David Vallenet

According to our database, David Vallenet authored at least 15 papers between 2003 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

A roadmap for the functional annotation of protein families: a community perspective.

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

Database J. Biol. Databases Curation, 2022

2021

Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

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

PLoS Comput. Biol., 2021

2020

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

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

PLoS Comput. Biol., 2020

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.

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

Nucleic Acids Res., 2020

2019

MicroScope - an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

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

Briefings Bioinform., 2019

2018

GROOLS: reactive graph reasoning for genome annotation through biological processes.

Jonathan Mercier, Adrien Josso, Claudine Médigue, David Vallenet

BMC Bioinform., 2018

2017

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

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

Nucleic Acids Res., 2017

2015

A new network representation of the metabolism to detect chemical transformation modules.

Maria Sorokina, Claudine Médigue, David Vallenet

BMC Bioinform., 2015

GROOLS: Reactive Graph Reasoning for Genome Annotation.

Jonathan Mercier, David Vallenet

Proceedings of the RuleML 2015 Challenge, 2015

2013

MicroScope - an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

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

Nucleic Acids Res., 2013

2012

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes.

Adam Alexander Thil Smith, Eugeni Belda, Alain Viari, Claudine Médigue, David Vallenet

PLoS Comput. Biol., 2012

2009

MicroScope: a platform for microbial genome annotation and comparative genomics.

David Vallenet, Stefan Engelen, Damien Mornico, Stéphane Cruveiller, Ludovic Fleury, Aurélie Lajus, Zoé Rouy, David Roche, Gregory Salvignol, Claude Scarpelli, Claudine Médigue

Database J. Biol. Databases Curation, 2009

2008

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data.

Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schächter

BMC Syst. Biol., 2008

2005

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Stéphane Cruveiller, Jérôme Le Saux, David Vallenet, Aurélie Lajus, Stéphanie Bocs, Claudine Médigue

Nucleic Acids Res., 2005

2003

AMIGene: Annotation of MIcrobial Genes.

Stéphanie Bocs, Stéphane Cruveiller, David Vallenet, Grégory Nuel, Claudine Médigue

Nucleic Acids Res., 2003