David Vallenet

Summary

Country: France

Publications

  1. pmc MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
    David Vallenet
    CEA, Institut de Génomique, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Nucleic Acids Res 41:D636-47. 2013
  2. pmc MaGe: a microbial genome annotation system supported by synteny results
    David Vallenet
    Atelier de Génomique Comparative, CNRS UMR8030, 2 rue Gaston Cremieux, 91057 Evry, Cedex, France
    Nucleic Acids Res 34:53-65. 2006
  3. pmc Comparative analysis of Acinetobacters: three genomes for three lifestyles
    David Vallenet
    Génomique Métabolique, CNRS UMR8030, CEA Institut de Génomique Genoscope, Evry, France
    PLoS ONE 3:e1805. 2008
  4. pmc NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis
    Christophe Rusniok
    Génomique des Microorganismes Pathogènes, Institut Pasteur, rue du Dr Roux, Paris 75015, France
    Genome Biol 10:R110. 2009
  5. pmc MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes
    Stephane Cruveiller
    Génoscope UMR CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Cremieux, F 91006 Evry, France
    Nucleic Acids Res 33:W471-9. 2005
  6. pmc A novel acyl-CoA beta-transaminase characterized from a metagenome
    Alain Perret
    Commissariat à l Énergie Atomique et aux Énergies Alternatives, Institut de Génomique, Genoscope, Evry, France
    PLoS ONE 6:e22918. 2011
  7. pmc Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
    Maxime Durot
    Genoscope Commissariat à l Energie Atomique and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, CP5706, 91057 Evry, Cedex, France
    BMC Syst Biol 2:85. 2008
  8. pmc From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later
    Valerie Barbe
    CEA, Institut de Génomique, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Microbiology 155:1758-75. 2009
  9. doi request reprint An updated metabolic view of the Bacillus subtilis 168 genome
    Eugeni Belda
    CEA, Institut de Génomique, Génoscope Laboratoire d Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Cremieux, Evry, France
    Microbiology 159:757-70. 2013
  10. pmc A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine
    Nuria Fonknechten
    CEA, DSV, IG, Genoscope, 2 rue Gaston Cremieux, Evry F 91057, France
    J Bacteriol 191:3162-7. 2009

Collaborators

Detail Information

Publications19

  1. pmc MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
    David Vallenet
    CEA, Institut de Génomique, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Nucleic Acids Res 41:D636-47. 2013
    ..An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest...
  2. pmc MaGe: a microbial genome annotation system supported by synteny results
    David Vallenet
    Atelier de Génomique Comparative, CNRS UMR8030, 2 rue Gaston Cremieux, 91057 Evry, Cedex, France
    Nucleic Acids Res 34:53-65. 2006
    ..In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage...
  3. pmc Comparative analysis of Acinetobacters: three genomes for three lifestyles
    David Vallenet
    Génomique Métabolique, CNRS UMR8030, CEA Institut de Génomique Genoscope, Evry, France
    PLoS ONE 3:e1805. 2008
    ..Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil...
  4. pmc NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis
    Christophe Rusniok
    Génomique des Microorganismes Pathogènes, Institut Pasteur, rue du Dr Roux, Paris 75015, France
    Genome Biol 10:R110. 2009
    ..This holds true for Neisseria meningitidis, one of the most feared human bacterial pathogens that causes meningitis and septicemia...
  5. pmc MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes
    Stephane Cruveiller
    Génoscope UMR CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Cremieux, F 91006 Evry, France
    Nucleic Acids Res 33:W471-9. 2005
    ..The MICheck website is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/micheck...
  6. pmc A novel acyl-CoA beta-transaminase characterized from a metagenome
    Alain Perret
    Commissariat à l Énergie Atomique et aux Énergies Alternatives, Institut de Génomique, Genoscope, Evry, France
    PLoS ONE 6:e22918. 2011
    ..To access new enzymatic reactions and new or alternative pathways, we investigated bacterial metabolism through analyses of uncultivated bacterial consortia...
  7. pmc Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
    Maxime Durot
    Genoscope Commissariat à l Energie Atomique and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, CP5706, 91057 Evry, Cedex, France
    BMC Syst Biol 2:85. 2008
    ..They provide a way to integrate various types of biological information in a single framework, providing a structured representation of available knowledge on the metabolism of the respective species...
  8. pmc From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later
    Valerie Barbe
    CEA, Institut de Génomique, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Microbiology 155:1758-75. 2009
    ..subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies...
  9. doi request reprint An updated metabolic view of the Bacillus subtilis 168 genome
    Eugeni Belda
    CEA, Institut de Génomique, Génoscope Laboratoire d Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Cremieux, Evry, France
    Microbiology 159:757-70. 2013
    ..ebi.ac.uk/chebi/). The newly annotated sequence is deposited at the International Nucleotide Sequence Data Collaboration with accession number AL009126.4...
  10. pmc A conserved gene cluster rules anaerobic oxidative degradation of L-ornithine
    Nuria Fonknechten
    CEA, DSV, IG, Genoscope, 2 rue Gaston Cremieux, Evry F 91057, France
    J Bacteriol 191:3162-7. 2009
    ..They encode L-ornithine racemase, (2R,4S)-2,4-diaminopentanoate dehydrogenase, and the two subunits of 2-amino-4-ketopentanoate thiolase. While described only for the Clostridiaceae to date, this pathway is shown to be more widespread...
  11. pmc Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
    Valerie Barbe
    Genoscope and CNRS UMR8030, 2 rue Gaston Cremieux, 91057 Evry, Cedex, France
    Nucleic Acids Res 32:5766-79. 2004
    ..This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism...
  12. pmc AMIGene: Annotation of MIcrobial Genes
    Stephanie Bocs
    Génoscope UMR CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Cremieux, F 91006 Evry, France
    Nucleic Acids Res 31:3723-6. 2003
    ..The AMIGene web site is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/amigene/index.html (Contact: sbocs@genoscope.cns.fr)...
  13. pmc Core and panmetabolism in Escherichia coli
    Gilles Vieira
    CNRS UMR 8030, Université d Evry, CEA, IG, Genoscope, F 91057 Evry Cedex, France
    J Bacteriol 193:1461-72. 2011
    ..Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models...
  14. doi request reprint Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
    Stefan Engelen
    AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Cremieux, 91000 Evry, France
    BMC Genomics 13:69. 2012
    ..Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase...
  15. pmc The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes
    Adam Alexander Thil Smith
    CEA DSV IG, Genoscope, Evry, France
    PLoS Comput Biol 8:e1002540. 2012
    ..A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12...
  16. pmc Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
    Claudine Medigue
    Genoscope, CNRS UMR 8030, Atelier de Génomique Comparative, 91006 Evry Cedex, France
    Genome Res 15:1325-35. 2005
    ..Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome...
  17. ncbi request reprint Identification of the last unknown genes in the fermentation pathway of lysine
    Annett Kreimeyer
    CNRS UMR 8030, Genoscope, 91057 Evry Cedex, France
    J Biol Chem 282:7191-7. 2007
    ..We identified twelve bacteria that possess these genes and thus are expected to ferment lysine, and their gene organization is discussed...
  18. pmc Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites
    Valerie Barbe
    CEA, DSV, IG, Genoscope, 2 rue Gaston Cremieux, CP5706, F 91057 Evry Cedex, France
    J Bacteriol 193:5055-6. 2011
    ..The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons...
  19. pmc A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1
    Veronique De Berardinis
    Genoscope, Institut de Génomique CEA, Evry, France
    Mol Syst Biol 4:174. 2008
    ..This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches...