    PUBMED: 18931103; PMC: 2612433; DOI: 10.1128/JB.01230-08

  • Genomic-scale prioritization of drug targets: the TDR Targets database.

    Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F et al.

    Nature reviews. Drug discovery 2008;7;11;900-7

    PUBMED: 18927591; PMC: 3184002; DOI: 10.1038/nrd2684

  • Presence of interstereocilial links in waltzer mutants suggests Cdh23 is not essential for tip link formation.

    Rzadzinska AK and Steel KP

    Neuroscience 2008;158;2;365-8

    PUBMED: 18996172; PMC: 2989438; DOI: 10.1016/j.neuroscience.2008.10.012

  • The genome of the simian and human malaria parasite Plasmodium knowlesi.

    Pain A, Böhme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA et al.

    Nature 2008;455;7214;799-803

    PUBMED: 18843368; PMC: 2656934; DOI: 10.1038/nature07306

  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

    Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell BG, Parkhill J and Rajandream MA

    Bioinformatics (Oxford, England) 2008;24;23;2672-6

    PUBMED: 18845581; PMC: 2606163; DOI: 10.1093/bioinformatics/btn529

  • A Myo6 mutation destroys coordination between the myosin heads, revealing new functions of myosin VI in the stereocilia of mammalian inner ear hair cells.

    Hertzano R, Shalit E, Rzadzinska AK, Dror AA, Song L, Ron U, Tan JT, Shitrit AS, Fuchs H, Hasson T et al.

    PLoS genetics 2008;4;10;e1000207

    PUBMED: 18833301; PMC: 2543112; DOI: 10.1371/journal.pgen.1000207

  • Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis.

    Balaresque P, Bowden GR, Parkin EJ, Omran GA, Heyer E, Quintana-Murci L, Roewer L, Stoneking M, Nasidze I, Carvalho-Silva DR et al.

    Human mutation 2008;29;10;1171-80

    PUBMED: 18470947; PMC: 2689608; DOI: 10.1002/humu.20757

  • High-resolution mapping of expression-QTLs yields insight into human gene regulation.

    Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M and Pritchard JK

    PLoS genetics 2008;4;10;e1000214

    PUBMED: 18846210; PMC: 2556086; DOI: 10.1371/journal.pgen.1000214

  • Sites of strong Rec12/Spo11 binding in the fission yeast genome are associated with meiotic recombination and with centromeres.

    Ludin K, Mata J, Watt S, Lehmann E, Bähler J and Kohli J

    Chromosoma 2008;117;5;431-44

    PUBMED: 18449558; PMC: 3671157; DOI: 10.1007/s00412-008-0159-3

  • The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae.

    Gross R, Guzman CA, Sebaihia M, dos Santos VA, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV et al.

    BMC genomics 2008;9;449

    PUBMED: 18826580; PMC: 2572626; DOI: 10.1186/1471-2164-9-449

  • Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification.

    Rosset S, Wells RS, Soria-Hernanz DF, Tyler-Smith C, Royyuru AK, Behar DM and Genographic Consortium

    Genetics 2008;180;3;1511-24

    PUBMED: 18791242; PMC: 2581953; DOI: 10.1534/genetics.108.091116

  • Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13.

    Barton A, Thomson W, Ke X, Eyre S, Hinks A, Bowes J, Plant D, Gibbons LJ, Wellcome Trust Case Control Consortium, YEAR Consortium et al.

    Nature genetics 2008;40;10;1156-9

    PUBMED: 18794857; PMC: 2662493; DOI: 10.1038/ng.218

  • Large recurrent microdeletions associated with schizophrenia.

    Stefansson H, Rujescu D, Cichon S, Pietiläinen OP, Ingason A, Steinberg S, Fossdal R, Sigurdsson E, Sigmundsson T, Buizer-Voskamp JE et al.

    Nature 2008;455;7210;232-6

    PUBMED: 18668039; PMC: 2687075; DOI: 10.1038/nature07229

  • A robust statistical method for case-control association testing with copy number variation.

    Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D and Hurles ME

    Nature genetics 2008;40;10;1245-52

    PUBMED: 18776912; PMC: 2784596; DOI: 10.1038/ng.206

  • Copy number variation and evolution in humans and chimpanzees.

    Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C et al.

    Genome research 2008;18;11;1698-710

    PUBMED: 18775914; PMC: 2577862; DOI: 10.1101/gr.082016.108

  • Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder.

    Ferreira MA, O'Donovan MC, Meng YA, Jones IR, Ruderfer DM, Jones L, Fan J, Kirov G, Perlis RH, Green EK et al.

    Nature genetics 2008;40;9;1056-8

    PUBMED: 18711365; PMC: 2703780; DOI: 10.1038/ng.209

  • Identifying protein domains with the Pfam database.

    Coggill P, Finn RD and Bateman A

    Current protocols in bioinformatics 2008;Chapter 2;Unit 2.5

    PUBMED: 18819075; DOI: 10.1002/0471250953.bi0205s23

  • Adaptive evolution of UGT2B17 copy-number variation.

    Xue Y, Sun D, Daly A, Yang F, Zhou X, Zhao M, Huang N, Zerjal T, Lee C, Carter NP et al.

    American journal of human genetics 2008;83;3;337-46

    PUBMED: 18760392; PMC: 2556428; DOI: 10.1016/j.ajhg.2008.08.004

  • MYO5B mutations cause microvillus inclusion disease and disrupt epithelial cell polarity.

    Müller T, Hess MW, Schiefermeier N, Pfaller K, Ebner HL, Heinz-Erian P, Ponstingl H, Partsch J, Röllinghoff B, Köhler H et al.

    Nature genetics 2008;40;10;1163-5

    PUBMED: 18724368; DOI: 10.1038/ng.225

  • Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing.

    Campbell PJ, Pleasance ED, Stephens PJ, Dicks E, Rance R, Goodhead I, Follows GA, Green AR, Futreal PA and Stratton MR

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;35;13081-6

    PUBMED: 18723673; PMC: 2529122; DOI: 10.1073/pnas.0801523105

  • Lifelong reduction of LDL-cholesterol related to a common variant in the LDL-receptor gene decreases the risk of coronary artery disease--a Mendelian Randomisation study.

    Linsel-Nitschke P, Götz A, Erdmann J, Braenne I, Braund P, Hengstenberg C, Stark K, Fischer M, Schreiber S, El Mokhtari NE et al.

    PloS one 2008;3;8;e2986

    PUBMED: 18714375; PMC: 2500189; DOI: 10.1371/journal.pone.0002986

  • Mapping short DNA sequencing reads and calling variants using mapping quality scores.

    Li H, Ruan J and Durbin R

    Genome research 2008;18;11;1851-8

    PUBMED: 18714091; PMC: 2577856; DOI: 10.1101/gr.078212.108

  • An evolutionary perspective on Y-chromosomal variation and male infertility.

    Tyler-Smith C

    International journal of andrology 2008;31;4;376-82

    PUBMED: 18399979; PMC: 2628431; DOI: 10.1111/j.1365-2605.2008.00889.x

  • Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast.

    Monahan BJ, Villén J, Marguerat S, Bähler J, Gygi SP and Winston F

    Nature structural & molecular biology 2008;15;8;873-80

    PUBMED: 18622392; PMC: 2559950; DOI: 10.1038/nsmb.1452

  • Genomic adaptation: a fungal perspective.

    Pain A and Hertz-Fowler C

    Nature reviews. Microbiology 2008;6;8;572-3

    PUBMED: 18628767; DOI: 10.1038/nrmicro1964

  • Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

    Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T et al.

    Nature biotechnology 2008;26;8;889-96

    PUBMED: 18688244; PMC: 2771753; DOI: 10.1038/nbt.1411

  • High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

    Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J et al.

    Nature genetics 2008;40;8;987-93

    PUBMED: 18660809; PMC: 2652037; DOI: 10.1038/ng.195

  • Organ-specific requirements for Hdac1 in liver and pancreas formation.

    Noël ES, Casal-Sueiro A, Busch-Nentwich E, Verkade H, Dong PD, Stemple DL and Ober EA

    Developmental biology 2008;322;2;237-50

    PUBMED: 18687323; PMC: 3710974; DOI: 10.1016/j.ydbio.2008.06.040

  • Mapping multiprotein complexes by affinity purification and mass spectrometry.

    Collins MO and Choudhary JS

    Current opinion in biotechnology 2008;19;4;324-30

    PUBMED: 18598764; DOI: 10.1016/j.copbio.2008.06.002

  • Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids.

    Letek M, Ocampo-Sosa AA, Sanders M, Fogarty U, Buckley T, Leadon DP, González P, Scortti M, Meijer WG, Parkhill J et al.

    Journal of bacteriology 2008;190;17;5797-805

    PUBMED: 18606735; PMC: 2519538; DOI: 10.1128/JB.00468-08

  • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

    Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM et al.

    Nature biotechnology 2008;26;7;779-85

    PUBMED: 18612301; PMC: 2644410; DOI: 10.1038/nbt1414

  • Sequence differentiation in regions identified by a genome scan for local adaptation.

    Wood HM, Grahame JW, Humphray S, Rogers J and Butlin RK

    Molecular ecology 2008;17;13;3123-35

    PUBMED: 18510587; DOI: 10.1111/j.1365-294X.2008.03755.x

  • Strong genetic evidence for a selective influence of GABAA receptors on a component of the bipolar disorder phenotype.

    Craddock N, Jones L, Jones IR, Kirov G, Green EK, Grozeva D, Moskvina V, Nikolov I, Hamshere ML, Vukcevic D et al.

    Molecular psychiatry 2008;15;2;146-53

    PUBMED: 19078961; PMC: 3967096; DOI: 10.1038/mp.2008.66

  • Use and misuse of the gene ontology annotations.

    Rhee SY, Wood V, Dolinski K and Draghici S

    Nature reviews. Genetics 2008;9;7;509-15

    PUBMED: 18475267; DOI: 10.1038/nrg2363

  • Vive la différence.

    Thomson NR

    Nature reviews. Microbiology 2008;6;7;502-3

    PUBMED: 18536729; DOI: 10.1038/nrmicro1929

  • Evaluating the role of LPIN1 variation in insulin resistance, body weight, and human lipodystrophy in U.K. Populations.

    Fawcett KA, Grimsey N, Loos RJ, Wheeler E, Daly A, Soos M, Semple R, Syddall H, Cooper C, Siniossoglou S et al.

    Diabetes 2008;57;9;2527-33

    PUBMED: 18591397; PMC: 2518506; DOI: 10.2337/db08-0422

  • Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.

    Smits G, Mungall AJ, Griffiths-Jones S, Smith P, Beury D, Matthews L, Rogers J, Pask AJ, Shaw G, VandeBerg JL et al.

    Nature genetics 2008;40;8;971-6

    PUBMED: 18587395; DOI: 10.1038/ng.168

  • Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.

    Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM et al.

    Nature genetics 2008;40;8;955-62

    PUBMED: 18587394; PMC: 2574810; DOI: 10.1038/ng.175

  • Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.

    Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S, Churcher C, Quail MA, Stevens M, Jones MA, Watson M et al.

    Genome research 2008;18;10;1624-37

    PUBMED: 18583645; PMC: 2556274; DOI: 10.1101/gr.077404.108

  • Chromosomal transposition of PiggyBac in mouse embryonic stem cells.

    Wang W, Lin C, Lu D, Ning Z, Cox T, Melvin D, Wang X, Bradley A and Liu P

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;27;9290-5

    PUBMED: 18579772; PMC: 2440425; DOI: 10.1073/pnas.0801017105

  • An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).

    Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M et al.

    Genome research 2008;18;9;1518-29

    PUBMED: 18577705; PMC: 2527707; DOI: 10.1101/gr.077479.108

  • Variation of the oxytocin/neurophysin I (OXT) gene in four human populations.

    Xu Y, Xue Y, Asan, Daly A, Wu L and Tyler-Smith C

    Journal of human genetics 2008;53;7;637-643

    PUBMED: 18566739; PMC: 2680061; DOI: 10.1007/s10038-008-0292-0

  • Long-range, high-throughput haplotype determination via haplotype-fusion PCR and ligation haplotyping.

    Turner DJ, Tyler-Smith C and Hurles ME

    Nucleic acids research 2008;36;13;e82

    PUBMED: 18562465; PMC: 2490767; DOI: 10.1093/nar/gkn373

  • Contemporary approaches for modifying the mouse genome.

    Adams DJ and van der Weyden L

    Physiological genomics 2008;34;3;225-38

    PUBMED: 18559964; PMC: 2519963; DOI: 10.1152/physiolgenomics.90242.2008

  • Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications.

    Balaresque P, Parkin EJ, Roewer L, Carvalho-Silva DR, Mitchell RJ, van Oorschot RA, Henke J, Stoneking M, Nasidze I, Wetton J et al.

    International journal of legal medicine 2008;123;1;15-23

    PUBMED: 18553096; PMC: 2680205; DOI: 10.1007/s00414-008-0253-3

  • Evolutionary expansion and anatomical specialization of synapse proteome complexity.

    Emes RD, Pocklington AJ, Anderson CN, Bayes A, Collins MO, Vickers CA, Croning MD, Malik BR, Choudhary JS, Armstrong JD and Grant SG

    Nature neuroscience 2008;11;7;799-806

    PUBMED: 18536710; PMC: 3624047; DOI: 10.1038/nn.2135

  • The evolution of the DLK1-DIO3 imprinted domain in mammals.

    Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, SAVOIR consortium et al.

    PLoS biology 2008;6;6;e135

    PUBMED: 18532878; PMC: 2408620; DOI: 10.1371/journal.pbio.0060135

  • Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype.

    Burns P, Gusnanto A, Macaulay IC, Rankin A, Tom B, Langford CF, Dudbridge F, Ouwehand WH, Watkins NA and Bloodomics Consortium

    Platelets 2008;19;4;258-67

    PUBMED: 18569861; DOI: 10.1080/09537100801947434

  • Microbiology in the post-genomic era.

    Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S and Rappuoli R

    Nature reviews. Microbiology 2008;6;6;419-30

    PUBMED: 18475305; DOI: 10.1038/nrmicro1901

  • Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice.

    Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG and Harrow JL

    Genome biology 2008;9;5;R91

    PUBMED: 18507838; PMC: 2441477; DOI: 10.1186/gb-2008-9-5-r91

  • Normal germ line establishment in mice carrying a deletion of the Ifitm/Fragilis gene family cluster.

    Lange UC, Adams DJ, Lee C, Barton S, Schneider R, Bradley A and Surani MA

    Molecular and cellular biology 2008;28;15;4688-96

    PUBMED: 18505827; PMC: 2493357; DOI: 10.1128/MCB.00272-08

  • Efficient targeted transcript discovery via array-based normalization of RACE libraries.

    Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR et al.

    Nature methods 2008;5;7;629-35

    PUBMED: 18500348; PMC: 2713501; DOI: 10.1038/nmeth.1216

  • Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes.

    Howarth KD, Blood KA, Ng BL, Beavis JC, Chua Y, Cooke SL, Raby S, Ichimura K, Collins VP, Carter NP and Edwards PA

    Oncogene 2008;27;23;3345-59

    PUBMED: 18084325; PMC: 2423006; DOI: 10.1038/sj.onc.1210993

  • Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.

    Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J and Bähler J

    Nature 2008;453;7199;1239-43

    PUBMED: 18488015; DOI: 10.1038/nature07002

  • X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment.

    Dibbens LM, Tarpey PS, Hynes K, Bayly MA, Scheffer IE, Smith R, Bomar J, Sutton E, Vandeleur L, Shoubridge C et al.

    Nature genetics 2008;40;6;776-81

    PUBMED: 18469813; PMC: 2756413; DOI: 10.1038/ng.149

  • The Gly482Ser genotype at the PPARGC1A gene and elevated blood pressure: a meta-analysis involving 13,949 individuals.

    Vimaleswaran KS, Luan J, Andersen G, Muller YL, Wheeler E, Brito EC, O'Rahilly S, Pedersen O, Baier LJ, Knowler WC et al.

    Journal of applied physiology (Bethesda, Md. : 1985) 2008;105;4;1352-8

    PUBMED: 18467552; PMC: 2576025; DOI: 10.1152/japplphysiol.90423.2008

  • Genome analysis of the platypus reveals unique signatures of evolution.

    Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT et al.

    Nature 2008;453;7192;175-83

    PUBMED: 18464734; PMC: 2803040; DOI: 10.1038/nature06936

  • Common variants near MC4R are associated with fat mass, weight and risk of obesity.

    Loos RJ, Lindgren CM, Li S, Wheeler E, Zhao JH, Prokopenko I, Inouye M, Freathy RM, Attwood AP, Beckmann JS et al.

    Nature genetics 2008;40;6;768-75

    PUBMED: 18454148; PMC: 2669167; DOI: 10.1038/ng.140

  • The minimum information about a genome sequence (MIGS) specification.

    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV et al.

    Nature biotechnology 2008;26;5;541-7

    PUBMED: 18464787; PMC: 2409278; DOI: 10.1038/nbt1360

  • BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals.

    Poser I, Sarov M, Hutchins JR, Hériché JK, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW et al.

    Nature methods 2008;5;5;409-15

    PUBMED: 18391959; PMC: 2871289; DOI: 10.1038/nmeth.1199

  • Consistently replicating locus linked to migraine on 10q22-q23.

    Anttila V, Nyholt DR, Kallela M, Artto V, Vepsäläinen S, Jakkula E, Wennerström A, Tikka-Kleemola P, Kaunisto MA, Hämäläinen E et al.

    American journal of human genetics 2008;82;5;1051-63

    PUBMED: 18423523; PMC: 2427232; DOI: 10.1016/j.ajhg.2008.03.003

  • From gene expression to disease risk.

    Dermitzakis ET

    Nature genetics 2008;40;5;492-3

    PUBMED: 18443581; DOI: 10.1038/ng0508-492

  • Identification of ten loci associated with height highlights new biological pathways in human growth.

    Lettre G, Jackson AU, Gieger C, Schumacher FR, Berndt SI, Sanna S, Eyheramendy S, Voight BF, Butler JL, Guiducci C et al.

    Nature genetics 2008;40;5;584-91

    PUBMED: 18391950; PMC: 2687076; DOI: 10.1038/ng.125

  • Phenotypical characteristics of idiopathic infantile nystagmus with and without mutations in FRMD7.

    Thomas S, Proudlock FA, Sarvananthan N, Roberts EO, Awan M, McLean R, Surendran M, Kumar AS, Farooq SJ, Degg C et al.

    Brain : a journal of neurology 2008;131;Pt 5;1259-67

    PUBMED: 18372314; DOI: 10.1093/brain/awn046

  • ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a.

    Gao X, Tate P, Hu P, Tjian R, Skarnes WC and Wang Z

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;18;6656-61

    PUBMED: 18448678; PMC: 2373334; DOI: 10.1073/pnas.0801802105

  • Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.

    Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, Prescott NJ, Nimmo ER, Massey D, Berzuini C, Johnson C et al.

    Nature genetics 2008;40;6;710-2

    PUBMED: 18438406; PMC: 2719289; DOI: 10.1038/ng.145

  • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

    Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C et al.

    Nature genetics 2008;40;6;722-9

    PUBMED: 18438408; PMC: 2705838; DOI: 10.1038/ng.128

  • The dawn of human matrilineal diversity.

    Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D et al.

    American journal of human genetics 2008;82;5;1130-40

    PUBMED: 18439549; PMC: 2427203; DOI: 10.1016/j.ajhg.2008.04.002

  • Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility.

    Barton A, Thomson W, Ke X, Eyre S, Hinks A, Bowes J, Gibbons L, Plant D, Wellcome Trust Case Control Consortium, Wilson AG et al.

    Human molecular genetics 2008;17;15;2274-9

    PUBMED: 18434327; PMC: 2465799; DOI: 10.1093/hmg/ddn128

  • The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants.

    Crossman LC, Gould VC, Dow JM, Vernikos GS, Okazaki A, Sebaihia M, Saunders D, Arrowsmith C, Carver T, Peters N et al.

    Genome biology 2008;9;4;R74

    PUBMED: 18419807; PMC: 2643945; DOI: 10.1186/gb-2008-9-4-r74

  • SrfB, a member of the Serum Response Factor family of transcription factors, regulates starvation response and early development in Dictyostelium.

    Galardi-Castilla M, Pergolizzi B, Bloomfield G, Skelton J, Ivens A, Kay RR, Bozzaro S and Sastre L

    Developmental biology 2008;316;2;260-74

    PUBMED: 18339368; DOI: 10.1016/j.ydbio.2008.01.026

  • Fission yeast MAP kinase Sty1 is recruited to stress-induced genes.

    Reiter W, Watt S, Dawson K, Lawrence CL, Bähler J, Jones N and Wilkinson CR

    The Journal of biological chemistry 2008;283;15;9945-56

    PUBMED: 18252721; PMC: 3668131; DOI: 10.1074/jbc.M710428200

  • Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis.

    Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, Johnson PD, Abdellah Z, Arrowsmith C, Chillingworth T, Churcher C et al.

    Genome research 2008;18;5;729-41

    PUBMED: 18403782; PMC: 2336800; DOI: 10.1101/gr.075069.107

  • Loss of Rassf1a cooperates with Apc(Min) to accelerate intestinal tumourigenesis.

    van der Weyden L, Arends MJ, Dovey OM, Harrison HL, Lefebvre G, Conte N, Gergely FV, Bradley A and Adams DJ

    Oncogene 2008;27;32;4503-8

    PUBMED: 18391979; PMC: 3706934; DOI: 10.1038/onc.2008.94

  • Genome-wide association analysis identifies 20 loci that influence adult height.

    Weedon MN, Lango H, Lindgren CM, Wallace C, Evans DM, Mangino M, Freathy RM, Perry JR, Stevens S, Hall AS et al.

    Nature genetics 2008;40;5;575-83

    PUBMED: 18391952; PMC: 2681221; DOI: 10.1038/ng.121

  • Phosphoproteomic analysis of the mouse brain cytosol reveals a predominance of protein phosphorylation in regions of intrinsic sequence disorder.

    Collins MO, Yu L, Campuzano I, Grant SG and Choudhary JS

    Molecular & cellular proteomics : MCP 2008;7;7;1331-48

    PUBMED: 18388127; DOI: 10.1074/mcp.M700564-MCP200

  • The functional impact of structural variation in humans.

    Hurles ME, Dermitzakis ET and Tyler-Smith C

    Trends in genetics : TIG 2008;24;5;238-45

    PUBMED: 18378036; PMC: 2869026; DOI: 10.1016/j.tig.2008.03.001

  • The Catalogue of Somatic Mutations in Cancer (COSMIC).

    Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA and Stratton MR

    Current protocols in human genetics 2008;Chapter 10;Unit 10.11

    PUBMED: 18428421; PMC: 2705836; DOI: 10.1002/0471142905.hg1011s57

  • The neglected role of antibody in protection against bacteremia caused by nontyphoidal strains of Salmonella in African children.

    MacLennan CA, Gondwe EN, Msefula CL, Kingsley RA, Thomson NR, White SA, Goodall M, Pickard DJ, Graham SM, Dougan G et al.

    The Journal of clinical investigation 2008;118;4;1553-62

    PUBMED: 18357343; PMC: 2268878; DOI: 10.1172/JCI33998

  • Apheresis donors and platelet function: inherent platelet responsiveness influences platelet quality.

    Garner SF, Jones CI, Stephens J, Burns P, Walton J, Bernard A, Angenent W, Ouwehand WH, Goodall AH and BLOODOMICS Consortium

    Transfusion 2008;48;4;673-80

    PUBMED: 18194381; DOI: 10.1111/j.1537-2995.2007.01591.x

  • Genomic 'valleys of death'.

    Bentley S

    Nature reviews. Microbiology 2008;6;4;260-1

    PUBMED: 18340971; DOI: 10.1038/nrmicro1881

  • Repeated replication and a prospective meta-analysis of the association between chromosome 9p21.3 and coronary artery disease.

    Schunkert H, Götz A, Braund P, McGinnis R, Tregouet DA, Mangino M, Linsel-Nitschke P, Cambien F, Hengstenberg C, Stark K et al.

    Circulation 2008;117;13;1675-84

    PUBMED: 18362232; PMC: 2689930; DOI: 10.1161/CIRCULATIONAHA.107.730614

  • Whole genome-amplified DNA: insights and imputation.

    Teo YY, Inouye M, Small KS, Fry AE, Potter SC, Dunstan SJ, Seielstad M, Barroso I, Wareham NJ, Rockett KA et al.

    Nature methods 2008;5;4;279-80

    PUBMED: 18376389; PMC: 2683750; DOI: 10.1038/nmeth0408-279

  • Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.

    Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PI, Abecasis GR, Almgren P, Andersen G et al.

    Nature genetics 2008;40;5;638-45

    PUBMED: 18372903; PMC: 2672416; DOI: 10.1038/ng.120

  • Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.

