Publications of AGC

• Bertin PN, Médigue C, Normand P (2008)
  Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems..
  Microbiology. 2008 Feb;154(Pt 2):347-59..

• Pelletier E, Kreimeyer A, Bocs S, Rouy Z, Gyapay G, Chouari R, Rivière D, Ganesan A, Daegelen P, Sghir A, Cohen GN, Médigue C, Weissenbach J, Le Paslier D (2008)
  “Candidatus Cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division..
  J Bacteriol. 2008 Apr;190(7):2572-9. Epub 2008 Feb 1..

• Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, Bataille E, Dossat C, Gas S, Kreimeyer A, Lenoble P, Oztas S, Poulain J, Segurens B, Robert C, Abergel C, Claverie JM, Raoult D, Médigue C, Weissenbach J, Cruveiller S (2008)
  Comparative analysis of Acinetobacters: three genomes for three lifestyles. .
  PLoS ONE. 2008 Mar 19;3(3):e1805..

• Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, Creno S, Kuczek ES, Bommezzadri S, Davis JC, McGrath A, Johnson MJ, Boursaux-Eude C, Seemann T, Rouy Z, Coppel RL, Rood JI, Lajus A, Davies JK, Médigue C, Adler B (2008)
  Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis..
  PLoS ONE. 2008 Feb 13;3(2):e1607..

• de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, Samair S, Lechaplais C, Gyapay G, Richez C, Durot M, Kreimeyer A, Le Fèvre F, Schächter V, Pezo V, Döring V, Scarpelli C, Médigue C, Cohen GN, Marlière P, Salanoubat M, Weissenbach J (2008)
  A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1..
  Mol Syst Biol. 2008;4:174. Epub 2008 Mar 4..

2007

• Médigue C, Moszer I. (2007)
  Annotation, comparison and databases for hundreds of bacterial genomes..
  Res Microbiol. 2007 Dec;158(10):724-36. Epub 2007 Oct 6. Review..

• Plainvert C, Bidet P, Peigne C, Barbe V, Médigue C, Denamur E, Bingen E, Bonacorsi S (2007)
  A new O-antigen gene cluster has a key role in the virulence of the Escherichia coli meningitis clone O45:K1:H7..
  J Bacteriol. 2007 Dec;189(23):8528-36. Epub 2007 Sep 28..

• Chauvaux S, Rosso ML, Frangeul L, Lacroix C, Labarre L, Schiavo A, Marceau M, Dillies MA, Foulon J, Coppée JY, Médigue C, Simonet M, Carniel E (2007)
  Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague..
  Microbiology. 2007 Sep;153(Pt 9):3112-24..

• Giraud E, Moulin L, Vallenet D, Barbe V, Cytryn E, Avarre JC, Jaubert M, Simon D, Cartieaux F, Prin Y, Bena G, Hannibal L, Fardoux J, Kojadinovic M, Vuillet L, Lajus A, Cruveiller S, Rouy Z, Mangenot S, Segurens B, Dossat C, Franck WL, Chang WS, Saunders E, Bruce D, Richardson P, Normand P, Dreyfus B, Pignol D, Stacey G, Emerich D, Verméglio A, Médigue C, Sadowsky M (2007)
  Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia..
  Science. 2007 Jun 1;316(5829):1307-12..

• Muller D, Médigue C, Koechler S, Barbe V, Barakat M, Talla E, Bonnefoy V, Krin E, Arsène-Ploetze F, Carapito C, Chandler M, Cournoyer B, Cruveiller S, Dossat C, Duval S, Heymann M, Leize E, Lieutaud A, Lièvremont D, Makita Y, Mangenot S, Nitschke W, Ortet P, Perdrial N, Schoepp B, Siguier P, Simeonova DD, Rouy Z, Segurens B, Turlin E, Vallenet D, Van Dorsselaer A, Weiss S, Weissenbach J, Lett MC, Danchin A, Bertin PN. (2007)
  A tale of two oxidation states: bacterial colonization of arsenic-rich environments. .
  PLoS Genet. 2007 Apr 13;3(4):e53. Epub 2007 Mar 5..

