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Bioinformatics Analyses for Genomics and Metabolism


Analyses Bio-Informatiques pour la Génomique et le Métabolisme

The LABGeM (Laboratory of Bioinformatics Analyses for Genomics and Metabolism) is a bioinformatics team of the Genomics Metabolics research unit of the Genoscope. Our activities concern the development of bioinformatics methods and databases for the analysis of prokaryotic genomes and their metabolism: comparative genomics, metagenomics, pangenomics, functional annotation, enzyme family and metabolic network analysis. In addition, we offer to a worldwide community of microbiologists a genome analysis service through the MicroScope platform (>5000 user accounts, >1200 citations). These tools help us make sense of the deluge of genomic data from which the function of many genes remains completely unknown. Several bioanalysis projects are conducted with academic and industrial partners for applications in environmental biology,  biotechnology and health.

Ongoing research activities focus on:
the development of meta-pangenomic approaches to study the diversity of species in various biomes
the exploration of the functional diversity of metabolic pathways and enzyme families from genomic or metagenomic resources.

Scientific platform and equipment
The MicroScope platform is a member of the French Institute of Bioinformatics (IFB) and associated with the France Genomique sequencing infrastructure. The platform is also integrated into the ELIXIR and IBISBA european infrastructures.

The lab  has access to Genoscope's IT infrastructure and to the CEA's very large computing centre at Bruyères-le-Châtel (CCRT).

Quality management
The Quality Management System of the LABGeM team has been certified according to the ISO 9001:2015 and NF X50-900:2016 standards (Lloyd's Register Quality Assurance France S.A.S.). The certification applies to LABGEM activities of research, developments, services and MicroScope training.

Published on 1 September 2021
Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea
Castelle CJ, Meheust R, Jaffe AL, Seitz K, Gong XZ, Baker BJ and Banfield JF
AI-based mobile application to fight antibiotic resistance
Pascucci M, Royer G, Adamek J, Al Asmar M, Aristizabal D, Blanche L, Bezzarga A, Boniface-Chang G, Brunner A, Curel C, Dulac-Arnold G, Fakhri RM, Malou N, Nordon C, Runge V, Samson F, Sebastian E, Soukieh D, Vert JP, Ambroise C and Madoui MA
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period
Royer G, Darty MM, Clermont O, Condamine B, Laouenan C, Decousser JW, Vallenet D, Lefort A, de Lastours V, Denamur E, Grp C and Grp S
Microdiversity of Enterococcus faecalis isolates in cases of infective endocarditis: selection of non-synonymous mutations and large deletions is associated with phenotypic modifications
Royer G, Roisin L, Demontant V, Lo S, Coutte L, Lim P, Pawlotsky JM, Jacquier H, Lepeule R, Rodriguez C and Woerther PL
A community resource for paired genomic and metabolomic data mining
Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrion VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Matus DGG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, Konig GM, Leao T, Lee SR, Lee YY, Li XJ, Little JC, Maloney KN, Mannle D, Martin HC, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sorensen SJ, Sosio M, Sussmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang MX, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crusemann M, Rogers S, Dorrestein PC, Medema MH and van der Hooft JJJ
Complete Genome Sequences of Two Pseudomonas Species Isolated from Marine Environments of the Pacific Ocean
Wang SZ, Cruaud C, Aury JM, Vallenet D, Poulain J, Vacherie B, Zaparucha A and Vergne-Vaxelaire C
Complete Genome Sequences of Two Pseudomonas Species Isolated from Marine Environments of the Pacific Ocean
Wang S-Z, Cruaud C, Aury J-M, Vallenet D, Poulain J, Vacherie B, Zaparucha A and Vergne-Vaxelaire C
panRGP: a pangenome-based method to predict genomic islands and explore their diversity
Bazin A, Gautreau G, Medigue C, Vallenet D and Calteau A
TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages
