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Items: 1 to 50 of 175

1.

PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level.

Royer G, Decousser JW, Branger C, Dubois M, Médigue C, Denamur E, Vallenet D.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000211.

2.

Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.

Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000203. Epub 2018 Aug 6.

3.

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.

4.

GROOLS: reactive graph reasoning for genome annotation through biological processes.

Mercier J, Josso A, Médigue C, Vallenet D.

BMC Bioinformatics. 2018 Apr 11;19(1):132. doi: 10.1186/s12859-018-2126-1.

5.

Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs.

Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C.

Front Microbiol. 2018 Feb 19;9:227. doi: 10.3389/fmicb.2018.00227. eCollection 2018.

6.

The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

Desroches M, Royer G, Roche D, Mercier-Darty M, Vallenet D, Médigue C, Bastard K, Rodriguez C, Clermont O, Denamur E, Decousser JW.

mSphere. 2018 Jan 31;3(1). pii: e00553-17. doi: 10.1128/mSphere.00553-17. eCollection 2018 Jan-Feb.

7.

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement.

Borriss R, Danchin A, Harwood CR, Médigue C, Rocha EPC, Sekowska A, Vallenet D.

Microb Biotechnol. 2018 Jan;11(1):3-17. doi: 10.1111/1751-7915.13043.

8.

Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria.

Ficko-Blean E, Préchoux A, Thomas F, Rochat T, Larocque R, Zhu Y, Stam M, Génicot S, Jam M, Calteau A, Viart B, Ropartz D, Pérez-Pascual D, Correc G, Matard-Mann M, Stubbs KA, Rogniaux H, Jeudy A, Barbeyron T, Médigue C, Czjzek M, Vallenet D, McBride MJ, Duchaud E, Michel G.

Nat Commun. 2017 Nov 22;8(1):1685. doi: 10.1038/s41467-017-01832-6.

9.

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. 2017 Sep 12. doi: 10.1093/bib/bbx113. [Epub ahead of print]

PMID:
28968784
10.

Corrigendum: Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.

Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V.

Nat Chem Biol. 2017 Sep 19;13(10):1137. doi: 10.1038/nchembio1017-1137c. No abstract available.

PMID:
28926556
11.

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.

12.

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.

Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V.

Nat Chem Biol. 2017 Aug;13(8):858-866. doi: 10.1038/nchembio.2397. Epub 2017 Jun 5. Erratum in: Nat Chem Biol. 2017 Sep 19;13(10 ):1137.

PMID:
28581482
13.

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
14.

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.

15.

Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain.

Remenant B, Borges F, Cailliez-Grimal C, Revol-Junelles AM, Marché L, Lajus A, Médigue C, Pilet MF, Prévost H, Zagorec M.

Genome Announc. 2016 Oct 13;4(5). pii: e01109-16. doi: 10.1128/genomeA.01109-16.

16.

Tempo and mode of genome evolution in a 50,000-generation experiment.

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE.

Nature. 2016 Aug 11;536(7615):165-70. Epub 2016 Aug 1.

17.

Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria.

Plucain J, Suau A, Cruveiller S, Médigue C, Schneider D, Le Gac M.

BMC Evol Biol. 2016 Apr 23;16:86. doi: 10.1186/s12862-016-0662-8.

18.

Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200.

Zhang SD, Santini CL, Zhang WJ, Barbe V, Mangenot S, Guyomar C, Garel M, Chen HT, Li XG, Yin QJ, Zhao Y, Armengaud J, Gaillard JC, Martini S, Pradel N, Vidaud C, Alberto F, Médigue C, Tamburini C, Wu LF.

Extremophiles. 2016 May;20(3):301-10. doi: 10.1007/s00792-016-0822-1. Epub 2016 Apr 2.

PMID:
27039108
19.

Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium.

Gerbore J, Brutel A, Lemainque A, Mairey B, Médigue C, Vallenet D, Lefort F, Grizard D.

Genome Announc. 2016 Mar 10;4(2). pii: e00058-16. doi: 10.1128/genomeA.00058-16.

20.

