Predicting transcription factor binding sites using local over-representation and comparative genomics. - Matthieu Defrance; Hélène Touzet (BMC Bioinform., 2006)

Algorithmes pour l'analyse de régions régulatrices dans le génome d'eucaryotes supérieurs. - Matthieu Defrance (2006)

RSAT: regulatory sequence analysis tools. - Morgane Thomas-Chollier; Olivier Sand; Jean-Valéry Turatsinze; Rekin's Janky; Matthieu Defrance; Eric Vervisch; Sylvain Brohée; Jacques van Helden (Nucleic Acids Res., 2008)

info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. - Matthieu Defrance; Jacques van Helden (Bioinform., 2009)

RSAT 2011: regulatory sequence analysis tools. - Morgane Thomas-Chollier; Matthieu Defrance; Alejandra Medina-Rivera; Olivier Sand; Carl Herrmann; Denis Thieffry; Jacques van Helden (Nucleic Acids Res., 2011)

A comprehensive overview of Infinium HumanMethylation450 data processing. - Sarah Dedeurwaerder; Matthieu Defrance; Martin Bizet; Emilie Calonne; Gianluca Bontempi; François Fuks (Briefings Bioinform., 2014)

RSAT 2015: Regulatory Sequence Analysis Tools. - Alejandra Medina-Rivera; Matthieu Defrance; Olivier Sand; Carl Herrmann; Jaime Abraham Castro-Mondragón; Jeremy Delerce; Sébastien Jaeger; Christophe Blanchet; Pierre Vincens; Christophe Caron; Daniel M. Staines; Bruno Contreras-Moreira; et al. (Nucleic Acids Res., 2015)

DNAModAnnot: a R toolbox for DNA modification filtering and annotation. - Alexis Hardy; Mélody Matelot; Amandine Touzeau; Christophe Klopp; Céline Lopez-Roques; Sandra Duharcourt; Matthieu Defrance (Bioinform., 2021)

Contrastive self-supervised clustering of scRNA-seq data. - Madalina Ciortan; Matthieu Defrance (BMC Bioinform., 2021)

GNN-based embedding for clustering scRNA-seq data. - Madalina Ciortan; Matthieu Defrance (Bioinform., 2022)