Bottai D, Frigui W, Sayes F, Di Luca M, Spadoni D, Pawlik A, Zoppo M, Orgeur M, Khanna V, Hardy D, Mangenot S, Barbe V, Medigue C, Ma L, Bouchier C, Tavanti A, Larrouy-Maumus G and Brosch R
Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it
de Lastours V, Laouenan C, Royer G, Carbonnelle E, Lepeule R, Esposito-Farese M, Clermont O, Duval X, Fantin B, Mentre F, Decousser JW, Denamur E, Lefort A and Grp S
Transformation of the recalcitrant pesticide chlordecone by Desulfovibrio sp.86 with a switch from ring-opening dechlorination to reductive sulfidation activity
Della-Negra O, Chaussonnerie S, Fonknechten N, Barbance A, Muselet D, Martin DE, Fouteau S, Fischer C, Saaidi PL and Le Paslier D
Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2
Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lievremont D, Coppee JY, Barbe V and Arsene-Ploetze F
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Medigue C, Calteau A, Cruveiller S, Matias C, Ambroise C, Rocha EPC and Vallenet D
Alterocin, an Antibiofilm Protein Secreted by Pseudoalteromonas sp. Strain 3J6
Jouault A, Gobet A, Simon M, Portier E, Perennou M, Corre E, Gaillard F, Vallenet D, Michel G, Fleury Y, Bazire A and Dufour A
Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex
Mercier-Darty M, Royer G, Lamy B, Charron C, Lemenand O, Gomart C, Fourreau F, Madec JY, Jumas-Bilak E, Decousser JW, Resapath N and Col BVHN
Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria
Monteil CL, Grouzdev DS, Perriere G, Alonso B, Rouy Z, Cruveiller S, Ginet N, Pignol D and Lefevre CT
Construction of a complete set of Neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen
Muir A, Gurung I, Cehovin A, Bazin A, Vallenet D and Pelicic V
Ancestral state reconstruction of metabolic pathways across pangenome ensembles
Psomopoulos FE, van Helden J, Medigue C, Chasapi A and Ouzounis CA
Modulated Response ofAspergillus fumigatusandStenotrophomonas maltophiliato Antimicrobial Agents in Polymicrobial Biofilm
Roisin L, Melloul E, Woerther PL, Royer G, Decousser JW, Guillot J, Dannaoui E and Botterel F
Outbreak of an Uncommon Rifampin-resistant bla(NDM-1)Citrobacter amalonaticus Strain in a Digestive Rehabilitation Center: The Putative Role of Rifaximin
Royer G, Fourreau F, Gomart C, Maurand A, Hacquin B, Ducellier D, Cizeau F, Lo S, Cordonnier-Jourdin C, Mercier-Darty M and Decousser JW
Modulation of Quorum Sensing as an Adaptation to Nodule Cell Infection during Experimental Evolution of Legume Symbionts
Tang MX, Bouchez O, Cruveiller S, Masson-Boivin C and Capela D
Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium
Teulet A, Gully D, Rouy Z, Camuel A, Koebnik R, Giraud E and Lassalle F
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 and Medigue C
Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations
Belkhelfa S, Roche D, Dubois I, Berger A, Delmas VA, Cattolico L, Perret A, Labadie K, Perdereau AC, Darii E, Pateau E, de Berardinis V, Salanoubat M, Bouzon M and Doring V
The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-beta-Lactamase-Producing Strains of Escherichia coli
Billard-Pomares T, Clermont O, Castellanos M, Magdoud F, Royer G, Condamine B, Fouteau S, Barbo V, Roche D, Cruveiller S, Medigue C, Pognard D, Glodt J, Dion S, Rigal O, Picard B, Denamur E and Branger C
Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways
Bourrel AS, Poirel L, Royer G, Darty M, Vuillemin X, Kieffer N, Clermont O, Denamur E, Nordmann P, Decousser JW, Lafaurie M, Bercot B, Walewski V, Lescat M, Carbonnelle E, Ousser F, Idri N, Ricard JD, Landraud L, Le Dorze M, Jacquier H, Cambau E, Lepeule R, Gomart C and Grp IR
Specialization of small non-conjugative plasmids in Escherichia coli according to their family types
Branger C, Ledda A, Billard-Pomares T, Doublet B, Barbe V, Roche D, Medigue C, Arlet G and Denamur E
Transcriptome and Volatilome Analysis During Growth of Brochothrix thermosphacta in Food: Role of Food Substrate and Strain Specificity for the Expression of Spoilage Functions
Illikoud N, Gohier R, Werner D, Barrachina C, Roche D, Jaffres E and Zagorec M
mcr-9, an Inducible Gene Encoding an Acquired Phosphoethanolamine Transferase in Escherichia coli, and Its Origin
