FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. - Philippe Gouret; Vérane Vitiello; Nathalie Balandraud; André Gilles; Pierre Pontarotti; Etienne G. J. Danchin (BMC Bioinform., 2005)

CASSIOPE: An expert system for conserved regions searches. - Virginie Lopez Rascol; Anthony Levasseur; Olivier Chabrol; Simona Grusea; Philippe Gouret; Etienne G. J. Danchin; Pierre Pontarotti (BMC Bioinform., 2009)

Identifying discriminative classification-based motifs in biological sequences. - Celine Vens; Marie-Noëlle Rosso; Etienne G. J. Danchin (Bioinform., 2011)

AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers. - Georgios D. Koutsovoulos; Solène Granjeon Noriot; Marc Bailly-Bechet; Etienne G. J. Danchin; Corinne Rancurel (PLoS Comput. Biol., 2022)