Berriman Group | Parasite Genomics

Berriman Group | Parasite Genomics

Berriman Group

berriman-group.jpgSanger Institute, Genome Research Limited
Berriman Group

Our Research and Approach

We use large-scale genome and transcriptome sequencing along with phenotyping to understand the biology of important parasites. We start with the production and analysis of high quality reference genomes. The malaria parasite P. falciparum is the gold standard for this – we have curated its genome for more than a decade – but the approach is being extended to other more neglected parasites including schistosomes and whipworms.

We then use comparisons between genomes, performed over different evolutionary scales, to address questions about parasite biology. We use draft genomes across diverse clades to survey the broad differences between parasites and finer grained comparisons between more closely related species to study the evolution of genes associated with specific clades of parasites or parasite traits.

For two exemplar helminth species – Schistosoma mansoni and Trichuris muris, representing flatworms and nematodes, we use full infection lifecycles established at the Institute to facilitate phenotyping and in-depth functional genomics studies, from which genes or proteins can be selected for detailed investigation.


Dr Matt Berriman
Group Leader

Matt leads the parasite genomics group who study the parasites that cause malaria and neglected tropical diseases. He uses large-scale comparative and functional genomics approaches to discover and study genes associated with major biological traits of parasites or with potential for exploitation as targets for intervention.

Holroyd, Nancy

Nancy Holroyd
Helminth Sequencing Project Coordination
Show Alumni


Beasley, Helen

No image available
Helen Beasley
Computer Biologist - Senior Genome Analyst

Brooks, Karen

Karen Brooks
Computer Biologist - Senior Genome Analyst

Key Projects, Collaborations, Tools & Data

Some of our main projects include the following efforts:

Programmes, Associate Research Programmes and Facilities

Partners and Funders

We collaborate with several internal and external groups, including:
Internal Partners


  • The genomic basis of parasitism in the Strongyloides clade of nematodes.

    Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N et al.

    Nature genetics 2016;48;3;299-307

  • Medicine. Halting harmful helminths.

    Hoffmann KF, Brindley PJ and Berriman M

    Science (New York, N.Y.) 2014;346;6206;168-9

  • 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 et al.

    Genome biology 2014;15;11;510

  • The genomes of four tapeworm species reveal adaptations to parasitism.

    Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A et al.

    Nature 2013;496;7443;57-63

  • 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

  • Genomic and Metabolomic Polymorphism among Experimentally Selected Paromomycin-Resistant Leishmania donovani Strains.

    Shaw CD, Imamura H, Downing T, Blackburn G, Westrop GD et al.

    Antimicrobial agents and chemotherapy 2019;64;1

  • 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 et al.

    PLoS neglected tropical diseases 2019;13;12;e0007900

  • The global diversity of Haemonchus contortus is shaped by human intervention and climate.

    Sallé G, Doyle SR, Cortet J, Cabaret J, Berriman M et al.

    Nature communications 2019;10;1;4811

  • The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.

    Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ et al.

    Science (New York, N.Y.) 2019;365;6455

  • 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 et al.

    BMC genomics 2019;20;1;218

  • Repeated clinical malaria episodes are associated with modification of the immune system in children.

    Bediako Y, Adams R, Reid AJ, Valletta JJ, Ndungu FM et al.

    BMC medicine 2019;17;1;60

  • An experimental human blood stage model for studying Plasmodium malariae infection.

    Woodford J, Collins KA, Odedra A, Wang C, Kyung JI et al.

    The Journal of infectious diseases 2019

  • Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni.

    Ittiprasert W, Mann VH, Karinshak SE, Coghlan A, Rinaldi G et al.

    eLife 2019;8

  • Comparative genomics of the major parasitic worms.

    International Helminth Genomes Consortium

    Nature genetics 2019;51;1;163-174

  • 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 et al.

    Frontiers in genetics 2019;10;826

  • 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 et al.

    PLoS pathogens 2019;15;1;e1007265

  • GeneDB and Wikidata.

    Manske M, Böhme U, Püthe C and Berriman M

    Wellcome open research 2019;4;114

  • 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

  • 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 et al.

