Matthew Berriman

Matthew Berriman

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Matthew Berriman

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Progression of the canonical reference malaria parasite genome from 2002-2019.

Wellcome Open Res 2019 28;4:58. Epub 2019 May 28.

Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.15194.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484455.2PMC
May 2019

Using WormBase ParaSite: An Integrated Platform for Exploring Helminth Genomic Data.

Methods Mol Biol 2018 ;1757:471-491

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-4939-7737-6_15DOI Listing
January 2019

Eradication genomics-lessons for parasite control.

Science 2018 07 12;361(6398):130-131. Epub 2018 Jul 12.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1126/science.aar6609DOI Listing
July 2018

Transcriptomic profiling of nematode parasites surviving vaccine exposure.

Int J Parasitol 2018 04 10;48(5):395-402. Epub 2018 Mar 10.

Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow, United Kingdom.

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http://dx.doi.org/10.1016/j.ijpara.2018.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909036PMC
April 2018

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

Int J Parasitol 2018 02 27;48(2):159-165. Epub 2017 Oct 27.

Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ijpara.2017.08.010DOI Listing
February 2018

Gene Expression in Is Regulated Predominantly by Gene Dosage.

MBio 2017 09 12;8(5). Epub 2017 Sep 12.

Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA

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http://dx.doi.org/10.1128/mBio.01393-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596349PMC
September 2017

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

Sci Data 2017 08 22;4:170118. Epub 2017 Aug 22.

BFS, Institute of Parasitology, Justus Liebig University, 35392 Giessen, Germany.

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http://dx.doi.org/10.1038/sdata.2017.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566097PMC
August 2017

WormBase ParaSite - a comprehensive resource for helminth genomics.

Mol Biochem Parasitol 2017 07 27;215:2-10. Epub 2016 Nov 27.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1016/j.molbiopara.2016.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5486357PMC
July 2017

Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca channel in neuromuscular function and regeneration.

Biochim Biophys Acta Mol Cell Res 2017 Jun 19;1864(6):1036-1045. Epub 2016 Oct 19.

Department of Pharmacology, University of Minnesota Medical School, MN 55455, United States; The Stem Cell Institute, University of Minnesota Medical School, MN 55455, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01674889163026
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http://dx.doi.org/10.1016/j.bbamcr.2016.10.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397384PMC
June 2017

Dataset for a de novo transcriptome assembly, utilized for defining the voltage-gated like ion channel superfamily.

Data Brief 2016 Dec 16;9:1044-1047. Epub 2016 Nov 16.

Department of Pharmacology, University of Minnesota Medical School, MN 55455, USA; The Stem Cell Institute, University of Minnesota Medical School, MN 55455, USA.

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http://dx.doi.org/10.1016/j.dib.2016.11.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124351PMC
December 2016

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

PLoS Pathog 2016 Nov 3;12(11):e1005971. Epub 2016 Nov 3.

Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1005971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094698PMC
November 2016

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

PLoS Pathog 2016 Oct 20;12(10):e1005931. Epub 2016 Oct 20.

Department of Microbiology, Immunology & Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1005931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072744PMC
October 2016

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

Nucleic Acids Res 2016 07 21;44(W1):W29-34. Epub 2016 Apr 21.

Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkw292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987884PMC
July 2016

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

PLoS Negl Trop Dis 2015 12;9(8):e0003975. Epub 2015 Aug 12.

Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pntd.0003975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534299PMC
April 2016

Nitroheterocyclic drug resistance mechanisms in Trypanosoma brucei.

J Antimicrob Chemother 2016 Mar 17;71(3):625-34. Epub 2015 Nov 17.

Division of Biological Chemistry and Drug Discovery, Wellcome Trust Building, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK

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http://jac.oxfordjournals.org/content/early/2015/11/17/jac.d
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http://www.jac.oxfordjournals.org/lookup/doi/10.1093/jac/dkv
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http://dx.doi.org/10.1093/jac/dkv376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743696PMC
March 2016

Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome.

PLoS Negl Trop Dis 2015 Dec 18;9(12):e0004299. Epub 2015 Dec 18.

School of Life Sciences, University of Dundee, Dundee, United Kingdom.

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http://dx.doi.org/10.1371/journal.pntd.0004299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689576PMC
December 2015

A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites.

BMC Genomics 2015 Apr 22;16:331. Epub 2015 Apr 22.

Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK.

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http://dx.doi.org/10.1186/s12864-015-1536-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428239PMC
April 2015

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

Nat Protoc 2015 Jan 11;10(1):106-33. Epub 2014 Dec 11.

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK.

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http://dx.doi.org/10.1038/nprot.2015.005DOI Listing
January 2015

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

DNA Res 2014 Dec 19;21(6):661-71. Epub 2014 Sep 19.

Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

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http://dx.doi.org/10.1093/dnares/dsu028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263299PMC
December 2014

Differential PfEMP1 expression is associated with cerebral malaria pathology.

PLoS Pathog 2014 Dec 4;10(12):e1004537. Epub 2014 Dec 4.

Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi; Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1004537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256257PMC
December 2014

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

Mol Cell Proteomics 2014 Oct 3;13(10):2736-51. Epub 2014 Jul 3.

From the ‡Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia;

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http://dx.doi.org/10.1074/mcp.M114.038950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4188999PMC
October 2014

Medicine. Halting harmful helminths.

Science 2014 Oct;346(6206):168-9

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1126/science.1261139DOI Listing
October 2014

International glossina genome initiative 2004-2014: a driver for post-genomic era research on the African continent.

PLoS Negl Trop Dis 2014 Aug 21;8(8):e3024. Epub 2014 Aug 21.

Yale School of Public Health, Department of Epidemiology and Public Health, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0003024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4140670PMC
August 2014

Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.

DNA Res 2014 Jun 18;21(3):243-54. Epub 2013 Dec 18.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK Faculty of Medicine, Division of Parasitology, Department of Infectious Disease, University of Miyazaki, Miyazaki 889-1692, Japan

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http://dx.doi.org/10.1093/dnares/dst054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060946PMC
June 2014

WormBase 2014: new views of curated biology.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D789-93. Epub 2013 Nov 4.

Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada, Genome Sequencing Center, Washington University, School of Medicine, St Louis, MO 63108, USA, Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, CA 91125, USA, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Department of Genetics Campus, Washington University School of Medicine, St. Louis, MO 63110, USA, Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/nar/gkt1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965043PMC
January 2014

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

PLoS Genet 2014 Jan 16;10(1):e1004092. Epub 2014 Jan 16.

Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894156PMC
January 2014

Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation.

Mol Microbiol 2013 Nov 30;90(3):519-37. Epub 2013 Sep 30.

Weatherall Institute of Molecular Medicine, Headington, Oxford, OX3 9DS, UK; National Institute of Allergy and Infectious Disease, NIH, Rockville, MD, 20892, USA.

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http://dx.doi.org/10.1111/mmi.12381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894959PMC
November 2013

Comparative study of transcriptome profiles of mechanical- and skin-transformed Schistosoma mansoni schistosomula.

PLoS Negl Trop Dis 2013 14;7(3):e2091. Epub 2013 Mar 14.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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http://dx.doi.org/10.1371/journal.pntd.0002091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597483PMC
August 2013

A cell-surface phylome for African trypanosomes.

PLoS Negl Trop Dis 2013 21;7(3):e2121. Epub 2013 Mar 21.

Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England, United Kingdom.

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http://dx.doi.org/10.1371/journal.pntd.0002121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605285PMC
August 2013

Vector transmission regulates immune control of Plasmodium virulence.

Nature 2013 Jun 29;498(7453):228-31. Epub 2013 May 29.

Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1038/nature12231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784817PMC
June 2013

BamView: visualizing and interpretation of next-generation sequencing read alignments.

Brief Bioinform 2013 Mar 16;14(2):203-12. Epub 2012 Jan 16.

Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/bib/bbr073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603209PMC
March 2013

RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

PLoS Negl Trop Dis 2012 25;6(10):e1854. Epub 2012 Oct 25.

Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America.

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https://dx.plos.org/10.1371/journal.pntd.0001854
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http://dx.doi.org/10.1371/journal.pntd.0001854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493385PMC
March 2013

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

Nucleic Acids Res 2013 Feb 28;41(3):1508-18. Epub 2012 Dec 28.

Parasite genomics group, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gks1340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561955PMC
February 2013

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

PLoS Pathog 2012 26;8(7):e1002820. Epub 2012 Jul 26.

Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1002820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406096PMC
January 2013

SchistoDB: an updated genome resource for the three key schistosomes of humans.

Nucleic Acids Res 2013 Jan 17;41(Database issue):D728-31. Epub 2012 Nov 17.

Centro de Excelência em Bioinformática, National Institute for Science and Technology in Tropical Diseases FIOCRUZ-Minas, Belo Horizonte, MG 30190-002, Brazil.

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http://dx.doi.org/10.1093/nar/gks1087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531198PMC
January 2013

Silencing of germline-expressed genes by DNA elimination in somatic cells.

Dev Cell 2012 Nov 1;23(5):1072-80. Epub 2012 Nov 1.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.devcel.2012.09.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3620533PMC
November 2012

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Nat Protoc 2012 Jun 7;7(7):1260-84. Epub 2012 Jun 7.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/nprot.2012.068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648784PMC
June 2012

High-throughput decoding of antitrypanosomal drug efficacy and resistance.

Nature 2012 Jan 25;482(7384):232-6. Epub 2012 Jan 25.

London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.

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http://dx.doi.org/10.1038/nature10771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303116PMC
January 2012