Kieffer N, Royer G, Decousser JW, Bourrel AS, Palmieri M, De La Rosa JMO, Jacquier H, Denamur E, Nordmann P and Poirel L
Physiological and evolutionary implications of tetrameric photosystem I in cyanobacteria
Li M, Calteau A, Semchonok DA, Witt TA, Nguyen JT, Sassoon N, Boekema EJ, Whitelegge J, Gugger M and Bruce BD
Advantage of the F2:A1:B- IncF Pandemic Plasmid over IncC Plasmids in In Vitro Acquisition and Evolution of bla(CTX-M )Gene-Bearing Plasmids in Escherichia coli
Maherault AC, Kemble H, Magnan M, Gachet B, Roche D, Le Nagard H, Tenaillon O, Denamur E, Branger C and Landraud L
A family of native amine dehydrogenases for the asymmetric reductive amination of ketones
Mayol O, Bastard K, Beloti L, Frese A, Turkenburg JP, Petit JL, Mariage A, Debard A, Pellouin V, Perret A, de Berardinis V, Zaparucha A, Grogan G and Vergne-Vaxelaire C
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data
Medigue 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 and Vallenet D
Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist
Monteil CL, Vallenet D, Menguy N, Benzerara K, Barbe V, Fouteau S, Cruaud C, Floriani M, Viollier E, Adryanczyk G, Leonhardt N, Faivre D, Pignol D, Lopez-Garcia P, Weld RJ and Lefevre CT
Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton
Pujic P, Alloisio N, Fournier P, Roche D, Sghaier H, Miotello G, Armengaud J, Berry AM and Normand P
Complete genome sequencing of Enterococcus faecalis strains suggests role of Ebp deletion in infective endocarditis relapse
Royer G, Melloul E, Roisin L, Courbin V, Jacquier H, Lepeule R, Coutte L, Darty M, Fihman V, Lim P, Decousser JW, Rodriguez C and Woerther PL
Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement
Borriss R, Danchin A, Harwood CR, Medigue C, Rocha EPC, Sekowska A and Vallenet D
Extended-spectrum beta-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, Medigue C, Castellanos M, Decre D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G and Denamur E
Parallels between experimental and natural evolution of legume symbionts
Clerissi C, Touchon M, Capela D, Tang MX, Cruveiller S, Parker MA, Moulin L, Masson-Boivin C and Rocha EPC
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, Medigue C, Bastard K, Rodriguez C, Clermont O, Denamur E and Decousser JW
Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs
Dias GM, Bidault A, Le Chevalier P, Choquet G, Sarkissian CD, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V and Paillard C
RecPhyloXML: a format for reconciled gene trees
Duchemin W, Gence G, Chifolleau AMA, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davin AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szollosi G, Zhang LX, Tannier E and Daubin V
Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia
Gully D, Czernic P, Cruveiller S, Mahe F, Longin C, Vallenet D, Francois P, Nidelet S, Rialle S, Giraud E, Arrighi JF, DasGupta M and Cartieaux F
Computational B-cell epitope identification and production of neutralizing murine antibodies against Atroxlysin-I
Kozlova EEG, Cerf L, Schneider FS, Viart BT, Nguyen C, Steiner BT, Lima SD, Molina F, Duarte CG, Felicori L, Chavez-Olortegui C and Machado-De-Avila RA
Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
Krin E, Pierle SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Medigue C, Coppee JY and Mazel D
GROOLS: reactive graph reasoning for genome annotation through biological processes
Mercier J, Josso A, Medigue C and Vallenet D
Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis
Monteil CL, Perriere G, Menguy N, Ginet N, Alonso B, Waisbord N, Cruveiller S, Pignol D and Lefevre CT
A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle
Partensky F, Six C, Ratin M, Garczarek L, Vaulot D, Probert I, Calteau A, Gourvil P, Marie D, Grebert T, Bouchier C, Le Panse S, Gachenot M, Rodriguez F and Garrido JL
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
Royer G, Decousser JW, Branger C, Dubois M, Medigue C, Denamur E and Vallenet D
The genomic and transcriptomic basis of the potential of Lactobacillus plantarum A6 to improve the nutritional quality of a cereal based fermented food
Turpin W, Weiman M, Guyot JP, Lajus A, Cruveiller S and Humblot C
