David Sherman

Summary

Affiliation: Laboratoire Bordelais de Recherche en Informatique
Country: France

Publications

  1. pmc Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
    David Sherman
    LaBRI, Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800, 351 Cours de la Liberation, 33405 Talence Cedex, France
    Nucleic Acids Res 32:D315-8. 2004
  2. pmc Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts
    David Sherman
    LaBRI, Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800, 351 Cours de la Liberation, 33405 Talence Cedex, France
    Nucleic Acids Res 34:D432-5. 2006
  3. pmc Fusion and fission of genes define a metric between fungal genomes
    Pascal Durrens
    MAGNOME Team, INRIA Centre de Recherche Bordeaux Sud Ouest, Laboratoire Bordelais de Recherche en Informatique, UMR 5800 CNRS, Domaine Universitaire, Talence Cedex, France
    PLoS Comput Biol 4:e1000200. 2008
  4. ncbi request reprint ProViz: protein interaction visualization and exploration
    Florian Iragne
    LaBRI UMR 5800, Université Bordeaux 1 351 cours de la Libération, 33405 Talence Cedex, France
    Bioinformatics 21:272-4. 2005
  5. ncbi request reprint Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts
    Florian Iragne
    LaBRI Université Bordeaux 1, France
    FEMS Yeast Res 8:132-9. 2008
  6. pmc Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
  7. pmc New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
    Roland Barriot
    Centre de Bioinformatique de Bordeaux, Université V Segalen Bordeaux 2, 146 rue Leo Saignat, 33076 Bordeaux, France
    Nucleic Acids Res 32:3581-9. 2004
  8. ncbi request reprint Genome evolution in yeasts
    Bernard Dujon
    Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
    Nature 430:35-44. 2004
  9. ncbi request reprint Common interchange standards for proteomics data: Public availability of tools and schema
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 4:490-1. 2004
  10. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004

Collaborators

Detail Information

Publications12

  1. pmc Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
    David Sherman
    LaBRI, Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800, 351 Cours de la Liberation, 33405 Talence Cedex, France
    Nucleic Acids Res 32:D315-8. 2004
    ..The Génolevures site includes a community area for specific studies by members of the international community...
  2. pmc Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts
    David Sherman
    LaBRI, Laboratoire Bordelais de Recherche en Informatique, UMR CNRS 5800, 351 Cours de la Liberation, 33405 Talence Cedex, France
    Nucleic Acids Res 34:D432-5. 2006
    ..The Génolevures site includes an area for specific studies by members of its international community...
  3. pmc Fusion and fission of genes define a metric between fungal genomes
    Pascal Durrens
    MAGNOME Team, INRIA Centre de Recherche Bordeaux Sud Ouest, Laboratoire Bordelais de Recherche en Informatique, UMR 5800 CNRS, Domaine Universitaire, Talence Cedex, France
    PLoS Comput Biol 4:e1000200. 2008
    ..The event localization counts for all the segments of the tree provide a metric that depicts the "recombinational" phylogeny among fungi. A possible interpretation of this metric as distance in adaptation space is proposed...
  4. ncbi request reprint ProViz: protein interaction visualization and exploration
    Florian Iragne
    LaBRI UMR 5800, Université Bordeaux 1 351 cours de la Libération, 33405 Talence Cedex, France
    Bioinformatics 21:272-4. 2005
    ..It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI...
  5. ncbi request reprint Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts
    Florian Iragne
    LaBRI Université Bordeaux 1, France
    FEMS Yeast Res 8:132-9. 2008
    ..In 60-80% of our results, further analysis is not required to determine whether the pathway is lost or conserved, so that our method can be systematically applied as a first step in developing species-specific models...
  6. pmc Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
    ....
  7. pmc New strategy for the representation and the integration of biomolecular knowledge at a cellular scale
    Roland Barriot
    Centre de Bioinformatique de Bordeaux, Université V Segalen Bordeaux 2, 146 rue Leo Saignat, 33076 Bordeaux, France
    Nucleic Acids Res 32:3581-9. 2004
    ..It was also used to retrieve the members of a complex (ribosome) based on the mining of expression profiles. These first results validate the relevance of the strategy and demonstrate the promising potential of BlastSets...
  8. ncbi request reprint Genome evolution in yeasts
    Bernard Dujon
    Unité de Génétique Moléculaire des Levures, URA 2171 CNRS and UFR 927 Université Pierre et Marie Curie
    Nature 430:35-44. 2004
    ....
  9. ncbi request reprint Common interchange standards for proteomics data: Public availability of tools and schema
    Sandra Orchard
    EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Proteomics 4:490-1. 2004
    ..A draft XML interchange format for mass spectrometry data has been written and is currently undergoing evaluation whilst work is ongoing to develop a proteomics data integration model, MIAPE...
  10. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  11. pmc IntAct: an open source molecular interaction database
    Henning Hermjakob
    European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D452-5. 2004
    ..All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact...
  12. ncbi request reprint Novel transporters from hemiascomycete yeasts
    Benoît De Hertogh
    Unité de Génétique GENA, Universite Catholique de Louvain, Louvain la Neuve, Belgique
    J Mol Microbiol Biotechnol 6:19-28. 2003
    ..Integr. Genomics 2002;2:154-170; http://cbi.labri.u-bordeaux.fr/Genolevures]. These novel hemiascomycete transporters comprise 3 channels, 23 secondary transporters, 5 primary transporters and 5 membrane proteins of unknown function...