Dr Matt Berriman

Matt leads a programme in the genomics of Neglected Tropical Disease parasites, including helminths such as Schistomosomes, tapeworms, roundworms, hookworms, threadworms and whipworms.

Matt graduated in 1994 from the University of Manchester with a degree in biochemistry.

He moved to the London School of Hygiene and Tropical Medicine at the University of Dundee to undertake a PhD with Professor Alan Fairlamb, biochemically characterising a putative drug target from the malaria parasite Plasmodium falciparum. After being awarded a Wellcome Trust Travelling Prize Fellowship, Matt moved to the laboratory of Professor George Cross at Rockefeller University in New York to study Trypanosome telomeres. At the end of 2000, he joined the Wellcome Trust Sanger Institute as a Senior Computer Biologist in the Pathogen Sequencing Unit. There, he analysed and annotated the genomes of Plasmodium falciparum and Trypanosoma brucei. From 2003, Matt took over the leadership of more than 20 eukaryotic pathogen sequencing projects, primarily focused on the medically important Apicomplexan and Kinetoplastid protozoa, which include malaria parasites and trypanosomes, respectively. Matt joined the faculty in 2008 and is leading a programme in the genomics of Neglected Tropical Disease parasites, which include parasitic helminths such as Schistomosomes, tapeworms, roundworms, hookworms, threadworms and whipworms.

Selected Publications

• 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, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston S, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders G, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS and Cotton JA

  Genome biology 2013;14;8;R88

  PUBMED: 23985316; DOI: 10.1186/gb-2013-14-8-r88

• 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

  PUBMED: 23980881; DOI: 10.1111/mmi.12381

• Vector transmission regulates immune control of Plasmodium virulence.

  Spence PJ, Jarra W, Lévy P, Reid AJ, Chappell L, Brugat T, Sanders M, Berriman M and Langhorne J

  Nature 2013;498;7453;228-31

  PUBMED: 23719378; DOI: 10.1038/nature12231

• 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; DOI: 10.1186/gb-2013-14-5-r47

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

  Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai J, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernández C, Holland PW, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, Kiss F, Koziol U, Lambert O, Liu K, Luo X, Luo Y, Macchiaroli N, Nichol S, Paps J, Parkinson J, Pouchkina-Stantcheva N, Riddiford N, Rosenzvit M, Salinas G, Wasmuth JD, Zamanian M, Zheng Y, Taenia solium Genome Consortium, Cai X, Soberón X, Olson PD, Laclette JP, Brehm K and Berriman M

  Nature 2013;496;7443;57-63

  PUBMED: 23485966; DOI: 10.1038/nature12031

• 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, Swerdlow HP and Quail MA

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

  PUBMED: 23224084; PMC: 3592063; DOI: 10.1128/JCM.02507-12

• 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

  PUBMED: 23275547; PMC: 3561955; DOI: 10.1093/nar/gks1340

• 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

• 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, Ouedraogo JB, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara SM, Marsh K, Jiang H, Su XZ, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White NJ, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail MA, Turner DJ, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan JC, Ferdig MT, Amambua-Ngwa A, Conway DJ, Takala-Harrison S, Plowe CV, Rayner JC, Rockett KA, Clark TG, Newbold CI, Berriman M, MacInnis B and Kwiatkowski DP

  Nature 2012;487;7407;375-9

  PUBMED: 22722859; PMC: 3738909; DOI: 10.1038/nature11174

• 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

• 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, Davidson C, Dillon GP, Holroyd NE, LoVerde PT, Lloyd C, McQuillan J, Oliveira G, Otto TD, Parker-Manuel SJ, Quail MA, Wilson RA, Zerlotini A, Dunne DW and Berriman M

  PLoS neglected tropical diseases 2012;6;1;e1455

  PUBMED: 22253936; PMC: 3254664; DOI: 10.1371/journal.pntd.0001455

• 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, Sanders M, Shanmugam D, Sohal A, Wasmuth JD, Brunk B, Grigg ME, Howard JC, Parkinson J, Roos DS, Trees AJ, Berriman M, Pain A and Wastling JM

