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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.


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.


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.


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.


RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.

de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L.

Genome Biol Evol. 2014 Apr;6(4):932-48. doi: 10.1093/gbe/evu069.


The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle.

Zoropogui A, Pujic P, Normand P, Barbe V, Belli P, Graindorge A, Roche D, Vallenet D, Mangenot S, Boiron P, Rodriguez-Nava V, Ribun S, Richard Y, Cournoyer B, Blaha D.

BMC Genomics. 2013 Apr 27;14:286. doi: 10.1186/1471-2164-14-286.


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.


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.


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.


Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius.

Alonso-Vega P, Normand P, Bacigalupe R, Pujic P, Lajus A, Vallenet D, Carro L, Coll P, Trujillo ME.

J Bacteriol. 2012 Aug;194(15):4135. doi: 10.1128/JB.00628-12.


The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

Smith AA, Belda E, Viari A, Medigue C, Vallenet D.

PLoS Comput Biol. 2012 May;8(5):e1002540. doi: 10.1371/journal.pcbi.1002540. Epub 2012 May 31.


Genome sequence of the human- and animal-pathogenic strain Nocardia cyriacigeorgica GUH-2.

Zoropogui A, Pujic P, Normand P, Barbe V, Beaman B, Beaman L, Boiron P, Colinon C, Deredjian A, Graindorge A, Mangenot S, Nazaret S, Neto M, Petit S, Roche D, Vallenet D, Rodríguez-Nava V, Richard Y, Cournoyer B, Blaha D.

J Bacteriol. 2012 Apr;194(8):2098-9. doi: 10.1128/JB.00161-12.


Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC.

Engelen S, Vallenet D, Médigue C, Danchin A.

BMC Genomics. 2012 Feb 14;13:69. doi: 10.1186/1471-2164-13-69.


Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles.

Remenant B, de Cambiaire JC, Cellier G, Jacobs JM, Mangenot S, Barbe V, Lajus A, Vallenet D, Medigue C, Fegan M, Allen C, Prior P.

PLoS One. 2011;6(9):e24356. doi: 10.1371/journal.pone.0024356. Epub 2011 Sep 8.


Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites.

Barbe V, Bouzon M, Mangenot S, Badet B, Poulain J, Segurens B, Vallenet D, Marlière P, Weissenbach J.

J Bacteriol. 2011 Sep;193(18):5055-6. doi: 10.1128/JB.05583-11.


A novel acyl-CoA beta-transaminase characterized from a metagenome.

Perret A, Lechaplais C, Tricot S, Perchat N, Vergne C, Pellé C, Bastard K, Kreimeyer A, Vallenet D, Zaparucha A, Weissenbach J, Salanoubat M.

PLoS One. 2011;6(8):e22918. doi: 10.1371/journal.pone.0022918. Epub 2011 Aug 3.


Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics.

Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsène-Ploetze F, Gallien S, Lauga B, Casiot C, Calteau A, Vallenet D, Bonnefoy V, Bruneel O, Chane-Woon-Ming B, Cleiss-Arnold J, Duran R, Elbaz-Poulichet F, Fonknechten N, Giloteaux L, Halter D, Koechler S, Marchal M, Mornico D, Schaeffer C, Smith AA, Van Dorsselaer A, Weissenbach J, Médigue C, Le Paslier D.

ISME J. 2011 Nov;5(11):1735-47. doi: 10.1038/ismej.2011.51. Epub 2011 May 12.


Core and panmetabolism in Escherichia coli.

Vieira G, Sabarly V, Bourguignon PY, Durot M, Le Fèvre F, Mornico D, Vallenet D, Bouvet O, Denamur E, Schachter V, Médigue C.

J Bacteriol. 2011 Mar;193(6):1461-72. doi: 10.1128/JB.01192-10. Epub 2011 Jan 14.


Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia.

Mornico D, Miché L, Béna G, Nouwen N, Verméglio A, Vallenet D, Smith AA, Giraud E, Médigue C, Moulin L.

Genes (Basel). 2011 Dec 21;3(1):35-61. doi: 10.3390/genes3010035.


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.

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