    Pearson MM, Sebaihia M, Churcher C, Quail MA, Seshasayee AS, Luscombe NM, Abdellah Z, Arrosmith C, Atkin B, Chillingworth T et al.

    Journal of bacteriology 2008;190;11;4027-37

    PUBMED: 18375554; PMC: 2395036; DOI: 10.1128/JB.01981-07

  • Y-chromosomal diversity in Lebanon is structured by recent historical events.

    Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DF, Blue-Smith J et al.

    American journal of human genetics 2008;82;4;873-82

    PUBMED: 18374297; PMC: 2427286; DOI: 10.1016/j.ajhg.2008.01.020

  • The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes.

    Liu Y, Tewari R, Ning J, Blagborough AM, Garbom S, Pei J, Grishin NV, Steele RE, Sinden RE, Snell WJ and Billker O

    Genes & development 2008;22;8;1051-68

    PUBMED: 18367645; PMC: 2335326; DOI: 10.1101/gad.1656508

  • Evolutionary plasticity of genetic interaction networks.

    Tischler J, Lehner B and Fraser AG

    Nature genetics 2008;40;4;390-1

    PUBMED: 18362882; DOI: 10.1038/ng.114

  • Pfam 10 years on: 10,000 families and still growing.

    Sammut SJ, Finn RD and Bateman A

    Briefings in bioinformatics 2008;9;3;210-9

    PUBMED: 18344544; DOI: 10.1093/bib/bbn010

  • Newly identified genetic risk variants for celiac disease related to the immune response.

    Hunt KA, Zhernakova A, Turner G, Heap GA, Franke L, Bruinenberg M, Romanos J, Dinesen LC, Ryan AW, Panesar D et al.

    Nature genetics 2008;40;4;395-402

    PUBMED: 18311140; PMC: 2673512; DOI: 10.1038/ng.102

  • A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae.

    Jones GM, Stalker J, Humphray S, West A, Cox T, Rogers J, Dunham I and Prelich G

    Nature methods 2008;5;3;239-41

    PUBMED: 18246075; DOI: 10.1038/nmeth.1181

  • Characterization of 6q deletions in mature B cell lymphomas and childhood acute lymphoblastic leukemia.

    Thelander EF, Ichimura K, Corcoran M, Barbany G, Nordgren A, Heyman M, Berglund M, Mungall A, Rosenquist R, Collins VP et al.

    Leukemia & lymphoma 2008;49;3;477-87

    PUBMED: 18297524; DOI: 10.1080/10428190701817282

  • Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

    Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F et al.

    Nature biotechnology 2008;26;3;305-12

    PUBMED: 18327244; PMC: 4367930; DOI: 10.1038/nbt1391

  • Single-cell genomics.

    Walker A and Parkhill J

    Nature reviews. Microbiology 2008;6;3;176-7

    PUBMED: 18283727; DOI: 10.1038/nrmicro1862

  • Large-scale screening for novel low-affinity extracellular protein interactions.

    Bushell KM, Söllner C, Schuster-Boeckler B, Bateman A and Wright GJ

    Genome research 2008;18;4;622-30

    PUBMED: 18296487; PMC: 2279249; DOI: 10.1101/gr.7187808

  • LDL-cholesterol concentrations: a genome-wide association study.

    Sandhu MS, Waterworth DM, Debenham SL, Wheeler E, Papadakis K, Zhao JH, Song K, Yuan X, Johnson T, Ashford S et al.

    Lancet (London, England) 2008;371;9611;483-91

    PUBMED: 18262040; PMC: 2292820; DOI: 10.1016/S0140-6736(08)60208-1

  • Mendelian randomisation studies of type 2 diabetes: future prospects.

    Sandhu MS, Debenham SL, Barroso I and Loos RJ

    Diabetologia 2008;51;2;211-3

    PUBMED: 18094955; PMC: 2681076; DOI: 10.1007/s00125-007-0903-x

  • Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

    Nousiainen HO, Kestilä M, Pakkasjärvi N, Honkala H, Kuure S, Tallila J, Vuopala K, Ignatius J, Herva R and Peltonen L

    Nature genetics 2008;40;2;155-7

    PUBMED: 18204449; PMC: 2684619; DOI: 10.1038/ng.2007.65

  • Robust, persistent transgene expression in human embryonic stem cells is achieved with AAVS1-targeted integration.

    Smith JR, Maguire S, Davis LA, Alexander M, Yang F, Chandran S, ffrench-Constant C and Pedersen RA

    Stem cells (Dayton, Ohio) 2008;26;2;496-504

    PUBMED: 18024421; DOI: 10.1634/stemcells.2007-0039

  • Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

    Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS et al.

    Nature genetics 2008;40;2;189-97

    PUBMED: 18193044; PMC: 2682493; DOI: 10.1038/ng.75

  • Habitual energy expenditure modifies the association between NOS3 gene polymorphisms and blood pressure.

    Vimaleswaran KS, Franks PW, Barroso I, Brage S, Ekelund U, Wareham NJ and Loos RJ

    American journal of hypertension 2008;21;3;297-302

    PUBMED: 18246059; PMC: 2714087; DOI: 10.1038/ajh.2007.69

  • Maternal footprints of Southeast Asians in North India.

    Thangaraj K, Chaubey G, Kivisild T, Selvi Rani D, Singh VK, Ismail T, Carvalho-Silva D, Metspalu M, Bhaskar LV, Reddy AG et al.

    Human heredity 2008;66;1;1-9

    PUBMED: 18223312; PMC: 2588665; DOI: 10.1159/000114160

  • A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

    Lee I, Lehner B, Crombie C, Wong W, Fraser AG and Marcotte EM

    Nature genetics 2008;40;2;181-8

    PUBMED: 18223650; DOI: 10.1038/ng.2007.70

  • Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold.

    Brosch M, Swamy S, Hubbard T and Choudhary J

    Molecular & cellular proteomics : MCP 2008;7;5;962-70

    PUBMED: 18216375; PMC: 2656932; DOI: 10.1074/mcp.M700293-MCP200

  • Protein interactions in human genetic diseases.

    Schuster-Böckler B and Bateman A

    Genome biology 2008;9;1;R9

    PUBMED: 18199329; PMC: 2395246; DOI: 10.1186/gb-2008-9-1-r9

  • urg1: a uracil-regulatable promoter system for fission yeast with short induction and repression times.

    Watt S, Mata J, López-Maury L, Marguerat S, Burns G and Bähler J

    PloS one 2008;3;1;e1428

    PUBMED: 18197241; PMC: 2174524; DOI: 10.1371/journal.pone.0001428

  • NestedMICA as an ab initio protein motif discovery tool.

    Doğruel M, Down TA and Hubbard TJ

    BMC bioinformatics 2008;9;19

    PUBMED: 18194537; PMC: 2267705; DOI: 10.1186/1471-2105-9-19

  • Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation.

    Bentley SD, Corton C, Brown SE, Barron A, Clark L, Doggett J, Harris B, Ormond D, Quail MA, May G et al.

    Journal of bacteriology 2008;190;6;2150-60

    PUBMED: 18192393; PMC: 2258862; DOI: 10.1128/JB.01598-07

  • Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1.

    Pickard D, Thomson NR, Baker S, Wain J, Pardo M, Goulding D, Hamlin N, Choudhary J, Threfall J and Dougan G

    Journal of bacteriology 2008;190;7;2580-7

    PUBMED: 18192390; PMC: 2293211; DOI: 10.1128/JB.01654-07

  • Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

    Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL et al.

    Immunogenetics 2008;60;1;1-18

    PUBMED: 18193213; PMC: 2206249; DOI: 10.1007/s00251-007-0262-2

  • The emerging landscape of breast cancer susceptibility.

    Stratton MR and Rahman N

    Nature genetics 2008;40;1;17-22

    PUBMED: 18163131; DOI: 10.1038/ng.2007.53

  • A novel CpG island set identifies tissue-specific methylation at developmental gene loci.

    Illingworth R, Kerr A, Desousa D, Jørgensen H, Ellis P, Stalker J, Jackson D, Clee C, Plumb R, Rogers J et al.

    PLoS biology 2008;6;1;e22

    PUBMED: 18232738; PMC: 2214817; DOI: 10.1371/journal.pbio.0060022

  • A Poultry Existence

    Seth-Smith H

    Nat Rev Microbiol 2008;6;8

  • A genome wide RNAi screen by time lapse microscopy in order to identify mitotic genes - Computational aspects and challenges

    Walter, T, Held, M, Neumann, B, Heriche, J. K, Conrad, C et al.

    2008 5th IEEE International Symposium on Biomedical Imaging. 2008;328-331

  • Accounting for non-genetic factors improves the power of eQTL studies

    Stegle, O, Kannan, A, Durbin, R, Winn, J.

    Lecture Notes in Computer Science. 2008;4955;411-422

  • Comparative genomics of the Rab protein family in Apicomplexan parasites

    Langsley G.

    Microbes and Infection. 2008

  • Contributions of the genome sequence of Erwinia amylovora to the fire blight community

    Bocsanczy, A. M., Beer, S. V., Perna, N. T., Biehl, B., Glasner, J. D. et al.

    Acta Horticulturae. 2008;793;163-170

  • Drug susceptibility testing using molecular techniques can enhance tuberculosis diagnosis in a community with a high tuberculosis incidence

    Johnson, R

    JIDC. 2008;2;40-45

  • Genomic resources and microarrays for the common carp Cyprinus carpio L

    Williams, D. R., Li, W., Hughes, M. A., Gonzalez, S. F., Vernon, C. et al.

    J Fish Biol. 2008;72;2095-2117

  • Graph clustering via a discrete uncoupling process

    Van Dongen, S.

    Siam Journal on Matrix Analysis and Applications. 2008;30;121-141

  • Image capture and fusion of 3D surface texture using wavelet transform

    Jian, M. W., Dong. J. Y..Wu, J. H.

    Proceedings of the 2007 International Conference on Wavelet Analysis and Pattern Recognition, ICWAPR '07. 2008;338-343

  • Invasive Salmonellosis in Humans

    Langridge, G.C., Wain, J., Nair, S.

    Ecosal. 2008;Module8.6.2.2

  • Meta-analysis of 32 genome-wide linkage studies of schizophrenia

    Ng, M. Y. M., Levinson, D. F, Faraone, S. V, Suarez, B. K. et al

    Molecular Psychiatry 2008

  • Opportunity knocks

    Seth-Smith H., Walker A.

    Nat Rev Microbiol. 2008;6;652-3

  • Scheduling in a dynamic heterogeneous distributed system using estimation error

    Page, A. J, Keane, T. M, Naughton, T. J.

    Journal of Parallel and Distributed Computing. 2008

  • The Grandest Genetics Experiment Ever Performed on Man? A Y-Chromosomal Perspective on Genetic Variation in India

    Carvalho-Silva D R, Tyler-Smith, C

    International Journal of Human Genetics. 2008;8;21-9

  • Whole-Genome analysis of pathogen evolution

    Parkhill J

    Evolution in Helth and Disease 2008;199-213

  • Whole-genome analysis of pathogen evolution

    Parkhill J

    Evolution in Health and Disease. 2008;199-214

  • Data growth and its impact on the SCOP database: new developments.

    Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C and Murzin AG

    Nucleic acids research 2008;36;Database issue;D419-25

    PUBMED: 18000004; PMC: 2238974; DOI: 10.1093/nar/gkm993

  • New case of interstitial deletion 12(q15-q21.2) in a girl with facial dysmorphism and mental retardation.

    Schluth C, Gesny R, Borck G, Redon R, Abadie V, Kleinfinger P, Munnich A, Lyonnet S and Colleaux L

    American journal of medical genetics. Part A 2008;146A;1;93-6

    PUBMED: 18076123; DOI: 10.1002/ajmg.a.31869

  • nGASP--the nematode genome annotation assessment project.

    Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium and Stein LD

    BMC bioinformatics 2008;9;549

    PUBMED: 19099578; PMC: 2651883; DOI: 10.1186/1471-2105-9-549

2007

  • Mosaic complementation demonstrates a regulatory role for myosin VIIa in actin dynamics of stereocilia.

    Prosser HM, Rzadzinska AK, Steel KP and Bradley A

    Molecular and cellular biology 2007;28;5;1702-12

    PUBMED: 18160714; PMC: 2258769; DOI: 10.1128/MCB.01282-07

  • Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.

    Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S et al.

    Genome research 2007;18;2;281-92

    PUBMED: 18096748; PMC: 2203626; DOI: 10.1101/gr.6836108

  • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

    Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S et al.

    Nucleic acids research 2007;36;Database issue;D793-9

    PUBMED: 18089548; PMC: 2238988; DOI: 10.1093/nar/gkm999

  • Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.

    De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, Dunham I, Gibbons RJ, Wood WG and Higgs DR

    Blood 2007;110;13;4503-10

    PUBMED: 17715390; DOI: 10.1182/blood-2007-06-097964

  • Testing of diabetes-associated WFS1 polymorphisms in the Diabetes Prevention Program.

    Florez JC, Jablonski KA, McAteer J, Sandhu MS, Wareham NJ, Barroso I, Franks PW, Altshuler D, Knowler WC and Diabetes Prevention Program Research Group

    Diabetologia 2007;51;3;451-7

    PUBMED: 18060660; PMC: 2483955; DOI: 10.1007/s00125-007-0891-x

  • Germline rates of de novo meiotic deletions and duplications causing several genomic disorders.

    Turner DJ, Miretti M, Rajan D, Fiegler H, Carter NP, Blayney ML, Beck S and Hurles ME

    Nature genetics 2007;40;1;90-5

    PUBMED: 18059269; PMC: 2669897; DOI: 10.1038/ng.2007.40

  • The association between polymorphisms in RLIP76 and drug response in epilepsy.

    Leschziner GD, Jorgensen AL, Andrew T, Williamson PR, Marson AG, Coffey AJ, Middleditch C, Balding DJ, Rogers J, Bentley DR et al.

    Pharmacogenomics 2007;8;12;1715-22

    PUBMED: 18086001; DOI: 10.2217/14622416.8.12.1715

  • microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells.

    Vigorito E, Perks KL, Abreu-Goodger C, Bunting S, Xiang Z, Kohlhaas S, Das PP, Miska EA, Rodriguez A, Bradley A et al.

    Immunity 2007;27;6;847-59

    PUBMED: 18055230; PMC: 4135426; DOI: 10.1016/j.immuni.2007.10.009

  • TreeFam: 2008 Update.

    Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R et al.

    Nucleic acids research 2007;36;Database issue;D735-40

    PUBMED: 18056084; PMC: 2238856; DOI: 10.1093/nar/gkm1005

  • Replication of the association between variants in WFS1 and risk of type 2 diabetes in European populations.

    Franks PW, Rolandsson O, Debenham SL, Fawcett KA, Payne F, Dina C, Froguel P, Mohlke KL, Willer C, Olsson T et al.

    Diabetologia 2007;51;3;458-63

    PUBMED: 18040659; PMC: 2670195; DOI: 10.1007/s00125-007-0887-6

  • The Pfam protein families database.

    Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL and Bateman A

    Nucleic acids research 2007;36;Database issue;D281-8

    PUBMED: 18039703; PMC: 2238907; DOI: 10.1093/nar/gkm960

  • Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.

    Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P et al.

    Nucleic acids research 2007;36;Database issue;D5-12

    PUBMED: 18039715; PMC: 2238915; DOI: 10.1093/nar/gkm1018

  • Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates.

    Thomson NR, Holden MT, Carder C, Lennard N, Lockey SJ, Marsh P, Skipp P, O'Connor CD, Goodhead I, Norbertzcak H et al.

    Genome research 2007;18;1;161-71

    PUBMED: 18032721; PMC: 2134780; DOI: 10.1101/gr.7020108

  • Determination and validation of principal gene products.

    Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J and Valencia A

    Bioinformatics (Oxford, England) 2007;24;1;11-7

    PUBMED: 18006548; PMC: 2734078; DOI: 10.1093/bioinformatics/btm547

  • The vertebrate genome annotation (Vega) database.

    Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T and Harrow JL

    Nucleic acids research 2007;36;Database issue;D753-60

    PUBMED: 18003653; PMC: 2238886; DOI: 10.1093/nar/gkm987

  • Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A.

    Nejentsev S, Howson JM, Walker NM, Szeszko J, Field SF, Stevens HE, Reynolds P, Hardy M, King E, Masters J et al.

    Nature 2007;450;7171;887-92

    PUBMED: 18004301; PMC: 2703779; DOI: 10.1038/nature06406

  • Ensembl 2008.

    Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T et al.

    Nucleic acids research 2007;36;Database issue;D707-14

    PUBMED: 18000006; PMC: 2238821; DOI: 10.1093/nar/gkm988

  • The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase.

    Gerken T, Girard CA, Tung YC, Webby CJ, Saudek V, Hewitson KS, Yeo GS, McDonough MA, Cunliffe S, McNeill LA et al.

    Science (New York, N.Y.) 2007;318;5855;1469-72

    PUBMED: 17991826; PMC: 2668859; DOI: 10.1126/science.1151710

  • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

    Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN et al.

    Nature 2007;450;7167;219-32

    PUBMED: 17994088; PMC: 2474711; DOI: 10.1038/nature06340

  • Evolution of genes and genomes on the Drosophila phylogeny.

    Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W et al.

    Nature 2007;450;7167;203-18

    PUBMED: 17994087; DOI: 10.1038/nature06341

  • MEROPS: the peptidase database.

    Rawlings ND, Morton FR, Kok CY, Kong J and Barrett AJ

    Nucleic acids research 2007;36;Database issue;D320-5

    PUBMED: 17991683; PMC: 2238837; DOI: 10.1093/nar/gkm954

  • BCL11B is required for positive selection and survival of double-positive thymocytes.

    Albu DI, Feng D, Bhattacharya D, Jenkins NA, Copeland NG, Liu P and Avram D

    The Journal of experimental medicine 2007;204;12;3003-15

    PUBMED: 17998389; PMC: 2118514; DOI: 10.1084/jem.20070863

  • Rheumatoid arthritis association at 6q23.

    Thomson W, Barton A, Ke X, Eyre S, Hinks A, Bowes J, Donn R, Symmons D, Hider S, Bruce IN et al.

    Nature genetics 2007;39;12;1431-3

    PUBMED: 17982455; PMC: 2674282; DOI: 10.1038/ng.2007.32

  • A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

    Baker S, Holt K, Whitehead S, Goodhead I, Perkins T, Stocker B, Hardy J and Dougan G

    Molecular microbiology 2007;66;5;1207-18

    PUBMED: 17976161; PMC: 2652032; DOI: 10.1111/j.1365-2958.2007.05995.x

  • Schistosoma mansoni genome: closing in on a final gene set.

    Haas BJ, Berriman M, Hirai H, Cerqueira GG, Loverde PT and El-Sayed NM

    Experimental parasitology 2007;117;3;225-8

    PUBMED: 17643433; DOI: 10.1016/j.exppara.2007.06.005

  • Sink or swim.

    Crossman LC

    Nature reviews. Microbiology 2007;5;11;834-5

    PUBMED: 17939228; DOI: 10.1038/nrmicro1777

  • Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota.

    Lawley TD, Bouley DM, Hoy YE, Gerke C, Relman DA and Monack DM

    Infection and immunity 2007;76;1;403-16

    PUBMED: 17967858; PMC: 2223630; DOI: 10.1128/IAI.01189-07

  • Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants.

    Wellcome Trust Case Control Consortium, Australo-Anglo-American Spondylitis Consortium (TASC), Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI et al.

    Nature genetics 2007;39;11;1329-37

    PUBMED: 17952073; PMC: 2680141; DOI: 10.1038/ng.2007.17

  • Paired-end mapping reveals extensive structural variation in the human genome.

    Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L et al.

    Science (New York, N.Y.) 2007;318;5849;420-6

    PUBMED: 17901297; PMC: 2674581; DOI: 10.1126/science.1149504

  • A second generation human haplotype map of over 3.1 million SNPs.

    International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P et al.

    Nature 2007;449;7164;851-61

    PUBMED: 17943122; PMC: 2689609; DOI: 10.1038/nature06258

  • Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation.

    Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M, Bähler J, Green RD and Kouzarides T

    Nature 2007;449;7164;928-32

    PUBMED: 17898715; PMC: 3350864; DOI: 10.1038/nature06160

  • Genome-wide detection and characterization of positive selection in human populations.

    Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R et al.

    Nature 2007;449;7164;913-8

    PUBMED: 17943131; PMC: 2687721; DOI: 10.1038/nature06250

  • Genomic expression patterns in cell separation mutants of Schizosaccharomyces pombe defective in the genes sep10 ( + ) and sep15 ( + ) coding for the Mediator subunits Med31 and Med8.

    Miklos I, Szilagyi Z, Watt S, Zilahi E, Batta G, Antunovics Z, Enczi K, Bähler J and Sipiczki M

    Molecular genetics and genomics : MGG 2007;279;3;225-38

    PUBMED: 17922236; DOI: 10.1007/s00438-007-0296-z

  • Reduced ENaC protein abundance contributes to the lower blood pressure observed in pendrin-null mice.

    Kim YH, Pech V, Spencer KB, Beierwaltes WH, Everett LA, Green ED, Shin W, Verlander JW, Sutliff RL and Wall SM

    American journal of physiology. Renal physiology 2007;293;4;F1314-24

    PUBMED: 17686956; DOI: 10.1152/ajprenal.00155.2007

  • Replication timing profile reflects the distinct functional and genomic features of the MHC class II region.

    Takousis P, Johonnett P, Williamson J, Sasieni P, Warnes G, Forshew T, Azuara V, Fisher A, Wu PJ, Jones T et al.

    Cell cycle (Georgetown, Tex.) 2007;6;19;2393-8

    PUBMED: 17938583; DOI: 10.4161/cc.6.19.4762

  • Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota.

    Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J et al.

    PLoS biology 2007;5;10;2177-89

    PUBMED: 17760501; PMC: 1951780; DOI: 10.1371/journal.pbio.0050244

  • Urbane decay.

    Walker A and Seth-Smith H

    Nature reviews. Microbiology 2007;5;10;748-9

    PUBMED: 17867225; DOI: 10.1038/nrmicro1763

  • Draft genome of the filarial nematode parasite Brugia malayi.

    Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D et al.

    Science (New York, N.Y.) 2007;317;5845;1756-60

    PUBMED: 17885136; PMC: 2613796; DOI: 10.1126/science.1145406

  • Population genomics of human gene expression.

    Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D et al.

    Nature genetics 2007;39;10;1217-24

    PUBMED: 17873874; PMC: 2683249; DOI: 10.1038/ng2142

  • In silico functional and structural characterisation of ferlin proteins by mapping disease-causing mutations and evolutionary information onto three-dimensional models of their C2 domains.

    Jiménez JL and Bashir R

    Journal of the neurological sciences 2007;260;1-2;114-23

    PUBMED: 17512949; DOI: 10.1016/j.jns.2007.04.016

  • Integrating sequence and structural biology with DAS.

    Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A and Hubbard TJ

    BMC bioinformatics 2007;8;333

    PUBMED: 17850653; PMC: 2031907; DOI: 10.1186/1471-2105-8-333

  • A genotype calling algorithm for the Illumina BeadArray platform.

    Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP and Clark TG

    Bioinformatics (Oxford, England) 2007;23;20;2741-6

    PUBMED: 17846035; PMC: 2666488; DOI: 10.1093/bioinformatics/btm443

  • Renin enhancer is crucial for full response in Renin expression to an in vivo stimulus.

    Markus MA, Goy C, Adams DJ, Lovicu FJ and Morris BJ

    Hypertension (Dallas, Tex. : 1979) 2007;50;5;933-8

    PUBMED: 17846348; DOI: 10.1161/HYPERTENSIONAHA.107.096891

  • Diet and the evolution of human amylase gene copy number variation.

    Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R et al.

    Nature genetics 2007;39;10;1256-60

    PUBMED: 17828263; PMC: 2377015; DOI: 10.1038/ng2123

  • Look who's talking too: graduates developing skills through communication.

    Tomazou EM and Powell GT

    Nature reviews. Genetics 2007;8;9;724-6

    PUBMED: 17680006; DOI: 10.1038/nrg2177

  • Serodiagnosis of Salmonella enterica serovar Typhi and S. enterica serovars Paratyphi A, B and C human infections.

    Chart H, Cheasty T, de Pinna E, Siorvanes L, Wain J, Alam D, Nizami Q, Bhutta Z and Threlfall EJ

    Journal of medical microbiology 2007;56;Pt 9;1161-6

    PUBMED: 17761477; DOI: 10.1099/jmm.0.47197-0

  • Variety is the spice of eukaryotic life.

    Berriman M and Pain A

    Nature reviews. Microbiology 2007;5;9;660-1

    PUBMED: 17703542; DOI: 10.1038/nrmicro1741

  • Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci.

