Co-auteurs

Nombre de documents

62

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 revue35 documents

  • Dinka Mandakovic, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, et al.. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Scientific Reports, Nature Publishing Group, 2018, 8 (1), pp.5875. 〈10.1038/s41598-018-23931-0〉. 〈hal-01774624〉
  • S. Thiriet-Rupert, Gregory Carrier, C. Trottier, Damien Eveillard, B. Schoefs, et al.. Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea. Algal Research - Biomass, Biofuels and Bioproducts, Elsevier, 2018, 30, pp.59 - 72. 〈10.1016/j.algal.2017.12.011〉. 〈hal-01677336〉
  • Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.. PLoS ONE, Public Library of Science, 2017, 12 (2), pp.e0171744. 〈hal-01478375〉
  • Julie Laniau, Clémence Frioux, Jacques Nicolas, Caroline Baroukh, María 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〉
  • Benoît Delahaye, Damien Eveillard, Nicholas Bouskill. On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore. mSystems, 2017, 2 (6), 〈10.1128/mSystems.00169-17〉. 〈hal-01658218〉
  • Sylvain Prigent, Clémence Frioux, Simon M Dittami, Sven Thiele, Abdelhalim Larhlimi, et al.. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Computational Biology, Public Library of Science, 2017, 13 (1), pp.32. 〈10.1371/journal.pcbi.1005276〉. 〈hal-01449100〉
  • François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Frontiers in Microbiology, Frontiers Media, 2017, 8, pp.article 1808. 〈10.3389/fmicb.2017.01808〉. 〈hal-01613034〉
  • Damien Eveillard, Joanna Jongwane. Un réseau social chez les planctons. Interstices, INRIA, 2016, 〈https://interstices.info/jcms/p_89505/un-reseau-social-chez-les-planctons〉. 〈hal-01350462〉
  • Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, et al.. Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.129-42. 〈hal-01260866〉
  • Alix Mas, Shahrad Jamshidi, Yvan Lagadeuc, Damien Eveillard, Philippe Vandenkoornhuyse. Beyond the Black Queen Hypothesis.. ISME Journal, Nature Publishing Group, 2016, 10 (9), pp.2085-2091. 〈10.1038/ismej.2016.22〉. 〈hal-01290210〉
  • Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, et al.. Plankton networks driving carbon export in the oligotrophic ocean. Nature, Nature Publishing Group, 2016, 532, pp.465-470. 〈10.1038/nature16942〉. 〈hal-01275276〉
  • 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, Elsevier, 2015, 311, pp.11-19. 〈10.1016/j.ecolmodel.2015.04.021〉. 〈hal-01158560〉
  • 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, Elsevier, 2015, 311, pp.11-19. 〈10.1016/j.ecolmodel.2015.04.021〉. 〈hal-01157450〉
  • Nicolas Mouquet, Yvan Lagadeuc, Vincent Devictor, Luc Doyen, Anne Duputié, et al.. Predictive ecology in a changing world . Journal of Applied Ecology, Wiley, 2015, 52 (5), pp.1293-1310. 〈10.1111/1365-2664.12482〉. 〈hal-01180277〉
  • Philippe Bordron, Mauricio Latorre, María Paz Cortés, Mauricio Gonzales, Sven Thiele, et al.. Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. MicrobiologyOpen, Wiley, 2015, 5 (1), pp.106-117. 〈http://onlinelibrary.wiley.com/doi/10.1002/mbo3.315/full〉. 〈10.1002/mbo3.315〉. 〈hal-01246173〉
  • Sylvain Prigent, Guillaume Collet, Simon M Dittami, Ludovic Delage, Floriane Ethis de Corny, et al.. The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.. Plant Journal, Wiley, 2014, 80 (2), pp.367-381. 〈10.1111/tpj.12627〉. 〈hal-01057153〉
  • 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〉
  • Thierry Tonon, Damien Eveillard. Marine systems biology.. Frontiers in Genetics, Frontiers, 2014, 6, pp.181. 〈hal-01161455〉
  • 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〉
  • 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〉
  • 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〉
  • 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〉
  • 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〉
  • 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〉
  • Jonathan Fromentin, Damien Eveillard, Olivier Roux. Hybrid Modeling of Gene Regulatory Networks: Mixing Temporal and Qualitative Biological Properties. BMC Systems Biology, BioMed Central, 2010, 4 (79), http://www.biomedcentral.com/1752-0509/4/79/abstract. 〈10.1186/1752-0509-4-79〉. 〈hal-00346588〉
  • Sf Martinez, A. Renodon-Cornière, J. Nomme, D. Eveillard, F. Fleury, et al.. Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination. Biochimie, Elsevier, 2010, 92 (12), pp.1832-1838. 〈hal-00549787〉
  • 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〉
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Temporal constraints of a gene regulatory network: refining a qualitative simulation. BioSystems, Special Issue on Gene Regulatory Networks, 2009, pp.10.1016/j.biosystems.2009.05.002. 〈10.1016/j.biosystems.2009.05.002〉. 〈hal-00423353〉
  • 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〉
  • 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〉
  • 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〉
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. A multi-scale constraint programming model of alternative splicing regulation. Theoretical Computer Science, Elsevier, 2004, Special issue: computational systems biology, 325 (1), pp.3-24. 〈10.1016/j.tcs.2004.03.062〉. 〈inria-00000916〉

