Codon adaptation index as a measure of dominating codon bias. - Alessandra Carbone; Andrei Yu. Zinovyev; François Képès (Bioinform., 2003)

Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication. - Nicolas Omont; François Képès (Bioinform., 2004)

Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. - Oriane Matte-Tailliez; Joan Hérisson; Nicolas Férey; Olivier Magneau; Pierre-Emmanuel Gros; François Képès; Rachid Gherbi (ICCSA (1), 2006)

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

Incremental and unifying modelling formalism for biological interaction networks. - Anastasia Yartseva; Hanna Klaudel; Raymond Devillers; François Képès (BMC Bioinform., 2007)

From MIN model to ordinary differential equations. - Anastasia Yartseva; Raymond Devillers; Hanna Klaudel; François Képès (J. Integr. Bioinform., 2007)

Chronique : Le programme d'épigénomique. - Gilles Bernot; François Képès (Tech. Sci. Informatiques, 2007)

Topology-based abstraction of complex biological systems: application to the Golgi apparatus. - Mathieu Poudret; Agnès Arnould; Jean-Paul Comet; Pascale Le Gall; Philippe Meseure; François Képès (Theory Biosci., 2008)

Spatial Information and Boolean Genetic Regulatory Networks. - Matthieu Manceny; Marc Aiguier; Pascale Le Gall; Joan Hérisson; Ivan Junier; François Képès (BICoB, 2009)

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)

Periodic pattern detection in sparse boolean sequences. - Ivan Junier; Joan Hérisson; François Képès (Algorithms Mol. Biol., 2010)

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization. - Ivan Junier; Olivier C. Martin; François Képès (PLoS Comput. Biol., 2010)

Boosting Binding Sites Prediction Using Gene's Positions. - Mohamed Elati; Rim Fekih; Rémy Nicolle; Ivan Junier; Joan Hérisson; François Képès (WABI, 2011)

Introduction to special issue ECCS'09 in Theory in Biosciences. - Markus Kirkilionis; François Képès (Theory Biosci., 2011)

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. - Vic Norris; Abdallah Zemirline; Patrick Amar; Jean Nicolas Audinot; Pascal Ballet; Eshel Ben-Jacob; Gilles Bernot; Guillaume Beslon; Armelle Cabin; Eric Fanchon; Jean-Louis Giavitto; Nicolas Glade; et al. (Theory Biosci., 2011)

Parallel stepwise stochastic simulation: harnessing GPUs to explore possible futures states of a chromosome folding model thanks to the possible futures algorithm (PFA). - Jonathan Passerat-Palmbach; Jonathan Caux; Yannick Le Pennec; Romain Reuillon; Ivan Junier; François Képès; David R. C. Hill (SIGSIM-PADS, 2013)

Analysis tools for the interplay between genome layout and regulation. - Costas Bouyioukos; Mohamed Elati; François Képès (BMC Bioinform., 2016)

GREAT: a web portal for Genome Regulatory Architecture Tools. - Costas Bouyioukos; François Bucchini; Mohamed Elati; François Képès (Nucleic Acids Res., 2016)