Nombre de documents


Systems biology, Systems Ecology & Computational Biology

I try to represent the behavior of living systems on different scales by various modeling approaches based on constraint programming. In my opinion, a living system should be formalized as an hybrid automaton under constraints.


My biological studies concern biological systems from molecular to ecological scales, with a special emphasis on marine systems.

Article dans une revue15 documents

  • Julie Laniau, Clémence Frioux, Jacques Nicolas, Caroline Baroukh, Maria-Paz Cortés, et al.. Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. PeerJ, PeerJ, 2017, 5, pp.e3860. 〈10.7717/peerj.3860〉. 〈hal-01635688〉
  • Silvia E. Newell, Damien Eveillard, Mark J. Mccarthy, Wayne S. Gardner, Zhanfei Liu, et al.. A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico. Environmental Microbiology Reports, Wiley, 2014, 6 (1), pp.106 - 112. 〈hal-00951509〉
  • Simon M Dittami, Damien Eveillard, Thierry Tonon. A metabolic approach to study algal-bacterial interactions in changing environments.. Molecular Ecology, Wiley, 2014, 23 (7), pp.1656-60. 〈10.1111/mec.12670〉. 〈hal-00936195〉
  • Richard A Long, Damien Eveillard, Shelli L M Franco, Eric Reeves, James L Pinckney. Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats.. FEMS Microbiology Ecology, Wiley-Blackwell, 2013, 83 (1), pp.74-81. 〈10.1111/j.1574-6941.2012.01457.x〉. 〈hal-00752749〉
  • 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, Wiley-Blackwell, 2012, 14 (3), pp.714-729. 〈10.1111/j.1462-2920.2011.02623.x〉. 〈hal-00661746〉
  • Thierry Tonon, Damien Eveillard, Sylvain Prigent, Jérémie Bourdon, Philippe Potin, et al.. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.. OMICS, Mary Ann Liebert, 2011, 15 (12), pp.883-892. 〈10.1089/omi.2011.0089〉. 〈hal-00661751〉
  • Jérémie Bourdon, Damien Eveillard, Anne Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network.. PLoS Computational Biology, Public Library of Science, 2011, 7 (9), pp.e1002157. 〈10.1371/journal.pcbi.1002157〉. 〈hal-00626708〉
  • Nicholas J Bouskill, Damien Eveillard, Gregory O'Mullan, George A Jackson, Bess B Ward. Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.. Environmental Microbiology, Wiley-Blackwell, 2011, 13 (4), pp.872-886. 〈10.1111/j.1462-2920.2010.02362.x〉. 〈hal-00626710〉
  • P. Bordron, D. Eveillard, I. Rusu. Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.. IET Systems Biology, Institution of Engineering and Technology, 2011, 5 (4), pp.261-268. 〈10.1049/iet-syb.2010.0070〉. 〈hal-00626709〉
  • Etienne Z Gnimpieba, 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, Royal Society of Chemistry, 2011, 7 (8), pp.2508-2521. 〈10.1039/c1mb05102d〉. 〈hal-00626712〉
  • Susan F Martinez, Axelle Renodon-Cornière, Julian Nomme, Damien Eveillard, Fabrice Fleury, et al.. Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination.. Biochimie, Elsevier, 2010, 92 (12), pp.1832-8. 〈10.1016/j.biochi.2010.08.006〉. 〈hal-00626711〉
  • Abalo Chango, Afif Abdel Nour, Souad Bousserouel, Damien Eveillard, Pauline M Anton, et al.. Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium.. Journal of Nutrition Biochemistry, 2009, 20 (4), pp.312-20. 〈10.1016/j.jnutbio.2008.04.004〉. 〈hal-00415914〉
  • Géraldine Del Mondo, Damien Eveillard, Irena Rusu. Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions.. Bioinformatics, Oxford University Press (OUP), 2009, 25 (7), pp.926-32. 〈10.1093/bioinformatics/btp083〉. 〈hal-00415905〉
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Temporal constraints of a gene regulatory network: Refining a qualitative simulation.. BioSystems, Elsevier, 2009, 98 (3), pp.149-159. 〈10.1016/j.biosystems.2009.05.002〉. 〈hal-00415921〉
  • Bess B. Ward, Damien Eveillard, Julie D. Kirshtein, Joshua D. Nelson, Mary A. Voytek, et al.. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. Environmental Microbiology, Wiley-Blackwell, 2007, 9 (10), pp.2522-2538. 〈hal-00346599〉

Communication dans un congrès2 documents

  • Thierry Tonon, P. Bonin, Sylvain Prigent, Z. Shao, Agnès Groisillier, et al.. Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology. Esil 2012: algal post-genomics, Apr 2012, Roscoff, France. 2012. 〈hal-00760640〉
  • Sébastien Angibaud, Damien Eveillard, Guillaume Fertin, Irena Rusu. Comparing Bacterial Genomes by Searching Their Common Intervals. Bioinformatics and Computational Biology, Apr 2009, New Orleans, United States. Springer Verlag, 5462, pp.102--113, 2009, Lecture Note in Bio-Informatics (LNBI). 〈10.1007/978-3-642-00727-9_12〉. 〈hal-00415955〉

Pré-publication, Document de travail2 documents

  • Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach. 10 pages. 2007. 〈hal-00199362〉
  • Jérémie Bourdon, Damien Eveillard. Toll Based Measures for Dynamical Graphs. 11 pages. 2007. 〈hal-00134078〉