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, Medigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M and De Berardinis V
Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria
Blanchard L, Guerin P, Roche D, Cruveiller S, Pignol D, Vallenet D, Armengaud J and de Groot A
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, Medigue C, Barbe V, Janssen DB and Vuilleumier S
Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont
Capela D, Marchetti M, Clerissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC and Masson-Boivin C
Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium
Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S and Bringel F
Expanding the reaction space of aldolases using hydroxypyruvate as a nucleophilic substrate
de Berardinis V, Guerard-Helaine C, Darii E, Bastard K, Helaine V, Mariage A, Petit JL, Poupard N, Sanchez-Moreno I, Stam M, Gefflaut T, Salanoubat M and Lemaire M
Structural Alteration of OmpR as a Source of Ertapenem Resistance in a CTX-M-15-Producing Escherichia coli O25b:H4 Sequence Type 131 Clinical Isolate
Dupont H, Choinier P, Roche D, Adiba S, Sookdeb M, Branger C, Denamur E and Mammeri H
Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria
Ficko-Blean E, Prechoux A, Thomas F, Rochat T, Larocque R, Zhu YT, Stam M, Genicot S, Jam M, Calteau A, Viart B, Ropartz D, Perez-Pascual D, Correc G, Matard-Mann M, Stubbs KA, Rogniaux H, Jeudy A, Barbeyron T, Medigue C, Czjzek M, Vallenet D, McBride MJ, Duchaud E and Michel G
Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat
Galia W, Leriche F, Cruveiller S, Garnier C, Navratil V, Dubost A, Blanquet-Diot S and Thevenot-Sergentet D
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 and Giraud E
The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria
Ji BY, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang LC, Tempel S, Li Y, Medigue C, Henrissat B, Coutinho PM, Barbe V, Talla E and Wu LF
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium
Lassalle F, Penel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Gueguen L, Vial L, Muller D, Daubin V and Nesme X
Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime
Marchetti M, Clerissi C, Yousfi Y, Gris C, Bouchez O, Rocha E, Cruveiller S, Jauneau A, Capela D and Masson-Boivin C
An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence
Mouammine A, Pages S, Lanois A, Gaudriault S, Jubelin G, Bonabaud M, Cruveiller S, Dubois E, Roche D, Legrand L, Brillard J and Givaudan A
Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains
Pancrace C, Barny MA, Ueoka R, Calteau A, Scalvenzi T, Pedron J, Barbe V, Piel J, Humbert JF and Gugger M
Rearranged Biosynthetic Gene Cluster and Synthesis of Hassallidin E in Planktothrix serta PCC 8927
Pancrace C, Jokela J, Sassoon N, Ganneau C, Desnos-Ollivier M, Wahlsten M, Hurnisto A, Calteau A, Bay S, Fewer DP, Sivonen K and Gugger M
DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence
Payelleville A, Lanois A, Gislard M, Dubois E, Roche D, Cruveiller S, Givaudan A and Brillard J
The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms
Perez-Pascual D, Lunazzi A, Magdelenat G, Rouy Z, Roulet A, Lopez-Roques C, Larocque R, Barbeyron T, Gobet A, Michel G, Bernardet JF and Duchaud E
Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme
Rochat T, Fujiwara-Nagata E, Calvez S, Dalsgaard I, Madsen L, Calteau A, Lunazzi A, Nicolas P, Wiklund T, Bernardet JF and Duchaud E
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 and Talla E
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 and Medigue C
In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum
Ailloud F, Lowe TM, Robene I, Cruveiller S, Allen C and Prior P
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Belda E, van Heck RGA, Lopez-Sanchez MJ, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, dos Santos V, de Lorenzo V, Danchin A and Medigue C
Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species
Bisch G, Ogier JC, Medigue C, Rouy Z, Vincent S, Tailliez P, Givaudan A and Gaudriault S
Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis
Bronnec V, Haddad N, Cruveiller S, Hernould M, Tresse O and Zagorec M
