Selected publications

 

  1. ๏Laniau Julie, Frioux Clémence, Nicolas Jacques, Baroukh Caroline, Cortés Maria-Paz, Got Jeanne, Trottier Camille, Eveillard Damien, Siegel Anne. Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. PeerJ. 2017;5: e3860. doi:10.7717/peerj.3860

  2. ๏Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard.  A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PLoS ONE, 12, e0171744, 2017.

  3. ๏Prigent,S. et al. (2017) Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput Biol, 13, e1005276.

  4. ๏Alix Mas, Shahrad Jamshidi, Yvan Lagadeuc, Damien Eveillard & Philippe Vandenkoornhuyse. Beyond the Black Queen Hypothesis. ISME J., 2016  doi:10.1038/ismej.2016.22


  1. ๏Marko Budinich,  Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard. Evolutionary Constraint-Based Formulation Requires New Bi-Level Solving Techniques. Computational Methods in Systems Biology, CMSB’15, Nantes, Springer LNBI 9308:279-281, 2015


  1. ๏Nicolas Mouquet, Yvan Lagadeuc, Vincent Devictor, Luc Doyen, Anne Duputié, Damien Eveillard, Denis Faure, et. al.. Predictive ecology in a changing world. Journal of Applied Ecology. vol. 52(5): 1293-1310, 2015


  1. ๏Shahrad Jamshidi, Jocelyn E. Behm, Damien Eveillard, E. Toby Kiers & Philippe Vandenkoornhuyse.  Using Hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism. Ecological Modelling vol. 311: 11- 19, 2015.


  1. ๏Thierry Tonon & Damien Eveillard. Marine Systems Biology. Frontiers in Genetics vol. 6(181): DOI 10.3389/fgene.2015.00181, 2015.


  1. ๏Jérémie Bourdon, Damien Eveillard & Anne Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network. PLoS Computational Biology vol. 7(9): e1002157, 2011.

  2. ๏Etienne Zohim, Damien Eveillard, Jean-Louis Guéant & Abalo Chango. Using Logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes. Molecular BioSystems, vol 7, 2508 - 2521, 2011 

  3. ๏Jérémie Bourdon & Damien Eveillard. Probabilistic Approaches for Investigating Biological Networks, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (eds M. Elloumi and A. Y. Zomaya), pp 893-913, John Wiley & Sons, Inc., Hoboken, NJ, USA, 2011. doi: 10.1002/9780470892107.ch38

  4. ๏Alexandre Goldsztejn, Olivier Mullier, Damien Eveillard, & Hiroshi Hosobe. Including ordinary differential equations based constraints in the standard CP framework. Principles and Practice of Constraint Programming, CP 2010, Springer LNCS 6308, 221-235. 2010

  5. ๏Jonathan Fromentin, Damien Eveillard & Olivier Roux. Hybrid modeling of biological networks: Mixing temporal and qualitative properties. BMC Systems Biology, vol 4 (79), 2010.

  6. ๏Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, Christine Sinoquet. Temporal constraints of a gene regulatory network: refining a qualitative simulation. Biosystems, vol 98 (3) pp 149-59, 2009.

  7. ๏Damien Eveillard, Jonathan Fromentin & Olivier Roux. Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches. Workshop on Constraint Based Methods for Bioinformatics (WCB08),  2008. also available as Technical Report HAL: hal-00277104, Mar 2008

  8. ๏Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach. RIAMS 2007, also available as Technical Report arXiv, q-bio.QM, Dec 2007. 10 pages.

  9. ๏Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr. A multi-scale constraint programming model of alternative splicing regulation. Theoretical Computer Science, 325(1):3—24, Sep 2004.

  10. ๏Alexander Bockmayr, Arnaud Courtois, Damien Eveillard, M Vezain. Building and analysing an integrative model of HIV-1 RNA alternative splicing. Computational Methods in Systems Biology, CMSB’04, Paris, Springer LNBI 3082:43–57, 2004.

  11. ๏Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant & Alexander Bockmayr. Multiscale modeling of alternative splicing regulation: Computational Methods in Systems Biology, CMSB'03, Rovereto, Italy, 2003. Springer LNCS 2602, 75-87. 2003

Ecological / Biological Modeling

Ecological / Biological system investigations & Bioinformatics

  1. ๏Thomas, François, Bordron, Philippe, Eveillard, Damien & Michel, Gurvan, Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Front Microbiol 8, 1808 (2017).

  2. ๏Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abelhalim Larhlimi, Simon Roux et al., Plankton network driving carbon export in the oligotrophic ocean. Nature. 532, 465--470, 2016.