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
21.

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.

22.

RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori.

Redko Y, Galtier E, Arnion H, Darfeuille F, Sismeiro O, Coppée JY, Médigue C, Weiman M, Cruveiller S, De Reuse H.

RNA Biol. 2016;13(2):243-53. doi: 10.1080/15476286.2015.1132141.

23.

A new network representation of the metabolism to detect chemical transformation modules.

Sorokina M, Medigue C, Vallenet D.

BMC Bioinformatics. 2015 Nov 14;16:385. doi: 10.1186/s12859-015-0809-4.

24.

Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.

Maddamsetti R, Hatcher PJ, Cruveiller S, Médigue C, Barrick JE, Lenski RE.

Mol Biol Evol. 2015 Nov;32(11):2897-904. doi: 10.1093/molbev/msv161. Epub 2015 Jul 20.

25.

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant.

Persson T, Battenberg K, Demina IV, Vigil-Stenman T, Vanden Heuvel B, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Cruz Hernandez MA, Mendoza Herrera A, Médigue C, Normand P, Pawlowski K, Berry AM.

PLoS One. 2015 May 28;10(5):e0127630. doi: 10.1371/journal.pone.0127630. eCollection 2015.

26.

16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage.

Fahy A, Giloteaux L, Bertin P, Le Paslier D, Médigue C, Weissenbach J, Duran R, Lauga B.

Microb Ecol. 2015 Jul;70(1):154-67. doi: 10.1007/s00248-014-0558-3. Epub 2015 Jan 16.

PMID:
25592635
27.

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.

28.

Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?

Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P.

PLoS One. 2014 Sep 30;9(9):e108522. doi: 10.1371/journal.pone.0108522. eCollection 2014.

29.

Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D.

MBio. 2014 Sep 9;5(5):e01377-14. doi: 10.1128/mBio.01377-14.

30.

Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum β-lactamase from an Escherichia coli strain.

Billard-Pomares T, Fouteau S, Jacquet ME, Roche D, Barbe V, Castellanos M, Bouet JY, Cruveiller S, Médigue C, Blanco J, Clermont O, Denamur E, Branger C.

Antimicrob Agents Chemother. 2014 Nov;58(11):6550-7. doi: 10.1128/AAC.03183-14. Epub 2014 Aug 18.

31.

Profiling the orphan enzymes.

Sorokina M, Stam M, Médigue C, Lespinet O, Vallenet D.

Biol Direct. 2014 Jun 6;9:10. doi: 10.1186/1745-6150-9-10. Review.

32.

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.

33.

Evolutionary history and genetic parallelism affect correlated responses to evolution.

Le Gac M, Cooper TF, Cruveiller S, Médigue C, Schneider D.

Mol Ecol. 2013 Jun;22(12):3292-3303.

PMID:
24624420
34.

Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

Plucain J, Hindré T, Le Gac M, Tenaillon O, Cruveiller S, Médigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE, Schneider D.

Science. 2014 Mar 21;343(6177):1366-9. doi: 10.1126/science.1248688. Epub 2014 Mar 6.

PMID:
24603152
35.

Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms.

Ramos PI, Picão RC, Almeida LG, Lima NC, Girardello R, Vivan AC, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Médigue C, Vasconcelos AT, Gales AC, Nicolás MF.

BMC Genomics. 2014 Jan 22;15:54. doi: 10.1186/1471-2164-15-54.

36.

Revealing the hidden functional diversity of an enzyme family.

Bastard K, Smith AA, Vergne-Vaxelaire C, Perret A, Zaparucha A, De Melo-Minardi R, Mariage A, Boutard M, Debard A, Lechaplais C, Pelle C, Pellouin V, Perchat N, Petit JL, Kreimeyer A, Medigue C, Weissenbach J, Artiguenave F, De Berardinis V, Vallenet D, Salanoubat M.

Nat Chem Biol. 2014 Jan;10(1):42-9. doi: 10.1038/nchembio.1387. Epub 2013 Nov 17.

PMID:
24240508
37.

A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa.