• Kreimeyer A, Perret A, Lechaplais C, Vallenet D, Médigue C, Salanoubat M, Weissenbach J. (2007)
  Identification of the last unknown genes in the fermentation pathway of lysine..
  J Biol Chem. 2007 Mar 9;282(10):7191-7. Epub 2006 Dec 13..

• Bourhy P, Salaün L, Lajus A, Médigue C, Boursaux-Eude C, Picardeau M (2007)
  A genomic island of the pathogen Leptospira interrogans serovar Lai can excise from its chromosome..
  Infect Immun. 2007 Feb;75(2):677-83. Epub 2006 Nov 21..

• Derbise A, Chenal-Francisque V, Pouillot F, Fayolle C, Prévost MC, Médigue C, Hinnebusch BJ, Carniel E (2007)
  A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus.
  Mol Microbiol. 2007 Feb;63(4):1145-57..

• Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR. (2007)
  Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
  Genome Res. 2007 Jan;17(1):7-15. Epub 2006 Dec 6.

2006

• Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Medigue C.
  MaGe - a microbial genome annotation system supported by synteny results.
  Nucleic Acids Res. 2006 Jan 10;34(1):53-65. Print 2006.

• Durand P, Labarre L, Meil A, Divol JL, Vandenbrouck Y, Viari A, Wojcik J. (2006)
  GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins.
  BMC Bioinformatics. 17;7(1):21.

• Labarre L., Vallenet D., Bruley S., Morgat A., Viari A. and Médigue C.
  Syntonizer: an interactive Web tool for identifying bacterial synteny group using multiple correspondences.
  (en préparation).

• Louvel H., Bommezzadri S., Zidane Z., Boursaux-Eude C., Creno S., Magnier A., Rouy Z., Médigue C., Saint Girons I., Bouchier C., and Picardeau M. (2006)
  Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp..
  J Bacteriol. 2006 Nov;188(22):7893-904. Epub 2006 Sep 15..

• Siroy A, Cosette P, Seyer D, Lemaître-Guillier C, Vallenet D, Van Dorsselaer A, Boyer-Mariotte S, Jouenne T, Dé E (2006)
  Global comparison of the membrane subproteomes between a multidrug-resistant Acinetobacter baumannii strain and a reference strain..
  J Proteome Res. 2006 Dec;5(12):3385-98..

• Strous M., Pelletier E, Mangenot S., Rattei R., Lehner A., Taylor M.W, Horn M., Daims H., Bartol-Mavel D., Wincker P., Barbe V., Fonknechten N., Vallenet D., Segurens B., Schenowitz-Truong C., Médigue C., Collingro A., Snel B., Dutilh B.E, Op den Camp H.J.M, van der Drift C., Cirpus I., van de Pas-Schoonen K.T, Harhangi H.R, van Niftrik L., Schmid M., Keltjens J., van de Vossenberg J., Kartal B., Frishman D., Huynen M.A, Mewes H.W, Weissenbach J., Jetten M.S.M., Wagner M., and Le Paslier D.(2006)
  Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
  Nature 440, 790-794 (6 April 2006).

• Vodovar N., Vallenet D., Cruveiller S., Rouy Z., Barbe V., Acosta C. Cattolico L., Jubin C., Lajus A., Segurens B., Vacherie B., Wincker P., Weissenbach J., Lemaitre B., Médigue C. and Boccard F. (2006)
  Complete genome sequence of the entomopathogen and metabolically versatile soil bacterium Pseudomonas entomophila.
  Nature Biotechnology (14 May 2006).

• Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, Poirel L, Richet H, Robert C, Mangenot S, Abergel C, Nordmann P, Weissenbach J, Raoult D, Claverie JM (2006)
  Comparative Genomics of Multidrug Resistance in Acinetobacter baumannii.
  PLoS Genet. 13;2(1):e7.

