Combined expression data with missing values and gene interaction network analysis: a Markovian integrated approach. - Juliette Blanchet; Matthieu Vignes (BIBE, 2007)

A Model-Based Approach to Gene Clustering with Missing Observation Reconstruction in a Markov Random Field Framework. - Juliette Blanchet; Matthieu Vignes (J. Comput. Biol., 2009)

Gene Clustering via Integrated Markov Models Combining Individual and Pairwise Features. - Matthieu Vignes; Florence Forbes (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent. - Matthieu Vignes; Juliette Blanchet; Damien Leroux; Florence Forbes (Bioinform., 2011)

Inférence de réseaux de régulation de gènes au travers de scores étendus dans les réseaux bayésiens. - Jimmy Vandel; Brigitte Mangin; Matthieu Vignes; Damien Leroux; Olivier Loudet; Marie-Laure Martin-Magniette; Simon de Givry (Rev. d'Intelligence Artif., 2012)

Exact and approximate inference in graphical models: variable elimination and beyond. - Nathalie Peyrard; Simon de Givry; Alain Franc; Stéphane Robin; Régis Sabbadin; Thomas Schiex; Matthieu Vignes (CoRR, 2015)

The sismonr Package: Simulation of In Silico Multi-Omic Networks in R. - Olivia Angelin-Bonnet; Patrick J. Biggs; Matthieu Vignes (BIBM, 2018)

Inferring large graphs using ℓ1 -penalized likelihood. - Magali Champion; Victor Picheny; Matthieu Vignes (Stat. Comput., 2018)

Correction to: Inferring large graphs using ℓ1-penalized likelihood. - Magali Champion; Victor Picheny; Matthieu Vignes (Stat. Comput., 2018)

sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R. - Olivia Angelin-Bonnet; Patrick J. Biggs; Samantha J. Baldwin; Susan Thomson 003; Matthieu Vignes (Bioinform., 2020)

A multi-objective genetic algorithm to find active modules in multiplex biological networks. - Elva María Novoa-del-Toro; Efrén Mezura-Montes; Matthieu Vignes; Morgane Térézol; Frédérique Magdinier; Laurent Tichit; Anaïs Baudot (PLoS Comput. Biol., 2021)