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Items: 43

1.

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.

Vallenet D, Calteau A, Dubois M, Amours P, Bazin A, Beuvin M, Burlot L, Bussell X, Fouteau S, Gautreau G, Lajus A, Langlois J, Planel R, Roche D, Rollin J, Rouy Z, Sabatet V, Médigue C.

Nucleic Acids Res. 2019 Oct 24. pii: gkz926. doi: 10.1093/nar/gkz926. [Epub ahead of print]

PMID:
31647104
2.

Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D.

BMC Genomics. 2018 May 21;19(1):373. doi: 10.1186/s12864-018-4716-8.

3.

MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

Médigue C, Calteau A, Cruveiller S, Gachet M, Gautreau G, Josso A, Lajus A, Langlois J, Pereira H, Planel R, Roche D, Rollin J, Rouy Z, Vallenet D.

Brief Bioinform. 2019 Jul 19;20(4):1071-1084. doi: 10.1093/bib/bbx113.

PMID:
28968784
4.

The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms.

Pérez-Pascual D, Lunazzi A, Magdelenat G, Rouy Z, Roulet A, Lopez-Roques C, Larocque R, Barbeyron T, Gobet A, Michel G, Bernardet JF, Duchaud E.

Front Microbiol. 2017 Aug 16;8:1542. doi: 10.3389/fmicb.2017.01542. eCollection 2017.

5.

Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21.

Bringel F, Postema CP, Mangenot S, Bibi-Triki S, Chaignaud P, Farhan Ul Haque M, Gruffaz C, Hermon L, Louhichi Y, Maucourt B, Muller EEL, Nadalig T, Lajus A, Rouy Z, Médigue C, Barbe V, Janssen DB, Vuilleumier S.

Genome Announc. 2017 Jul 27;5(30). pii: e00622-17. doi: 10.1128/genomeA.00622-17.

6.

Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with Aeschynomene Legumes.

Gully D, Teulet A, Busset N, Nouwen N, Fardoux J, Rouy Z, Vallenet D, Cruveiller S, Giraud E.

Genome Announc. 2017 Jul 27;5(30). pii: e00421-17. doi: 10.1128/genomeA.00421-17.

7.

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes.

Tran TTT, Mangenot S, Magdelenat G, Payen E, Rouy Z, Belahbib H, Grail BM, Johnson DB, Bonnefoy V, Talla E.

Front Microbiol. 2017 Jun 13;8:1009. doi: 10.3389/fmicb.2017.01009. eCollection 2017.

8.

The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria.

Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigue C, Henrissat B, Coutinho PM, Barbe V, Talla E, Wu LF.

Environ Microbiol. 2017 Mar;19(3):1103-1119. doi: 10.1111/1462-2920.13637. Epub 2017 Feb 1.

PMID:
27902881
9.

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D517-D528. doi: 10.1093/nar/gkw1101. Epub 2016 Nov 29.

10.

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.

Belda E, van Heck RG, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins Dos Santos VA, de Lorenzo V, Danchin A, Médigue C.

Environ Microbiol. 2016 Oct;18(10):3403-3424. doi: 10.1111/1462-2920.13230. Epub 2016 Apr 28.

PMID:
26913973
11.

Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species.

Bisch G, Ogier JC, Médigue C, Rouy Z, Vincent S, Tailliez P, Givaudan A, Gaudriault S.

Genome Biol Evol. 2016 Jan 14;8(1):148-60. doi: 10.1093/gbe/evv248.

12.

Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease.

Gomez-Valero L, Rusniok C, Rolando M, Neou M, Dervins-Ravault D, Demirtas J, Rouy Z, Moore RJ, Chen H, Petty NK, Jarraud S, Etienne J, Steinert M, Heuner K, Gribaldo S, Médigue C, Glöckner G, Hartland EL, Buchrieser C.

Genome Biol. 2014;15(11):505.

13.

Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii.

Ogier JC, Pagès S, Bisch G, Chiapello H, Médigue C, Rouy Z, Teyssier C, Vincent S, Tailliez P, Givaudan A, Gaudriault S.

Genome Biol Evol. 2014 Jun 5;6(6):1495-513. doi: 10.1093/gbe/evu119.

14.

Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain.