Humbert JF, Barbe V, Latifi A, Gugger M, Calteau A, Coursin T, Lajus A, Castelli V, Oztas S, Samson G, Longin C, Medigue C, de Marsac NT.

PLoS One. 2013 Aug 12;8(8):e70747. doi: 10.1371/journal.pone.0070747. eCollection 2013.

38.

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
39.

Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits.

Goudenège D, Labreuche Y, Krin E, Ansquer D, Mangenot S, Calteau A, Médigue C, Mazel D, Polz MF, Le Roux F.

ISME J. 2013 Oct;7(10):1985-96. doi: 10.1038/ismej.2013.90. Epub 2013 Jun 6.

40.

Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN.

Genome Biol Evol. 2013;5(5):934-53. doi: 10.1093/gbe/evt061.

41.

Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8.

Kits KD, Kalyuzhnaya MG, Klotz MG, Jetten MS, Op den Camp HJ, Vuilleumier S, Bringel F, Dispirito AA, Murrell JC, Bruce D, Cheng JF, Copeland A, Goodwin L, Hauser L, Lajus A, Land ML, Lapidus A, Lucas S, Médigue C, Pitluck S, Woyke T, Zeytun A, Stein LY.

Genome Announc. 2013 Apr 11;1(2):e0017013. doi: 10.1128/genomeA.00170-13.

42.

An updated metabolic view of the Bacillus subtilis 168 genome.

Belda E, Sekowska A, Le Fèvre F, Morgat A, Mornico D, Ouzounis C, Vallenet D, Médigue C, Danchin A.

Microbiology. 2013 Apr;159(Pt 4):757-70. doi: 10.1099/mic.0.064691-0. Epub 2013 Feb 21.

PMID:
23429746
43.

Experimental evolution of nodule intracellular infection in legume symbionts.

Guan SH, Gris C, Cruveiller S, Pouzet C, Tasse L, Leru A, Maillard A, Médigue C, Batut J, Masson-Boivin C, Capela D.

ISME J. 2013 Jul;7(7):1367-77. doi: 10.1038/ismej.2013.24. Epub 2013 Feb 21.

44.

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.

45.

Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T).

Amin O, Fardeau ML, Valette O, Hirschler-Réa A, Barbe V, Médigue C, Vacherie B, Ollivier B, Bertin PN, Dolla A.

Genome Announc. 2013 Jan;1(1). pii: e00114-12. doi: 10.1128/genomeA.00114-12. Epub 2013 Jan 24.

46.

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis.

Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R.

Nat Genet. 2013 Feb;45(2):172-9. doi: 10.1038/ng.2517. Epub 2013 Jan 6.

47.

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load.

Wielgoss S, Barrick JE, Tenaillon O, Wiser MJ, Dittmar WJ, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):222-7. doi: 10.1073/pnas.1219574110. Epub 2012 Dec 17.

48.

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.

49.

Genome sequence of radiation-resistant Modestobacter marinus strain BC501, a representative actinobacterium that thrives on calcareous stone surfaces.

Normand P, Gury J, Pujic P, Chouaia B, Crotti E, Brusetti L, Daffonchio D, Vacherie B, Barbe V, Médigue C, Calteau A, Ghodhbane-Gtari F, Essoussi I, Nouioui I, Abbassi-Ghozzi I, Gtari M.

J Bacteriol. 2012 Sep;194(17):4773-4. doi: 10.1128/JB.01029-12.

50.

Complete genome sequences of six strains of the genus Methylobacterium.

Marx CJ, Bringel F, Chistoserdova L, Moulin L, Farhan Ul Haque M, Fleischman DE, Gruffaz C, Jourand P, Knief C, Lee MC, Muller EE, Nadalig T, Peyraud R, Roselli S, Russ L, Goodwin LA, Ivanova N, Kyrpides N, Lajus A, Land ML, Médigue C, Mikhailova N, Nolan M, Woyke T, Stolyar S, Vorholt JA, Vuilleumier S.

J Bacteriol. 2012 Sep;194(17):4746-8. doi: 10.1128/JB.01009-12.

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