  3. ๏Philippe Bordron,  Mauricio Latorre, Maria-Paz Cortés, Mauricio González, Sven Thiele, Anne Siegel, Alejandro Maass & Damien Eveillard. Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. MicrobiologyOpen. vol 5(1):106-17, 2016. doi: 10.1002/mbo3.315

  4. ๏Acuña V, Aravena A, Guziolowski C, Eveillard D, Siegel A, Maass A. Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinformatics.17: 35, 2016 doi:10.1186/s12859-016-0885-0

  5. ๏Sylvain Prigent, Guillaume Collet, Simon Dittami, Ludovic Delage, Floriane Ethis de Corny, Olivier Dameron, Damien Eveillard, Sven Thiele, Jeanne Cambefort, Catherin Boyen, Anne Siegel & Thierry Tonon.  The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. The Plant Journal, 80(2) pp. 367-381, 2014

  6. ๏Simon Dittami, Damien Eveillard & Thierry Tonon. A metabolic approach to study algal-bacterial interactions in changing environments. Molecular Ecology vol.7 pp. 1656-60, 2014

  7. ๏Silvia E. Newell, Damien Eveillard, Mark J. McCarthy, Wayne S. Gardner, Zhanfei Liu & Bess B. Ward.  A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico. Environmental Microbiology Reports, vol.6(1) pp. 106-112, 2014

  8. ๏Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel & Sven Thiele. Extending the metabolic network of Ectocarpus siliculosus using Answer Set Programming. International Conference on Logic Programming and Nonmonotonic Reasonning, LPMNR‘2013, Corunna, Spain 2013. Springer LNAI 8148, pp 245-256, 2013.

  9. ๏Philippe Bordron, Damien Eveillard, Alejandro Maass & Anne Siegel. An ASP application in integrative biology: identification of functional gene units. International Conference on Logic Programming and Nonmonotonic Reasonning, LPMNR‘2013, Corunna, Spain 2013. Springer LNAI 8148, pp 206-218, 2013.

  10. ๏Richard Long, Damien Eveillard, Shelli Franco, Eric Reeves & James Pinckney. Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats. FEMS Microbiology Ecology, vol.83 pp. 74-81, 2013

  11. ๏Nicholas J. Bouskill, Damien Eveillard, Diana Chien, Amal Jayakumar & Bess B. Ward. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments. Environmental Microbiology vol. 14 (13) pp. 714-729, 2012

  12. ๏Thierry Tonon, Damien Eveillard, Sylvain Prigent, Jérémie Bourdon, Philippe Potin, Catherine Boyen & Anne Siegel. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. Omics: A journal of Integrative Biology vol. 15 (12) pp. 1-10, 2011

  13. ๏Philippe Bordron, Damien Eveillard & Irena Rusu. Integrated analysis of the gene neighboring impact on bacterial metabolic networks. IET Systems Biology. vol.5(4) pp. 261 - 268, 2011.

  14. ๏Philippe Bordron, Damien Eveillard & Irena Rusu. SIPPER: a flexible method to integrate heterogeneous data into a metabolic network. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICABS), 40 - 45, 2011.

  15. ๏Nicholas J. Bouskill, Damien Eveillard, Gregory O’Mullan, George A. Jackson & Bess B. Ward. Seasonal and annual reoccurrence in Ammonia-oxidizing bacterial population structure.  Environmental Microbiology, vol.13 (4), pp 872 -886, 2011.

  16. ๏Sébastien Angibaud, Philippe Bordron, Damien Eveillard, Guillaume Fertin & Irena Rusu. Integration of omics data to investigate common intervals. International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011), IEEE, pp. 101-105, 2011. rp023_ICBBB2011-X00036.pdf

  17. ๏Susan F. Martinez, Axelle Renodon-Cornière, Julian Nomme, Damien Eveillard, Fabrice Fleury, Masayuki Takahashi & Pierre Weigel. Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination. Biochimie vol. 92 (12) pp. 1832-8, 2010.

  18. ๏Géraldine Del Mondo, Damien Eveillard & Irena Rusu. Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions. Bioinformatics, vol. 25 (7) pp. 926-32, 2009.

  19. ๏Abalo Chango, Afif Abdel Nour, Souad Bousserouel, Damien Eveillard, Pauline M. Anton, Jean-Louis Guéant. Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium. Journal of Nutritional Biochemistry, vol. 20 (4) pp. 312-20, 2009.

  20. ๏Sébastien Angibaud, Damien Eveillard, Guillaume Fertin & Irena Rusu. Comparing Bacterial Genomes by Searching their Common Intervals. International Conference on Bioinformatics and Computational Biology (BICoB) 2009, volume 5462, Springer LNBI,102--113, 2009.

  21. ๏Bess B Ward, Damien Eveillard, Julie D Kirshtein, Joshua D Nelson, Mary A Voytek, George A Jackson. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environmental Microbiology, 9(10):2522–38, 2007.