M Berriman

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms
    Priti P Parikh
    The Kno, E, sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA
    J Biomed Semantics 3:5. 2012
  2. pmc Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS)
    Jennifer Lawton
    Division of Parasitology, MRC National Institute for Medical Research, London, UK
    BMC Genomics 13:125. 2012
  3. pmc Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
    Alessandro Guida
    School of Medicine and Medical Science, Conway Institute, UniversityCollege Dublin, Belfield, Dublin 4, Ireland
    BMC Genomics 12:628. 2011
  4. pmc Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel
    Alan D Winter
    Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK
    BMC Genomics 13:4. 2012
  5. pmc Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    Isheng J Tsai
    Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 11:R41. 2010
  6. pmc Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes
    Marco van het Hoog
    Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
    Genome Biol 8:R52. 2007
  7. pmc Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans)
    Geoffrey M Attardo
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
    BMC Genomics 11:160. 2010
  8. pmc Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa)
    Andrew P Jackson
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    BMC Genomics 9:594. 2008
  9. pmc An insight into the sialome of Glossina morsitans morsitans
    Juliana Alves-Silva
    Vector Group, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
    BMC Genomics 11:213. 2010
  10. pmc GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
    David M A Martin
    Post Genomics and Molecular Interactions Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    BMC Bioinformatics 5:178. 2004

Detail Information

Publications23

  1. pmc The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms
    Priti P Parikh
    The Kno, E, sis Center, Department of Computer Science and Engineering, Wright State University, Dayton, OH, USA
    J Biomed Semantics 3:5. 2012
    ..abstract:..
  2. pmc Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS)
    Jennifer Lawton
    Division of Parasitology, MRC National Institute for Medical Research, London, UK
    BMC Genomics 13:125. 2012
    ..In order to fully understand the role(s) of CIR proteins during P. chabaudi infection, a detailed characterization of the cir gene family was required...
  3. pmc Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
    Alessandro Guida
    School of Medicine and Medical Science, Conway Institute, UniversityCollege Dublin, Belfield, Dublin 4, Ireland
    BMC Genomics 12:628. 2011
    ..The transcriptional response of C. parapsilosis to hypoxic (low oxygen) conditions, such as those encountered in the host, is also relatively unexplored...
  4. pmc Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel
    Alan D Winter
    Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences University of Glasgow, Garscube Estate, Bearsden Road, Glasgow, G61 1QH, UK
    BMC Genomics 13:4. 2012
    ..Here we describe the the miRNA repertoire of two important parasitic nematodes as an essential first step in addressing this question...
  5. pmc Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    Isheng J Tsai
    Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 11:R41. 2010
    ..The continuity of a draft genome can thus be substantially improved, often without the need to generate new data...
  6. pmc Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes
    Marco van het Hoog
    Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
    Genome Biol 8:R52. 2007
    ..However, sequences of specific chromosomes were not determined...
  7. pmc Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans)
    Geoffrey M Attardo
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
    BMC Genomics 11:160. 2010
    ..3438 expressed sequence tags were sequenced and analyzed...
  8. pmc Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa)
    Andrew P Jackson
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    BMC Genomics 9:594. 2008
    ..Various coding regions were sequenced to provide a preliminary insight into the bodonid genome sequence, relative to trypanosomatid sequences...
  9. pmc An insight into the sialome of Glossina morsitans morsitans
    Juliana Alves-Silva
    Vector Group, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
    BMC Genomics 11:213. 2010
    ..Adult tsetse flies feed exclusively on vertebrate blood and are important vectors of human and animal diseases. Thus far, only limited information exists regarding the Glossina sialome, or any other fly belonging to the Hippoboscidae...
  10. pmc GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
    David M A Martin
    Post Genomics and Molecular Interactions Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
    BMC Bioinformatics 5:178. 2004
    ..GOtcha predicts GO term associations with term-specific probability (P-score) measures of confidence. Term-specific probabilities are a novel feature of GOtcha and allow the identification of conflicts or uncertainty in annotation...
  11. ncbi request reprint Viewing and annotating sequence data with Artemis
    Matt Berriman
    The Wellcome Trust Sanger Institute, Genome Campus, Hinxton CB10 1SA, UK
    Brief Bioinform 4:124-32. 2003
    ....
  12. ncbi request reprint The genome of the African trypanosome Trypanosoma brucei
    Matthew Berriman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Science 309:416-22. 2005
    ..brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified...
  13. ncbi request reprint Data mining parasite genomes
    M Berriman
    Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, CB10 ISA, UK
    Parasitology 128:S23-31. 2004
    ..If these roles are accurately reflected in genome annotation, they can be used by researchers to frame queries and interrogate the data further...
  14. pmc The genome of the blood fluke Schistosoma mansoni
    Matthew Berriman
    Wellcome Trust Sanger Institute, Cambridge CB10 1SD, UK
    Nature 460:352-8. 2009
    ..The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease...
  15. pmc The genome of the simian and human malaria parasite Plasmodium knowlesi
    A Pain
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nature 455:799-803. 2008
    ..One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry...
  16. ncbi request reprint Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13
    N Hall
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 419:527-31. 2002
    ..We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts...
  17. pmc The Gene Ontology (GO) database and informatics resource
    M A Harris
    GO EBI, Hinxton, UK
    Nucleic Acids Res 32:D258-61. 2004
    ..The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses...
  18. pmc Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum
    Tobias Mourier
    Ancient DNA and Evolution Group, Department of Biology, University of Copenhagen, Copenhagen DK 2100, Denmark
    Genome Res 18:281-92. 2008
    ..reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism's life cycle...
  19. pmc Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii
    Asis Khan
    Department of Molecular Microbiology, Center for Infectious Diseases, Washington University School of Medicine St Louis, MO 63110, USA
    Nucleic Acids Res 33:2980-92. 2005
    ..The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies...
  20. ncbi request reprint Continuing tsetse and Trypanosoma genome sequencing projects
    Christiane Hertz-Fowler
    Trends Parasitol 20:308-9; author reply 309-10. 2004
  21. ncbi request reprint A case for a Glossina genome project
    Serap Aksoy
    Yale University School of Medicine, 60 College Street, 606 LEPH, New Haven, CT 06520, USA
    Trends Parasitol 21:107-11. 2005
    ..An international consortium is now in place to further efforts to lead to a full genome project...
  22. ncbi request reprint The genome of the protist parasite Entamoeba histolytica
    Brendan Loftus
    TIGR, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nature 433:865-8. 2005
    ..Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen...
  23. ncbi request reprint Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes
    Daniel E Neafsey
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Mol Biol Evol 22:1621-6. 2005
    ..Divergence rates of different classes of silent sites in these Plasmodium genomes are determined by a combination of mutational and selective pressures...