seq++: analyzing biological sequences with a range of Markov-related models. - Vincent Miele; Pierre-Yves Bourguignon; David Robelin; Grégory Nuel; Hugues Richard (Bioinform., 2005)

Property-Driven Statistics of Biological Networks. - Pierre-Yves Bourguignon; Vincent Danos; François Képès; Serge Smidtas; Vincent Schächter (Trans. Comp. Sys. Biology, 2006)

Challenges in experimental data integration within genome-scale metabolic models. - Pierre-Yves Bourguignon; Areejit Samal; François Képès; Jürgen Jost; Olivier C. Martin (Algorithms Mol. Biol., 2010)

Inhomogeneous Parsimonious Markov Models. - Ralf Eggeling; André Gohr; Pierre-Yves Bourguignon; Edgar Wingender; Ivo Grosse (ECML/PKDD (1), 2013)

Point estimates in phylogenetic reconstructions. - Philipp Benner; Miroslav Bacák; Pierre-Yves Bourguignon (Bioinform., 2014)