Multiscale Modeling of Alternative Splicing Regulation. - Damien Eveillard; Delphine Ropers; Hidde de Jong; Christiane Branlant; Alexander Bockmayr (CMSB, 2003)

Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing. - Alexander Bockmayr; Arnaud Courtois; Damien Eveillard; M. Vezain (CMSB, 2004)

A multi-scale constraint programming model of alternative splicing regulation. - Damien Eveillard; Delphine Ropers; Hidde de Jong; Christiane Branlant; Alexander Bockmayr (Theor. Comput. Sci., 2004)

Comparing Bacterial Genomes by Searching Their Common Intervals. - Sébastien Angibaud; Damien Eveillard; Guillaume Fertin; Irena Rusu (BICoB, 2009)

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions. - Géraldine Del Mondo; Damien Eveillard; Irena Rusu (Bioinform., 2009)

Temporal constraints of a gene regulatory network: Refining a qualitative simulation. - Jamil Ahmad; Jérémie Bourdon; Damien Eveillard; Jonathan Fromentin; Olivier F. Roux; Christine Sinoquet (Biosyst., 2009)

Including Ordinary Differential Equations Based Constraints in the Standard CP Framework. - Alexandre Goldsztejn; Olivier Mullier; Damien Eveillard; Hiroshi Hosobe (CP, 2010)

Hybrid modeling of biological networks: mixing temporal and qualitative biological properties. - Jonathan Fromentin; Damien Eveillard; Olivier F. Roux (BMC Syst. Biol., 2010)

SIPPER: A flexible method to integrate heterogeneous data into a metabolic network. - Philippe Bordron; Damien Eveillard; Irena Rusu (ICCABS, 2011)

Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network. - Jérémie Bourdon; Damien Eveillard; Anne Siegel (PLoS Comput. Biol., 2011)

An ASP Application in Integrative Biology: Identification of Functional Gene Units. - Philippe Bordron; Damien Eveillard; Alejandro Maass; Anne Siegel; Sven Thiele (LPNMR, 2013)

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming. - Guillaume Collet; Damien Eveillard; Martin Gebser; Sylvain Prigent 001; Torsten Schaub; Anne Siegel; Sven Thiele (LPNMR, 2013)

OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques. - Marko Budinich; Jérémie Bourdon; Abdelhalim Larhlimi; Damien Eveillard (CMSB, 2015)

Deciphering transcriptional regulations coordinating the response to environmental changes. - Vicente Acuña; Andrés Aravena; Carito Guziolowski; Damien Eveillard; Anne Siegel; Alejandro Maass (BMC Bioinform., 2016)

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. - Sylvain Prigent 001; Clémence Frioux; Simon M. Dittami; Sven Thiele; Abdelhalim Larhlimi; Guillaume Collet; Fabien Gutknecht; Jeanne Got; Damien Eveillard; Jérémie Bourdon; Frédéric Plewniak; Thierry Tonon; et al. (PLoS Comput. Biol., 2017)

From Systems Biology to Systems Ecology: A Computational Journey Through Biological Scales. (De la biologie systémique à l'écologie systémique : un voyage informatique à travers les échelles biologiques). - Damien Eveillard (2020)