  PLoS pathogens 2012;8;3;e1002567

  PUBMED: 22457617; PMC: 3310773; DOI: 10.1371/journal.ppat.1002567

• 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

• 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, Quail MA, Rijal S, Sanders M, Schönian G, Stark O, Sundar S, Vanaerschot M, Hertz-Fowler C, Dujardin JC and Berriman M

  Genome research 2011;21;12;2143-56

  PUBMED: 22038251; PMC: 3227103; DOI: 10.1101/gr.123430.111

• 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

• 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

• 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, Newbold C and Llinás M

  Molecular microbiology 2010;76;1;12-24

  PUBMED: 20141604; PMC: 2859250; DOI: 10.1111/j.1365-2958.2009.07026.x

• 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

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

  Warimwe GM, Keane TM, Fegan G, Musyoki JN, Newton CR, Pain A, Berriman M, Marsh K and Bull PC

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

  PUBMED: 20018734; PMC: 2792160; DOI: 10.1073/pnas.0907590106

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

  Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D, Harris D, Aslett M, Barrell JF, Butler G, Citiulo F, Coleman DC, de Groot PW, Goodwin TJ, Quail MA, McQuillan J, Munro CA, Pain A, Poulter RT, Rajandream MA, Renauld H, Spiering MJ, Tivey A, Gow NA, Barrell B, Sullivan DJ and Berriman M

  Genome research 2009;19;12;2231-44

  PUBMED: 19745113; PMC: 2792176; DOI: 10.1101/gr.097501.109

• 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, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG and El-Sayed NM

  Nature 2009;460;7253;352-8

  PUBMED: 19606141; PMC: 2756445; DOI: 10.1038/nature08160

• 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

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

  Redman E, Grillo V, Saunders G, Packard E, Jackson F, Berriman M and Gilleard JS

  Genetics 2008;180;4;1877-87

  PUBMED: 18854587; PMC: 2600929; DOI: 10.1534/genetics.108.094623

• 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, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC and Verlinde CL

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

  PUBMED: 18927591; PMC: 3184002; DOI: 10.1038/nrd2684

• 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, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG and Berriman M

  Nature 2008;455;7214;799-803

  PUBMED: 18843368; PMC: 2656934; DOI: 10.1038/nature07306

• 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, Ivens A, Newbold C and Pain A

  Genome research 2008;18;2;281-92

  PUBMED: 18096748; PMC: 2203626; DOI: 10.1101/gr.6836108

• 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

  PUBMED: 19068121; PMC: 2621209; DOI: 10.1186/1471-2164-9-594

• 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, Heath P, Kartvelishvili M, Mungall K, Harris D, Hauser H, Sanders M, Saunders D, Seeger K, Sharp S, Taylor JE, Walker D, White B, Young R, Cross GA, Rudenko G, Barry JD, Louis EJ and Berriman M

  PloS one 2008;3;10;e3527

  PUBMED: 18953401; PMC: 2567434; DOI: 10.1371/journal.pone.0003527

• 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, Kerhornou A, Ivens A, Fraser A, Rajandream MA, Carver T, Norbertczak H, Chillingworth T, Hance Z, Jagels K, Moule S, Ormond D, Rutter S, Squares R, Whitehead S, Rabbinowitsch E, Arrowsmith C, White B, Thurston S, Bringaud F, Baldauf SL, Faulconbridge A, Jeffares D, Depledge DP, Oyola SO, Hilley JD, Brito LO, Tosi LR, Barrell B, Cruz AK, Mottram JC, Smith DF and Berriman M

  Nature genetics 2007;39;7;839-47

  PUBMED: 17572675; PMC: 2592530; DOI: 10.1038/ng2053

• 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, Kyes S, Krishna S, Newbold C, Dermitzakis ET and Berriman M

  Nature genetics 2007;39;1;120-5

  PUBMED: 17159978; PMC: 2663918; DOI: 10.1038/ng1931

• 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, Böhme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE and El-Sayed NM

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

  PUBMED: 16020726; DOI: 10.1126/science.1112642

Related links

• Helminth Genomes Initiative
• Reference helminth genomes
• Caenorhabditis genomes
• Protozoan genomes
• Global Health Research