    Wellcome open research 2019;4;159

  • 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 et al.

    Genome research 2018;28;9;1383-1394

  • Biology and genome of a newly discovered sibling species of Caenorhabditis elegans.

    Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Liu D et al.

    Nature communications 2018;9;1;3216

  • Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis.

    Wyllie S, Thomas M, Patterson S, Crouch S, De Rycker M et al.

    Nature 2018

  • 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

  • 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 et al.

    The Journal of infectious diseases 2018;218;2;259-264

  • 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 et al.

    Nature microbiology 2018;3;6;687-697

  • 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 et al.

    Genome research 2018;28;4;547-560

  • Transcriptomic profiling of nematode parasites surviving vaccine exposure.

    Sallé G, Laing R, Cotton JA, Maitland K, Martinelli A et al.

    International journal for parasitology 2018;48;5;395-402

  • Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.

    Reid AJ, Talman AM, Bennett HM, Gomes AR, Sanders MJ et al.

    eLife 2018;7

  • Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni.

    Wendt GR, Collins JN, Pei J, Pearson MS, Bennett HM et al.

    eLife 2018;7

  • A method for single pair mating in an obligate parasitic nematode.

    Sargison ND, Redman E, Morrison AA, Bartley DJ, Jackson F et al.

    International journal for parasitology 2018;48;2;159-165

  • WormBase 2017: molting into a new stage.

    Lee RYN, Howe KL, Harris TW, Arnaboldi V, Cain S et al.

    Nucleic acids research 2018;46;D1;D869-D874

  • 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 et al.

    PloS one 2018;13;7;e0201263

  • 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 et al.

    Wellcome open research 2018;3;142

  • Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres.

    Otto TD, Böhme U, Sanders M, Reid A, Bruske EI et al.

    Wellcome open research 2018;3;52

  • Pre-clinical evaluation of a P. berghei-based whole-sporozoite malaria vaccine candidate.

    Mendes AM, Reuling IJ, Andrade CM, Otto TD, Machado M et al.

    NPJ vaccines 2018;3;54

  • Tissue-specific transcriptome analyses provide new insights into GPCR signalling in adult Schistosoma mansoni.

    Hahnel S, Wheeler N, Lu Z, Wangwiwatsin A, McVeigh P et al.

    PLoS pathogens 2018;14;1;e1006718

  • 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

  • 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 et al.

    Journal of global antimicrobial resistance 2017;11;148-151

  • Gene Expression in Leishmania Is Regulated Predominantly by Gene Dosage.

    Iantorno SA, Durrant C, Khan A, Sanders MJ, Beverley SM et al.

    mBio 2017;8;5

  • A gene expression atlas of adult Schistosoma mansoni and their gonads.

    Lu Z, Sessler F, Holroyd N, Hahnel S, Quack T et al.

    Scientific data 2017;4;170118

  • Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine.

    Rutledge GG, Marr I, Huang GKL, Auburn S, Marfurt J et al.

    Emerging infectious diseases 2017;23;8;1300-1307

  • WormBase ParaSite - a comprehensive resource for helminth genomics.

    Howe KL, Bolt BJ, Shafie M, Kersey P and Berriman M

    Molecular and biochemical parasitology 2017;215;2-10

  • 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 et al.

    mBio 2017;8;3

  • 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 et al.

    PLoS neglected tropical diseases 2017;11;5;e0005559

  • 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 et al.

    Antimicrobial agents and chemotherapy 2017;61;3

  • Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution.

    Rutledge GG, Böhme U, Sanders M, Reid AJ, Cotton JA et al.

    Nature 2017;542;7639;101-104

  • The exported chaperone Hsp70-x supports virulence functions for Plasmodium falciparum blood stage parasites.

    Charnaud SC, Dixon MWA, Nie CQ, Chappell L, Sanders PR et al.

    PloS one 2017;12;7;e0181656

  • 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 et al.

    Malaria journal 2016;15;1;597

  • 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

  • The genome of Onchocerca volvulus, agent of river blindness.

    Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A et al.