    Mavroidi A, Aanensen DM, Godoy D, Skovsted IC, Kaltoft MS, Reeves PR, Bentley SD and Spratt BG

    Journal of bacteriology 2007;189;21;7841-55

    PUBMED: 17766424; PMC: 2168730; DOI: 10.1128/JB.00836-07

  • Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci.

    Aanensen DM, Mavroidi A, Bentley SD, Reeves PR and Spratt BG

    Journal of bacteriology 2007;189;21;7856-76

    PUBMED: 17766420; PMC: 2168755; DOI: 10.1128/JB.00837-07

  • Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

    Tarpey PS, Raymond FL, Nguyen LS, Rodriguez J, Hackett A, Vandeleur L, Smith R, Shoubridge C, Edkins S, Stevens C et al.

    Nature genetics 2007;39;9;1127-33

    PUBMED: 17704778; PMC: 2872770; DOI: 10.1038/ng2100

  • Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome.

    Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J et al.

    Journal of bacteriology 2007;189;22;8186-95

    PUBMED: 17675389; PMC: 2168654; DOI: 10.1128/JB.00690-07

  • Mapping the platelet profile for functional genomic studies and demonstration of the effect size of the GP6 locus.

    Jones CI, Garner SF, Angenent W, Bernard A, Berzuini C, Burns P, Farndale RW, Hogwood J, Rankin A, Stephens JC et al.

    Journal of thrombosis and haemostasis : JTH 2007;5;8;1756-65

    PUBMED: 17663743; DOI: 10.1111/j.1538-7836.2007.02632.x

  • Say hello to our little friends.

    Walker A

    Nature reviews. Microbiology 2007;5;8;572-3

    PUBMED: 17633442; DOI: 10.1038/nrmicro1720

  • Genomewide association analysis of coronary artery disease.

    Samani NJ, Erdmann J, Hall AS, Hengstenberg C, Mangino M, Mayer B, Dixon RJ, Meitinger T, Braund P, Wichmann HE et al.

    The New England journal of medicine 2007;357;5;443-53

    PUBMED: 17634449; PMC: 2719290; DOI: 10.1056/NEJMoa072366

  • Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.

    Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC et al.

    PloS one 2007;2;7;e617

    PUBMED: 17637833; PMC: 1910612; DOI: 10.1371/journal.pone.0000617

  • The genome of Salmonella enterica serovar Typhi.

    Baker S and Dougan G

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2007;45 Suppl 1;S29-33

    PUBMED: 17582565; DOI: 10.1086/518143

  • Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet.

    Tett A, Spiers AJ, Crossman LC, Ager D, Ciric L, Dow JM, Fry JC, Harris D, Lilley A, Oliver A et al.

    The ISME journal 2007;1;4;331-40

    PUBMED: 18043644; PMC: 2656933; DOI: 10.1038/ismej.2007.47

  • The Ras-association domain family (RASSF) members and their role in human tumourigenesis.

    van der Weyden L and Adams DJ

    Biochimica et biophysica acta 2007;1776;1;58-85

    PUBMED: 17692468; PMC: 2586335; DOI: 10.1016/j.bbcan.2007.06.003

  • A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21.

    van Heel DA, Franke L, Hunt KA, Gwilliam R, Zhernakova A, Inouye M, Wapenaar MC, Barnardo MC, Bethel G, Holmes GK et al.

    Nature genetics 2007;39;7;827-9

    PUBMED: 17558408; PMC: 2274985; DOI: 10.1038/ng2058

  • The population genetics of structural variation.

    Conrad DF and Hurles ME

    Nature genetics 2007;39;7 Suppl;S30-6

    PUBMED: 17597779; PMC: 2716079; DOI: 10.1038/ng2042

  • Challenges and standards in integrating surveys of structural variation.

    Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME and Feuk L

    Nature genetics 2007;39;7 Suppl;S7-15

    PUBMED: 17597783; PMC: 2698291; DOI: 10.1038/ng2093

  • Common variants in WFS1 confer risk of type 2 diabetes.

    Sandhu MS, Weedon MN, Fawcett KA, Wasson J, Debenham SL, Daly A, Lango H, Frayling TM, Neumann RJ, Sherva R et al.

    Nature genetics 2007;39;8;951-3

    PUBMED: 17603484; PMC: 2672152; DOI: 10.1038/ng2067

  • Methods and strategies for analyzing copy number variation using DNA microarrays.

    Carter NP

    Nature genetics 2007;39;7 Suppl;S16-21

    PUBMED: 17597776; PMC: 2697494; DOI: 10.1038/ng2028

  • Genome-wide association study identifies novel breast cancer susceptibility loci.

    Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R et al.

    Nature 2007;447;7148;1087-93

    PUBMED: 17529967; PMC: 2714974; DOI: 10.1038/nature05887

  • Definition of the zebrafish genome using flow cytometry and cytogenetic mapping.

    Freeman JL, Adeniyi A, Banerjee R, Dallaire S, Maguire SF, Chi J, Ng BL, Zepeda C, Scott CE, Humphray S et al.

    BMC genomics 2007;8;195

    PUBMED: 17597531; PMC: 1925092; DOI: 10.1186/1471-2164-8-195

  • Comparative genomic analysis of three Leishmania species that cause diverse human disease.

    Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, Quail MA, Peters N, Adlem E, Tivey A, Aslett M et al.

    Nature genetics 2007;39;7;839-47

    PUBMED: 17572675; PMC: 2592530; DOI: 10.1038/ng2053

  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

    ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al.

    Nature 2007;447;7146;799-816

    PUBMED: 17571346; PMC: 2212820; DOI: 10.1038/nature05874

  • Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

    Wellcome Trust Case Control Consortium

    Nature 2007;447;7145;661-78

    PUBMED: 17554300; PMC: 2719288; DOI: 10.1038/nature05911

  • Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.

    Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, Bailey R, Nejentsev S, Field SF, Payne F et al.

    Nature genetics 2007;39;7;857-64

    PUBMED: 17554260; PMC: 2492393; DOI: 10.1038/ng2068

  • Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

    Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, Roberts RG, Nimmo ER, Cummings FR, Soars D et al.

    Nature genetics 2007;39;7;830-2

    PUBMED: 17554261; PMC: 2628541; DOI: 10.1038/ng2061

  • Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.

    Wong WS and Nielsen R

    Bioinformatics (Oxford, England) 2007;23;16;2031-7

    PUBMED: 17550911; DOI: 10.1093/bioinformatics/btm299

  • Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

    Raval A, Tanner SM, Byrd JC, Angerman EB, Perko JD, Chen SS, Hackanson B, Grever MR, Lucas DM, Matkovic JJ et al.

    Cell 2007;129;5;879-90

    PUBMED: 17540169; DOI: 10.1016/j.cell.2007.03.043

  • Esophageal atresia, hypoplasia of zygomatic complex, microcephaly, cup-shaped ears, congenital heart defect, and mental retardation--new MCA/MR syndrome in two affected sibs and a mildly affected mother?

    Wieczorek D, Shaw-Smith C, Kohlhase J, Schmitt W, Buiting K, Coffey A, Howard E, Hehr U and Gillessen-Kaesbach G

    American journal of medical genetics. Part A 2007;143A;11;1135-42

    PUBMED: 17497718; DOI: 10.1002/ajmg.a.31752

  • Identification of common genetic variation that modulates alternative splicing.

    Hull J, Campino S, Rowlands K, Chan MS, Copley RR, Taylor MS, Rockett K, Elvidge G, Keating B, Knight J and Kwiatkowski D

    PLoS genetics 2007;3;6;e99

    PUBMED: 17571926; PMC: 1904363; DOI: 10.1371/journal.pgen.0030099

  • Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizations.

    Gusnanto A, Tom B, Burns P, Macaulay I, Thijssen-Timmer DC, Tijssen MR, Langford C, Watkins N, Ouwehand W, Berzuini C and Dudbridge F

    Computational biology and chemistry 2007;31;3;178-85

    PUBMED: 17499550; DOI: 10.1016/j.compbiolchem.2007.03.005

  • Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

    Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J et al.

    Genome research 2007;17;6;746-59

    PUBMED: 17567994; PMC: 1891335; DOI: 10.1101/gr.5660607

  • Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

    Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M et al.

    Genome research 2007;17;6;839-51

    PUBMED: 17568002; PMC: 1891343; DOI: 10.1101/gr.5586307

  • Environmental and genetic modifiers of squint penetrance during zebrafish embryogenesis.

    Pei W, Williams PH, Clark MD, Stemple DL and Feldman B

    Developmental biology 2007;308;2;368-78

    PUBMED: 17583692; PMC: 1994576; DOI: 10.1016/j.ydbio.2007.05.026

  • Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.

    Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT, Mitchell WJ, Carter AT, Bentley SD, Mason DR, Crossman L et al.

    Genome research 2007;17;7;1082-92

    PUBMED: 17519437; PMC: 1899119; DOI: 10.1101/gr.6282807

  • Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers.

    Maser RS, Choudhury B, Campbell PJ, Feng B, Wong KK, Protopopov A, O'Neil J, Gutierrez A, Ivanova E, Perna I et al.

    Nature 2007;447;7147;966-71

    PUBMED: 17515920; PMC: 2714968; DOI: 10.1038/nature05886

  • Completing the map of human genetic variation.

    Human Genome Structural Variation Working Group, Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M et al.

    Nature 2007;447;7141;161-5

    PUBMED: 17495918; PMC: 2685471; DOI: 10.1038/447161a

  • Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.

    Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A et al.

    Nature 2007;447;7141;167-77

    PUBMED: 17495919; DOI: 10.1038/nature05805

  • Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.

    Coghlan A and Durbin R

    Bioinformatics (Oxford, England) 2007;23;12;1468-75

    PUBMED: 17483502; PMC: 2880447; DOI: 10.1093/bioinformatics/btm133

  • Definition of a minimal region of deletion of chromosome 7 in uterine leiomyomas by tiling-path microarray CGH and mutation analysis of known genes in this region.

    Vanharanta S, Wortham NC, Langford C, El-Bahrawy M, van der Spuy Z, Sjöberg J, Lehtonen R, Karhu A, Tomlinson IP and Aaltonen LA

    Genes, chromosomes & cancer 2007;46;5;451-8

    PUBMED: 17285575; DOI: 10.1002/gcc.20427

  • Different evolutionary histories of the two classical class I genes BF1 and BF2 illustrate drift and selection within the stable MHC haplotypes of chickens.

    Shaw I, Powell TJ, Marston DA, Baker K, van Hateren A, Riegert P, Wiles MV, Milne S, Beck S and Kaufman J

    Journal of immunology (Baltimore, Md. : 1950) 2007;178;9;5744-52

    PUBMED: 17442958; DOI: 10.4049/jimmunol.178.9.5744

  • Genome-wide association study of prostate cancer identifies a second risk locus at 8q24.

    Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, Minichiello MJ, Fearnhead P, Yu K, Chatterjee N et al.

    Nature genetics 2007;39;5;645-9

    PUBMED: 17401363; DOI: 10.1038/ng2022

  • Insights into modern disease from our distant evolutionary past.

    Yngvadottir B

    European journal of human genetics : EJHG 2007;15;5;603-6

    PUBMED: 17356547; DOI: 10.1038/sj.ejhg.5201811

  • Specialist fungi, versatile genomes.

    Hertz-Fowler C and Pain A

    Nature reviews. Microbiology 2007;5;5;332-3

    PUBMED: 17436472; DOI: 10.1038/nrmicro1669

  • Requirement of bic/microRNA-155 for normal immune function.

    Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA et al.

    Science (New York, N.Y.) 2007;316;5824;608-11

    PUBMED: 17463290; PMC: 2610435; DOI: 10.1126/science.1139253

  • Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.

    Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, Lango H, Timpson NJ, Perry JR, Rayner NW, Freathy RM et al.

    Science (New York, N.Y.) 2007;316;5829;1336-41

    PUBMED: 17463249; PMC: 3772310; DOI: 10.1126/science.1142364

  • Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins.

    Macaulay IC, Tijssen MR, Thijssen-Timmer DC, Gusnanto A, Steward M, Burns P, Langford CF, Ellis PD, Dudbridge F, Zwaginga JJ et al.

    Blood 2007;109;8;3260-9

    PUBMED: 17192395; PMC: 6485507; DOI: 10.1182/blood-2006-07-036269

  • Evolutionary and biomedical insights from the rhesus macaque genome.

    Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC et al.

    Science (New York, N.Y.) 2007;316;5822;222-34

    PUBMED: 17431167; DOI: 10.1126/science.1139247

  • A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity.

    Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, Perry JR, Elliott KS, Lango H, Rayner NW et al.

    Science (New York, N.Y.) 2007;316;5826;889-94

    PUBMED: 17434869; PMC: 2646098; DOI: 10.1126/science.1141634

  • A recombineering based approach for high-throughput conditional knockout targeting vector construction.

    Chan W, Costantino N, Li R, Lee SC, Su Q, Melvin D, Court DL and Liu P

    Nucleic acids research 2007;35;8;e64

    PUBMED: 17426124; PMC: 1885671; DOI: 10.1093/nar/gkm163

  • A new function for the fragile X mental retardation protein in regulation of PSD-95 mRNA stability.

    Zalfa F, Eleuteri B, Dickson KS, Mercaldo V, De Rubeis S, di Penta A, Tabolacci E, Chiurazzi P, Neri G, Grant SG and Bagni C

    Nature neuroscience 2007;10;5;578-87

    PUBMED: 17417632; PMC: 2804293; DOI: 10.1038/nn1893

  • TCF7L2 polymorphisms modulate proinsulin levels and beta-cell function in a British Europid population.

    Loos RJ, Franks PW, Francis RW, Barroso I, Gribble FM, Savage DB, Ong KK, O'Rahilly S and Wareham NJ

    Diabetes 2007;56;7;1943-7

    PUBMED: 17416797; PMC: 2668957; DOI: 10.2337/db07-0055

  • A comprehensive antibody panel for immunohistochemical analysis of formalin-fixed, paraffin-embedded hematopoietic neoplasms of mice: analysis of mouse specific and human antibodies cross-reactive with murine tissue.

    Kunder S, Calzada-Wack J, Hölzlwimmer G, Müller J, Kloss C, Howat W, Schmidt J, Höfler H, Warren M and Quintanilla-Martinez L

    Toxicologic pathology 2007;35;3;366-75

    PUBMED: 17455084; DOI: 10.1080/01926230701230296

  • A more convenient truth.

    Seth-Smith H

    Nature reviews. Microbiology 2007;5;4;248-50

    PUBMED: 17366694; DOI: 10.1038/nrmicro1644

  • An RNA G-quadruplex in the 5' UTR of the NRAS proto-oncogene modulates translation.

    Kumari S, Bugaut A, Huppert JL and Balasubramanian S

    Nature chemical biology 2007;3;4;218-21

    PUBMED: 17322877; PMC: 2206252; DOI: 10.1038/nchembio864

  • Distinct cytokine-driven responses of activated blood gammadelta T cells: insights into unconventional T cell pleiotropy.

    Vermijlen D, Ellis P, Langford C, Klein A, Engel R, Willimann K, Jomaa H, Hayday AC and Eberl M

    Journal of immunology (Baltimore, Md. : 1950) 2007;178;7;4304-14

    PUBMED: 17371987; PMC: 3915340

  • Immunohistochemical characterization of cytokeratins in the abnormal corneal endothelium of posterior polymorphous corneal dystrophy patients.

    Jirsova K, Merjava S, Martincova R, Gwilliam R, Ebenezer ND, Liskova P and Filipec M

    Experimental eye research 2007;84;4;680-6

    PUBMED: 17289024; DOI: 10.1016/j.exer.2006.12.006

  • Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.

    Holt KE, Thomson NR, Wain J, Phan MD, Nair S, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D et al.

    Journal of bacteriology 2007;189;11;4257-64

    PUBMED: 17384186; PMC: 1913411; DOI: 10.1128/JB.00232-07

  • Mutations in ZDHHC9, which encodes a palmitoyltransferase of NRAS and HRAS, cause X-linked mental retardation associated with a Marfanoid habitus.

    Raymond FL, Tarpey PS, Edkins S, Tofts C, O'Meara S, Teague J, Butler A, Stevens C, Barthorpe S, Buck G et al.

    American journal of human genetics 2007;80;5;982-7

    PUBMED: 17436253; PMC: 1852737; DOI: 10.1086/513609

  • The implications of alternative splicing in the ENCODE protein complement.

    Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A et al.

    Proceedings of the National Academy of Sciences of the United States of America 2007;104;13;5495-500

    PUBMED: 17372197; PMC: 1838448; DOI: 10.1073/pnas.0700800104

  • Genome plasticity of BCG and impact on vaccine efficacy.

    Brosch R, Gordon SV, Garnier T, Eiglmeier K, Frigui W, Valenti P, Dos Santos S, Duthoy S, Lacroix C, Garcia-Pelayo C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2007;104;13;5596-601

    PUBMED: 17372194; PMC: 1838518; DOI: 10.1073/pnas.0700869104

  • The V103I polymorphism of the MC4R gene and obesity: population based studies and meta-analysis of 29 563 individuals.

    Young EH, Wareham NJ, Farooqi S, Hinney A, Hebebrand J, Scherag A, O'rahilly S, Barroso I and Sandhu MS

    International journal of obesity (2005) 2007;31;9;1437-41

    PUBMED: 17356525; PMC: 2683751; DOI: 10.1038/sj.ijo.0803609

  • Wnt5a functions in planar cell polarity regulation in mice.

    Qian D, Jones C, Rzadzinska A, Mark S, Zhang X, Steel KP, Dai X and Chen P

    Developmental biology 2007;306;1;121-33

    PUBMED: 17433286; PMC: 1978180; DOI: 10.1016/j.ydbio.2007.03.011

  • Network activity-independent coordinated gene expression program for synapse assembly.

    Valor LM, Charlesworth P, Humphreys L, Anderson CN and Grant SG

    Proceedings of the National Academy of Sciences of the United States of America 2007;104;11;4658-63

    PUBMED: 17360580; PMC: 1810326; DOI: 10.1073/pnas.0609071104

  • Analysis of genetic variation in Akt2/PKB-beta in severe insulin resistance, lipodystrophy, type 2 diabetes, and related metabolic phenotypes.

    Tan K, Kimber WA, Luan J, Soos MA, Semple RK, Wareham NJ, O'Rahilly S and Barroso I

    Diabetes 2007;56;3;714-9

    PUBMED: 17327441; PMC: 2672155; DOI: 10.2337/db06-0921

  • Bacterial therapeutics.

    Bentley S and Sebaihia M

    Nature reviews. Microbiology 2007;5;3;170-1

    PUBMED: 17310535; DOI: 10.1038/nrmicro1633

  • Common ABCB1 polymorphisms are not associated with multidrug resistance in epilepsy using a gene-wide tagging approach.

    Leschziner GD, Andrew T, Leach JP, Chadwick D, Coffey AJ, Balding DJ, Bentley DR, Pirmohamed M and Johnson MR

    Pharmacogenetics and genomics 2007;17;3;217-20

    PUBMED: 17460550; DOI: 10.1097/01.fpc.0000230408.23146.b1

  • hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

    Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P et al.

    Genomics 2007;89;3;307-15

    PUBMED: 17207965; DOI: 10.1016/j.ygeno.2006.11.012

  • Lamin A/C polymorphisms, type 2 diabetes, and the metabolic syndrome: case-control and quantitative trait studies.

    Mesa JL, Loos RJ, Franks PW, Ong KK, Luan J, O'Rahilly S, Wareham NJ and Barroso I

    Diabetes 2007;56;3;884-9

    PUBMED: 17327461; PMC: 2668858; DOI: 10.2337/db06-1055

  • Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.

    Mouse Phenotype Database Integration Consortium, Hancock JM, Adams NC, Aidinis V, Blake A, Bogue M, Brown SD, Chesler EJ, Davidson D, Duran C et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2007;18;3;157-63

    PUBMED: 17436037; DOI: 10.1007/s00335-007-9004-x

  • Relative impact of nucleotide and copy number variation on gene expression phenotypes.

    Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C et al.

    Science (New York, N.Y.) 2007;315;5813;848-53

    PUBMED: 17289997; PMC: 2665772; DOI: 10.1126/science.1136678

  • Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization.

    Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ, Madeira AM, Mungall K, Billington K, Yee WY, Bankier AT et al.

    Genome research 2007;17;3;311-9

    PUBMED: 17284678; PMC: 1800922; DOI: 10.1101/gr.5823007

  • Interleukin-2 gene variation impairs regulatory T cell function and causes autoimmunity.

    Yamanouchi J, Rainbow D, Serra P, Howlett S, Hunter K, Garner VE, Gonzalez-Munoz A, Clark J, Veijola R, Cubbon R et al.

    Nature genetics 2007;39;3;329-37

    PUBMED: 17277778; PMC: 2886969; DOI: 10.1038/ng1958

  • SCOOP: a simple method for identification of novel protein superfamily relationships.

    Bateman A and Finn RD

    Bioinformatics (Oxford, England) 2007;23;7;809-14

    PUBMED: 17277330; PMC: 2603044; DOI: 10.1093/bioinformatics/btm034

  • This place is big enough for both of us.

    Walker A and Crossman LC

    Nature reviews. Microbiology 2007;5;2;90-2

    PUBMED: 17225354; DOI: 10.1038/nrmicro1601

  • Clinical and molecular genetic spectrum of congenital deficiency of the leptin receptor.

    Farooqi IS, Wangensteen T, Collins S, Kimber W, Matarese G, Keogh JM, Lank E, Bottomley B, Lopez-Fernandez J, Ferraz-Amaro I et al.

    The New England journal of medicine 2007;356;3;237-47

    PUBMED: 17229951; PMC: 2670197; DOI: 10.1056/NEJMoa063988

  • ProServer: a simple, extensible Perl DAS server.

    Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J and Pettett R

    Bioinformatics (Oxford, England) 2007;23;12;1568-70

    PUBMED: 17237073; PMC: 2989875; DOI: 10.1093/bioinformatics/btl650

  • An H-NS-like stealth protein aids horizontal DNA transmission in bacteria.

    Doyle M, Fookes M, Ivens A, Mangan MW, Wain J and Dorman CJ

    Science (New York, N.Y.) 2007;315;5809;251-2

    PUBMED: 17218529; DOI: 10.1126/science.1137550

  • Comment on "A common genetic variant is associated with adult and childhood obesity".

    Loos RJ, Barroso I, O'rahilly S and Wareham NJ

    Science (New York, N.Y.) 2007;315;5809;187; author reply 187

    PUBMED: 17218509; PMC: 2719286; DOI: 10.1126/science.1130012

  • Adiponectin receptor genes: mutation screening in syndromes of insulin resistance and association studies for type 2 diabetes and metabolic traits in UK populations.

    Collins SC, Luan J, Thompson AJ, Daly A, Semple RK, O'Rahilly S, Wareham NJ and Barroso I

    Diabetologia 2007;50;3;555-62

    PUBMED: 17216283; PMC: 1794135; DOI: 10.1007/s00125-006-0534-7

  • PPARGC1A coding variation may initiate impaired NEFA clearance during glucose challenge.

    Franks PW, Ekelund U, Brage S, Luan J, Schafer AJ, O'Rahilly S, Barroso I and Wareham NJ

    Diabetologia 2007;50;3;569-73

    PUBMED: 17216277; PMC: 2682771; DOI: 10.1007/s00125-006-0580-1

  • The Israeli-Palestinian Science Organization.

    Wiesel T, Agre P, Arrow KJ, Atiyah M, Brézin E, Charfi FF, Cohen-Tanoudji C, Daar A, Jacob F, Kahneman D et al.

    Science (New York, N.Y.) 2007;315;5808;39

    PUBMED: 17204624; DOI: 10.1126/science.315.5808.39b

  • Interaction analysis of the CBLB and CTLA4 genes in type 1 diabetes.

    Payne F, Cooper JD, Walker NM, Lam AC, Smink LJ, Nutland S, Stevens HE, Hutchings J and Todd JA

    Journal of leukocyte biology 2007;81;3;581-3

    PUBMED: 17209142; DOI: 10.1189/jlb.0906577

  • A high utility integrated map of the pig genome.

    Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M et al.

    Genome biology 2007;8;7;R139

    PUBMED: 17625002; PMC: 2323232; DOI: 10.1186/gb-2007-8-7-r139

  • A recessive genetic screen for host factors required for retroviral infection in a library of insertionally mutated Blm-deficient embryonic stem cells.

    Wang W and Bradley A

    Genome biology 2007;8;4;R48

    PUBMED: 17407599; PMC: 1895998; DOI: 10.1186/gb-2007-8-4-r48

  • A Sall4 mutant mouse model useful for studying the role of Sall4 in early embryonic development and organogenesis.

