EUGÈNE'HOM: a generic similarity-based gene finder using multiple homologous sequences. - Sylvain Foissac; Philippe Bardou; Annick Moisan; Marie-Josée Cros; Thomas Schiex (Nucleic Acids Res., 2003)

Integrating alternative splicing detection into gene prediction. - Sylvain Foissac; Thomas Schiex (BMC Bioinform., 2005)

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. - Sylvain Foissac; Michael Sammeth (Nucleic Acids Res., 2007)

A General Definition and Nomenclature for Alternative Splicing Events. - Michael Sammeth; Sylvain Foissac; Roderic Guigó (PLoS Comput. Biol., 2008)

Enhancer/gene relationships: Need for more reliable genome-wide reference sets. - Tristan Hoellinger; Camille Mestre; Hugues Aschard; Wilfried Le Goff; Sylvain Foissac; Thomas Faraut; Sarah Djebali (Frontiers Bioinform., 2023)

A comprehensive review and benchmark of differential analysis tools for Hi-C data. - Elise Jorge; Sylvain Foissac; Pierre Neuvial; Matthias Zytnicki; Nathalie Vialaneix (Briefings Bioinform., 2025)