    Nature microbiology 2016;2;16216

  • 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 et al.

    Wellcome open research 2016;1;4

  • Activation of Bicyclic Nitro-drugs by a Novel Nitroreductase (NTR2) in Leishmania.

    Wyllie S, Roberts AJ, Norval S, Patterson S, Foth BJ et al.

    PLoS pathogens 2016;12;11;e1005971

  • 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

  • HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni.

    Suttiprapa S, Rinaldi G, Tsai IJ, Mann VH, Dubrovsky L et al.

    PLoS pathogens 2016;12;10;e1005931

  • 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 et al.

    Scientific reports 2016;6;31150

  • Companion: a web server for annotation and analysis of parasite genomes.

    Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.

    Nucleic acids research 2016;44;W1;W29-34

  • Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent.

    Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S et al.

    eLife 2016;5

  • The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences.

    Kensche PR, Hoeijmakers WA, Toenhake CG, Bras M, Chappell L et al.

    Nucleic acids research 2016;44;5;2110-24

  • The genomic basis of parasitism in the Strongyloides clade of nematodes.

    Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N et al.

    Nature genetics 2016;48;3;299-307

  • 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

  • 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 et al.

    Scientific reports 2016;6;20954

  • Population genomics reveals the origin and asexual evolution of human infective trypanosomes.

    Weir W, Capewell P, Foth B, Clucas C, Pountain A et al.

    eLife 2016;5;e11473

  • Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism.

    Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F et al.

    Current biology : CB 2016;26;2;161-172

  • WormBase 2016: expanding to enable helminth genomic research.

    Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ et al.

    Nucleic acids research 2016;44;D1;D774-80

  • Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax.

    Jackson AP, Goyard S, Xia D, Foth BJ, Sanders M et al.

    PLoS neglected tropical diseases 2015;9;8;e0003975

  • 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 et al.

    BMC genomics 2015;16;331

  • What helminth genomes have taught us about parasite evolution.

    Zarowiecki M and Berriman M

    Parasitology 2015;142 Suppl 1;S85-97

  • Genome-scale RNAi screens for high-throughput phenotyping in bloodstream-form African trypanosomes.

    Glover L, Alsford S, Baker N, Turner DJ, Sanchez-Flores A et al.

    Nature protocols 2015;10;1;106-33

  • TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei.

    Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B et al.

    Nucleic acids research 2015;43;Database issue;D637-44

  • Differential PfEMP1 expression is associated with cerebral malaria pathology.

    Tembo DL, Nyoni B, Murikoli RV, Mukaka M, Milner DA et al.

    PLoS pathogens 2014;10;12;e1004537

  • Optimized whole-genome amplification strategy for extremely AT-biased template.

    Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL et al.

    DNA research : an international journal for rapid publication of reports on genes and genomes 2014;21;6;661-71

  • Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum.

    Vaidya AB, Morrisey JM, Zhang Z, Das S, Daly TM et al.

    Nature communications 2014;5;5521

  • A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

    Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B et al.

    BMC biology 2014;12;86

  • Medicine. Halting harmful helminths.

    Hoffmann KF, Brindley PJ and Berriman M

    Science (New York, N.Y.) 2014;346;6206;168-9

  • Genomic analysis of the causative agents of coccidiosis in domestic chickens.

    Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP et al.

    Genome research 2014;24;10;1676-85

  • Secreted proteomes of different developmental stages of the gastrointestinal nematode Nippostrongylus brasiliensis.

    Sotillo J, Sanchez-Flores A, Cantacessi C, Harcus Y, Pickering D et al.

    Molecular & cellular proteomics : MCP 2014;13;10;2736-51

  • Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

    Otto TD, Rayner JC, Böhme U, Pain A, Spottiswoode N et al.

    Nature communications 2014;5;4754

  • 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

  • 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 et al.

    Nature genetics 2014;46;7;693-700

  • 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 et al.

    Nucleic acids research 2014;42;11;7113-31

  • 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 2014;21;3;243-54

  • 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

  • Human African trypanosomiasis research gets a boost: unraveling the tsetse genome.