    Warren M, Wang W, Spiden S, Chen-Murchie D, Tannahill D, Steel KP and Bradley A

    Genesis (New York, N.Y. : 2000) 2007;45;1;51-8

    PUBMED: 17216607; PMC: 2593393; DOI: 10.1002/dvg.20264

  • EDITORIAL

    Bateman, A

    Nucleic Acids Res.. 2007;35;D1

  • Gene Prediction

    Rajandream M

    Bioinformatics 2007;71-102

  • Helminth initiative for drug discovery

    Berriman M

    Expert Opinion on Drug Discovery. 2007;2;Suppl 1

  • Pharmacogenomics of non-small cell lung cancer

    Spicer J

    Current Pharmacogenomics. 2007;5;228-234

  • Prediction of noncoding transcripts

    Bateman A

    Bioinformatics. 2007;103-116

  • Speciation in the Genus Bordetella as deduced from comparative genome analyses

    Preston A

    Bordetella: Molecular Microbiology. 2007;1-16

  • The Straphylococci: A Postgenomic View

    Linday J A

    Bacterial Pathogenomics. 2007;120-40

  • Y Chromosome

    Tyler-Smith C

    Encyclopedia of Life Sciences. 2007

  • Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

    Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET et al.

    Genome biology 2007;8;10;R228

    PUBMED: 17961237; PMC: 2246302; DOI: 10.1186/gb-2007-8-10-r228

  • Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

    Fiegler H, Redon R and Carter NP

    Nature protocols 2007;2;3;577-87

    PUBMED: 17406619; PMC: 2688820; DOI: 10.1038/nprot.2007.53

  • Convergent adaptation of human lactase persistence in Africa and Europe.

    Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M et al.

    Nature genetics 2007;39;1;31-40

    PUBMED: 17159977; PMC: 2672153; DOI: 10.1038/ng1946

  • Critical assessment of methods of protein structure prediction-Round VII.

    Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T and Tramontano A

    Proteins 2007;69 Suppl 8;3-9

    PUBMED: 17918729; PMC: 2653632; DOI: 10.1002/prot.21767

  • Generation of an inducible and optimized piggyBac transposon system.

    Cadiñanos J and Bradley A

    Nucleic acids research 2007;35;12;e87

    PUBMED: 17576687; PMC: 1919496; DOI: 10.1093/nar/gkm446

  • Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.

    Hart EA, Caccamo M, Harrow JL, Humphray SJ, Gilbert JG, Trevanion S, Hubbard T, Rogers J and Rothschild MF

    Genome biology 2007;8;8;R168

    PUBMED: 17705864; PMC: 2374978; DOI: 10.1186/gb-2007-8-8-r168

  • Molecular analysis of the VSX1 gene in familial keratoconus.

    Liskova P, Ebenezer ND, Hysi PG, Gwilliam R, El-Ashry MF, Moodaley LC, Hau S, Twa M, Tuft SJ and Bhatacharya SS

    Molecular vision 2007;13;1887-91

    PUBMED: 17960127

  • New developments in the InterPro database.

    Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R et al.

    Nucleic acids research 2007;35;Database issue;D224-8

    PUBMED: 17202162; PMC: 1899100; DOI: 10.1093/nar/gkl841

  • New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.

    Kryshtafovych A, Prlic A, Dmytriv Z, Daniluk P, Milostan M, Eyrich V, Hubbard T and Fidelis K

    Proteins 2007;69 Suppl 8;19-26

    PUBMED: 17705273; PMC: 2656758; DOI: 10.1002/prot.21653

  • Ocean's elevenses.

    Seth-Smith H

    Nature reviews. Microbiology 2007;5;1;9

    PUBMED: 17171852; DOI: 10.1038/nrmicro1589

  • Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans.

    Vavouri T, Walter K, Gilks WR, Lehner B and Elgar G

    Genome biology 2007;8;2;R15

    PUBMED: 17274809; PMC: 1852409; DOI: 10.1186/gb-2007-8-2-r15

  • ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.

    Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R et al.

    Nature methods 2007;4;1;13-7

    PUBMED: 17195019; DOI: 10.1038/nmeth0107-13

  • SISYPHUS--structural alignments for proteins with non-trivial relationships.

    Andreeva A, Prlić A, Hubbard TJ and Murzin AG

    Nucleic acids research 2007;35;Database issue;D253-9

    PUBMED: 17068077; PMC: 1635320; DOI: 10.1093/nar/gkl746

  • WebACT: an online genome comparison suite.

    Abbott JC, Aanensen DM and Bentley SD

    Methods in molecular biology (Clifton, N.J.) 2007;395;57-74

    PUBMED: 17993667

  • Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan.

    Firasat S, Khaliq S, Mohyuddin A, Papaioannou M, Tyler-Smith C, Underhill PA and Ayub Q

    European journal of human genetics : EJHG 2007;15;1;121-6

    PUBMED: 17047675; PMC: 2588664; DOI: 10.1038/sj.ejhg.5201726

2006

  • PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene.

    Rahman N, Seal S, Thompson D, Kelly P, Renwick A, Elliott A, Reid S, Spanova K, Barfoot R, Chagtai T et al.

    Nature genetics 2006;39;2;165-7

    PUBMED: 17200668; PMC: 2871593; DOI: 10.1038/ng1959

  • F0 generation mice fully derived from gene-targeted embryonic stem cells allowing immediate phenotypic analyses.

    Poueymirou WT, Auerbach W, Frendewey D, Hickey JF, Escaravage JM, Esau L, Doré AT, Stevens S, Adams NC, Dominguez MG et al.

    Nature biotechnology 2006;25;1;91-9

    PUBMED: 17187059; DOI: 10.1038/nbt1263

  • Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

    Bentley SD, Vernikos GS, Snyder LA, Churcher C, Arrowsmith C, Chillingworth T, Cronin A, Davis PH, Holroyd NE, Jagels K et al.

    PLoS genetics 2006;3;2;e23

    PUBMED: 17305430; PMC: 1797815; DOI: 10.1371/journal.pgen.0030023

  • High resolution array-CGH analysis of single cells.

    Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, Carter NP and Speicher MR

    Nucleic acids research 2006;35;3;e15

    PUBMED: 17178751; PMC: 1807964; DOI: 10.1093/nar/gkl1030

  • The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

    Thomson NR, Howard S, Wren BW, Holden MT, Crossman L, Challis GL, Churcher C, Mungall K, Brooks K, Chillingworth T et al.

    PLoS genetics 2006;2;12;e206

    PUBMED: 17173484; PMC: 1698947; DOI: 10.1371/journal.pgen.0020206

  • Genome variation and evolution of the malaria parasite Plasmodium falciparum.

    Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall K, Uhlemann AC et al.

    Nature genetics 2006;39;1;120-5

    PUBMED: 17159978; PMC: 2663918; DOI: 10.1038/ng1931

  • Ensembl 2007.

    Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T et al.

    Nucleic acids research 2006;35;Database issue;D610-7

    PUBMED: 17148474; PMC: 1761443; DOI: 10.1093/nar/gkl996

  • Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Down TA, Bergman CM, Su J and Hubbard TJ

    PLoS computational biology 2006;3;1;e7

    PUBMED: 17238282; PMC: 1779301; DOI: 10.1371/journal.pcbi.0030007

  • Colonic irritation.

    Sebaihia M and Thomson NR

    Nature reviews. Microbiology 2006;4;12;882-3

    PUBMED: 17120341; DOI: 10.1038/nrmicro1571

  • Evolutionary history of Salmonella typhi.

    Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S, Chinh NT, Le TA, Acosta CJ, Farrar J, Dougan G and Achtman M

    Science (New York, N.Y.) 2006;314;5803;1301-4

    PUBMED: 17124322; PMC: 2652035; DOI: 10.1126/science.1134933

  • Global variation in copy number in the human genome.

    Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W et al.

    Nature 2006;444;7118;444-54

    PUBMED: 17122850; PMC: 2669898; DOI: 10.1038/nature05329

  • Accurate and reliable high-throughput detection of copy number variation in the human genome.

    Fiegler H, Redon R, Andrews D, Scott C, Andrews R, Carder C, Clark R, Dovey O, Ellis P, Feuk L et al.

    Genome research 2006;16;12;1566-74

    PUBMED: 17122085; PMC: 1665640; DOI: 10.1101/gr.5630906

  • Genome assembly comparison identifies structural variants in the human genome.

    Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L et al.

    Nature genetics 2006;38;12;1413-8

    PUBMED: 17115057; PMC: 2674632; DOI: 10.1038/ng1921

  • Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.

    Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, Zhang J, Liu G, Ihara S, Nakamura H, Hurles ME et al.

    Genome research 2006;16;12;1575-84

    PUBMED: 17122084; PMC: 1665641; DOI: 10.1101/gr.5629106

  • Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.

    Ikediobi ON, Davies H, Bignell G, Edkins S, Stevens C, O'Meara S, Santarius T, Avis T, Barthorpe S, Brackenbury L et al.

    Molecular cancer therapeutics 2006;5;11;2606-12

    PUBMED: 17088437; PMC: 2705832; DOI: 10.1158/1535-7163.MCT-06-0433

  • The grapes of wrath.

    Holden M, Lindsay J and Bentley S

    Nature reviews. Microbiology 2006;4;11;806-7

    PUBMED: 17042109; DOI: 10.1038/nrmicro1535

  • The LRC haplotype project: a resource for killer immunoglobulin-like receptor-linked association studies.

    Horton R, Coggill P, Miretti MM, Sambrook JG, Traherne JA, Ward R, Sims S, Palmer S, Sehra H, Harrow J et al.

    Tissue antigens 2006;68;5;450-2

    PUBMED: 17092261; PMC: 2734079; DOI: 10.1111/j.1399-0039.2006.00697.x

  • A shared Y-chromosomal heritage between Muslims and Hindus in India.

    Gutala R, Carvalho-Silva DR, Jin L, Yngvadottir B, Avadhanula V, Nanne K, Singh L, Chakraborty R and Tyler-Smith C

    Human genetics 2006;120;4;543-51

    PUBMED: 16951948; PMC: 2590854; DOI: 10.1007/s00439-006-0234-x

  • Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles.

    Seal S, Thompson D, Renwick A, Elliott A, Kelly P, Barfoot R, Chagtai T, Jayatilake H, Ahmed M, Spanova K et al.

    Nature genetics 2006;38;11;1239-41

    PUBMED: 17033622; DOI: 10.1038/ng1902

  • DNA methylation profiling of human chromosomes 6, 20 and 22.

    Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA et al.

    Nature genetics 2006;38;12;1378-85

    PUBMED: 17072317; PMC: 3082778; DOI: 10.1038/ng1909

  • Insights into social insects from the genome of the honeybee Apis mellifera.

    Honeybee Genome Sequencing Consortium

    Nature 2006;443;7114;931-49

    PUBMED: 17073008; PMC: 2048586

  • Otoferlin, defective in a human deafness form, is essential for exocytosis at the auditory ribbon synapse.

    Roux I, Safieddine S, Nouvian R, Grati M, Simmler MC, Bahloul A, Perfettini I, Le Gall M, Rostaing P, Hamard G et al.

    Cell 2006;127;2;277-89

    PUBMED: 17055430; DOI: 10.1016/j.cell.2006.08.040

  • Animal, vegetable or mineral?

    Cerdeño-Tárraga AM and Bentley S

    Nature reviews. Microbiology 2006;4;10;725-6

    PUBMED: 16983803; DOI: 10.1038/nrmicro1508

  • Minimizing the risk of reporting false positives in large-scale RNAi screens.

    Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N et al.

    Nature methods 2006;3;10;777-9

    PUBMED: 16990807; DOI: 10.1038/nmeth1006-777

  • Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus.

    Tarpey P, Thomas S, Sarvananthan N, Mallya U, Lisgo S, Talbot CJ, Roberts EO, Awan M, Surendran M, McLean RJ et al.

    Nature genetics 2006;38;11;1242-4

    PUBMED: 17013395; PMC: 2592600; DOI: 10.1038/ng1893

  • Non-DNA binding, dominant-negative, human PPARgamma mutations cause lipodystrophic insulin resistance.

    Agostini M, Schoenmakers E, Mitchell C, Szatmari I, Savage D, Smith A, Rajanayagam O, Semple R, Luan J, Bath L et al.

    Cell metabolism 2006;4;4;303-11

    PUBMED: 17011503; PMC: 1821092; DOI: 10.1016/j.cmet.2006.09.003

  • Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.

    Holden MT, Scott A, Cherevach I, Chillingworth T, Churcher C, Cronin A, Dowd L, Feltwell T, Hamlin N, Holroyd S et al.

    Journal of bacteriology 2006;189;4;1473-7

    PUBMED: 17012393; PMC: 1797351; DOI: 10.1128/JB.01227-06

  • Mapping trait loci by use of inferred ancestral recombination graphs.

    Minichiello MJ and Durbin R

    American journal of human genetics 2006;79;5;910-22

    PUBMED: 17033967; PMC: 1698562; DOI: 10.1086/508901

  • A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination.

    Lindsay SJ, Khajavi M, Lupski JR and Hurles ME

    American journal of human genetics 2006;79;5;890-902

    PUBMED: 17033965; PMC: 1698570; DOI: 10.1086/508709

  • A machine learning strategy to identify candidate binding sites in human protein-coding sequence.

    Down T, Leong B and Hubbard TJ

    BMC bioinformatics 2006;7;419

    PUBMED: 17002805; PMC: 1592515; DOI: 10.1186/1471-2105-7-419

  • A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC.

    de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M et al.

    Nature genetics 2006;38;10;1166-72

    PUBMED: 16998491; PMC: 2670196; DOI: 10.1038/ng1885

  • PARL Leu262Val is not associated with fasting insulin levels in UK populations.

    Fawcett KA, Wareham NJ, Luan J, Syddall H, Cooper C, O'Rahilly S, Day IN, Sandhu MS and Barroso I

    Diabetologia 2006;49;11;2649-52

    PUBMED: 17019603; PMC: 2672784; DOI: 10.1007/s00125-006-0443-9

  • Polymorphisms in the gene encoding sterol regulatory element-binding factor-1c are associated with type 2 diabetes.

    Harding AH, Loos RJ, Luan J, O'Rahilly S, Wareham NJ and Barroso I

    Diabetologia 2006;49;11;2642-8

    PUBMED: 17019602; PMC: 2668914; DOI: 10.1007/s00125-006-0430-1

  • Ultra-high resolution array painting facilitates breakpoint sequencing.

    Gribble SM, Kalaitzopoulos D, Burford DC, Prigmore E, Selzer RR, Ng BL, Matthews NS, Porter KM, Curley R, Lindsay SJ et al.

    Journal of medical genetics 2006;44;1;51-8

    PUBMED: 16971479; PMC: 2597908; DOI: 10.1136/jmg.2006.044909

  • Distinct element analysis of attrition of granular solids under shear deformation

    Zemin Ning and Mojtaba Ghadiri

    Chemical Engineering Science 2006;61;5991–6001

    DOI: doi:10.1016/j.ces.2006.03.056; URL: https://www.sciencedirect.com/scien...ce/article/pii/S000925090600337X

  • Factors affecting flow karyotype resolution.

    Ng BL and Carter NP

    Cytometry. Part A : the journal of the International Society for Analytical Cytology 2006;69;9;1028-36

    PUBMED: 16969800; DOI: 10.1002/cyto.a.20330

  • Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability.

    Shaw-Smith C, Pittman AM, Willatt L, Martin H, Rickman L, Gribble S, Curley R, Cumming S, Dunn C, Kalaitzopoulos D et al.

    Nature genetics 2006;38;9;1032-7

    PUBMED: 16906163; DOI: 10.1038/ng1858

  • Where there's muck there's microbes.

    Seth-Smith H and Bentley S

    Nature reviews. Microbiology 2006;4;9;646-7

    PUBMED: 16913069; DOI: 10.1038/nrmicro1497

  • Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.

    Khan A, Böhme U, Kelly KA, Adlem E, Brooks K, Simmonds M, Mungall K, Quail MA, Arrowsmith C, Chillingworth T et al.

    Genome research 2006;16;9;1119-25

    PUBMED: 16902086; PMC: 1557770; DOI: 10.1101/gr.5318106

  • Renin enhancer is critical for control of renin gene expression and cardiovascular function.

    Adams DJ, Head GA, Markus MA, Lovicu FJ, van der Weyden L, Köntgen F, Arends MJ, Thiru S, Mayorov DN and Morris BJ

    The Journal of biological chemistry 2006;281;42;31753-61

    PUBMED: 16895910; DOI: 10.1074/jbc.M605720200

  • EGASP: the human ENCODE Genome Annotation Assessment Project.

    Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E et al.

    Genome biology 2006;7 Suppl 1;S2.1-31

    PUBMED: 16925836; PMC: 1810551; DOI: 10.1186/gb-2006-7-s1-s2

  • GENCODE: producing a reference annotation for ENCODE.

    Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al.

    Genome biology 2006;7 Suppl 1;S4.1-9

    PUBMED: 16925838; PMC: 1810553; DOI: 10.1186/gb-2006-7-s1-s4

  • Two quantitative trait loci affecting progressive hearing loss in 101/H mice.

    Mashimo T, Erven AE, Spiden SL, Guénet JL and Steel KP

    Mammalian genome : official journal of the International Mammalian Genome Society 2006;17;8;841-50

    PUBMED: 16897347; DOI: 10.1007/s00335-004-2438-5

  • ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles.

    Renwick A, Thompson D, Seal S, Kelly P, Chagtai T, Ahmed M, North B, Jayatilake H, Barfoot R, Spanova K et al.

    Nature genetics 2006;38;8;873-5

    PUBMED: 16832357; DOI: 10.1038/ng1837

  • Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction.

    Sebaihia M, Preston A, Maskell DJ, Kuzmiak H, Connell TD, King ND, Orndorff PE, Miyamoto DM, Thomson NR, Harris D et al.

    Journal of bacteriology 2006;188;16;6002-15

    PUBMED: 16885469; PMC: 1540077; DOI: 10.1128/JB.01927-05

  • Functional knockout of the matrilin-3 gene causes premature chondrocyte maturation to hypertrophy and increases bone mineral density and osteoarthritis.

    van der Weyden L, Wei L, Luo J, Yang X, Birk DE, Adams DJ, Bradley A and Chen Q

    The American journal of pathology 2006;169;2;515-27

    PUBMED: 16877353; PMC: 1698783; DOI: 10.2353/ajpath.2006.050981

  • TranscriptSNPView: a genome-wide catalog of mouse coding variation.

    Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J et al.

    Nature genetics 2006;38;8;853

    PUBMED: 16874317; PMC: 2610433; DOI: 10.1038/ng0806-853a

  • Expression of mammalian GPCRs in C. elegans generates novel behavioural responses to human ligands.

    Teng MS, Dekkers MP, Ng BL, Rademakers S, Jansen G, Fraser AG and McCafferty J

    BMC biology 2006;4;22

    PUBMED: 16857046; PMC: 1550261; DOI: 10.1186/1741-7007-4-22

  • Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways.

    Lehner B, Crombie C, Tischler J, Fortunato A and Fraser AG

    Nature genetics 2006;38;8;896-903

    PUBMED: 16845399; DOI: 10.1038/ng1844

  • Geminin is essential to prevent endoreduplication and to form pluripotent cells during mammalian development.

    Gonzalez MA, Tachibana KE, Adams DJ, van der Weyden L, Hemberger M, Coleman N, Bradley A and Laskey RA

    Genes & development 2006;20;14;1880-4

    PUBMED: 16847348; PMC: 1522086; DOI: 10.1101/gad.379706

  • Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.

    Vernikos GS and Parkhill J

    Bioinformatics (Oxford, England) 2006;22;18;2196-203

    PUBMED: 16837528; DOI: 10.1093/bioinformatics/btl369

  • Nonrandom distribution of Burkholderia pseudomallei clones in relation to geographical location and virulence.

    Vesaratchavest M, Tumapa S, Day NP, Wuthiekanun V, Chierakul W, Holden MT, White NJ, Currie BJ, Spratt BG, Feil EJ and Peacock SJ

    Journal of clinical microbiology 2006;44;7;2553-7

    PUBMED: 16825379; PMC: 1489466; DOI: 10.1128/JCM.00629-06

  • Peddling the nitrogen cycle.

    Crossman L and Thomson N

    Nature reviews. Microbiology 2006;4;7;494-5

    PUBMED: 16835960; DOI: 10.1038/nrmicro1456

  • YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms.

    Penkett CJ, Morris JA, Wood V and Bähler J

    Nucleic acids research 2006;34;Web Server issue;W330-4

    PUBMED: 16845020; PMC: 1538793; DOI: 10.1093/nar/gkl311

  • The Genetics of Type 2 Diabetes

    Stevenson,C., Barroso,I. and Wareham,N.;

    Nutritional Genomics: Impact on Health and Disease 2006;Chapter 13;222-65

    DOI: 10.1002/3527608109.ch13; URL: https://onlinelibrary.wiley.com/doi/...10.1002/3527608109.ch13/summary

  • Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii.

    Boyle JP, Rajasekar B, Saeij JPJ, Ajioka JW, Berriman M, Paulsen I, Roos DS, Sibley LD, White MW and Boothroyd JC

    Proceedings of the National Academy of Sciences of the United States of America 2006;103;27;10514-10519

    PUBMED: 16801557; PMC: 1502489; DOI: 10.1073/pnas.0510319103

  • The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.

    Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N, Stabler R, Thomson NR, Roberts AP, Cerdeño-Tárraga AM, Wang H et al.

    Nature genetics 2006;38;7;779-86

    PUBMED: 16804543; DOI: 10.1038/ng1830

  • Genetic screens for mutations affecting development of Xenopus tropicalis.

    Goda T, Abu-Daya A, Carruthers S, Clark MD, Stemple DL and Zimmerman LB

    PLoS genetics 2006;2;6;e91

    PUBMED: 16789825; PMC: 1475704; DOI: 10.1371/journal.pgen.0020091

  • Assaying chromosomal inversions by single-molecule haplotyping.

    Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C and Hurles ME

    Nature methods 2006;3;6;439-45

    PUBMED: 16721377; PMC: 2690135; DOI: 10.1038/nmeth881

  • The DNA sequence and biological annotation of human chromosome 1.

    Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, Howe KL, Woodfine K, Spencer CC et al.

    Nature 2006;441;7091;315-21

    PUBMED: 16710414; DOI: 10.1038/nature04727

  • Data sharing and intellectual property in a genomic epidemiology network: policies for large-scale research collaboration.

    Chokshi DA, Parker M and Kwiatkowski DP

    Bulletin of the World Health Organization 2006;84;5;382-7

    PUBMED: 16710548; PMC: 2627357; DOI: 10.2471/blt.06.029843

  • Budget genome.

    Crossman L

    Nature reviews. Microbiology 2006;4;5;326-7

    PUBMED: 16722005; DOI: 10.1038/nrmicro1396

  • Loss of TSLC1 causes male infertility due to a defect at the spermatid stage of spermatogenesis.

    van der Weyden L, Arends MJ, Chausiaux OE, Ellis PJ, Lange UC, Surani MA, Affara N, Murakami Y, Adams DJ and Bradley A

    Molecular and cellular biology 2006;26;9;3595-609

    PUBMED: 16611999; PMC: 1447413; DOI: 10.1128/MCB.26.9.3595-3609.2006

  • Staking claims in the biotechnology Klondike.

    Sulston J

    Bulletin of the World Health Organization 2006;84;5;412-3

    PUBMED: 16710554; PMC: 2627350; DOI: /S0042-96862006000500024

  • Pseudo-messenger RNA: phantoms of the transcriptome.

    Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, Wahlestedt C, Bajic VB, Kai C, Kawai J, Carninci P et al.

    PLoS genetics 2006;2;4;e23

    PUBMED: 16683022; PMC: 1449882; DOI: 10.1371/journal.pgen.0020023

  • The genome of Rhizobium leguminosarum has recognizable core and accessory components.

    Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson AR, Todd JD, Poole PS et al.

    Genome biology 2006;7;4;R34

    PUBMED: 16640791; PMC: 1557990; DOI: 10.1186/gb-2006-7-4-r34

  • DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

    Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK et al.

    Nature 2006;440;7087;1045-9

    PUBMED: 16625196; PMC: 2610434; DOI: 10.1038/nature04689

  • Tmc1 is necessary for normal functional maturation and survival of inner and outer hair cells in the mouse cochlea.

    Marcotti W, Erven A, Johnson SL, Steel KP and Kros CJ

    The Journal of physiology 2006;574;Pt 3;677-98

    PUBMED: 16627570; PMC: 1817746; DOI: 10.1113/jphysiol.2005.095661

  • A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy.

    Hunter C, Smith R, Cahill DP, Stephens P, Stevens C, Teague J, Greenman C, Edkins S, Bignell G, Davies H et al.

