AMIGene: Annotation of MIcrobial Genes. - Stéphanie Bocs; Stéphane Cruveiller; David Vallenet; Grégory Nuel; Claudine Médigue (Nucleic Acids Res., 2003)

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)

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)

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)

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)

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; et al. (Nucleic Acids Res., 2013)

GROOLS: Reactive Graph Reasoning for Genome Annotation. - Jonathan Mercier; David Vallenet (Challenge+DC@RuleML, 2015)

A new network representation of the metabolism to detect chemical transformation modules. - Maria Sorokina; Claudine Médigue; David Vallenet (BMC Bioinform., 2015)

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; et al. (Nucleic Acids Res., 2017)

GROOLS: reactive graph reasoning for genome annotation through biological processes. - Jonathan Mercier; Adrien Josso; Claudine Médigue; David Vallenet (BMC Bioinform., 2018)

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; et al. (Briefings Bioinform., 2019)

panRGP: a pangenome-based method to predict genomic islands and explore their diversity. - Adelme Bazin; Guillaume Gautreau; Claudine Médigue; David Vallenet; Alexandra Calteau (Bioinform., 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; et al. (Nucleic Acids Res., 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; et al. (PLoS Comput. Biol., 2020)

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; et al. (PLoS Comput. Biol., 2021)

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; et al. (Database J. Biol. Databases Curation, 2022)