Adhesion, Biofilm Formation, and Genomic Features of Campylobacter jejuni Bf, an Atypical Strain Able to Grow under Aerobic Conditions
Bronnec V, Turonova H, Bouju A, Cruveiller S, Rodrigues R, Demnerova K, Tresse O, Haddad N and Zagorec M
Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium
Gerbore J, Brutel A, Lemainque A, Mairey B, Medigue C, Vallenet D, Lefort F and Grizard D
Genome announcements 4 (2), , 2016
Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria
Plucain J, Suau A, Cruveiller S, Medigue C, Schneider D and Le Gac M
RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori
Redko Y, Galtier E, Arnion H, Darfeuille F, Sismeiro O, Coppee JY, Medigue C, Weiman M, Cruveiller S and De Reuse H
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, Medigue C, Schneider D and Lenski RE
Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics
Vanhove AS, Rubio TP, Nguyen AN, Lemire A, Roche D, Nicod J, Vergnes A, Poirier AC, Disconzi E, Bachere E, Le Roux F, Jacq A, Charriere GM and Destoumieux-Garzon D
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, Medigue C, Tamburini C and Wu LF
Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity
Ailloud F, Lowe T, Cellier G, Roche D, Allen C and Prior P
Small RNA Deep-Sequencing Analyses Reveal a New Regulator of Virulence in Agrobacterium fabrum C58
Dequivre M, Diel B, Villard C, Sismeiro O, Durot M, Coppee JY, Nesme X, Vial L and Hommais F
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, Medigue C, Weissenbach J, Duran R and Lauga B
Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges
Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L and Pruvost O
A single regulatory gene is sufficient to alter Vibrio aestuarianus pathogenicity in oysters
Goudenege D, Travers MA, Lemire A, Petton B, Haffner P, Labreuche Y, Tourbiez D, Mangenot S, Calteau A, Mazel D, Nicolas JL, Jacq A and Le roux F
Environmental Microbiology 17 (11), 4189-4199, 2015
Populations, not clones, are the unit of vibrio pathogenesis in naturally infected oysters
Lemire A, Goudenege D, Versigny T, Petton B, Calteau A, Labreuche Y and Le Roux F
The Conserved nhaAR Operon Is Drastically Divergent between B2 and Non-B2 Escherichia coli and Is Involved in Extra-Intestinal Virulence (vol 9, e108738, 2014)
Lescat M, Reibel F, Pintard C, Dion S, Glodt J, Gateu C and Cruveiller S
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, Medigue C, Barrick JE and Lenski RE
Updates in Rhea-a manually curated resource of biochemical reactions
Morgat A, Axelsen KB, Lombardot T, Alcantara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I and Bridge A
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, Heuvel BV, Pujic P, Facciotti MT, Wilbanks EG, O'Brien A, Fournier P, Hernandez MAC, Herrera AM, Medigue C, Normand P, Pawlowski K and Berry AM
A new network representation of the metabolism to detect chemical transformation modules
Sorokina M, Medigue C and Vallenet D
Revealing the hidden functional diversity of an enzyme family
Bastard K, Smith AAT, 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 and Salanoubat M
Characterization of a P1-Like Bacteriophage Carrying an SHV-2 Extended-Spectrum beta-Lactamase from an Escherichia coli Strain
Billard-Pomares T, Fouteau S, Jacquet ME, Roche D, Barbe V, Castellanos M, Bouet JY, Cruveiller S, Medigue C, Blanco J, Clermont O, Denamur E and Branger C
Large alpha-aminonitrilase activity screening of nitrilase superfamily members: Access to conversion and enantiospecificity by LC-MS
Bordier F, Stam M, Darii E, Tricot S, Fossey A, Rohault J, Debard A, Mariage A, Pellouin V, Petit JL, Perret A, Vallenet D, Salanoubat M, Weissenbach J, Vergne-Vaxelaire C, de Berardinis V and Zaparucha A
Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria
Calteau A, Fewer DP, Latifi A, Coursin T, Laurent T, Jokela J, Kerfeld CA, Sivonen K, Piel J and Gugger M
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 and Blanchard L
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 HL, Petty NK, Jarraud S, Etienne J, Steinert M, Heuner K, Gribaldo S, Medigue C, Glockner G, Hartland EL and Buchrieser C
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