    Aksoy S, Attardo G, Berriman M, Christoffels A, Lehane M et al.

    PLoS neglected tropical diseases 2014;8;4;e2624

  • A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium.

    Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C et al.

    Nature 2014;507;7491;253-257

  • A comprehensive evaluation of assembly scaffolding tools.

    Hunt M, Newbold C, Berriman M and Otto TD

    Genome biology 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 et al.

    Genome biology 2014;15;3;R43

  • 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 et al.

    PLoS biology 2014;12;3;e1001806

  • 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 et al.

    Genome biology 2014;15;11;510

  • Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population.

    Rogers MB, Downing T, Smith BA, Imamura H, Sanders M et al.

    PLoS genetics 2014;10;1;e1004092

  • WormBase 2014: new views of curated biology.

    Harris TW, Baran J, Bieri T, Cabunoc A, Chan J et al.

    Nucleic acids research 2014;42;Database issue;D789-93

  • 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 et al.

    Science (New York, N.Y.) 2013;342;6164;1385-9

  • 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 et al.

    Molecular microbiology 2013;90;3;519-37

  • 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 et al.

    Genome biology 2013;14;8;R88

  • Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.

    Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S et al.

    Nature genetics 2013;45;6;648-55

  • 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

  • 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 et al.

    International journal for parasitology 2013;43;6;465-75

  • The genomes of four tapeworm species reveal adaptations to parasitism.

    Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A et al.

    Nature 2013;496;7443;57-63

  • Efficient depletion of host DNA contamination in malaria clinical sequencing.

    Oyola SO, Gu Y, Manske M, Otto TD, O'Brien J et al.

    Journal of clinical microbiology 2013;51;3;745-51

  • Genes involved in host-parasite interactions can be revealed by their correlated expression.

    Reid AJ and Berriman M

    Nucleic acids research 2013;41;3;1508-18

  • 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

  • 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 et al.

    The Journal of infectious diseases 2012;206;5;752-5

  • Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.

    Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J et al.

    Nature 2012;487;7407;375-9

  • 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

  • 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 et al.

    BMC genomics 2012;13;125

  • Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus.

    Rinaldi G, Eckert SE, Tsai IJ, Suttiprapa S, Kines KJ et al.

    PLoS pathogens 2012;8;7;e1002820

  • 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

  • The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.

    Jackson AP, Sanders M, Berry A, McQuillan J, Aslett MA et al.

    PLoS neglected tropical diseases 2010;4;4;e658

  • New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

    Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR et al.

    Molecular microbiology 2010;76;1;12-24

  • Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans.

    Liu R, Lehane S, He X, Lehane M, Hertz-Fowler C et al.

    Cellular and molecular life sciences : CMLS 2010;67;6;919-29

  • 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

  • Plasmodium falciparum var gene expression is modified by host immunity.

    Warimwe GM, Keane TM, Fegan G, Musyoki JN, Newton CR et al.

    Proceedings of the National Academy of Sciences of the United States of America 2009;106;51;21801-6

  • Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans.

    Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D et al.

    Genome research 2009;19;12;2231-44

  • 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

  • The genome of the blood fluke Schistosoma mansoni.

    Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP et al.

    Nature 2009;460;7253;352-8

  • Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

    Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S et al.

    Nature 2009;459;7247;657-62

  • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.

    Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M and Turner DJ

    Nature methods 2009;6;4;291-5

  • DNAPlotter: circular and linear interactive genome visualization.

    Carver T, Thomson N, Bleasby A, Berriman M and Parkhill J

    Bioinformatics (Oxford, England) 2009;25;1;119-20

  • Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa).

    Jackson AP, Quail MA and Berriman M

    BMC genomics 2008;9;594

  • Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

    Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.

    Bioinformatics (Oxford, England) 2008;24;23;2672-6

  • Genetics of mating and sex determination in the parasitic nematode Haemonchus contortus.

    Redman E, Grillo V, Saunders G, Packard E, Jackson F et al.

    Genetics 2008;180;4;1877-87

  • Genomic-scale prioritization of drug targets: the TDR Targets database.

    Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS et al.

