MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
Vallenet, David, Calteau, Alexandra, Dubois, Mathieu, Amours, Paul, Bazin, Adelme, Beuvin, Mylène, Burlot, Laura, Bussell, Xavier, Fouteau, Stéphanie, Gautreau, Guillaume, Lajus, Aurélie, Langlois, Jordan, Planel, Rémi, Roche, David, Rollin, Johan, Rouy, Zoe, Sabatet, Valentin, Médigue, Claudine
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes
Vallenet, David, Calteau, Alexandra, Cruveiller, Stéphane, Gachet, Mathieu, Lajus, Aurélie, Josso, Adrien, Mercier, Jonathan, Renaux, Alexandre, Rollin, Johan, Rouy, Zoe, Roche, David, Scarpelli, Claude, Médigue, Claudine
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Gautreau, Guillaume, Bazin, Adelme, Gachet, Mathieu, Planel, Rémi, Burlot, Laura, Dubois, Mathieu, Perrin, Amandine, Médigue, Claudine, Calteau, Alexandra, Cruveiller, Stéphane, Matias, Catherine, Ambroise, Christophe, Rocha, Eduardo P C, Vallenet, David
Published in PLoS computational biology (19.03.2020)
Published in PLoS computational biology (19.03.2020)
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Journal Article
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
Vallenet, David, Belda, Eugeni, Calteau, Alexandra, Cruveiller, Stéphane, Engelen, Stefan, Lajus, Aurélie, Le Fèvre, François, Longin, Cyrille, Mornico, Damien, Roche, David, Rouy, Zoé, Salvignol, Gregory, Scarpelli, Claude, Thil Smith, Adam Alexander, Weiman, Marion, Médigue, Claudine
Published in Nucleic acids research (01.01.2013)
Published in Nucleic acids research (01.01.2013)
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Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria
Ficko-Blean, Elizabeth, Préchoux, Aurélie, Thomas, François, Rochat, Tatiana, Larocque, Robert, Zhu, Yongtao, Stam, Mark, Génicot, Sabine, Jam, Murielle, Calteau, Alexandra, Viart, Benjamin, Ropartz, David, Pérez-Pascual, David, Correc, Gaëlle, Matard-Mann, Maria, Stubbs, Keith A., Rogniaux, Hélène, Jeudy, Alexandra, Barbeyron, Tristan, Médigue, Claudine, Czjzek, Mirjam, Vallenet, David, McBride, Mark J., Duchaud, Eric, Michel, Gurvan
Published in Nature communications (22.11.2017)
Published in Nature communications (22.11.2017)
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From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later
Barbe, Valerie, Cruveiller, Stephane, Kunst, Frank, Lenoble, Patricia, Meurice, Guillaume, Sekowska, Agnieszka, Vallenet, David, Wang, Tingzhang, Moszer, Ivan, Medigue, Claudine, Danchin, Antoine
Published in Microbiology (Society for General Microbiology) (01.06.2009)
Published in Microbiology (Society for General Microbiology) (01.06.2009)
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A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening
Elisée, Eddy, Ducrot, Laurine, Méheust, Raphaël, Bastard, Karine, Fossey-Jouenne, Aurélie, Grogan, Gideon, Pelletier, Eric, Petit, Jean-Louis, Stam, Mark, de Berardinis, Véronique, Zaparucha, Anne, Vallenet, David, Vergne-Vaxelaire, Carine
Published in Nature communications (10.06.2024)
Published in Nature communications (10.06.2024)
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Journal Article
GROOLS: reactive graph reasoning for genome annotation through biological processes
Mercier, Jonathan, Josso, Adrien, Médigue, Claudine, Vallenet, David
Published in BMC bioinformatics (11.04.2018)
Published in BMC bioinformatics (11.04.2018)
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Journal Article
A novel binary pesticidal protein from Chryseobacterium arthrosphaerae controls western corn rootworm by a different mode of action to existing commercial pesticidal proteins
Jabeur, Rania, Guyon, Virginie, Toth, Szabolcs, Pereira, Adriano E, Huynh, Man P, Selmani, Zakia, Boland, Erin, Bosio, Mickael, Beuf, Laurent, Clark, Pete, Vallenet, David, Achouak, Wafa, Audiffrin, Carine, Torney, François, Paul, Wyatt, Heulin, Thierry, Hibbard, Bruce E, Toepfer, Stefan, Sallaud, Christophe
Published in PloS one (17.02.2023)
Published in PloS one (17.02.2023)
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Journal Article
Comparative genomics of multidrug resistance in Acinetobacter baumannii
Fournier, Pierre-Edouard, Vallenet, David, Barbe, Valérie, Audic, Stéphane, Ogata, Hiroyuki, Poirel, Laurent, Richet, Hervé, Robert, Catherine, Mangenot, Sophie, Abergel, Chantal, Nordmann, Patrice, Weissenbach, Jean, Raoult, Didier, Claverie, Jean-Michel