Ji B, Zhang SD, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang WJ, Rioux JB, Ginet N, Sabaty M, Mangenot S, Pradel N, Tian J, Yang J, Zhang L, Zhang W, Pan H, Henrissat B, Coutinho PM, Li Y, Xiao T, Médigue C, Barbe V, Pignol D, Talla E, Wu LF.

Environ Microbiol. 2014 Feb;16(2):525-44. doi: 10.1111/1462-2920.12180. Epub 2013 Jul 10.

PMID:
23841906
15.

Draft Genome Sequence and Annotation of the Entomopathogenic Bacterium Xenorhabdus nematophila Strain F1.

Lanois A, Ogier JC, Gouzy J, Laroui C, Rouy Z, Givaudan A, Gaudriault S.

Genome Announc. 2013 Jun 20;1(3). pii: e00342-13. doi: 10.1128/genomeA.00342-13.

16.

Complete Genome Sequence of the Piezophilic, Mesophilic, Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13(T.).

Ji B, Gimenez G, Barbe V, Vacherie B, Rouy Z, Amrani A, Fardeau ML, Bertin P, Alazard D, Leroy S, Talla E, Ollivier B, Dolla A, Pradel N.

Genome Announc. 2013 Jan;1(1). pii: e00226-12. doi: 10.1128/genomeA.00226-12. Epub 2013 Feb 21.

17.

Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies.

Sugawara M, Epstein B, Badgley BD, Unno T, Xu L, Reese J, Gyaneshwar P, Denny R, Mudge J, Bharti AK, Farmer AD, May GD, Woodward JE, Médigue C, Vallenet D, Lajus A, Rouy Z, Martinez-Vaz B, Tiffin P, Young ND, Sadowsky MJ.

Genome Biol. 2013 Feb 20;14(2):R17. doi: 10.1186/gb-2013-14-2-r17.

18.

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D636-47. doi: 10.1093/nar/gks1194. Epub 2012 Nov 27.

19.

Draft genome sequence of the purple photosynthetic bacterium Phaeospirillum molischianum DSM120, a particularly versatile bacterium.

Duquesne K, Prima V, Ji B, Rouy Z, Médigue C, Talla E, Sturgis JN.

J Bacteriol. 2012 Jul;194(13):3559-60. doi: 10.1128/JB.00605-12.

20.

Insights into the 1.59-Mbp largest plasmid of Azospirillum brasilense CBG497.

Acosta-Cruz E, Wisniewski-Dyé F, Rouy Z, Barbe V, Valdés M, Mavingui P.

Arch Microbiol. 2012 Sep;194(9):725-36. doi: 10.1007/s00203-012-0805-2. Epub 2012 Apr 6.

PMID:
22481309
21.

Whole-genome sequence of Wolbachia strain wAlbB, an endosymbiont of tiger mosquito vector Aedes albopictus.

Mavingui P, Valiente Moro C, Tran-Van V, Wisniewski-Dyé F, Raquin V, Minard G, Tran FH, Voronin D, Rouy Z, Bustos P, Lozano L, Barbe V, González V.

J Bacteriol. 2012 Apr;194(7):1840. doi: 10.1128/JB.00036-12.

22.

Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.

Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB.

PLoS Genet. 2011 Dec;7(12):e1002430. doi: 10.1371/journal.pgen.1002430. Epub 2011 Dec 22.

23.

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation.

Wisniewski-Dyé F, Lozano L, Acosta-Cruz E, Borland S, Drogue B, Prigent-Combaret C, Rouy Z, Barbe V, Herrera AM, González V, Mavingui P.

Genes (Basel). 2012 Sep 28;3(4):576-602. doi: 10.3390/genes3040576.

24.

Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z.

Vuilleumier S, Khmelenina VN, Bringel F, Reshetnikov AS, Lajus A, Mangenot S, Rouy Z, Op den Camp HJ, Jetten MS, Dispirito AA, Dunfield P, Klotz MG, Semrau JD, Stein LY, Barbe V, Médigue C, Trotsenko YA, Kalyuzhnaya MG.

J Bacteriol. 2012 Jan;194(2):551-2. doi: 10.1128/JB.06392-11.

25.

The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes.

Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Léon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Médigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H.

PLoS One. 2011;6(11):e27909. doi: 10.1371/journal.pone.0027909. Epub 2011 Nov 18.