    Cancer research 2006;66;8;3987-91

    PUBMED: 16618716; PMC: 7212022; DOI: 10.1158/0008-5472.CAN-06-0127

  • Hot and sexy moulds!

    Pain A, Böhme U and Berriman M

    Nature reviews. Microbiology 2006;4;4;244-5

    PUBMED: 16602146; DOI: 10.1038/nrmicro1388

  • Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome.

    Collins MO, Husi H, Yu L, Brandon JM, Anderson CN, Blackstock WP, Choudhary JS and Grant SG

    Journal of neurochemistry 2006;97 Suppl 1;16-23

    PUBMED: 16635246; DOI: 10.1111/j.1471-4159.2005.03507.x

  • Human chromosome 11 DNA sequence and analysis including novel gene identification.

    Taylor TD, Noguchi H, Totoki Y, Toyoda A, Kuroki Y, Dewar K, Lloyd C, Itoh T, Takeda T, Kim DW et al.

    Nature 2006;440;7083;497-500

    PUBMED: 16554811; DOI: 10.1038/nature04632

  • Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes.

    Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E, Collins M, Donohoe K, Harris D, Murphy L, Quail MA et al.

    PLoS genetics 2006;2;3;e31

    PUBMED: 16532061; PMC: 1391919; DOI: 10.1371/journal.pgen.0020031

  • The genomic sequence and analysis of the swine major histocompatibility complex.

    Renard C, Hart E, Sehra H, Beasley H, Coggill P, Howe K, Harrow J, Gilbert J, Sims S, Rogers J et al.

    Genomics 2006;88;1;96-110

    PUBMED: 16515853; DOI: 10.1016/j.ygeno.2006.01.004

  • Molecular analysis of fluoroquinolone-resistant Salmonella Paratyphi A isolate, India.

    Nair S, Unnikrishnan M, Turner K, Parija SC, Churcher C, Wain J and Harish N

    Emerging infectious diseases 2006;12;3;489-91

    PUBMED: 16704790; PMC: 3291429; DOI: 10.3201/eid1205.050560

  • Genomic anatomy of the Tyrp1 (brown) deletion complex.

    Smyth IM, Wilming L, Lee AW, Taylor MS, Gautier P, Barlow K, Wallis J, Martin S, Glithero R, Phillimore B et al.

    Proceedings of the National Academy of Sciences of the United States of America 2006;103;10;3704-9

    PUBMED: 16505357; PMC: 1450144; DOI: 10.1073/pnas.0600199103

  • Spread of an inactive form of caspase-12 in humans is due to recent positive selection.

    Xue Y, Daly A, Yngvadottir B, Liu M, Coop G, Kim Y, Sabeti P, Chen Y, Stalker J, Huckle E et al.

    American journal of human genetics 2006;78;4;659-70

    PUBMED: 16532395; PMC: 1424700; DOI: 10.1086/503116

  • A deficiency in the region homologous to human 17q21.33-q23.2 causes heart defects in mice.

    Yu YE, Morishima M, Pao A, Wang DY, Wen XY, Baldini A and Bradley A

    Genetics 2006;173;1;297-307

    PUBMED: 16489219; PMC: 1461454; DOI: 10.1534/genetics.105.054833

  • Male demography in East Asia: a north-south contrast in human population expansion times.

    Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, Du R, Fu S, Li P, Hurles ME et al.

    Genetics 2006;172;4;2431-9

    PUBMED: 16489223; PMC: 1456369; DOI: 10.1534/genetics.105.054270

  • Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs.

    Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ and Schier AF

    Science (New York, N.Y.) 2006;312;5770;75-9

    PUBMED: 16484454; DOI: 10.1126/science.1122689

  • An explosive-degrading cytochrome P450 activity and its targeted application for the phytoremediation of RDX.

    Rylott EL, Jackson RG, Edwards J, Womack GL, Seth-Smith HM, Rathbone DA, Strand SE and Bruce NC

    Nature biotechnology 2006;24;2;216-9

    PUBMED: 16429147; DOI: 10.1038/nbt1184

  • The rise and fall of the ape Y chromosome?

    Tyler-Smith C, Howe K and Santos FR

    Nature genetics 2006;38;2;141-3

    PUBMED: 16444252; DOI: 10.1038/ng0206-141

  • Schistosoma mansoni (Platyhelminthes, Trematoda) nuclear receptors: sixteen new members and a novel subfamily.

    Wu W, Niles EG, El-Sayed N, Berriman M and LoVerde PT

    Gene 2006;366;2;303-15

    PUBMED: 16406405; DOI: 10.1016/j.gene.2005.09.013

  • COSMIC 2005.

    Forbes S, Clements J, Dawson E, Bamford S, Webb T, Dogan A, Flanagan A, Teague J, Wooster R, Futreal PA and Stratton MR

    British journal of cancer 2006;94;2;318-22

    PUBMED: 16421597; PMC: 2361125; DOI: 10.1038/sj.bjc.6602928

  • Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

    Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, Stewart CA, Ashurst JL, Atrazhev AM, Coggill P, Palmer S et al.

    PLoS genetics 2006;2;1;e9

    PUBMED: 16440057; PMC: 1331980; DOI: 10.1371/journal.pgen.0020009

  • Meta-analysis of the Gly482Ser variant in PPARGC1A in type 2 diabetes and related phenotypes.

    Barroso I, Luan J, Sandhu MS, Franks PW, Crowley V, Schafer AJ, O'Rahilly S and Wareham NJ

    Diabetologia 2006;49;3;501-5

    PUBMED: 16435105; DOI: 10.1007/s00125-005-0130-2

  • Genetic and genomic prospects for Xenopus tropicalis research.

    Carruthers S and Stemple DL

    Seminars in cell & developmental biology 2006;17;1;146-53

    PUBMED: 16427790; DOI: 10.1016/j.semcdb.2005.11.009

  • The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour.

    Pocklington AJ, Cumiskey M, Armstrong JD and Grant SG

    Molecular systems biology 2006;2;2006.0023

    PUBMED: 16738568; PMC: 1681474; DOI: 10.1038/msb4100041

  • The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.

    Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S et al.

    Nucleic acids research 2006;34;Database issue;D642-8

    PUBMED: 16381950; PMC: 1347459; DOI: 10.1093/nar/gkj097

  • Chromosome-engineered mouse models

    Liu, P.

    Genomic Disorders 2006;VI;373-387

    DOI: 10.1007/978-1-59745-039-3_26; URL: https://link.springer.com/chapter.../10.1007%2F978-1-59745-039-3_26

  • Detection of novel Y SNPs provides further insights into Y chromosomal variation in Pakistan.

    Mohyuddin A, Ayub Q, Underhill PA, Tyler-Smith C and Mehdi SQ

    Journal of human genetics 2006;51;4;375-8

    PUBMED: 16470330; DOI: 10.1007/s10038-005-0357-2

  • Ensembl 2006.

    Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T et al.

    Nucleic acids research 2006;34;Database issue;D556-61

    PUBMED: 16381931; PMC: 1347495; DOI: 10.1093/nar/gkj133

  • Essential and overlapping roles for laminin alpha chains in notochord and blood vessel formation.

    Pollard SM, Parsons MJ, Kamei M, Kettleborough RN, Thomas KA, Pham VN, Bae MK, Scott A, Weinstein BM and Stemple DL

    Developmental biology 2006;289;1;64-76

    PUBMED: 16321372; DOI: 10.1016/j.ydbio.2005.10.006

  • Recombination hotspots in nonallelic homologous recombination

    HURLES,M.E. and Lupski,J.R.;

    Genomic Disorders: The Genomic Basis of Disease 2006;Chapter 24;341-355

    DOI: 10.1007/978-1-59745-039-3_24; URL: https://link.springer.com/chapter.../10.1007/978-1-59745-039-3_24#page-1

  • RNAi screens in Caenorhabditis elegans in a 96-well liquid format and their application to the systematic identification of genetic interactions.

    Lehner B, Tischler J and Fraser AG

    Nature protocols 2006;1;3;1617-20

    PUBMED: 17406454; DOI: 10.1038/nprot.2006.245

  • Single Nucleotide Polymorphism Analysis by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

    Whittaker,P., Bumpstead,S., Downes,K., Ghori,J. and Deloukas,P.;

    Cell Biology 2006;3;Chapter 48;463–470

    DOI: 10.1016/B978-012164730-8/50176-3

  • TreeFam: a curated database of phylogenetic trees of animal gene families.

    Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L et al.

    Nucleic acids research 2006;34;Database issue;D572-80

    PUBMED: 16381935; PMC: 1347480; DOI: 10.1093/nar/gkj118

  • Y-chromosomal rearrangements and azoospermia

    Hurles,M.E. and Tyler-Smith,C.

    Genomic Disorders: The Genomic Basis of Disease 2006;19;273-288

    DOI: 10.1007/978-1-59745-039-3_19; URL: https://link.springer.com/chapter.../10.1007/978-1-59745-039-3_19#page-1

2005

  • Conserved noncoding sequences are selectively constrained and not mutation cold spots.

    Drake JA, Bird C, Nemesh J, Thomas DJ, Newton-Cheh C, Reymond A, Excoffier L, Attar H, Antonarakis SE, Dermitzakis ET and Hirschhorn JN

    Nature genetics 2005;38;2;223-7

    PUBMED: 16380714; DOI: 10.1038/ng1710

  • Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.

    Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C et al.

    Nature 2005;438;7071;1151-6

    PUBMED: 16372009; DOI: 10.1038/nature04332

  • Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.

    Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J et al.

    Nature 2005;438;7071;1105-15

    PUBMED: 16372000; DOI: 10.1038/nature04341

  • Genome-wide associations of gene expression variation in humans.

    Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S et al.

    PLoS genetics 2005;1;6;e78

    PUBMED: 16362079; PMC: 1315281; DOI: 10.1371/journal.pgen.0010078

  • Tectonic, a novel regulator of the Hedgehog pathway required for both activation and inhibition.

    Reiter JF and Skarnes WC

    Genes & development 2005;20;1;22-7

    PUBMED: 16357211; PMC: 1356097; DOI: 10.1101/gad.1363606

  • Genome sequence, comparative analysis and haplotype structure of the domestic dog.

    Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC et al.

    Nature 2005;438;7069;803-19

    PUBMED: 16341006; DOI: 10.1038/nature04338

  • Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus.

    Wen G, Ramser J, Taudien S, Gausmann U, Blechschmidt K, Frankish A, Ashurst J, Meindl A and Platzer M

    Mammalian genome : official journal of the International Mammalian Genome Society 2005;16;12;934-41

    PUBMED: 16341673; DOI: 10.1007/s00335-005-0090-3

  • Notch, epidermal growth factor receptor, and beta1-integrin pathways are coordinated in neural stem cells.

    Campos LS, Decker L, Taylor V and Skarnes W

    The Journal of biological chemistry 2005;281;8;5300-9

    PUBMED: 16332675; DOI: 10.1074/jbc.M511886200

  • A high-resolution survey of deletion polymorphism in the human genome.

    Conrad DF, Andrews TD, Carter NP, Hurles ME and Pritchard JK

    Nature genetics 2005;38;1;75-81

    PUBMED: 16327808; DOI: 10.1038/ng1697

  • Chromosome evolution in eukaryotes: a multi-kingdom perspective.

    Coghlan A, Eichler EE, Oliver SG, Paterson AH and Stein L

    Trends in genetics : TIG 2005;21;12;673-82

    PUBMED: 16242204; DOI: 10.1016/j.tig.2005.09.009

  • Complex disease: pleiotropic gene effects in obesity and type 2 diabetes.

    Barroso I

    European journal of human genetics : EJHG 2005;13;12;1243-4

    PUBMED: 16251891; DOI: 10.1038/sj.ejhg.5201514

  • Food for thought.

    Holden M, Rajandream MA and Bentley S

    Nature reviews. Microbiology 2005;3;12;912-3

    PUBMED: 16350281; DOI: 10.1038/nrmicro1292

  • Recent spread of a Y-chromosomal lineage in northern China and Mongolia.

    Xue Y, Zerjal T, Bao W, Zhu S, Lim SK, Shu Q, Xu J, Du R, Fu S, Li P et al.

    American journal of human genetics 2005;77;6;1112-6

    PUBMED: 16380921; PMC: 1285168; DOI: 10.1086/498583

  • EMPReSS: standardized phenotype screens for functional annotation of the mouse genome.

    Brown SD, Chambon P, de Angelis MH and Eumorphia Consortium

    Nature genetics 2005;37;11;1155

    PUBMED: 16254554; DOI: 10.1038/ng1105-1155

  • Fungi behaving badly.

    Pain A

    Nature reviews. Microbiology 2005;3;11;832-3

    PUBMED: 16273665; DOI: 10.1038/nrmicro1270

  • Global hypomethylation of the genome in XX embryonic stem cells.

    Zvetkova I, Apedaile A, Ramsahoye B, Mermoud JE, Crompton LA, John R, Feil R and Brockdorff N

    Nature genetics 2005;37;11;1274-9

    PUBMED: 16244654; DOI: 10.1038/ng1663

  • Mutations of C-RAF are rare in human cancer because C-RAF has a low basal kinase activity compared with B-RAF.

    Emuss V, Garnett M, Mason C and Marais R

    Cancer research 2005;65;21;9719-26

    PUBMED: 16266992; DOI: 10.1158/0008-5472.CAN-05-1683

  • Plasmodium falciparum variant surface antigen expression patterns during malaria.

    Bull PC, Berriman M, Kyes S, Quail MA, Hall N, Kortok MM, Marsh K and Newbold CI

    PLoS pathogens 2005;1;3;e26

    PUBMED: 16304608; PMC: 1287908; DOI: 10.1371/journal.ppat.0010026

  • An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets.

    Zeggini E, Rayner W, Morris AP, Hattersley AT, Walker M, Hitman GA, Deloukas P, Cardon LR and McCarthy MI

    Nature genetics 2005;37;12;1320-2

    PUBMED: 16258542; DOI: 10.1038/ng1670

  • A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction.

    Adams DJ, Quail MA, Cox T, van der Weyden L, Gorick BD, Su Q, Chan WI, Davies R, Bonfield JK, Law F et al.

    Genomics 2005;86;6;753-8

    PUBMED: 16257172; DOI: 10.1016/j.ygeno.2005.08.003

  • A haplotype map of the human genome.

    International HapMap Consortium

    Nature 2005;437;7063;1299-320

    PUBMED: 16255080; PMC: 1880871; DOI: 10.1038/nature04226

  • AMPA receptor trafficking and GluR1.

    Grant SG

    Science (New York, N.Y.) 2005;310;5746;234-5; author reply 234-5

    PUBMED: 16224003; DOI: 10.1126/science.310.5746.234

  • Shotgun haplotyping: a novel method for surveying allelic sequence variation.

    Lindsay SJ, Bonfield JK and Hurles ME

    Nucleic acids research 2005;33;18;e152

    PUBMED: 16221968; PMC: 1253838; DOI: 10.1093/nar/gni152

  • Multiple mutations in mouse Chd7 provide models for CHARGE syndrome.

    Bosman EA, Penn AC, Ambrose JC, Kettleborough R, Stemple DL and Steel KP

    Human molecular genetics 2005;14;22;3463-76

    PUBMED: 16207732; DOI: 10.1093/hmg/ddi375

  • The new cytogenetics: blurring the boundaries with molecular biology.

    Speicher MR and Carter NP

    Nature reviews. Genetics 2005;6;10;782-92

    PUBMED: 16145555; DOI: 10.1038/nrg1692

  • Microbial mariners.

    Holden M, Thomson N and Bentley S

    Nature reviews. Microbiology 2005;3;10;748-9

    PUBMED: 16231859; DOI: 10.1038/nrmicro1262

  • The molecular clock mediates leptin-regulated bone formation.

    Fu L, Patel MS, Bradley A, Wagner EF and Karsenty G

    Cell 2005;122;5;803-15

    PUBMED: 16143109; DOI: 10.1016/j.cell.2005.06.028

  • Two ways to trap a gene in mice.

    Skarnes WC

    Proceedings of the National Academy of Sciences of the United States of America 2005;102;37;13001-2

    PUBMED: 16150712; PMC: 1201614; DOI: 10.1073/pnas.0506279102

  • The transcriptional landscape of the mammalian genome.

    Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C et al.

    Science (New York, N.Y.) 2005;309;5740;1559-63

    PUBMED: 16141072; DOI: 10.1126/science.1112014

  • The RASSF1A isoform of RASSF1 promotes microtubule stability and suppresses tumorigenesis.

    van der Weyden L, Tachibana KK, Gonzalez MA, Adams DJ, Ng BL, Petty R, Venkitaraman AR, Arends MJ and Bradley A

    Molecular and cellular biology 2005;25;18;8356-67

    PUBMED: 16135822; PMC: 1234312; DOI: 10.1128/MCB.25.18.8356-8367.2005

  • Adding some SPICE to DAS.

    Prlić A, Down TA and Hubbard TJ

    Bioinformatics (Oxford, England) 2005;21 Suppl 2;ii40-1

    PUBMED: 16204122; PMC: 2656757; DOI: 10.1093/bioinformatics/bti1106

  • How homologous recombination generates a mutable genome.

    Hurles M

    Human genomics 2005;2;3;179-86

    PUBMED: 16197735; PMC: 3525126; DOI: 10.1186/1479-7364-2-3-179

  • Somatic mutations of the protein kinase gene family in human lung cancer.

    Davies H, Hunter C, Smith R, Stephens P, Greenman C, Bignell G, Teague J, Butler A, Edkins S, Stevens C et al.

    Cancer research 2005;65;17;7591-5

    PUBMED: 16140923; DOI: 10.1158/0008-5472.CAN-05-1855

  • Variation in the eNOS gene modifies the association between total energy expenditure and glucose intolerance.

    Franks PW, Luan J, Barroso I, Brage S, Gonzalez Sanchez JL, Ekelund U, Ríos MS, Schafer AJ, O'Rahilly S and Wareham NJ

    Diabetes 2005;54;9;2795-801

    PUBMED: 16123371; DOI: 10.2337/diabetes.54.9.2795

  • Complete genome sequence and lytic phase transcription profile of a Coccolithovirus.

    Wilson WH, Schroeder DC, Allen MJ, Holden MT, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H et al.

    Science (New York, N.Y.) 2005;309;5737;1090-2

    PUBMED: 16099989; DOI: 10.1126/science.1113109

  • Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping.

    Hitte C, Madeoy J, Kirkness EF, Priat C, Lorentzen TD, Senger F, Thomas D, Derrien T, Ramirez C, Scott C et al.

    Nature reviews. Genetics 2005;6;8;643-8

    PUBMED: 16012527; DOI: 10.1038/nrg1658

  • Massive attack.

    Thomson N, Cerdeño-Tárraga A and Bentley S

    Nature reviews. Microbiology 2005;3;8;586-7

    PUBMED: 16094740; DOI: 10.1038/nrmicro1212

  • ssahaSNP - a polymorphism detection tool on a whole genome scale

    Z. Ning, M. Caccamo and J.C. Mullikin

    Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE 2005;251 - 252

    DOI: 10.1109/CSBW.2005.128; URL: https://ieeexplore.ieee.org/xpl/lo...gin.jsp?tp=&arnumber=1540618&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D1540618

  • The genome of the African trypanosome Trypanosoma brucei.

    Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B et al.

    Science (New York, N.Y.) 2005;309;5733;416-22

    PUBMED: 16020726; DOI: 10.1126/science.1112642

  • The genome of the kinetoplastid parasite, Leishmania major.

    Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R et al.

    Science (New York, N.Y.) 2005;309;5733;436-42

    PUBMED: 16020728; PMC: 1470643; DOI: 10.1126/science.1112680

  • Comparative genomics of trypanosomatid parasitic protozoa.

    El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C et al.

    Science (New York, N.Y.) 2005;309;5733;404-9

    PUBMED: 16020724; DOI: 10.1126/science.1112181

  • Wolbachia variability and host effects on crossing type in Culex mosquitoes.

    Sinkins SP, Walker T, Lynd AR, Steven AR, Makepeace BL, Godfray HC and Parkhill J

    Nature 2005;436;7048;257-60

    PUBMED: 16015330; DOI: 10.1038/nature03629

  • Genome of the host-cell transforming parasite Theileria annulata compared with T. parva.

    Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, Weir W, Kerhornou A, Aslett M, Bishop R, Bouchier C et al.

    Science (New York, N.Y.) 2005;309;5731;131-3

    PUBMED: 15994557; DOI: 10.1126/science.1110418

  • Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.

    Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M et al.

    Science (New York, N.Y.) 2005;309;5731;134-7

    PUBMED: 15994558; DOI: 10.1126/science.1110439

  • Myosin VI is required for normal retinal function.

    Kitamoto J, Libby RT, Gibbs D, Steel KP and Williams DS

    Experimental eye research 2005;81;1;116-20

    PUBMED: 15978262; DOI: 10.1016/j.exer.2005.02.014

  • ACT: the Artemis Comparison Tool.

    Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J

    Bioinformatics (Oxford, England) 2005;21;16;3422-3

    PUBMED: 15976072; DOI: 10.1093/bioinformatics/bti553

  • Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators.

    Kaló P, Gleason C, Edwards A, Marsh J, Mitra RM, Hirsch S, Jakab J, Sims S, Long SR, Rogers J et al.

    Science (New York, N.Y.) 2005;308;5729;1786-9

    PUBMED: 15961668; DOI: 10.1126/science.1110951

  • Comparative apicomplexan genomics.

    Pain A, Crossman L and Parkhill J

    Nature reviews. Microbiology 2005;3;6;454-5

    PUBMED: 15934186; DOI: 10.1038/nrmicro1174

  • Structure and function of the notochord: an essential organ for chordate development.

    Stemple DL

    Development (Cambridge, England) 2005;132;11;2503-12

    PUBMED: 15890825; DOI: 10.1242/dev.01812

  • VEGA, the genome browser with a difference.

    Loveland J

    Briefings in bioinformatics 2005;6;2;189-93

    PUBMED: 15975227; DOI: 10.1093/bib/6.2.189

  • A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer.

    Stephens P, Edkins S, Davies H, Greenman C, Cox C, Hunter C, Bignell G, Teague J, Smith R, Stevens C et al.

    Nature genetics 2005;37;6;590-2

    PUBMED: 15908952; DOI: 10.1038/ng1571

  • Differentiating campomelic dysplasia from Cumming syndrome.

    Watiker V, Lachman RS, Wilcox WR, Barroso I, Schafer AJ and Scherer G

    American journal of medical genetics. Part A 2005;135;1;110-2

    PUBMED: 15754354; DOI: 10.1002/ajmg.a.30650

  • MicroRNAs regulate brain morphogenesis in zebrafish.

    Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville S, Hammond SM, Bartel DP and Schier AF

    Science (New York, N.Y.) 2005;308;5723;833-8

    PUBMED: 15774722; DOI: 10.1126/science.1109020

  • The genome of the social amoeba Dictyostelium discoideum.

    Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q et al.

    Nature 2005;435;7038;43-57

    PUBMED: 15875012; PMC: 1352341; DOI: 10.1038/nature03481

  • Genetics of Type 2 diabetes.

    Barroso I

    Diabetic medicine : a journal of the British Diabetic Association 2005;22;5;517-35

    PUBMED: 15842505; DOI: 10.1111/j.1464-5491.2005.01550.x

  • GI genomes.

    Cerdeño-Tárraga A, Claesson MJ, Sebaihia M and Thomson NR

    Nature reviews. Microbiology 2005;3;5;368-9

    PUBMED: 15871171; DOI: 10.1038/nrmicro1153

  • Sox2 is required for sensory organ development in the mammalian inner ear.

    Kiernan AE, Pelling AL, Leung KK, Tang AS, Bell DM, Tease C, Lovell-Badge R, Steel KP and Cheah KS

    Nature 2005;434;7036;1031-5

    PUBMED: 15846349; DOI: 10.1038/nature03487

  • The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.

    Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD, Livingstone M, Cerdeño-Tárraga AM, Harris B, Doggett J, Ormond D et al.

    Genome research 2005;15;5;629-40

    PUBMED: 15837807; PMC: 1088291; DOI: 10.1101/gr.3684805

  • Visualizing profile-profile alignment: pairwise HMM logos.

    Schuster-Böckler B and Bateman A

    Bioinformatics (Oxford, England) 2005;21;12;2912-3

    PUBMED: 15827079; DOI: 10.1093/bioinformatics/bti434

  • Don't mix radiocarbon and calendar years.

    Tyler-Smith C, Hurles ME and Jobling MA

    Nature 2005;434;7034;697

    PUBMED: 15815601; DOI: 10.1038/434697c

  • Livelihood hazards.

    Sebaihia M, Thomson NR, Crossman L and Parkhill J

    Nature reviews. Microbiology 2005;3;4;278-9

    PUBMED: 15818892; DOI: 10.1038/nrmicro1132

  • Mutation in the transcriptional coactivator EYA4 causes dilated cardiomyopathy and sensorineural hearing loss.