Published in PLoS computational biology (01.01.2006)
Published in PLoS computational biology (01.01.2006)
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Construction of a complete set of Neisseria meningitidis mutants and its use for the phenotypic profiling of this human pathogen
Muir, Alastair, Gurung, Ishwori, Cehovin, Ana, Bazin, Adelme, Vallenet, David, Pelicic, Vladimir
Published in Nature communications (02.11.2020)
Published in Nature communications (02.11.2020)
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Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies
Sugawara, Masayuki, Epstein, Brendan, Badgley, Brian D, Unno, Tatsuya, Xu, Lei, Reese, Jennifer, Gyaneshwar, Prasad, Denny, Roxanne, Mudge, Joann, Bharti, Arvind K, Farmer, Andrew D, May, Gregory D, Woodward, Jimmy E, Médigue, Claudine, Vallenet, David, Lajus, Aurélie, Rouy, Zoé, Martinez-Vaz, Betsy, Tiffin, Peter, Young, Nevin D, Sadowsky, Michael J
Published in Genome biology (01.01.2013)
Published in Genome biology (01.01.2013)
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Journal Article
Comparative analysis of Acinetobacters: three genomes for three lifestyles
Vallenet, David, Nordmann, Patrice, Barbe, Valérie, Poirel, Laurent, Mangenot, Sophie, Bataille, Elodie, Dossat, Carole, Gas, Shahinaz, Kreimeyer, Annett, Lenoble, Patricia, Oztas, Sophie, Poulain, Julie, Segurens, Béatrice, Robert, Catherine, Abergel, Chantal, Claverie, Jean-Michel, Raoult, Didier, Médigue, Claudine, Weissenbach, Jean, Cruveiller, Stéphane
Published in PloS one (19.03.2008)
Published in PloS one (19.03.2008)
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Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles
Remenant, Benoît, de Cambiaire, Jean-Charles, Cellier, Gilles, Jacobs, Jonathan M, Mangenot, Sophie, Barbe, Valérie, Lajus, Aurélie, Vallenet, David, Medigue, Claudine, Fegan, Mark, Allen, Caitilyn, Prior, Philippe
Published in PloS one (08.09.2011)
Published in PloS one (08.09.2011)
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Journal Article
Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period
Royer, Guilhem, Darty, Mélanie Mercier, Clermont, Olivier, Condamine, Bénédicte, Laouenan, Cédric, Decousser, Jean-Winoc, Vallenet, David, Lefort, Agnès, de Lastours, Victoire, Denamur, Erick
Published in Genome medicine (05.05.2021)
Published in Genome medicine (05.05.2021)
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Journal Article
Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Gautreau, Guillaume, Bazin, Adelme, Gachet, Mathieu, Planel, Rémi, Burlot, Laura, Dubois, Mathieu, Perrin, Amandine, Médigue, Claudine, Calteau, Alexandra, Cruveiller, Stéphane, Matias, Catherine, Ambroise, Christophe, Rocha, Eduardo P C, Vallenet, David
Published in PLoS computational biology (10.12.2021)
Published in PLoS computational biology (10.12.2021)
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Journal Article
Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis
Bastard, Karine, Perret, Alain, Mariage, Aline, Bessonnet, Thomas, Pinet-Turpault, Agnès, Petit, Jean-Louis, Darii, Ekaterina, Bazire, Pascal, Vergne-Vaxelaire, Carine, Brewee, Clémence, Debard, Adrien, Pellouin, Virginie, Besnard-Gonnet, Marielle, Artiguenave, François, Médigue, Claudine, Vallenet, David, Danchin, Antoine, Zaparucha, Anne, Weissenbach, Jean, Salanoubat, Marcel, de Berardinis, Véronique
Published in Nature chemical biology (01.08.2017)
Published in Nature chemical biology (01.08.2017)
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Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources
Vuilleumier, Stéphane, Chistoserdova, Ludmila, Lee, Ming-Chun, Bringel, Françoise, Lajus, Aurélie, Zhou, Yang, Gourion, Benjamin, Barbe, Valérie, Chang, Jean, Cruveiller, Stéphane, Dossat, Carole, Gillett, Will, Gruffaz, Christelle, Haugen, Eric, Hourcade, Edith, Levy, Ruth, Mangenot, Sophie, Muller, Emilie, Nadalig, Thierry, Pagni, Marco, Penny, Christian, Peyraud, Rémi, Robinson, David G, Roche, David, Rouy, Zoé, Saenampechek, Channakhone, Salvignol, Grégory, Vallenet, David, Wu, Zaining, Marx, Christopher J, Vorholt, Julia A, Olson, Maynard V, Kaul, Rajinder, Weissenbach, Jean, Médigue, Claudine, Lidstrom, Mary E
Published in PloS one (18.05.2009)
Published in PloS one (18.05.2009)
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