Communication dans un congrès16 documents

  • Victoria Potdevin, Marie Chevallier, Ruben Garrido Oter, Anne Siegel, Stéphane Hacquard, et al.. Toward a better understanding of the plant microbiota. 4ème colloque de Génomique Environnementale, Sep 2017, Marseille, France. 〈https://ge2017.sciencesconf.org/〉. 〈hal-01576743〉
  • Damien Eveillard, Lionel Guidi, Lucie Bittner, Samuel Chaffron, Jeroen Raes, et al.. Revealing and analyzing networks of marine microbial ecosystems . Conférence Jacques Monod - Marine Ecosystems Biology, 2015, Roscoff, France. 〈hal-01176727〉
  • Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, Sven Thiele. An ASP application in integrative biology: identification of functional gene units. LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain. 2013. 〈hal-00853762〉
  • Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, et al.. Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming. LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain. 2013. 〈hal-00853752〉
  • 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〉
  • Philippe Bordron, Damien Eveillard, Irena Rusu. SIPPER: A flexible method to integrate heterogeneous data into a metabolic network. Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on, Feb 2011, Orlando, United States. pp.40 - 45, 2011, 〈10.1109/ICCABS.2011.5729937〉. 〈hal-00585102〉
  • Sébastien Angibaud, Philippe Bordron, Damien Eveillard, Guillaume Fertin, Irena Rusu. Integration of omics data to investigate common intervals. IEEE. 1st International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011), 2011, Singapore, Singapore. pp.101-105, 2011. 〈hal-00606226〉
  • 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, CP2010, Sep 2010, St Andrews, United Kingdom. Springer Verlag, 6308, pp.221--235, 2010. 〈hal-00520054〉
  • Sébastien Angibaud, Damien Eveillard, Guillaume Fertin, Irena Rusu. Comparing Bacterial Genomes by Searching their Common Intervals. Springer-Verlag. 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), 2009, New Orleans, United States. Springer-Verlag, Lecture Notes in BioInformatics (LNBI) (5462), pp.102-113, 2009, Lecture Notes in BioInformatics (LNBI). 〈hal-00416466〉
  • 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〉
  • Damien Eveillard, Jonathan Fromentin, Olivier Roux. Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches. Workshop on Constraint Based Methods for Bioinformatics (WCB08), 2008, Paris, France. pp.10, 2008. 〈hal-00277104〉
  • Damien Eveillard, Abdelhalim Larhlimi, Delphine Ropers, Stéphanie Billaut, Sandrine Peyrefitte. KOALAB: A new method for regulatory motif search. Illustration on alternative splicing regulation in HIV-1. 5èmes Journées Ouvertes Biologie Informatique Mathématiques - JOBIM 2004, Jun 2004, Montréal, Canada, 2004. 〈inria-00000915〉
  • Alexander Bockmayr, Arnaud Courtois, Damien Eveillard, Myriam Vezain. Building and analysing an integrative model of HIV-1 RNA alternative splicing. Vincent Danos & Vincent Schachter. International Conference on Computational Methods in Systems Biology - CMSB 2004, May 2004, Paris/France, Springer-Verlag, 3082, pp.43--57, 2004, Lecture Notes in Bioinformatics. 〈10.1007/b107287〉. 〈inria-00000917〉
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. Multiscale modeling of alternative splicing regulation. Corrado Priami. International Workshop on Computational Methods in Systems Biology - CMSB'03, 2003, Rovereto, Italie, Springer-Verlag, 2602, pp.75-87, 2003, Lecture Notes in Computer Science. 〈inria-00099792〉
  • Damien Eveillard, Arnaud Courtois, Alexander Bockmayr. Hybrid concurrent constraint programming: A well-suited formalism for modelling alternative splicing regulation (Abstract). Modeling and Simulation of Biological Regulatory Processes - ECCB Satellite Meeting, 2003, Paris, France, 2003. 〈inria-00099705〉
  • Damien Eveillard, Yann Guermeur. Traitement statistique des résultats SELEX. Journées Ouvertes en Biologie Informatiques et Mathématiques - JOBIM 2002, Jun 2002, Saint Malo - France, pp.277--283, 2002. 〈inria-00000918〉