    Schönberger J, Wang L, Shin JT, Kim SD, Depreux FF, Zhu H, Zon L, Pizard A, Kim JB, Macrae CA et al.

    Nature genetics 2005;37;4;418-22

    PUBMED: 15735644; DOI: 10.1038/ng1527

  • Null and conditional semaphorin 3B alleles using a flexible puroDeltatk loxP/FRT vector.

    van der Weyden L, Adams DJ, Harris LW, Tannahill D, Arends MJ and Bradley A

    Genesis (New York, N.Y. : 2000) 2005;41;4;171-8

    PUBMED: 15789413; DOI: 10.1002/gene.20111

  • The nuclear rim protein Amo1 is required for proper microtubule cytoskeleton organisation in fission yeast.

    Pardo M and Nurse P

    Journal of cell science 2005;118;Pt 8;1705-14

    PUBMED: 15797925; DOI: 10.1242/jcs.02305

  • The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages.

    Hurles ME, Sykes BC, Jobling MA and Forster P

    American journal of human genetics 2005;76;5;894-901

    PUBMED: 15793703; PMC: 1199379; DOI: 10.1086/430051

  • Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.

    Sönnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E et al.

    Nature 2005;434;7032;462-9

    PUBMED: 15791247; DOI: 10.1038/nature03353

  • Acquired mutation of the tyrosine kinase JAK2 in human myeloproliferative disorders.

    Baxter EJ, Scott LM, Campbell PJ, East C, Fourouclas N, Swanton S, Vassiliou GS, Bench AJ, Boyd EM, Curtin N et al.

    Lancet (London, England) 2005;365;9464;1054-61

    PUBMED: 15781101; DOI: 10.1016/S0140-6736(05)71142-9

  • The DNA sequence of the human X chromosome.

    Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP et al.

    Nature 2005;434;7031;325-37

    PUBMED: 15772651; PMC: 2665286; DOI: 10.1038/nature03440

  • NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.

    Down TA and Hubbard TJ

    Nucleic acids research 2005;33;5;1445-53

    PUBMED: 15760844; PMC: 1064142; DOI: 10.1093/nar/gki282

  • Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome.

    Dhami P, Coffey AJ, Abbs S, Vermeesch JR, Dumanski JP, Woodward KJ, Andrews RM, Langford C and Vetrie D

    American journal of human genetics 2005;76;5;750-62

    PUBMED: 15756638; PMC: 1199365; DOI: 10.1086/429588

  • Extensive DNA inversions in the B. fragilis genome control variable gene expression.

    Cerdeño-Tárraga AM, Patrick S, Crossman LC, Blakely G, Abratt V, Lennard N, Poxton I, Duerden B, Harris B, Quail MA et al.

    Science (New York, N.Y.) 2005;307;5714;1463-5

    PUBMED: 15746427; DOI: 10.1126/science.1107008

  • The immunoglobulin heavy-chain locus in zebrafish: identification and expression of a previously unknown isotype, immunoglobulin Z.

    Danilova N, Bussmann J, Jekosch K and Steiner LA

    Nature immunology 2005;6;3;295-302

    PUBMED: 15685175; DOI: 10.1038/ni1166

  • Diversity at every level.

    Crossman L, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2005;3;3;196-7

    PUBMED: 15742523; DOI: 10.1038/nrmicro1479

  • Mutations of the catalytic subunit of RAB3GAP cause Warburg Micro syndrome.

    Aligianis IA, Johnson CA, Gissen P, Chen D, Hampshire D, Hoffmann K, Maina EN, Morgan NV, Tee L, Morton J et al.

    Nature genetics 2005;37;3;221-3

    PUBMED: 15696165; DOI: 10.1038/ng1517

  • The genome of the protist parasite Entamoeba histolytica.

    Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ et al.

    Nature 2005;433;7028;865-8

    PUBMED: 15729342; DOI: 10.1038/nature03291

  • PPARGC1A genotype (Gly482Ser) predicts exceptional endurance capacity in European men.

    Lucia A, Gómez-Gallego F, Barroso I, Rabadán M, Bandrés F, San Juan AF, Chicharro JL, Ekelund U, Brage S, Earnest CP et al.

    Journal of applied physiology (Bethesda, Md. : 1985) 2005;99;1;344-8

    PUBMED: 15705733; DOI: 10.1152/japplphysiol.00037.2005

  • The complete genome sequence of Francisella tularensis, the causative agent of tularemia.

    Larsson P, Oyston PC, Chain P, Chu MC, Duffield M, Fuxelius HH, Garcia E, Hälltorp G, Johansson D, Isherwood KE et al.

    Nature genetics 2005;37;2;153-9

    PUBMED: 15640799; DOI: 10.1038/ng1499

  • Brothers in arms.

    Thomson N, Holden M and Parkhill J

    Nature reviews. Microbiology 2005;3;2;100-1

    PUBMED: 15693175; DOI: 10.1038/nrmicro1092

  • Conserved non-genic sequences - an unexpected feature of mammalian genomes.

    Dermitzakis ET, Reymond A and Antonarakis SE

    Nature reviews. Genetics 2005;6;2;151-7

    PUBMED: 15716910; DOI: 10.1038/nrg1527

  • Genetic factors in type 2 diabetes: the end of the beginning?

    O'Rahilly S, Barroso I and Wareham NJ

    Science (New York, N.Y.) 2005;307;5708;370-3

    PUBMED: 15662000; DOI: 10.1126/science.1104346

  • A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.

    Hall N, Karras M, Raine JD, Carlton JM, Kooij TW, Berriman M, Florens L, Janssen CS, Pain A, Christophides GK et al.

    Science (New York, N.Y.) 2005;307;5706;82-6

    PUBMED: 15637271; DOI: 10.1126/science.1103717

  • The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number.

    Collins NE, Liebenberg J, de Villiers EP, Brayton KA, Louw E, Pretorius A, Faber FE, van Heerden H, Josemans A, van Kleef M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2005;102;3;838-43

    PUBMED: 15637156; PMC: 545511; DOI: 10.1073/pnas.0406633102

  • The Vertebrate Genome Annotation (Vega) database.

    Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S et al.

    Nucleic acids research 2005;33;Database issue;D459-65

    PUBMED: 15608237; PMC: 540089; DOI: 10.1093/nar/gki135

  • BRCTx is a novel, highly conserved RAD18-interacting protein.

    Adams DJ, van der Weyden L, Gergely FV, Arends MJ, Ng BL, Tannahill D, Kanaar R, Markus A, Morris BJ and Bradley A

    Molecular and cellular biology 2005;25;2;779-88

    PUBMED: 15632077; PMC: 543416; DOI: 10.1128/MCB.25.2.779-788.2005

  • Critical assessment of methods of protein structure prediction (CASP)--round 6.

    Moult J, Fidelis K, Rost B, Hubbard T and Tramontano A

    Proteins 2005;61 Suppl 7;3-7

    PUBMED: 16187341; DOI: 10.1002/prot.20716

  • Enemies within.

    Bentley S, Sebaihia M and Crossman L

    Nature reviews. Microbiology 2005;3;1;8-9

    PUBMED: 15635776; DOI: 10.1038/nrmicro1071

  • Ensembl 2005.

    Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F et al.

    Nucleic acids research 2005;33;Database issue;D447-53

    PUBMED: 15608235; PMC: 540092; DOI: 10.1093/nar/gki138

  • Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.

    Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, Tang X, Wang J, Xiong Z, Dong J et al.

    Nucleic acids research 2005;33;19;6445-58

    PUBMED: 16275786; PMC: 1278947; DOI: 10.1093/nar/gki954

  • Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species.

    Debenham SL, Hart EA, Ashurst JL, Howe KL, Quail MA, Ollier WE and Binns MM

    Genomics 2005;85;1;48-59

    PUBMED: 15607421; DOI: 10.1016/j.ygeno.2004.09.009

  • Rfam: annotating non-coding RNAs in complete genomes.

    Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR and Bateman A

    Nucleic acids research 2005;33;Database issue;D121-4

    PUBMED: 15608160; PMC: 540035; DOI: 10.1093/nar/gki081

  • Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen.

    Lucchini S, Liu H, Jin Q, Hinton JC and Yu J

    Infection and immunity 2005;73;1;88-102

    PUBMED: 15618144; PMC: 538992; DOI: 10.1128/IAI.73.1.88-102.2005

2004

  • Polybromo protein BAF180 functions in mammalian cardiac chamber maturation.

    Wang Z, Zhai W, Richardson JA, Olson EN, Meneses JJ, Firpo MT, Kang C, Skarnes WC and Tjian R

    Genes & development 2004;18;24;3106-16

    PUBMED: 15601824; PMC: 535920; DOI: 10.1101/gad.1238104

  • The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation.

    Bateman A, Holden MT and Yeats C

    Bioinformatics (Oxford, England) 2004;21;8;1301-3

    PUBMED: 15598841; DOI: 10.1093/bioinformatics/bti206

  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

    International Chicken Genome Sequencing Consortium

    Nature 2004;432;7018;695-716

    PUBMED: 15592404; DOI: 10.1038/nature03154

  • A transcriptomic analysis of the phylum Nematoda.

    Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Barrell B, Waterston RH et al.

    Nature genetics 2004;36;12;1259-67

    PUBMED: 15543149; DOI: 10.1038/ng1472

  • Gene map of the extended human MHC.

    Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC, Wright MW et al.

    Nature reviews. Genetics 2004;5;12;889-99

    PUBMED: 15573121; DOI: 10.1038/nrg1489

  • Genomic pot pourri.

    Bentley S, Crossman L, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;12;928-9

    PUBMED: 15580690; DOI: 10.1038/nrmicro1051

  • Proteomic analysis of in vivo phosphorylated synaptic proteins.

    Collins MO, Yu L, Coba MP, Husi H, Campuzano I, Blackstock WP, Choudhary JS and Grant SG

    The Journal of biological chemistry 2004;280;7;5972-82

    PUBMED: 15572359; DOI: 10.1074/jbc.M411220200

  • Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotes transcription termination.

    Teixeira A, Tahiri-Alaoui A, West S, Thomas B, Ramadass A, Martianov I, Dye M, James W, Proudfoot NJ and Akoulitchev A

    Nature 2004;432;7016;526-30

    PUBMED: 15565159; DOI: 10.1038/nature03032

  • Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage.

    Sanders SL, Portoso M, Mata J, Bähler J, Allshire RC and Kouzarides T

    Cell 2004;119;5;603-14

    PUBMED: 15550243; DOI: 10.1016/j.cell.2004.11.009

  • DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

    Rakyan VK, Hildmann T, Novik KL, Lewin J, Tost J, Cox AV, Andrews TD, Howe KL, Otto T, Olek A et al.

    PLoS biology 2004;2;12;e405

    PUBMED: 15550986; PMC: 529316; DOI: 10.1371/journal.pbio.0020405

  • 5,000 RNAi experiments on a chip.

    Lehner B and Fraser AG

    Nature methods 2004;1;2;103-4

    PUBMED: 15782169; DOI: 10.1038/nmeth1104-103

  • Eukaryotes: not beyond compare.

    Pain A, Bentley S and Parkhill J

    Nature reviews. Microbiology 2004;2;11;856-7

    PUBMED: 15523762; DOI: 10.1038/nrmicro1028

  • The ENCODE (ENCyclopedia Of DNA Elements) Project.

    ENCODE Project Consortium

    Science (New York, N.Y.) 2004;306;5696;636-40

    PUBMED: 15499007; DOI: 10.1126/science.1105136

  • Finishing the euchromatic sequence of the human genome.

    International Human Genome Sequencing Consortium

    Nature 2004;431;7011;931-45

    PUBMED: 15496913; DOI: 10.1038/nature03001

  • The use of genome annotation data and its impact on biological conclusions.

    Tettelin H and Parkhill J

    Nature genetics 2004;36;10;1028-9

    PUBMED: 15454934; DOI: 10.1038/ng1004-1028b

  • Chromosome 21 and down syndrome: from genomics to pathophysiology.

    Antonarakis SE, Lyle R, Dermitzakis ET, Reymond A and Deutsch S

    Nature reviews. Genetics 2004;5;10;725-38

    PUBMED: 15510164; DOI: 10.1038/nrg1448

  • Differential requirements for COPI transport during vertebrate early development.

    Coutinho P, Parsons MJ, Thomas KA, Hirst EM, Saúde L, Campos I, Williams PH and Stemple DL

    Developmental cell 2004;7;4;547-58

    PUBMED: 15469843; DOI: 10.1016/j.devcel.2004.07.020

  • Genetic equity.

    Harris J and Sulston J

    Nature reviews. Genetics 2004;5;10;796-800

    PUBMED: 15510171; DOI: 10.1038/nrg1454

  • Pathogens in decay.

    Cerdeño-Tárraga A, Thomson N and Parkhill J

    Nature reviews. Microbiology 2004;2;10;774-5

    PUBMED: 15468460; DOI: 10.1038/nrmicro1009

  • Lung cancer: intragenic ERBB2 kinase mutations in tumours.

    Stephens P, Hunter C, Bignell G, Edkins S, Davies H, Teague J, Stevens C, O'Meara S, Smith R, Parker A et al.

    Nature 2004;431;7008;525-6

    PUBMED: 15457249; DOI: 10.1038/431525b

  • Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.

    Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;39;14240-5

    PUBMED: 15377794; PMC: 521101; DOI: 10.1073/pnas.0403302101

  • What can we learn from noncoding regions of similarity between genomes?

    Down TA and Hubbard TJ

    BMC bioinformatics 2004;5;131

    PUBMED: 15369604; PMC: 523850; DOI: 10.1186/1471-2105-5-131

  • Identification of mammalian microRNA host genes and transcription units.

    Rodriguez A, Griffiths-Jones S, Ashurst JL and Bradley A

    Genome research 2004;14;10A;1902-10

    PUBMED: 15364901; PMC: 524413; DOI: 10.1101/gr.2722704

  • Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse.

    Mallon AM, Wilming L, Weekes J, Gilbert JG, Ashurst J, Peyrefitte S, Matthews L, Cadman M, McKeone R, Sellick CA et al.

    Genome research 2004;14;10A;1888-901

    PUBMED: 15364904; PMC: 524412; DOI: 10.1101/gr.2478604

  • Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers.

    Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP and Bickmore WA

    Cell 2004;118;5;555-66

    PUBMED: 15339661; DOI: 10.1016/j.cell.2004.08.011

  • The European dimension for the mouse genome mutagenesis program.

    Auwerx J, Avner P, Baldock R, Ballabio A, Balling R, Barbacid M, Berns A, Bradley A, Brown S, Carmeliet P et al.

    Nature genetics 2004;36;9;925-7

    PUBMED: 15340424; PMC: 2716028; DOI: 10.1038/ng0904-925

  • The knockout mouse project.

    Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT et al.

    Nature genetics 2004;36;9;921-4

    PUBMED: 15340423; PMC: 2716027; DOI: 10.1038/ng0904-921

  • As normal as normal can be?

    Carter NP

    Nature genetics 2004;36;9;931-2

    PUBMED: 15340426; DOI: 10.1038/ng0904-931

  • The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases.

    Dillon SC and Bateman A

    BMC bioinformatics 2004;5;109

    PUBMED: 15307895; PMC: 516016; DOI: 10.1186/1471-2105-5-109

  • Improved techniques for the identification of pseudogenes.

    Coin L and Durbin R

    Bioinformatics (Oxford, England) 2004;20 Suppl 1;i94-100

    PUBMED: 15262786; DOI: 10.1093/bioinformatics/bth942

  • The SSAHA trace server

    Z. Ning, W. Spooner, A. Spargo, S. Leonard, M. Rae. and A. Cox

    Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE 2004;544 - 545

    DOI: 10.1109/CSB.2004.1332490; URL: https://ieeexplore.ieee.org/xpl/lo...gin.jsp?tp=&arnumber=1332490&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F9262%2F29416%2F01332490.pdf%3Farnumber%3D1332490

  • Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops.

    Murrell A, Heeson S and Reik W

    Nature genetics 2004;36;8;889-93

    PUBMED: 15273689; DOI: 10.1038/ng1402

  • Periodic gene expression program of the fission yeast cell cycle.

    Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P and Bähler J

    Nature genetics 2004;36;8;809-17

    PUBMED: 15195092; DOI: 10.1038/ng1377

  • The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website.

    Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR and Wooster R

    British journal of cancer 2004;91;2;355-8

    PUBMED: 15188009; PMC: 2409828; DOI: 10.1038/sj.bjc.6601894

  • Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.

    Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ, Holeva MC, Thomson NR, Bentley SD, Churcher LJ, Mungall K et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;30;11105-10

    PUBMED: 15263089; PMC: 503747; DOI: 10.1073/pnas.0402424101

  • Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots.

    Hurles ME, Willey D, Matthews L and Hussain SS

    Genome biology 2004;5;8;R55

    PUBMED: 15287977; PMC: 507880; DOI: 10.1186/gb-2004-5-8-r55

  • Mutagenic insertion and chromosome engineering resource (MICER).

    Adams DJ, Biggs PJ, Cox T, Davies R, van der Weyden L, Jonkers J, Smith J, Plumb B, Taylor R, Nishijima I et al.

    Nature genetics 2004;36;8;867-71

    PUBMED: 15235602; DOI: 10.1038/ng1388

  • Cancer: understanding the target.

    Stratton MR and Futreal PA

    Nature 2004;430;6995;30

    PUBMED: 15229590; DOI: 10.1038/430030a

  • Chalk and cheese.

    Crossman L, Cerdeño-Tárraga A and Thomson NR

    Nature reviews. Microbiology 2004;2;7;528-9

    PUBMED: 15248310; DOI: 10.1038/nrmicro932

  • Fine mapping, gene content, comparative sequencing, and expression analyses support Ctla4 and Nramp1 as candidates for Idd5.1 and Idd5.2 in the nonobese diabetic mouse.

    Wicker LS, Chamberlain G, Hunter K, Rainbow D, Howlett S, Tiffen P, Clark J, Gonzalez-Munoz A, Cumiskey AM, Rosa RL et al.

    Journal of immunology (Baltimore, Md. : 1950) 2004;173;1;164-73

    PUBMED: 15210771; DOI: 10.4049/jimmunol.173.1.164

  • Mismatch repair genes identified using genetic screens in Blm-deficient embryonic stem cells.

    Guo G, Wang W and Bradley A

    Nature 2004;429;6994;891-5

    PUBMED: 15215866; DOI: 10.1038/nature02653

  • Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance.

    Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;26;9786-91

    PUBMED: 15213324; PMC: 470752; DOI: 10.1073/pnas.0402521101

  • A public gene trap resource for mouse functional genomics.

    Skarnes WC, von Melchner H, Wurst W, Hicks G, Nord AS, Cox T, Young SG, Ruiz P, Soriano P, Tessier-Lavigne M et al.

    Nature genetics 2004;36;6;543-4

    PUBMED: 15167922; PMC: 2716026; DOI: 10.1038/ng0604-543

  • New environments, versatile genomes.

    Cerdeño-Tárraga A, Crossman L and Parkhill J

    Nature reviews. Microbiology 2004;2;6;446-7

    PUBMED: 15181901; DOI: 10.1038/nrmicro910

  • A family with severe insulin resistance and diabetes due to a mutation in AKT2.

    George S, Rochford JJ, Wolfrum C, Gray SL, Schinner S, Wilson JC, Soos MA, Murgatroyd PR, Williams RM, Acerini CL et al.

    Science (New York, N.Y.) 2004;304;5675;1325-8

    PUBMED: 15166380; PMC: 2258004; DOI: 10.1126/science.1096706

  • The DNA sequence and comparative analysis of human chromosome 10.

    Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L, Steward CA, Sims SK, Jones MC, Searle S, Scott C et al.

    Nature 2004;429;6990;375-81

    PUBMED: 15164054; DOI: 10.1038/nature02462

  • DNA sequence and analysis of human chromosome 9.

    Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE et al.

    Nature 2004;429;6990;369-74

    PUBMED: 15164053; PMC: 2734081; DOI: 10.1038/nature02465

  • Genomes for medicine.

    Bentley DR

    Nature 2004;429;6990;440-5

    PUBMED: 15164068; DOI: 10.1038/nature02622

  • The Wnt co-receptors Lrp5 and Lrp6 are essential for gastrulation in mice.

    Kelly OG, Pinson KI and Skarnes WC

    Development (Cambridge, England) 2004;131;12;2803-15

    PUBMED: 15142971; DOI: 10.1242/dev.01137

  • Complete MHC haplotype sequencing for common disease gene mapping.

    Stewart CA, Horton R, Allcock RJ, Ashurst JL, Atrazhev AM, Coggill P, Dunham I, Forbes S, Halls K, Howson JM et al.

    Genome research 2004;14;6;1176-87

    PUBMED: 15140828; PMC: 419796; DOI: 10.1101/gr.2188104

  • Domain insertions in protein structures.

    Aroul-Selvam R, Hubbard T and Sasidharan R

    Journal of molecular biology 2004;338;4;633-41

    PUBMED: 15099733; PMC: 2665287; DOI: 10.1016/j.jmb.2004.03.039

  • The bordetellae: lessons from genomics.

    Preston A, Parkhill J and Maskell DJ

    Nature reviews. Microbiology 2004;2;5;379-90

    PUBMED: 15100691; DOI: 10.1038/nrmicro886

  • The Ensembl automatic gene annotation system.

    Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, Searle SM and Clamp M

    Genome research 2004;14;5;942-50

    PUBMED: 15123590; PMC: 479124; DOI: 10.1101/gr.1858004

  • The Ensembl Web site: mechanics of a genome browser.

    Stalker J, Gibbins B, Meidl P, Smith J, Spooner W, Hotz HR and Cox AV

    Genome research 2004;14;5;951-5

    PUBMED: 15123591; PMC: 479125; DOI: 10.1101/gr.1863004

  • The otter annotation system.

    Searle SM, Gilbert J, Iyer V and Clamp M

    Genome research 2004;14;5;963-70

    PUBMED: 15123593; PMC: 479127; DOI: 10.1101/gr.1864804

  • Bioinformatics of proteases in the MEROPS database.

    Barrett AJ

    Current opinion in drug discovery & development 2004;7;3;334-41

    PUBMED: 15216937

  • Strength in diversity.

    Pain A, Crossman L, Sebaihia M, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;5;358-9

    PUBMED: 15134078; DOI: 10.1038/nrmicro889

  • The fine-scale structure of recombination rate variation in the human genome.

    McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR and Donnelly P

    Science (New York, N.Y.) 2004;304;5670;581-4

    PUBMED: 15105499; DOI: 10.1126/science.1092500

  • Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

    Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M et al.

    PLoS biology 2004;2;6;e162

    PUBMED: 15103394; PMC: 393292; DOI: 10.1371/journal.pbio.0020162

  • An overview of Ensembl.

    Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T et al.

    Genome research 2004;14;5;925-8

    PUBMED: 15078858; PMC: 479121; DOI: 10.1101/gr.1860604

  • The DNA sequence and analysis of human chromosome 13.

    Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S et al.

    Nature 2004;428;6982;522-8

    PUBMED: 15057823; PMC: 2665288; DOI: 10.1038/nature02379

  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

    Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE et al.

    Nature 2004;428;6982;493-521

    PUBMED: 15057822; DOI: 10.1038/nature02426

  • Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features.

    Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt L, Fiegler H, Firth H, Sanlaville D, Winter R, Colleaux L et al.

    Journal of medical genetics 2004;41;4;241-8

    PUBMED: 15060094; PMC: 1735726; DOI: 10.1136/jmg.2003.017731

  • RNA interference: human genes hit the big screen.

    Fraser A

    Nature 2004;428;6981;375-8

    PUBMED: 15042071; DOI: 10.1038/428375a

  • Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF.

    Wan PT, Garnett MJ, Roe SM, Lee S, Niculescu-Duvaz D, Good VM, Jones CM, Marshall CJ, Springer CJ, Barford D et al.

    Cell 2004;116;6;855-67

    PUBMED: 15035987; DOI: 10.1016/s0092-8674(04)00215-6

  • A census of human cancer genes.

    Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N and Stratton MR

    Nature reviews. Cancer 2004;4;3;177-83

    PUBMED: 14993899; PMC: 2665285; DOI: 10.1038/nrc1299

  • Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.

    Liu M, Gingery M, Doulatov SR, Liu Y, Hodes A, Baker S, Davis P, Simmonds M, Churcher C, Mungall K et al.

    Journal of bacteriology 2004;186;5;1503-17

    PUBMED: 14973019; PMC: 344406; DOI: 10.1128/JB.186.5.1503-1517.2004

  • Sequencing the environment.

    Crossman L, Sebaihia M, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;3;184-5

    PUBMED: 15751186; DOI: 10.1038/nrmicro847

  • Gene structure conservation aids similarity based gene prediction.

