SPADEVizR: an R package for visualization, analysis and integration of SPADE results. - Guillaume Gautreau; David Pejoski; Roger Le Grand; Antonio Cosma; Anne-Sophie Beignon; Nicolas Tchitchek (Bioinform., 2017)

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)

Integrating Complex Pangenome Graphs. - Jérôme Arnoux; Angela Bonifati; Alexandra Calteau; Stefania Dumbrava; Guillaume Gautreau (ICDEW, 2024)