Publications
(Since the arrival of the group at UMR 8030 in February 2002)

2006
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 structure reflects host biogeography in three plant symbionts Frankia sp. strains. "
Genome Research. (in presse).

Derbise A, Chenal-Francisque V, Fayolle C, Pouillot F, Prévost M.C, Médigue C, Hinnebusch B.J and Carniel E.
"An Infectious Filamentous Phage Associated with the Transformation of Yersinia pestis from an Enteropathogen into the Deadly Plague Bacillus"
Molecular Microbiology. (in presse)

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. (in presse).

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

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, W471-479.

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: 4209-15.

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. 49:4876-83.

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.
"Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis."
Proc Natl Acad Sci U S A. 2004. 101: 13826-31.

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, 339-53

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.

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.