    Meyer IM and Durbin R

    Nucleic acids research 2004;32;2;776-83

    PUBMED: 14764925; PMC: 373336; DOI: 10.1093/nar/gkh211

  • A new trade framework for global healthcare R&D.

    Hubbard T and Love J

    PLoS biology 2004;2;2;E52

    PUBMED: 14966544; PMC: 340954; DOI: 10.1371/journal.pbio.0020052

  • Pathogenomics of non-pathogens.

    Holden M, Crossman L, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;2;91

    PUBMED: 15040257; DOI: 10.1038/nrmicro825

  • TILLING--a high-throughput harvest for functional genomics.

    Stemple DL

    Nature reviews. Genetics 2004;5;2;145-50

    PUBMED: 14726927; DOI: 10.1038/nrg1273

  • A map of the interactome network of the metazoan C. elegans.

    Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T et al.

    Science (New York, N.Y.) 2004;303;5657;540-3

    PUBMED: 14704431; PMC: 1698949; DOI: 10.1126/science.1091403

  • The impact of SNP density on fine-scale patterns of linkage disequilibrium.

    Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D et al.

    Human molecular genetics 2004;13;6;577-88

    PUBMED: 14734624; DOI: 10.1093/hmg/ddh060

  • A genome annotation-driven approach to cloning the human ORFeome.

    Collins JE, Wright CL, Edwards CA, Davis MP, Grinham JA, Cole CG, Goward ME, Aguado B, Mallya M, Mokrab Y et al.

    Genome biology 2004;5;10;R84

    PUBMED: 15461802; PMC: 545604; DOI: 10.1186/gb-2004-5-10-r84

  • Applications of combined DNA microarray and chromosome sorting technologies.

    Gribble SM, Fiegler H, Burford DC, Prigmore E, Yang F, Carr P, Ng BL, Sun T, Kamberov ES, Makarov VL et al.

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2004;12;1;35-43

    PUBMED: 14984100; DOI: 10.1023/b:chro.0000009325.69828.83

  • Chromosome paints from single copies of chromosomes.

    Gribble S, Ng BL, Prigmore E, Burford DC and Carter NP

    Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2004;12;2;143-51

    PUBMED: 15053484; DOI: 10.1023/b:chro.0000013167.12527.f0

  • Ensembl 2004.

    Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J et al.

    Nucleic acids research 2004;32;Database issue;D468-70

    PUBMED: 14681459; PMC: 308772; DOI: 10.1093/nar/gkh038

  • SCOP database in 2004: refinements integrate structure and sequence family data.

    Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C and Murzin AG

    Nucleic acids research 2004;32;Database issue;D226-9

    PUBMED: 14681400; PMC: 308773; DOI: 10.1093/nar/gkh039

  • Shrinking genomics.

    Thomson NR, Sebaihia M, Cerdeño-Tárraga AM, Holden MT and Parkhill J

    Nature reviews. Microbiology 2004;2;1;11

    PUBMED: 15035003; DOI: 10.1038/nrmicro800

2003

  • The International HapMap Project.

    International HapMap Consortium

    Nature 2003;426;6968;789-96

    PUBMED: 14685227; DOI: 10.1038/nature02168

  • QUAD system offers fair shares to all authors.

    Verhagen JV, Wallace KJ, Collins SC and Scott TR

    Nature 2003;426;6967;602

    PUBMED: 14668833; DOI: 10.1038/426602a

  • Pathogenomics.

    Crossman L, Cerdeño-Tárraga A, Bentley S and Parkhill J

    Nature reviews. Microbiology 2003;1;3;176-7

    PUBMED: 15035020; DOI: 10.1038/nrmicro778

  • The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

    Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A et al.

    PLoS biology 2003;1;2;E45

    PUBMED: 14624247; PMC: 261899; DOI: 10.1371/journal.pbio.0000045

  • The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

    Cerdeño-Tárraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M, Bentley SD, Besra GS, Churcher C, James KD, De Zoysa A et al.

    Nucleic acids research 2003;31;22;6516-23

    PUBMED: 14602910; PMC: 275568; DOI: 10.1093/nar/gkg874

  • A DNA damage checkpoint response in telomere-initiated senescence.

    d'Adda di Fagagna F, Reaper PM, Clay-Farrace L, Fiegler H, Carr P, Von Zglinicki T, Saretzki G, Carter NP and Jackson SP

    Nature 2003;426;6963;194-8

    PUBMED: 14608368; DOI: 10.1038/nature02118

  • Fitting the niche by genomic adaptation.

    Thomson N, Bentley S, Holden M and Parkhill J

    Nature reviews. Microbiology 2003;1;2;92-3

    PUBMED: 15035037; DOI: 10.1038/nrmicro756

  • The DNA sequence and analysis of human chromosome 6.

    Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE et al.

    Nature 2003;425;6960;805-11

    PUBMED: 14574404; DOI: 10.1038/nature02055

  • Automatic inference of protein quaternary structure from crystals

    Ponstingl, H, Kabir, T and Thornton, JM

    JOURNAL OF APPLIED CRYSTALLOGRAPHY 2003;36;5;1116-1122

    DOI: 10.1107/S0021889803012421

  • The value of comparison.

    Thomson N, Sebaihia M, Cerdeño-Tárraga A, Bentley S, Crossman L and Parkhill J

    Nature reviews. Microbiology 2003;1;1;11-2

    PUBMED: 15040174; DOI: 10.1038/nrmicro734

  • Candidate gene association study in type 2 diabetes indicates a role for genes involved in beta-cell function as well as insulin action.

    Barroso I, Luan J, Middelberg RP, Harding AH, Franks PW, Jakes RW, Clayton D, Schafer AJ, O'Rahilly S and Wareham NJ

    PLoS biology 2003;1;1;E20

    PUBMED: 14551916; PMC: 212698; DOI: 10.1371/journal.pbio.0000020

  • Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes.

    Lehane MJ, Aksoy S, Gibson W, Kerhornou A, Berriman M, Hamilton J, Soares MB, Bonaldo MF, Lehane S and Hall N

    Genome biology 2003;4;10;R63

    PUBMED: 14519198; PMC: 328452; DOI: 10.1186/gb-2003-4-10-r63

  • ddbRNA: detection of conserved secondary structures in multiple alignments.

    di Bernardo D, Down T and Hubbard T

    Bioinformatics (Oxford, England) 2003;19;13;1606-11

    PUBMED: 12967955; DOI: 10.1093/bioinformatics/btg229

  • Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile.

    Jenner RG, Maillard K, Cattini N, Weiss RA, Boshoff C, Wooster R and Kellam P

    Proceedings of the National Academy of Sciences of the United States of America 2003;100;18;10399-404

    PUBMED: 12925741; PMC: 193573; DOI: 10.1073/pnas.1630810100

  • Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

    Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, Harris DE, Holden MT, Churcher CM, Bentley SD, Mungall KL et al.

    Nature genetics 2003;35;1;32-40

    PUBMED: 12910271; DOI: 10.1038/ng1227

  • The complete genome sequence of Mycobacterium bovis.

    Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M, Duthoy S, Grondin S, Lacroix C, Monsempe C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2003;100;13;7877-82

    PUBMED: 12788972; PMC: 164681; DOI: 10.1073/pnas.1130426100

  • Identification of a structurally distinct CD101 molecule encoded in the 950-kb Idd10 region of NOD mice.

    Penha-Gonçalves C, Moule C, Smink LJ, Howson J, Gregory S, Rogers J, Lyons PA, Suttie JJ, Lord CJ, Peterson LB et al.

    Diabetes 2003;52;6;1551-6

    PUBMED: 12765969; DOI: 10.2337/diabetes.52.6.1551

  • Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.

    Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M, RIKEN GER Group and GSL Members

    Genome research 2003;13;6B;1301-6

    PUBMED: 12819127; PMC: 403720; DOI: 10.1101/gr.1011603

  • Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma.

    Zhang Y, Leaves NI, Anderson GG, Ponting CP, Broxholme J, Holt R, Edser P, Bhattacharyya S, Dunham A, Adcock IM et al.

    Nature genetics 2003;34;2;181-6

    PUBMED: 12754510; DOI: 10.1038/ng1166

  • Sequence-based cancer genomics: progress, lessons and opportunities.

    Strausberg RL, Simpson AJ and Wooster R

    Nature reviews. Genetics 2003;4;6;409-18

    PUBMED: 12776211; DOI: 10.1038/nrg1085

  • Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease.

    Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, Rainbow DB, Hunter KM, Smith AN, Di Genova G et al.

    Nature 2003;423;6939;506-11

    PUBMED: 12724780; DOI: 10.1038/nature01621

  • Genomics: Relative pathogenic values.

    Parkhill J and Berry C

    Nature 2003;423;6935;23-5

    PUBMED: 12721608; DOI: 10.1038/423023a

  • DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones.

    Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP and Carter NP

    Genes, chromosomes & cancer 2003;36;4;361-74

    PUBMED: 12619160; DOI: 10.1002/gcc.10155

  • Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei.

    Bentley SD, Maiwald M, Murphy LD, Pallen MJ, Yeats CA, Dover LG, Norbertczak HT, Besra GS, Quail MA, Harris DE et al.

    Lancet (London, England) 2003;361;9358;637-44

    PUBMED: 12606174; DOI: 10.1016/S0140-6736(03)12597-4

  • Systematic functional analysis of the Caenorhabditis elegans genome using RNAi.

    Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M et al.

    Nature 2003;421;6920;231-7

    PUBMED: 12529635; DOI: 10.1038/nature01278

  • The phusion assembler.

    Mullikin JC and Ning Z

    Genome research 2003;13;1;81-90

    PUBMED: 12529309; PMC: 430959; DOI: 10.1101/gr.731003

  • CASP5 target classification.

    Kinch LN, Qi Y, Hubbard TJ and Grishin NV

    Proteins 2003;53 Suppl 6;340-51

    PUBMED: 14579323; PMC: 2656935; DOI: 10.1002/prot.10555

  • Ensembl 2002: accommodating comparative genomics.

    Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V et al.

    Nucleic acids research 2003;31;1;38-42

    PUBMED: 12519943; PMC: 165530; DOI: 10.1093/nar/gkg083

  • Gene annotation: prediction and testing.

    Ashurst JL and Collins JE

    Annual review of genomics and human genetics 2003;4;69-88

    PUBMED: 14527297; DOI: 10.1146/annurev.genom.4.070802.110300

  • Reevaluating human gene annotation: a second-generation analysis of chromosome 22.

    Collins JE, Goward ME, Cole CG, Smink LJ, Huckle EJ, Knowles S, Bye JM, Beare DM and Dunham I

    Genome research 2003;13;1;27-36

    PUBMED: 12529303; PMC: 430954; DOI: 10.1101/gr.695703

  • Rfam: an RNA family database.

    Griffiths-Jones S, Bateman A, Marshall M, Khanna A and Eddy SR

    Nucleic acids research 2003;31;1;439-41

    PUBMED: 12520045; PMC: 165453; DOI: 10.1093/nar/gkg006

2002

  • The mosaic structure of variation in the laboratory mouse genome.

    Wade CM, Kulbokas EJ, Kirby AW, Zody MC, Mullikin JC, Lander ES, Lindblad-Toh K and Daly MJ

    Nature 2002;420;6915;574-8

    PUBMED: 12466852; DOI: 10.1038/nature01252

  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

    Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H et al.

    Nature 2002;420;6915;563-73

    PUBMED: 12466851; DOI: 10.1038/nature01266

  • Initial sequencing and comparative analysis of the mouse genome.

    Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M et al.

    Nature 2002;420;6915;520-62

    PUBMED: 12466850; DOI: 10.1038/nature01262

  • Mining the mouse genome.

    Bradley A

    Nature 2002;420;6915;512-4

    PUBMED: 12466846; DOI: 10.1038/420512a

  • Tools for targeted manipulation of the mouse genome.

    van der Weyden L, Adams DJ and Bradley A

    Physiological genomics 2002;11;3;133-64

    PUBMED: 12464689; DOI: 10.1152/physiolgenomics.00074.2002

  • Human genome. HapMap launched with pledges of $100 million.

    Couzin J

    Science (New York, N.Y.) 2002;298;5595;941-2

    PUBMED: 12411675; DOI: 10.1126/science.298.5595.941a

  • Mutation of TBCE causes hypoparathyroidism-retardation-dysmorphism and autosomal recessive Kenny-Caffey syndrome.

    Parvari R, Hershkovitz E, Grossman N, Gorodischer R, Loeys B, Zecic A, Mortier G, Gregory S, Sharony R, Kambouris M et al.

    Nature genetics 2002;32;3;448-52

    PUBMED: 12389028; DOI: 10.1038/ng1012

  • QuickTree: building huge Neighbour-Joining trees of protein sequences.

    Howe K, Bateman A and Durbin R

    Bioinformatics (Oxford, England) 2002;18;11;1546-7

    PUBMED: 12424131; DOI: 10.1093/bioinformatics/18.11.1546

  • The genome sequence of the malaria mosquito Anopheles gambiae.

    Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R et al.

    Science (New York, N.Y.) 2002;298;5591;129-49

    PUBMED: 12364791; DOI: 10.1126/science.1076181

  • Genome sequence of the human malaria parasite Plasmodium falciparum.

    Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S et al.

    Nature 2002;419;6906;498-511

    PUBMED: 12368864; PMC: 3836256; DOI: 10.1038/nature01097

  • Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

    Hall N, Pain A, Berriman M, Churcher C, Harris B, Harris D, Mungall K, Bowman S, Atkin R, Baker S et al.

    Nature 2002;419;6906;527-31

    PUBMED: 12368867; DOI: 10.1038/nature01095

  • Comparative ab initio prediction of gene structures using pair HMMs.

    Meyer IM and Durbin R

    Bioinformatics (Oxford, England) 2002;18;10;1309-18

    PUBMED: 12376375; DOI: 10.1093/bioinformatics/18.10.1309

  • Cancer: stuck at first base.

    van der Weyden L, Jonkers J and Bradley A

    Nature 2002;419;6903;127-8

    PUBMED: 12226650; DOI: 10.1038/419127a

  • The PASTA domain: a beta-lactam-binding domain.

    Yeats C, Finn RD and Bateman A

    Trends in biochemical sciences 2002;27;9;438

    PUBMED: 12217513; DOI: 10.1016/s0968-0004(02)02164-3

  • The transcriptional program of meiosis and sporulation in fission yeast.

    Mata J, Lyne R, Burns G and Bähler J

    Nature genetics 2002;32;1;143-7

    PUBMED: 12161753; DOI: 10.1038/ng951

  • GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.

    Howe KL, Chothia T and Durbin R

    Genome research 2002;12;9;1418-27

    PUBMED: 12213779; PMC: 186661; DOI: 10.1101/gr.149502

  • A physical map of the mouse genome.

    Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA et al.

    Nature 2002;418;6899;743-50

    PUBMED: 12181558; DOI: 10.1038/nature00957

  • A first-generation linkage disequilibrium map of human chromosome 22.

    Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S et al.

    Nature 2002;418;6897;544-8

    PUBMED: 12110843; DOI: 10.1038/nature00864

  • Sequence and analysis of chromosome 2 of Dictyostelium discoideum.

    Glöckner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C, Parra G, Abril JF et al.

    Nature 2002;418;6893;79-85

    PUBMED: 12097910; DOI: 10.1038/nature00847

  • The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei.

    Berriman M, Hall N, Sheader K, Bringaud F, Tiwari B, Isobe T, Bowman S, Corton C, Clark L, Cross GA et al.

    Molecular and biochemical parasitology 2002;122;2;131-40

    PUBMED: 12106867; DOI: 10.1016/s0166-6851(02)00092-0

  • A global analysis of Caenorhabditis elegans operons.

    Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M and Kim SK

    Nature 2002;417;6891;851-4

    PUBMED: 12075352; DOI: 10.1038/nature00831

  • Mutations of the BRAF gene in human cancer.

    Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W et al.

    Nature 2002;417;6892;949-54

    PUBMED: 12068308; DOI: 10.1038/nature00766

  • Restricting genome data won't stop bioterrorism.

    Read TD and Parkhill J

    Nature 2002;417;6887;379

    PUBMED: 12024189; DOI: 10.1038/417379a

  • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

    Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D et al.

    Nature 2002;417;6885;141-7

    PUBMED: 12000953; DOI: 10.1038/417141a

  • Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations.

    Meijers-Heijboer H, van den Ouweland A, Klijn J, Wasielewski M, de Snoo A, Oldenburg R, Hollestelle A, Houben M, Crepin E, van Veghel-Plandsoen M et al.

    Nature genetics 2002;31;1;55-9

    PUBMED: 11967536; DOI: 10.1038/ng879

  • The significance of performance ranking in CASP--response to Marti-Renom et al.

    Moult J, Fidelis K, Zemla A, Hubbard T and Tramontano A

    Structure (London, England : 1993) 2002;10;3;291-2; discussion 292-3

    PUBMED: 12005428; DOI: 10.1016/s0969-2126(02)00728-1

  • Computational detection and location of transcription start sites in mammalian genomic DNA.

    Down TA and Hubbard TJ

    Genome research 2002;12;3;458-61

    PUBMED: 11875034; PMC: 155284; DOI: 10.1101/gr.216102

  • MaxBench: evaluation of sequence and structure comparison methods.

    Leplae R and Hubbard TJ

    Bioinformatics (Oxford, England) 2002;18;3;494-5

    PUBMED: 11934754; DOI: 10.1093/bioinformatics/18.3.494

  • The genome sequence of Schizosaccharomyces pombe.

    Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S et al.

    Nature 2002;415;6874;871-80

    PUBMED: 11859360; DOI: 10.1038/nature724

  • p53 mutant mice that display early ageing-associated phenotypes.

    Tyner SD, Venkatachalam S, Choi J, Jones S, Ghebranious N, Igelmann H, Lu X, Soron G, Cooper B, Brayton C et al.

    Nature 2002;415;6867;45-53

    PUBMED: 11780111; DOI: 10.1038/415045a

  • The Ensembl genome database project.

    Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al.

    Nucleic acids research 2002;30;1;38-41

    PUBMED: 11752248; PMC: 99161; DOI: 10.1093/nar/30.1.38

  • Databases and tools for browsing genomes.

    Birney E, Clamp M and Hubbard T

    Annual review of genomics and human genetics 2002;3;293-310

    PUBMED: 12194990; DOI: 10.1146/annurev.genom.3.030502.101529

  • Induced mitotic recombination: a switch in time.

    Adams DJ and Bradley A

    Nature genetics 2002;30;1;6-7

    PUBMED: 11753379; DOI: 10.1038/ng0102-6

  • SCOP database in 2002: refinements accommodate structural genomics.

    Lo Conte L, Brenner SE, Hubbard TJ, Chothia C and Murzin AG

    Nucleic acids research 2002;30;1;264-7

    PUBMED: 11752311; PMC: 99154; DOI: 10.1093/nar/30.1.264

2001

  • The DNA sequence and comparative analysis of human chromosome 20.

    Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL et al.

    Nature 2001;414;6866;865-71

    PUBMED: 11780052; DOI: 10.1038/414865a

  • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT et al.

    Nature 2001;413;6858;848-52

    PUBMED: 11677608; DOI: 10.1038/35101607

  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL et al.

    Nature 2001;413;6855;523-7

    PUBMED: 11586360; DOI: 10.1038/35097083

  • An SSLP marker-anchored BAC framework map of the mouse genome.

    Cai WW, Chow CW, Damani S, Gregory SG, Marra M and Bradley A

    Nature genetics 2001;29;2;133-4

    PUBMED: 11586294; DOI: 10.1038/ng1001-133

  • Engineering chromosomal rearrangements in mice.

    Yu Y and Bradley A

    Nature reviews. Genetics 2001;2;10;780-90

    PUBMED: 11584294; DOI: 10.1038/35093564

  • SSAHA: a fast search method for large DNA databases.

    Ning Z, Cox AJ and Mullikin JC

    Genome research 2001;11;10;1725-9

    PUBMED: 11591649; PMC: 311141; DOI: 10.1101/gr.194201

  • A Text-Independent Speaker Verification System Using Support Vector Machines Classifier

    Yong Gu and Trevor Thomas

    7th European Conference on Speech Communication and Technology, Aalborg, Denmark, September 3-7, 2001 2001

  • Word Level Confidence Measures Using N -Best Sub-Hypotheses Likelihood Ratio

    Beng T. Tan, Yong Gu, and Trevor Thomas

    7th European Conference on Speech Communication and Technology, Aalborg, Denmark, September 3-7, 2001 2001

  • Disruption of an imprinted gene cluster by a targeted chromosomal translocation in mice.

    Cleary MA, van Raamsdonk CD, Levorse J, Zheng B, Bradley A and Tilghman SM

    Nature genetics 2001;29;1;78-82

    PUBMED: 11528397; DOI: 10.1038/ng715

  • Granular powders and solids: Insights from numerical simulations

    W. Hoyle, M. Ghadiri, S. J. Antony, R. Moreno and Z. Ning

    Powders and Solids : Developments in Handling and Processing Technologies 2001

    DOI: 10.1039/9781847551733-00070; URL: https://pubs.rsc.org/en/conten...t/chapter/bk9780854048014-00070/978-0-85404-801-4#!divabstract

  • Breast cancer genetics: what we know and what we need.

    Nathanson KL, Wooster R, Weber BL and Nathanson KN

    Nature medicine 2001;7;5;552-6

    PUBMED: 11329055; DOI: 10.1038/87876

  • A superfamily of variant genes encoded in the subtelomeric region of Plasmodium vivax.

    del Portillo HA, Fernandez-Becerra C, Bowman S, Oliver K, Preuss M, Sanchez CP, Schneider NK, Villalobos JM, Rajandream MA, Harris D et al.

    Nature 2001;410;6830;839-42

    PUBMED: 11298455; DOI: 10.1038/35071118

  • Tbx1 haploinsufficieny in the DiGeorge syndrome region causes aortic arch defects in mice.

    Lindsay EA, Vitelli F, Su H, Morishima M, Huynh T, Pramparo T, Jurecic V, Ogunrinu G, Sutherland HF, Scambler PJ et al.

    Nature 2001;410;6824;97-101

    PUBMED: 11242049; DOI: 10.1038/35065105

  • Massive gene decay in the leprosy bacillus.

    Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honoré N, Garnier T, Churcher C, Harris D et al.

    Nature 2001;409;6823;1007-11

    PUBMED: 11234002; DOI: 10.1038/35059006

  • A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

    Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL et al.

    Nature 2001;409;6822;928-33

    PUBMED: 11237013; DOI: 10.1038/35057149

  • The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

    Bentley DR, Deloukas P, Dunham A, French L, Gregory SG, Humphray SJ, Mungall AJ, Ross MT, Carter NP, Dunham I et al.

    Nature 2001;409;6822;942-3

    PUBMED: 11237015; DOI: 10.1038/35057165

  • Cancer and genomics.

    Futreal PA, Kasprzyk A, Birney E, Mullikin JC, Wooster R and Stratton MR

    Nature 2001;409;6822;850-2

    PUBMED: 11237008; DOI: 10.1038/35057046

  • Comparison of human genetic and sequence-based physical maps.

    Yu A, Zhao C, Fan Y, Jang W, Mungall AJ, Deloukas P, Olsen A, Doggett NA, Ghebranious N, Broman KW and Weber JL

    Nature 2001;409;6822;951-3

    PUBMED: 11237020; DOI: 10.1038/35057185

  • Initial sequencing and analysis of the human genome.

    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al.

    Nature 2001;409;6822;860-921

    PUBMED: 11237011; DOI: 10.1038/35057062

  • Integration of cytogenetic landmarks into the draft sequence of the human genome.

    Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M et al.

    Nature 2001;409;6822;953-8

    PUBMED: 11237021; DOI: 10.1038/35057192

  • Mining the draft human genome.

    Birney E, Bateman A, Clamp ME and Hubbard TJ

    Nature 2001;409;6822;827-8

    PUBMED: 11236999; PMC: 2658632; DOI: 10.1038/35057004

  • Functional annotation of a full-length mouse cDNA collection.

    Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H et al.

    Nature 2001;409;6821;685-90

    PUBMED: 11217851; DOI: 10.1038/35055500

  • Contact Mechanics and Coefficients of Restitution

    Colin Thornton, Zemin Ning, Chuan-yu Wu , Mohammed Nasrullah and Long-yuan Li

    Lecture Notes in Physics 2001;564;184-194

    URL: https://link.springer.com/chapter.../10.1007/3-540-44506-4_9

  • A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence.

    Dawson E, Chen Y, Hunt S, Smink LJ, Hunt A, Rice K, Livingston S, Bumpstead S, Bruskiewich R, Sham P et al.

    Genome research 2001;11;1;170-8

    PUBMED: 11156626; PMC: 311026; DOI: 10.1101/gr.156901

  • Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts.

