GROOLS: reactive graph reasoning for genome annotation through biological processes

by Jonathan Mercier, Adrien Josso, Claudine Médigue, David Vallenet
Published 2018-04-01

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

by Adam Alexander Thil Smith, Eugeni Belda, Alain Viari, Claudine Medigue, David Vallenet
Published 2012-05-01

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

by Martha E Trujillo, Rodrigo Bacigalupe, Petar Pujic, Yasuhiro Igarashi, Patricia Benito, Raúl Riesco, Claudine Médigue, Philippe Normand
Published 2014-01-01

Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

by Damien Mornico, Lionel Moulin, Claudine Médigue, Alexander A.T. Smith, David Vallenet, André Verméglio, Gilles Béna, Nico Nouwen, Lucie Miché, Eric Giraud
Published 2011-12-01

Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

by Philipp Engel, Walter Salzburger, Marius Liesch, Chao-Chin Chang, Soichi Maruyama, Christa Lanz, Alexandra Calteau, Aurélie Lajus, Claudine Médigue, Stephan C Schuster, Christoph Dehio
Published 2011-02-01

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

by Benoît Remenant, Jean-Charles de Cambiaire, Gilles Cellier, Jonathan M Jacobs, Sophie Mangenot, Valérie Barbe, Aurélie Lajus, David Vallenet, Claudine Medigue, Mark Fegan, Caitilyn Allen, Philippe Prior
Published 2011-01-01

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

by Jean-François Humbert, Valérie Barbe, Amel Latifi, Muriel Gugger, Alexandra Calteau, Therese Coursin, Aurélie Lajus, Vanina Castelli, Sophie Oztas, Gaëlle Samson, Cyrille Longin, Claudine Medigue, Nicole Tandeau de Marsac
Published 2013-01-01

Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation

by Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée, Didier Mazel
Published 2018-05-01

Experimental evolution of a plant pathogen into a legume symbiont.

by Marta Marchetti, Delphine Capela, Michelle Glew, Stéphane Cruveiller, Béatrice Chane-Woon-Ming, Carine Gris, Ton Timmers, Véréna Poinsot, Luz B Gilbert, Philipp Heeb, Claudine Médigue, Jacques Batut, Catherine Masson-Boivin
Published 2010-01-01

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

by Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P C Rocha, David Vallenet
Published 2020-03-01

TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages

by Daria Bottai, Wafa Frigui, Fadel Sayes, Mariagrazia Di Luca, Dalila Spadoni, Alexandre Pawlik, Marina Zoppo, Mickael Orgeur, Varun Khanna, David Hardy, Sophie Mangenot, Valerie Barbe, Claudine Medigue, Laurence Ma, Christiane Bouchier, Arianna Tavanti, Gerald Larrouy-Maumus, Roland Brosch
Published 2020-02-01

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

by Graciela M. Dias, Graciela M. Dias, Adeline Bidault, Patrick Le Chevalier, Gwenaëlle Choquet, Clio Der Sarkissian, Ludovic Orlando, Ludovic Orlando, Claudine Medigue, Valerie Barbe, Sophie Mangenot, Cristiane C. Thompson, Fabiano L. Thompson, Annick Jacq, Vianney Pichereau, Christine Paillard
Published 2018-02-01

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

by Tomas Persson, Kai Battenberg, Irina V Demina, Theoden Vigil-Stenman, Brian Vanden Heuvel, Petar Pujic, Marc T Facciotti, Elizabeth G Wilbanks, Anna O'Brien, Pascale Fournier, Maria Antonia Cruz Hernandez, Alberto Mendoza Herrera, Claudine Médigue, Philippe Normand, Katharina Pawlowski, Alison M Berry
Published 2015-01-01

Comparative analysis of Acinetobacters: three genomes for three lifestyles.

by David Vallenet, Patrice Nordmann, Valérie Barbe, Laurent Poirel, Sophie Mangenot, Elodie Bataille, Carole Dossat, Shahinaz Gas, Annett Kreimeyer, Patricia Lenoble, Sophie Oztas, Julie Poulain, Béatrice Segurens, Catherine Robert, Chantal Abergel, Jean-Michel Claverie, Didier Raoult, Claudine Médigue, Jean Weissenbach, Stéphane Cruveiller
Published 2008-03-01

Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82.

by Sylvie Miquel, Eric Peyretaillade, Laurent Claret, Amélie de Vallée, Carole Dossat, Benoit Vacherie, El Hajji Zineb, Beatrice Segurens, Valerie Barbe, Pierre Sauvanet, Christel Neut, Jean-Frédéric Colombel, Claudine Medigue, Francisco J M Mojica, Pierre Peyret, Richard Bonnet, Arlette Darfeuille-Michaud
Published 2010-01-01

The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments.

by Paul J Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed A Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue, Safiyh Taghavi, Sean McCorkle, John Dunn, Daniël van der Lelie, Max Mergeay
Published 2010-05-01

Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis.

by Mathieu Picardeau, Dieter M Bulach, Christiane Bouchier, Richard L Zuerner, Nora Zidane, Peter J Wilson, Sophie Creno, Elizabeth S Kuczek, Simona Bommezzadri, John C Davis, Annette McGrath, Matthew J Johnson, Caroline Boursaux-Eude, Torsten Seemann, Zoé Rouy, Ross L Coppel, Julian I Rood, Aurélie Lajus, John K Davies, Claudine Médigue, Ben Adler
Published 2008-02-01

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

by Elizabeth Ficko-Blean, Aurélie Préchoux, François Thomas, Tatiana Rochat, Robert Larocque, Yongtao Zhu, Mark Stam, Sabine Génicot, Murielle Jam, Alexandra Calteau, Benjamin Viart, David Ropartz, David Pérez-Pascual, Gaëlle Correc, Maria Matard-Mann, Keith A. Stubbs, Hélène Rogniaux, Alexandra Jeudy, Tristan Barbeyron, Claudine Médigue, Mirjam Czjzek, David Vallenet, Mark J. McBride, Eric Duchaud, Gurvan Michel
Published 2017-11-01

A tale of two oxidation states: bacterial colonization of arsenic-rich environments.

by Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, Violaine Bonnefoy, Evelyne Krin, Florence Arsène-Ploetze, Christine Carapito, Michael Chandler, Benoît Cournoyer, Stéphane Cruveiller, Caroline Dossat, Simon Duval, Michael Heymann, Emmanuelle Leize, Aurélie Lieutaud, Didier Lièvremont, Yuko Makita, Sophie Mangenot, Wolfgang Nitschke, Philippe Ortet, Nicolas Perdrial, Barbara Schoepp, Patricia Siguier, Diliana D Simeonova, Zoé Rouy, Béatrice Segurens, Evelyne Turlin, David Vallenet, Alain Van Dorsselaer, Stéphanie Weiss, Jean Weissenbach, Marie-Claire Lett, Antoine Danchin, Philippe N Bertin
Published 2007-04-01

Structure, function, and evolution of the Thiomonas spp. genome.

by Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Muller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, Philippe N Bertin
Published 2010-02-01