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 | | | | 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 | Bmc Genomics 19 (), e373, 2018 | | | 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 | | | | Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp QH-2 strain | Ji BY, 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 JS, Yang J, Zhang LC, Zhang WY, Pan HM, Henrissat B, Coutinho PM, Li Y, Xiao T, Medigue C, Barbe V, Pignol D, Talla E and Wu LF | | | | The Conserved nhaAR Operon Is Drastically Divergent between B2 and Non-B2 Escherichia coli and Is Involved in Extra-Intestinal Virulence | Lescat M, Reibel F, Pintard C, Dion S, Glodt J, Gateau C, Launay A, Ledda A, Cruvellier S, Tourret J and Tenaillon O | | | | Attenuated Virulence and Genomic Reductive Evolution in the Entomopathogenic Bacterial Symbiont Species, Xenorhabdus poinarii | Ogier J-C, Pages S, Bisch G, Chiapello H, Medigue C, Rouy Z, Teyssier C, Vincent S, Tailliez P, Givaudan A and Gaudriault S | | | | Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli | Plucain J, Hindre T, Le Gac M, Tenaillon O, Cruveiller S, Medigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE and Schneider D | | | | Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli | Raeside C, Gaffe J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Medigue C, Lenski RE, Barrick JE and Schneider D | | | | 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 PIP, Picao RC, de Almeida LGP, Lima NCB, Girardello R, Vivan ACP, Xavier DE, Barcellos FG, Pelisson M, Vespero EC, Medigue C, de Vasconcelos ATR, Gales AC and Nicolas MF | | | | Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer | Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EPC and Masson-Boivin C | | | | Profiling the orphan enzymes | Sorokina M, Stam M, Medigue C, Lespinet O and Vallenet D | | | | Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach | Stuani L, Lechaplais C, Salminen AV, Segurens B, Durot M, Castelli V, Pinet A, Labadie K, Cruveiller S, Weissenbach J, de Berardinis V, Salanoubat M and Perret A | | |
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