    Lesk AM, Lo Conte L and Hubbard TJ

    Proteins 2001;Suppl 5;98-118

    PUBMED: 11835487; DOI: 10.1002/prot.10056

  • Critical assessment of methods of protein structure prediction (CASP): round IV.

    Moult J, Fidelis K, Zemla A and Hubbard T

    Proteins 2001;Suppl 5;2-7

    PUBMED: 11835476

  • Prediction targets of CASP4.

    Murzin A and Hubbard TJ

    Proteins 2001;Suppl 5;8-12

    PUBMED: 11835477; DOI: 10.1002/prot.10055

2000

  • Cancer predisposition caused by elevated mitotic recombination in Bloom mice.

    Luo G, Santoro IM, McDaniel LD, Nishijima I, Mills M, Youssoufian H, Vogel H, Schultz RA and Bradley A

    Nature genetics 2000;26;4;424-9

    PUBMED: 11101838; DOI: 10.1038/82548

  • Functional genomic analysis of C. elegans chromosome I by systematic RNA interference.

    Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M and Ahringer J

    Nature 2000;408;6810;325-30

    PUBMED: 11099033; DOI: 10.1038/35042517

  • Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III.

    Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E et al.

    Nature 2000;408;6810;331-6

    PUBMED: 11099034; DOI: 10.1038/35042526

  • Attrition of granular solids in a shear cell

    M. Ghadiri, Z. Ning, S.J Kenter and E Puikc

    Chemical Engineering Science 2000;55;5445–5456

    DOI: 10.1016/S0009-2509(00)00168-8; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0009250900001688

  • Advances on HMM-based Text-dependent Speaker Verification

    Yong Gu and Trevor Thomas

    Proceedings ICSLP2000 2000

  • Competition-based score analysis for utterance verificationin name recognition

    Yong Gu and Trevor Thomas

    Proceedings ICSLP 2000

  • SPEAKER VERIFICATION IN OPERATIONAL ENVIRONMENTS - MONITORING FOR IMPROVED SERVICE OPERATION

    Yong Gu, Hans Jongebloed, Dorota Iskra, Els den Os, Lou Boves

    Proceedings ICSLP2000 2000;Vol. 2;Vol. 2, p.450-453

  • Artemis: sequence visualization and annotation.

    Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B

    Bioinformatics (Oxford, England) 2000;16;10;944-5

    PUBMED: 11120685; DOI: 10.1093/bioinformatics/16.10.944

  • Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain.

    Cerutti L, Mian N and Bateman A

    Trends in biochemical sciences 2000;25;10;481-2

    PUBMED: 11050429; DOI: 10.1016/s0968-0004(00)01641-8

  • An SNP map of human chromosome 22.

    Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, Rice CM, Burton J, Matthews LH, Pavitt R, Plumb RW, Sims SK et al.

    Nature 2000;407;6803;516-20

    PUBMED: 11029003; DOI: 10.1038/35035089

  • A Competition-based Score Measurement for Speaker Verification

    Yong Gu and Trevor Thomas

    Proceedings of EUSIPCO 2000, Tenth European Signal Processing Conference, Tampere, Finland 2000

  • In defense of complete genomes.

    Parkhill J

    Nature biotechnology 2000;18;5;493-4

    PUBMED: 10802612; DOI: 10.1038/75346

  • A browser for expression data.

    Pocock MR and Hubbard TJ

    Bioinformatics (Oxford, England) 2000;16;4;402-3

    PUBMED: 10869040; DOI: 10.1093/bioinformatics/16.4.402

  • Distinct element analysis of bulk crushing: effect of particle properties and loading rate

    C. Couroyer, Z. Ning and M. Ghadiri

    Powder Technology 2000;109;241–254

    DOI: 10.1016/S0032-5910(99)00240-5; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0032591099002405

  • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.

    Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G, Basham D, Brown D, Chillingworth T et al.

    Nature 2000;404;6777;502-6

    PUBMED: 10761919; DOI: 10.1038/35006655

  • The genome sequence of Drosophila melanogaster.

    Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al.

    Science (New York, N.Y.) 2000;287;5461;2185-95

    PUBMED: 10731132

  • From sequence to chromosome: the tip of the X chromosome of D. melanogaster.

    Benos PV, Gatt MK, Ashburner M, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demailles J et al.

    Science (New York, N.Y.) 2000;287;5461;2220-2

    PUBMED: 10731137

  • Open annotation offers a democratic solution to genome sequencing.

    Hubbard T and Birney E

    Nature 2000;403;6772;825

    PUBMED: 10706254; DOI: 10.1038/35002770

  • The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

    Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S et al.

    Nature 2000;403;6770;665-8

    PUBMED: 10688204; DOI: 10.1038/35001088

  • Analysis of vertebrate SCL loci identifies conserved enhancers.

    Göttgens B, Barton LM, Gilbert JG, Bench AJ, Sanchez MJ, Bahn S, Mistry S, Grafham D, McMurray A, Vaudin M et al.

    Nature biotechnology 2000;18;2;181-6

    PUBMED: 10657125; DOI: 10.1038/72635

  • LMNA, encoding lamin A/C, is mutated in partial lipodystrophy.

    Shackleton S, Lloyd DJ, Jackson SN, Evans R, Niermeijer MF, Singh BM, Schmidt H, Brabant G, Kumar S, Durrington PN et al.

    Nature genetics 2000;24;2;153-6

    PUBMED: 10655060; DOI: 10.1038/72807

  • Entering the post-genomic era of malaria research.

    Horrocks P, Bowman S, Kyes S, Waters AP and Craig A

    Bulletin of the World Health Organization 2000;78;12;1424-37

    PUBMED: 11196489; PMC: 2560662

  • SCOP: a structural classification of proteins database.

    Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG and Chothia C

    Nucleic acids research 2000;28;1;257-9

    PUBMED: 10592240; PMC: 102479; DOI: 10.1093/nar/28.1.257

1999

  • Genetic definition and sequence analysis of Arabidopsis centromeres.

    Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD et al.

    Science (New York, N.Y.) 1999;286;5449;2468-74

    PUBMED: 10617454

  • Word Confusability Measures for Vocabulary Selection in Speech Recognition

    Beng T. Tan, Yong Gu, and Trevor Thomas

    Proc. IEEE Workshop on Automtic Speech Recognition and Understanding (ASRU), Colordo, USA 1999

  • The DNA sequence of human chromosome 22.

    Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ et al.

    Nature 1999;402;6761;489-95

    PUBMED: 10591208; DOI: 10.1038/990031

  • From genomics to epigenomics: a loftier view of life.

    Beck S, Olek A and Walter J

    Nature biotechnology 1999;17;12;1144

    PUBMED: 10585673; DOI: 10.1038/70651

  • Breakage of macroporous alumina beads under compressive loading: simulation and experimental validation

    Charlotte Couroyera, Zemin Ninga, Mojtaba Ghadiria, Nathalie Brunardb, Frédéric Kolendab, Denis Bortzmeyerc and Philippe Laval

    Powder Technology 1999;105;57–65

    DOI: 10.1016/S0032-5910(99)00118-7; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0032591099001187

  • Effect of interface energy on the impact strength of agglomerates

    J. Subero, Z. Ning, M. Ghadiri and C. Thornton

    Powder Technology 1999;105;66–73

    DOI: 10.1016/S0032-5910(99)00119-9; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0032591099001199

  • The chicken B locus is a minimal essential major histocompatibility complex.

    Kaufman J, Milne S, Göbel TW, Walker BA, Jacob JP, Auffray C, Zoorob R and Beck S

    Nature 1999;401;6756;923-5

    PUBMED: 10553909; DOI: 10.1038/44856

  • Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium.

    No authors listed

    Nature 1999;401;6756;921-3

    PUBMED: 10553908; DOI: 10.1038/44853

  • Sequencing. Gels and genomes.

    Rogers J

    Science (New York, N.Y.) 1999;286;5439;429

    PUBMED: 10577205

  • A new member of the IL-1 receptor family highly expressed in hippocampus and involved in X-linked mental retardation.

    Carrié A, Jun L, Bienvenu T, Vinet MC, McDonell N, Couvert P, Zemni R, Cardona A, Van Buggenhout G, Frints S et al.

    Nature genetics 1999;23;1;25-31

    PUBMED: 10471494; DOI: 10.1038/12623

  • The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum.

    Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, Churcher CM, Craig A, Davies RM, Devlin K, Feltwell T et al.

    Nature 1999;400;6744;532-8

    PUBMED: 10448855; DOI: 10.1038/22964

  • A YAC-based physical map of the mouse genome.

    Nusbaum C, Slonim DK, Harris KL, Birren BW, Steen RG, Stein LD, Miller J, Dietrich WF, Nahf R, Wang V et al.

    Nature genetics 1999;22;4;388-93

    PUBMED: 10431246; DOI: 10.1038/11967

  • Mutations in SLC19A2 cause thiamine-responsive megaloblastic anaemia associated with diabetes mellitus and deafness.

    Labay V, Raz T, Baron D, Mandel H, Williams H, Barrett T, Szargel R, McDonald L, Shalata A, Nosaka K et al.

    Nature genetics 1999;22;3;300-4

    PUBMED: 10391221; DOI: 10.1038/10372

  • Techview: DNA sequencing. Sequencing the genome, fast.

    Mullikin JC and McMurragy AA

    Science (New York, N.Y.) 1999;283;5409;1867-9

    PUBMED: 10206892

  • A Hybrid Score Measurement for HMM-Based Speaker Verification

    Yong Gu & Threvor Thomas

    Acoustics, Speech, and Signal Processing, 1999. Proceedings., 1999 IEEE International Conference 1999;Volume:1;317 - 320 vol.1

    DOI: 10.1109/ICASSP.1999.758126

  • Nonmethylated transposable elements and methylated genes in a chordate genome.

    Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, Clark VH and Bird A

    Science (New York, N.Y.) 1999;283;5405;1164-7

    PUBMED: 10024242

  • Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction.

    Orengo CA, Bray JE, Hubbard T, LoConte L and Sillitoe I

    Proteins 1999;Suppl 3;149-70

    PUBMED: 10526364; DOI: 10.1002/(sici)1097-0134(1999)37:3+<149::aid-prot20>3.3.co;2-8

  • Data mining parasite genomes: haystack searching with a computer.

    Lawson D

    Parasitology 1999;118 Suppl;S15-8

    PUBMED: 10466134

  • Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

    Bateman A, Birney E, Durbin R, Eddy SR, Finn RD and Sonnhammer EL

    Nucleic acids research 1999;27;1;260-2

    PUBMED: 9847196; PMC: 148151

  • RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions.

    Hubbard TJ

    Proteins 1999;Suppl 3;15-21

    PUBMED: 10526348; DOI: 10.1002/(sici)1097-0134(1999)37:3+<15::aid-prot4>3.3.co;2-q

  • SCOP: a Structural Classification of Proteins database.

    Hubbard TJ, Ailey B, Brenner SE, Murzin AG and Chothia C

    Nucleic acids research 1999;27;1;254-6

    PUBMED: 9847194; PMC: 148149; DOI: 10.1093/nar/27.1.254

1998

  • Genome sequence of the nematode C. elegans: a platform for investigating biology.

    C. elegans Sequencing Consortium

    Science (New York, N.Y.) 1998;282;5396;2012-8

    PUBMED: 9851916; DOI: 10.1126/science.282.5396.2012

  • Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.

    Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T and Chothia C

    Journal of molecular biology 1998;284;4;1201-10

    PUBMED: 9837738; DOI: 10.1006/jmbi.1998.2221

  • An implementation and evaluation of an on-line speaker verification system for field trials

    Yong Gu & Trevor Thomas

    The 5th International Conference on Spoken Language Processing, Sydney Convention Centre, Sydney, Australia, 30th November - 4th December 1998 1998

  • SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data.

    Hubbard TJ, Ailey B, Brenner SE, Murzin AG and Chothia C

    Acta crystallographica. Section D, Biological crystallography 1998;54;Pt 6 Pt 1;1147-54

    PUBMED: 10089491; DOI: 10.1107/s0907444998009172

  • Toward a complete human genome sequence.

    Sanger Center and Genome Sequencing Center

    Genome research 1998;8;11;1097-108

    PUBMED: 9847074; DOI: 10.1101/gr.8.11.1097

  • A physical map of 30,000 human genes.

    Deloukas P, Schuler GD, Gyapay G, Beasley EM, Soderlund C, Rodriguez-Tomé P, Hui L, Matise TC, McKusick KB, Beckmann JS et al.

    Science (New York, N.Y.) 1998;282;5389;744-6

    PUBMED: 9784132; DOI: 10.1126/science.282.5389.744

  • The Human Genome Project: reaching the finish line.

    Waterston R and Sulston JE

    Science (New York, N.Y.) 1998;282;5386;53-4

    PUBMED: 9786797

  • Disintegration of weak lactose agglomerates for inhalation applications

    R. Boerefijn, Z. Ning and M. Ghadiri

    International Journal of Pharmaceutics 1998;172;199–209

    DOI: 10.1016/S0378-5173(98)00207-5; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0378517398002075

  • Host response to EBV infection in X-linked lymphoproliferative disease results from mutations in an SH2-domain encoding gene.

    Coffey AJ, Brooksbank RA, Brandau O, Oohashi T, Howell GR, Bye JM, Cahn AP, Durham J, Heath P, Wray P et al.

    Nature genetics 1998;20;2;129-35

    PUBMED: 9771704; DOI: 10.1038/2424

  • Inversin, a novel gene in the vertebrate left-right axis pathway, is partially deleted in the inv mouse.

    Morgan D, Turnpenny L, Goodship J, Dai W, Majumder K, Matthews L, Gardner A, Schuster G, Vien L, Harrison W et al.

    Nature genetics 1998;20;2;149-56

    PUBMED: 9771707; DOI: 10.1038/2450

  • Mutations in a gene encoding a novel protein tyrosine phosphatase cause progressive myoclonus epilepsy.

    Minassian BA, Lee JR, Herbrick JA, Huizenga J, Soder S, Mungall AJ, Dunham I, Gardner R, Fong CY, Carpenter S et al.

    Nature genetics 1998;20;2;171-4

    PUBMED: 9771710; DOI: 10.1038/2470

  • Simulation Of Flexible Fibers By Discrete Cylindrical Segments

    Zemin Ning and John R. Melrose

    Computational Methods for Smart Structures and Materials 1998

    URL: https://www.witpress.com/elibrar...y/wit-transactions-on-the-built-environment/38

  • Implementation and evaluation of a voice-activated dialling system

    Beng T Tan, Yong Gu, and Trevor Thomas

    Interactive Voice Technology for Telecommunications Applications, IEEE IVTTA '98. Proceedings. 1998

    DOI: 10.1109/IVTTA.1998.727698

  • A theoretical model for the stick/bounce behaviour of adhesive, elastic-plastic spheres

    Colin Thornton and Zemin Ning

    Powder Technology 1998;99;154–162

    DOI: 10.1016/S0032-5910(98)00099-0; URL: https://www.sciencedirect.com/scien...ce/article/pii/S0032591098000990

  • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE et al.

    Nature 1998;393;6685;537-44

    PUBMED: 9634230; DOI: 10.1038/31159

  • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.

    Brenner SE, Chothia C and Hubbard TJ

    Proceedings of the National Academy of Sciences of the United States of America 1998;95;11;6073-8

    PUBMED: 9600919; PMC: 27587; DOI: 10.1073/pnas.95.11.6073

  • Using neural networks for prediction of the subcellular location of proteins.

    Reinhardt A and Hubbard T

    Nucleic acids research 1998;26;9;2230-6

    PUBMED: 9547285; PMC: 147531; DOI: 10.1093/nar/26.9.2230

  • GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency.

    Leplae R, Hubbard T and Tramontano A

    Proteins 1998;30;4;339-51

    PUBMED: 9533618; DOI: 10.1002/(sici)1097-0134(19980301)30:4<339::aid-prot1>3.0.co;2-e

  • SPEM: a parser for EMBL style flat file database entries.

    Pocock MR, Hubbard T and Birney E

    Bioinformatics (Oxford, England) 1998;14;9;823-4

    PUBMED: 9918956; DOI: 10.1093/bioinformatics/14.9.823

1997

  • Intermediate sequences increase the detection of homology between sequences.

    Park J, Teichmann SA, Hubbard T and Chothia C

    Journal of molecular biology 1997;273;1;349-54

    PUBMED: 9367767; DOI: 10.1006/jmbi.1997.1288

  • Distinct element simulation of impact breakage of lactose agglomerates

    Z. Ning, R. Boerefijn, M. Ghadiri and C. Thornton

    Advanced Powder Technology 1997

    DOI: 10.1163/156855297X00020; URL: https://booksandjournals.brillonline.com/...content/journals/10.1163/156855297x00020

  • Detection of protein-ligand NOEs with small, weakly binding ligands by combined relaxation and diffusion filtering

    Ponstingl, H and Otting, G

    J Biomol NMR 1997;9;4;441-444

    DOI: 10.1023/A:1018363030177

  • Population statistics of protein structures: lessons from structural classifications.

    Brenner SE, Chothia C and Hubbard TJ

    Current opinion in structural biology 1997;7;3;369-76

    PUBMED: 9204279; DOI: 10.1016/s0959-440x(97)80054-1

  • The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.

    Jacq C, Alt-Mörbe J, Andre B, Arnold W, Bahr A, Ballesta JP, Bargues M, Baron L, Becker A, Biteau N et al.

    Nature 1997;387;6632 Suppl;75-8

    PUBMED: 9169867

  • The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.

    Churcher C, Bowman S, Badcock K, Bankier A, Brown D, Chillingworth T, Connor R, Devlin K, Gentles S, Hamlin N et al.

    Nature 1997;387;6632 Suppl;84-7

    PUBMED: 9169870

  • The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.

    Bowman S, Churcher C, Badcock K, Brown D, Chillingworth T, Connor R, Dedman K, Devlin K, Gentles S, Hamlin N et al.

    Nature 1997;387;6632 Suppl;90-3

    PUBMED: 9169872

  • The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.

    Bussey H, Storms RK, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell B, Badcock K et al.

    Nature 1997;387;6632 Suppl;103-5

    PUBMED: 9169875

  • New horizons in sequence analysis.

    Hubbard TJ

    Current opinion in structural biology 1997;7;2;190-3

    PUBMED: 9094334; DOI: 10.1016/s0959-440x(97)80024-3

  • The relationship between chromosome structure and function at a human telomeric region.

    Flint J, Thomas K, Micklem G, Raynham H, Clark K, Doggett NA, King A and Higgs DR

    Nature genetics 1997;15;3;252-7

    PUBMED: 9054936; DOI: 10.1038/ng0397-252

  • Instability of highly expanded CAG repeats in mice transgenic for the Huntington's disease mutation.

    Mangiarini L, Sathasivam K, Mahal A, Mott R, Seller M and Bates GP

    Nature genetics 1997;15;2;197-200

    PUBMED: 9020849; DOI: 10.1038/ng0297-197

  • Critical assessment of methods of protein structure prediction (CASP): round II.

    Moult J, Hubbard T, Bryant SH, Fidelis K and Pedersen JT

    Proteins 1997;Suppl 1;2-6

    PUBMED: 9485489

  • Numerical criteria for the evaluation of ab initio predictions of protein structure.

    Zemla A, Venclovas C, Reinhardt A, Fidelis K and Hubbard TJ

    Proteins 1997;Suppl 1;140-50

    PUBMED: 9485506; DOI: 10.1002/(sici)1097-0134(1997)1+<140::aid-prot19>3.3.co;2-y

1996

  • A gene map of the human genome.

    Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E et al.

    Science (New York, N.Y.) 1996;274;5287;540-6

    PUBMED: 8849440

  • Genome maps 7. The human transcript map. Wall chart.

    Schuler GD, Boguski MS, Hudson TJ, Hui L, Ma J, Castle AB, Wu X, Silva J, Nusbaum HC, Birren BB et al.

    Science (New York, N.Y.) 1996;274;5287;547-62

    PUBMED: 8928009

  • Life with 6000 genes.

    Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al.

    Science (New York, N.Y.) 1996;274;5287;546, 563-7

    PUBMED: 8849441

  • The Saccharomyces cerevisiae genome on the World Wide Web.

    Walsh S and Barrell B

    Trends in genetics : TIG 1996;12;7;276-7

    PUBMED: 8763500

  • Characterization of DRP2, a novel human dystrophin homologue.

    Roberts RG, Freeman TC, Kendall E, Vetrie DL, Dixon AK, Shaw-Smith C, Bone Q and Bobrow M

    Nature genetics 1996;13;2;223-6

    PUBMED: 8640231; DOI: 10.1038/ng0696-223

1995

  • A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.

    Sonnhammer EL and Durbin R

    Gene 1995;167;1-2;GC1-10

    PUBMED: 8566757; DOI: 10.1016/0378-1119(95)00714-8

  • Identification of the breast cancer susceptibility gene BRCA2.

    Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, Collins N, Gregory S, Gumbs C and Micklem G

    Nature 1995;378;6559;789-92

    PUBMED: 8524414; DOI: 10.1038/378789a0

  • Sequence variation of the human Y chromosome.

    Whitfield LS, Sulston JE and Goodfellow PN

    Nature 1995;378;6555;379-80

    PUBMED: 7477372; DOI: 10.1038/378379a0

  • A high-density YAC contig map of human chromosome 22.

    Collins JE, Cole CG, Smink LJ, Garrett CL, Leversha MA, Soderlund CA, Maslen GL, Everett LA, Rice KM, Coffey AJ et al. et al.

    Nature 1995;377;6547 Suppl;367-79

    PUBMED: 7566101; DOI: 10.1038/377367a0

  • Free exchange.

    Waterston B and Sulston J

    Nature 1995;376;6536;111

    PUBMED: 7603552; DOI: 10.1038/376111d0

  • Comparative sequence analysis of the human and pufferfish Huntington's disease genes.

    Baxendale S, Abdulla S, Elgar G, Buck D, Berks M, Micklem G, Durbin R, Bates G, Brenner S and Beck S

    Nature genetics 1995;10;1;67-76

    PUBMED: 7647794; DOI: 10.1038/ng0595-67

1994

  • A workbench for large-scale sequence homology analysis.

    Sonnhammer EL and Durbin R

    Computer applications in the biosciences : CABIOS 1994;10;3;301-7

    PUBMED: 7922687; DOI: 10.1093/bioinformatics/10.3.301

  • 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.

    Wilson R, Ainscough R, Anderson K, Baynes C, Berks M, Bonfield J, Burton J, Connell M, Copsey T, Cooper J et al. et al.

    Nature 1994;368;6466;32-8

    PUBMED: 7906398; DOI: 10.1038/368032a0

1993

  • Yeast origin recognition complex is involved in DNA replication and transcriptional silencing.

    Micklem G, Rowley A, Harwood J, Nasmyth K and Diffley JF

    Nature 1993;366;6450;87-9

    PUBMED: 8232543; DOI: 10.1038/366087a0

  • Regulation of linkages between the erythrocyte membrane and its skeleton by 2,3-diphosphoglycerate.

    Moriyama R, Lombardo CR, Workman RF and Low PS

    The Journal of biological chemistry 1993;268;15;10990-6

    PUBMED: 8496163

  • The Caenorhabditis elegans genome sequencing project: first steps in automation.

    Watson A, Smaldon N, Lucke R and Hawkins T

    Nature 1993;362;6420;569-70

    PUBMED: 8464500; DOI: 10.1038/362569a0

1992

  • A survey of expressed genes in Caenorhabditis elegans.

    Waterston R, Martin C, Craxton M, Huynh C, Coulson A, Hillier L, Durbin R, Green P, Shownkeen R, Halloran N et al. et al.

    Nature genetics 1992;1;2;114-23

    PUBMED: 1302004; DOI: 10.1038/ng0592-114

  • The C. elegans genome sequencing project: a beginning.

    Sulston J, Du Z, Thomas K, Wilson R, Hillier L, Staden R, Halloran N, Green P, Thierry-Mieg J, Qiu L et al. et al.

    Nature 1992;356;6364;37-41

    PUBMED: 1538779; DOI: 10.1038/356037a0

1989

  • Speaker Normalisation via a Linear Transformation on a Perceptual Feature Space and its Benefits in ASR

    Yong Gu & John Mason

    First European Conference on Speech Communication and Technology, Paris, France 1989

1988

  • A Speaker-Correlation Weighted RPS Distance Measure for Speech Recognition

    Yong Gu and John Mason

    IEEE International Symposium on Information Theory 1988

    DOI: 10.1109/ISIT.1988.22256

0

  • Using social network analysis to complete literature reviews: a new systematic approach for independent researchers to detect and interpret prominent research programs within large collections of relevant literature

    Cowhitt,T., Butler,T. and Wilson,E.

    International Journal of Social Research Methodology 0

    DOI: 10.1080/13645579.2019.1704356