Chapitre d'ouvrage4 documents

  • Damien Eveillard, Anne Siegel, Philippe Vandenkoornhuyse. L'écologie des systèmes. Mokrane Bouzeghoub et Rémy Mosseri. Les Big Data à Découvert, CNRS éditions, 2017, 978-2-271-11464-8. 〈hal-01575603〉
  • Damien Eveillard, Xavier Raynaud, Jérémie Bourdon, Alain Franc, Frederic Plewniak. Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes. La génomique environnemetale : la révolution du séquençage à haut débit , 2016. 〈hal-01777358〉
  • Damien Eveillard, Xavier Raynaud, Jérémie Bourdon, Alain Franc, Frederic Plewniak. XII Des données haut-débit à la modélisation des écosystèmes. Prospective Génomique Environnementale, pp.83-89, 2013. 〈hal-01176570〉
  • Jérémie Bourdon, Damien Eveillard. Probabilistic Approaches for Investigating Biological Networks. Mourad Elloumi, Albert Y. Zomaya. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley, pp.1066, 2011. 〈hal-00531568〉

Pré-publication, Document de travail4 documents

  • Marko Budinich, Jérémie Bourdon, Damien Eveillard. Impact of the species compartment definition on quantitative modeling of microbial communities. LINA-COMBI; ACLN. 2015. 〈hal-01145858〉
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Qualitative modelling and analysis of gene regulatory networks: application to the adaptation of Escherichia coli bacterium to carbon availability. first submitted under the present form to obtain a HAL number for the cover page. 2009. 〈hal-00359530〉
  • Jérémie Bourdon, Damien Eveillard. Toll Based Measures for Dynamical Graphs. 11 pages. 2007. 〈hal-00134078〉
  • Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach. 10 pages. 2007. 〈hal-00199362〉

Rapport3 documents

  • Marko Budinich, Damien Eveillard, Jérémie Bourdon, Abdelhalim Larhlimi. MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network. 2013. 〈hal-00839321〉
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. A Multi-Site Constraint Programming Model of Alternative Splicing Regulation. [Research Report] RR-4830, INRIA. 2003. 〈inria-00071756〉
  • Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr. Modeling the effects of SR proteins on alternative splicing. [Intern report] A02-R-117 || eveillard02b, 2002, 8 p. 〈inria-00101060〉