Publications
(depuis l'intégration du groupe au sein de l'UMR8030, Février 2002)

2007

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

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

Normand P, Lapierre P, Tisa L, Lavire C, Alloisio N, Cournoye B, Marechal J, Pujic P, Gogarten J.P, Huang Y, Mastronunzio J, Bickhard D, Bassi C, Rawnsley T, Niemann J, Francino M.P, Lapidus A, Martinez M, Goltsman E, Choisne N, Schenowitz C, Couloux A, Demange N, Cruveiller C, Labarre L, Rouy Z, Vallenet D, Mullin B, Kopp O, Wang Y, Tomkins J, Berry A, Valverde C, Wall L, Sellstedt A, Tavares F, Daubin V, Médigue C, and Benson D.R.
"Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography."
Genome Research. 2007 Jan;17(1):7-15.

P. Normand, C. Queiroux, L. Tisa, D. Benson, Z. Rouy, S. Cruveiller, and C. Médigue
"Exploring the genomes of Frankia."
Physiologia Plantarum (sous presse).

Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, Violaine Bonnefoy, Evelyne Krin, Florence Arsène-Ploetze, Christine Carapito, Michael Chandler, Benoît Cournoyer, Stéphane Cruveiller, Caroline Dossat, Simon Duval, Michael Heymann, Emmanuelle Leize, Aurélie Lieutaud, Didier Lièvremont, Yuko Makita, Sophie Mangenot, Wolfgang Nitschke, Philippe Ortet, Nicolas Perdrial, Barbara Schoepp, Patricia Siguier, Diliana D. Simeonova, Zoé Rouy, Béatrice Segurens, Evelyne Turlin, David Vallenet, Alain Van Dorsselaer, Stéphanie Weiss, Jean Weissenbach, Marie-Claire Lett, Antoine Danchin, Philippe N. Bertin
"A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments"
PLoS Genetics (sous presse)

Eric Giraud, Lionel Moulin, David Vallenet, Valérie Barbe, Eddie Cytryn, Jean-Christophe Avarre, Marianne Jaubert, Damien Simon, Fabienne Cartieaux, Yves Prin, Gilles Bena, Laure Hannibal, Joel Fardoux, Mila Kojadinovic, Laurie Vuillet, Aurélie Lajus, Stéphane Cruveiller, Zoe Rouy, Sophie Mangenot, Béatrice Segurens, Carole Dossat, William L. Franck, Woo-Suk Chang, Elizabeth Saunders, David Bruce, Paul Richardson, Philippe Normand, Bernard Dreyfus, David Pignol, Gary Stacey, David Emerich, André Verméglio, Claudine Médigue, and Michael Sadowsky.
"Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia"
Science (en révision)


2006
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.
"Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp."
Journal of Bacteriology. 2006. 188(22):7893-904.

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.
"Complete genome sequence of the entomopathogen and metabolically versatile soil bacterium Pseudomonas entomophila"
Nature Biotechnology. 2006. 24:673-679.

Strous M, Pelletier E, Mangenot S, Rattei R, Lehner A, Taylor MW, 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 BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, and Le Paslier D.
"Deciphering the evolution and metabolism of an anammox bacterium from a community genome"
Nature. 2006 apr. 440:790-794.

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.
"Comparative Genomics of Multidrug Resistance in Acinetobacter baumannii"
PLoS Genet. 2006. 13;2(1):e7.

Vallenet, D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, and Médigue C.
"MaGe - a microbial genome annotation system supported by synteny results"
Nucleic Acids Research. 2006. 34:53-65.

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

Pascal G, Médigue C and Danchin A.
"Persistant biaises in the amino acid composition of prokaryotic proteins"
BioAssays. 2006. 28(7):726-38

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2005
Médigue C.
"L'annotation des génomes procaryotes"
Biofutur. 2005. 251:23-27.

Pascal G, Médigue C, and Danchin A.
"Universal biases in protein composition of model prokaryotes"
Proteins. 2005. 60(1):27-35.

Cruveiller S, Le Saux J,Vallenet D, Lajus A, Bocs S, and Médigue C.
"MICheck : A web tool for fast check of syntactic annotations of bacterial genomes"
Nucleic Acids Research. 2005. 33:471-479.

Boyer F, Morgat A, Labarre L, Pothier J, and Viari A.
"Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data"
Bioinformatics. 2005. 21:4209-4215.

Médigue C, Krin E, Pascal G, Barbe V, Bernsel A, Bertin PN, Cheung F, Cruveiller S, D'Amico S, Duilio A, Fang G, Feller G, Ho C, Mangenot S, Marino G, Nilsson J, Parilli E, Rocha EPC, Rouy Z, Sekowska A, Tutino ML, Vallenet D, Von Heijne G, and Danchin A.
"Coping with the cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125"
Genome Research. 2005. 15:1325-1335.

Siroy A, Molle V, Lemaitre-Guillier C, Vallenet D, Pestel-Caron M, Cozzone AJ, Jouenne T, De E.
"Channel formation by CarO, the carbapenem resistance-associated outer membrane protein of Acinetobacter baumannii"
Antimicrob Agents Chemother. 2005. 49:4876-4883.

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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.
"Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis"
Proc Natl Acad Sci U S A. 2004. 101:13826-13831.

Barbe V, Vallenet D, Fonknechten N, Kreimeyer A, Oztas S, Labarre L, Robert C, Duprat S, Wincker P, Ornston L.N, Weissenbach J, Marlière P, Cohen GN, and Médigue C.
"Singular features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium"
Nucleic Acid Research. 2004. 32:5766-5779.

2003
Yuen KY, Pascal G, Wong SY, Glaser P, Woo P, Kunst F, Tsoi HW, Cheung EYL, Médigue C, and Danchin A.
"Exploring the Penicillium marneffei genome"
Achives of Microbiology. 2003. 179:339-353

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

Bocs S, Cruveiller S, Vallenet D, Nuel G, and Médigue C.
"AMIGene: Annotation of MIcrobial Genes"
Nucleic Acids Research. 2003. 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, and Kunst F.
"The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens"
Nature Biotechnology. 2003. 11:1307-1313.

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2002 :
Bocs S, Danchin A, and Médigue C.
"Re-annotation of genomes microbial CoDing Sequences : finding new genes and inaccurately annotated genes"
BMC BioInformatics. 2002. 3:5.

Médigue C, Bocs S, Labarre L, Mathé C, Vallenet D.
"L'annotation in silico des séquences génomiques"
Médecine et Sciences. 2002. 18:237-250.

Médigue C, Wong BCY, Lin MCM, Gu Q, Bocs S and Danchin A.
"The secE Gene of Helicobacter pylori"
Journal of Bacteriology. 2002. 184:2837-2840.

Camus JC, Pryor MJ, Médigue C, and Cole S.
"Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv"
Microbiology. 2002. 148:2967-2973.