    Nature reviews. Drug discovery 2008;7;11;900-7

  • The genome of the simian and human malaria parasite Plasmodium knowlesi.

    Pain A, Böhme U, Berry AE, Mungall K, Finn RD et al.

    Nature 2008;455;7214;799-803

  • Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.

    Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP et al.

    Genome research 2008;18;2;281-92

  • Telomeric expression sites are highly conserved in Trypanosoma brucei.

    Hertz-Fowler C, Figueiredo LM, Quail MA, Becker M, Jackson A et al.

    PloS one 2008;3;10;e3527

  • 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

  • Variety is the spice of eukaryotic life.

    Berriman M and Pain A

    Nature reviews. Microbiology 2007;5;9;660-1

  • Comparative genomic analysis of three Leishmania species that cause diverse human disease.

    Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC et al.

    Nature genetics 2007;39;7;839-47

  • Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization.

    Ling KH, Rajandream MA, Rivailler P, Ivens A, Yap SJ et al.

    Genome research 2007;17;3;311-9

  • Genome variation and evolution of the malaria parasite Plasmodium falciparum.

    Jeffares DC, Pain A, Berry A, Cox AV, Stalker J et al.

    Nature genetics 2007;39;1;120-5

  • Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.

    Khan A, Böhme U, Kelly KA, Adlem E, Brooks K et al.

    Genome research 2006;16;9;1119-25

  • 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 et al.

    Proceedings of the National Academy of Sciences of the United States of America 2006;103;27;10514-10519

  • Hot and sexy moulds!

    Pain A, Böhme U and Berriman M

    Nature reviews. Microbiology 2006;4;4;244-5

  • 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

  • Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.

    Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS et al.

    Nature 2005;438;7071;1151-6

  • Plasmodium falciparum variant surface antigen expression patterns during malaria.

    Bull PC, Berriman M, Kyes S, Quail MA, Hall N et al.

    PLoS pathogens 2005;1;3;e26

  • The genome of the African trypanosome Trypanosoma brucei.

    Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H et al.

    Science (New York, N.Y.) 2005;309;5733;416-22

  • The genome of the kinetoplastid parasite, Leishmania major.

    Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G et al.

    Science (New York, N.Y.) 2005;309;5733;436-42

  • Comparative genomics of trypanosomatid parasitic protozoa.

    El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J et al.

    Science (New York, N.Y.) 2005;309;5733;404-9

  • Genome of the host-cell transforming parasite Theileria annulata compared with T. parva.

    Pain A, Renauld H, Berriman M, Murphy L, Yeats CA et al.

    Science (New York, N.Y.) 2005;309;5731;131-3

  • Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.

    Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM et al.

    Science (New York, N.Y.) 2005;309;5731;134-7

  • 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

  • The genome of the social amoeba Dictyostelium discoideum.

    Eichinger L, Pachebat JA, Glöckner G, Rajandream MA, Sucgang R et al.

    Nature 2005;435;7038;43-57

  • The genome of the protist parasite Entamoeba histolytica.

    Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J et al.

    Nature 2005;433;7028;865-8

  • A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.

    Hall N, Karras M, Raine JD, Carlton JM, Kooij TW et al.

    Science (New York, N.Y.) 2005;307;5706;82-6

  • The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism.

    Hall N, Berriman M, Lennard NJ, Harris BR, Hertz-Fowler C et al.

    Nucleic acids research 2003;31;16;4864-73

  • Viewing and annotating sequence data with Artemis.

    Berriman M and Rutherford K

    Briefings in bioinformatics 2003;4;2;124-32

  • 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 et al.

    Genome biology 2003;4;10;R63

  • Genome sequence of the human malaria parasite Plasmodium falciparum.

    Gardner MJ, Hall N, Fung E, White O, Berriman M et al.

    Nature 2002;419;6906;498-511

  • Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.

    Hall N, Pain A, Berriman M, Churcher C, Harris B et al.

    Nature 2002;419;6906;527-31

  • The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei.

    Berriman M, Hall N, Sheader K, Bringaud F, Tiwari B et al.

    Molecular and biochemical parasitology 2002;122;2;131-40