Sanger Institute, Genome Research Limited


Berriman, Matt
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.

Key Projects, Collaborations, Tools & Data

Some of our main projects include the following efforts:

Research Programmes

Partners and Funders

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


  • 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, Sanchez-Flores A et al.

    Nature 2013;496;7443;57-63

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

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

    Nucleic acids research 2015

  • WormBase 2016: expanding to enable helminth genomic research.

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

    Nucleic acids research 2015

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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;253-7

  • 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

  • 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

  • A comprehensive evaluation of assembly scaffolding tools.

    Hunt M, Newbold C, Berriman M and Otto TD

    Genome biology 2014;15;3;R42

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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, Sanchez-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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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 JP, Ajioka JW, Berriman M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2006;103;27;10514-9

  • 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

  • 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 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

  • 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