26.

Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes.

Gomez-Valero L, Rusniok C, Jarraud S, Vacherie B, Rouy Z, Barbe V, Medigue C, Etienne J, Buchrieser C.

BMC Genomics. 2011 Nov 1;12:536. doi: 10.1186/1471-2164-12-536.

27.

Complete nucleotide sequence of plasmid pTN48, encoding the CTX-M-14 extended-spectrum β-lactamase from an Escherichia coli O102-ST405 strain.

Billard-Pomares T, Tenaillon O, Le Nagard H, Rouy Z, Cruveiller S, Médigue C, Arlet G, Denamur E, Branger C.

Antimicrob Agents Chemother. 2011 Mar;55(3):1270-3. doi: 10.1128/AAC.01108-10. Epub 2010 Dec 20.

28.

Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus.

Ogier JC, Calteau A, Forst S, Goodrich-Blair H, Roche D, Rouy Z, Suen G, Zumbihl R, Givaudan A, Tailliez P, Médigue C, Gaudriault S.

BMC Genomics. 2010 Oct 15;11:568. doi: 10.1186/1471-2164-11-568.

29.

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma.

Thiberge JM, Boursaux-Eude C, Lehours P, Dillies MA, Creno S, Coppée JY, Rouy Z, Lajus A, Ma L, Burucoa C, Ruskoné-Foumestraux A, Courillon-Mallet A, De Reuse H, Boneca IG, Lamarque D, Mégraud F, Delchier JC, Médigue C, Bouchier C, Labigne A, Raymond J.

BMC Genomics. 2010 Jun 10;11:368. doi: 10.1186/1471-2164-11-368.

30.

Structure, function, and evolution of the Thiomonas spp. genome.

Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN.

PLoS Genet. 2010 Feb 26;6(2):e1000859. doi: 10.1371/journal.pgen.1000859.

31.

MicroScope: a platform for microbial genome annotation and comparative genomics.

Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C.

Database (Oxford). 2009;2009:bap021. Epub 2009 Nov 25.

32.

Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Médigue C, Lidstrom ME.

PLoS One. 2009;4(5):e5584. doi: 10.1371/journal.pone.0005584. Epub 2009 May 18.

33.

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E.

PLoS Genet. 2009 Jan;5(1):e1000344. doi: 10.1371/journal.pgen.1000344. Epub 2009 Jan 23.

34.

Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia.

Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, Carrère S, Cruveiller S, Dossat C, Lajus A, Marchetti M, Poinsot V, Rouy Z, Servin B, Saad M, Schenowitz C, Barbe V, Batut J, Médigue C, Masson-Boivin C.

Genome Res. 2008 Sep;18(9):1472-83. doi: 10.1101/gr.076448.108. Epub 2008 May 19.

35.

Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis.

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.

PLoS One. 2008 Feb 13;3(2):e1607. doi: 10.1371/journal.pone.0001607.

36.

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.

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.

J Bacteriol. 2008 Apr;190(7):2572-9. doi: 10.1128/JB.01248-07. Epub 2008 Feb 1.

37.

Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia.

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.

Science. 2007 Jun 1;316(5829):1307-12.

38.

A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

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.

PLoS Genet. 2007 Apr 13;3(4):e53. Epub 2007 Mar 5.

39.

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

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.

Genome Res. 2007 Jan;17(1):7-15. Epub 2006 Dec 6.

40.

Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp.

Louvel H, Bommezzadri S, Zidane N, Boursaux-Eude C, Creno S, Magnier A, Rouy Z, Médigue C, Saint Girons I, Bouchier C, Picardeau M.

J Bacteriol. 2006 Nov;188(22):7893-904. Epub 2006 Sep 15.

41.

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila.

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, Boccard F.

Nat Biotechnol. 2006 Jun;24(6):673-9. Epub 2006 May 14.

PMID:
16699499
42.

MaGe: a microbial genome annotation system supported by synteny results.

Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Médigue C.

Nucleic Acids Res. 2006 Jan 10;34(1):53-65. Print 2006.

43.

Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.

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, Parrilli E, Rocha EP, Rouy Z, Sekowska A, Tutino ML, Vallenet D, von Heijne G, Danchin A.

Genome Res. 2005 Oct;15(10):1325-35. Epub 2005 Sep 16.

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