David Vallenet

17 papers Journal 16Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
ASMC: investigating the amino acid diversity of enzyme active sites.
Bioinform.
Thomas Bailly, Eddy Elisée, David Vallenet
2022 J jnl
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
2021 J jnl
Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
PLoS Comput. Biol.
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
2020 J jnl
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.
Nucleic Acids Res.
David Vallenet, Alexandra Calteau, Mathieu Dubois, Paul Amours, Adelme Bazin, Mylène Beuvin, Laura Burlot, Xavier Bussell, Stéphanie Fouteau, Guillaume Gautreau, Aurélie Lajus, Jordan Langlois, Rémi Planel, David Roche, Johan Rollin, Zoé Rouy, Valentin Sabatet, Claudine Médigue
2020 J jnl
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.
PLoS Comput. Biol.
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
2020 J jnl
panRGP: a pangenome-based method to predict genomic islands and explore their diversity.
Bioinform.
Adelme Bazin, Guillaume Gautreau, Claudine Médigue, David Vallenet, Alexandra Calteau
2019 J jnl
MicroScope - an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.
Briefings Bioinform.
Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Guillaume Gautreau, Adrien Josso, Aurélie Lajus, Jordan Langlois, Hugo Pereira, Rémi Planel, David Roche, Johan Rollin, Zoé Rouy, David Vallenet
2018 J jnl
GROOLS: reactive graph reasoning for genome annotation through biological processes.
BMC Bioinform.
Jonathan Mercier, Adrien Josso, Claudine Médigue, David Vallenet
2017 J jnl
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.
Nucleic Acids Res.
David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoé Rouy, David Roche, Claude Scarpelli, Claudine Médigue
2015 J jnl
A new network representation of the metabolism to detect chemical transformation modules.
BMC Bioinform.
Maria Sorokina, Claudine Médigue, David Vallenet
2015 — conf
GROOLS: Reactive Graph Reasoning for Genome Annotation.
Challenge+DC@RuleML
Jonathan Mercier, David Vallenet
2013 J jnl
MicroScope - an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.
Nucleic Acids Res.
David Vallenet, Eugeni Belda, Alexandra Calteau, Stéphane Cruveiller, Stefan Engelen, Aurélie Lajus, François Le Fèvre, Cyrille Longin, Damien Mornico, David Roche, Zoé Rouy, Gregory Salvignol, Claude Scarpelli, Adam Alexander Thil Smith, Marion Weiman, Claudine Médigue
2012 J jnl
The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes.
PLoS Comput. Biol.
Adam Alexander Thil Smith, Eugeni Belda, Alain Viari, Claudine Médigue, David Vallenet
2009 J jnl
MicroScope: a platform for microbial genome annotation and comparative genomics.
Database J. Biol. Databases Curation
David Vallenet, Stefan Engelen, Damien Mornico, Stéphane Cruveiller, Ludovic Fleury, Aurélie Lajus, Zoé Rouy, David Roche, Gregory Salvignol, Claude Scarpelli, Claudine Médigue
2008 J jnl
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data.
BMC Syst. Biol.
Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schächter
2005 J jnl
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.
Nucleic Acids Res.
Stéphane Cruveiller, Jérôme Le Saux, David Vallenet, Aurélie Lajus, Stéphanie Bocs, Claudine Médigue
2003 J jnl
AMIGene: Annotation of MIcrobial Genes.
Nucleic Acids Res.
Stéphanie Bocs, Stéphane Cruveiller, David Vallenet, Grégory Nuel, Claudine Médigue