2005

• Cruveiller, S., J., Le Saux, D., Vallenet, A., Lajus, S. Bocs And Médigue C. (2005)
  MICheck: A web tool for fast check of syntactic annotations of bacterial genomes.
  Nucleic Acids Res. 2005 Jul 1;33 (Web Server issue):W471-9.

• Boyer F, Morgat A, Labarre L, Pothier J, and Viari A. (2005)
  Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data.
  Bioinformatics. 21: 4209-15.

• Médigue C (2005)
  L’annotation des génomes procaryotes.
  Biofutur, 251, 23-27

• Médigue C., E. Krin, G. Pascal, V. Barbe, A. Bernsel, PN. Bertin, F. Cheung, S. Cruveiller, S.D’Amico, A. Duilio, G.Fang, G. Feller, C. Ho , S. Mangenot, G. Marino, J. Nilsson, E. Parilli, E. P.C. Rocha, Z. Rouy, A. Sekowska, M.L. Tutino, D. Vallenet, G. von Heijne, and A. Danchin.
  Coping with the cold : the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125 .
  Genome Research. 2005 Oct;15(10):1325-35. Epub 2005 Sep 16.

• Pascal G, Medigue C, Danchin A.
  Universal biases in protein composition of model prokaryotes.
  Proteins. 2005 Jul 1;60(1):27-35.

• Siroy A, Molle V, Lemaitre-Guillier C, Vallenet D, Pestel-Caron M, Cozzone AJ, Jouenne T, De E. (2005)
  Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii.
  Antimicrob Agents Chemother. 49:4876-83.

2004

• Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Médigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E.(2004)
  Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis .
  Proc Natl Acad Sci U S A 101(38) 13826-31.

• Barbe V, Vallenet D, Fonknechten N, Kreimeyer A, Oztas S, Labarre L, Cruveiller S, Robert C, Duprat S, Wincker P, Ornston LN, Weissenbach J, Marliere P, Cohen GN, and Médigue C. (2004)
  Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium.
  Nucleic Acids Res. 32(19) 5766-79.

2003

• Durand P, Médigue C., Morgat A., Vandenbrouck Y., Viari A., and Rechenmann F. (2003)
  «Integration of data and methods for genome analysis».
  Curr Opin Drug discov Devel., 6, 346-352.

• Bocs, S., Cruveiller, S., Vallenet, D., Nuel, G. and Médigue C. (2003)
  AMIGENE: Annotation of Microbial Genes.
  Nucleic Acids Res. 13(31) 3723-3726.

• Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles JF, Dassa E, Derose R, Derzelle S, Freyssinet G, Gaudriault S, Médigue C, Lanois A, Powell K, Siguier P, Vincent R, Wingate V, Zouine M, Glaser P, Boemare N, Danchin A, Kunst F. (2003)
  The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens .
  Nat Biotechnol. 21(11) 1307-13.

• Yuen KY, Pascal G, Wong SS, Glaser P, Woo PC, Kunst F, Cai JJ, Cheung EY, Medigue C, Danchin A.
  Exploring the Penicillium marneffei genome.
  Arch Microbiol. 2003 May;179(5):339-53.

2002

• Camus JC, Pryor MJ, Médigue C, and Cole ST. (2002)
  Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv .
  Microbiology 148, 2967-73.

• Bocs S, Danchin A, Médigue C. (2002)
  Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.
  BMC Bioinformatics 3(1) 5.
  (Lien vers les Résultats de Réannotation ).

• Médigue C, Wong BC, Lin MC, Bocs S, Danchin A.
  The secE gene of Helicobacter pylori.
  J Bacteriol. 2002 May;184(10):2837-40.

• Médigue C., Bocs S., Labarre L., Mathé C., Vallenet D. (2002)
  L’annotation in silico des séquences génomiques.
  Médecine et Sciences, 18, 237-250.