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Number of documents

96

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.


Journal articles56 documents

  • Antoine Régimbeau, Marko Budinich, Abdelhalim Larhlimi, Juan José Pierella Karlusich, Olivier Aumont, et al.. Contribution of genome‐scale metabolic modelling to niche theory. Ecology Letters, Wiley, 2022, 25 (6), pp.1352-1364. ⟨10.1111/ele.13954⟩. ⟨hal-03635158⟩
  • Daniel J Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Frémont, et al.. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife, eLife Sciences Publication, In press, ⟨10.1101/867739⟩. ⟨hal-02399723⟩
  • Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, et al.. Environmental vulnerability of the global ocean epipelagic plankton community interactome. Science Advances , American Association for the Advancement of Science (AAAS), 2021, 7 (35), ⟨10.1126/sciadv.abg1921⟩. ⟨hal-03458184⟩
  • Seaver Wang, Weiyi Tang, Erwan Delage, Scott Gifford, Hannah Whitby, et al.. Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic. Scientific Reports, Nature Publishing Group, 2021, 11 (1), ⟨10.1038/s41598-021-84969-1⟩. ⟨hal-03166895⟩
  • Simon M. Dittami, Enrique Arboleda, J.-C. Auguet, Arite Bigalke, Enora Briand, et al.. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ, PeerJ, 2021, 9, pp.e10911. ⟨10.7717/peerj.10911⟩. ⟨hal-03166872⟩
  • Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, et al.. Environmental vulnerability of the global ocean epipelagic plankton community interactome. Science Advances , American Association for the Advancement of Science (AAAS), 2021, 7 (35), pp.eabg1921. ⟨10.1126/sciadv.abg1921⟩. ⟨hal-03329022⟩
  • yajuan Lin, Carly Moreno, Adrian Marchetti, Hugh Ducklow, Oscar Schofield, et al.. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula. Nature Communications, Nature Publishing Group, 2021, 12, pp.4948. ⟨10.1038/s41467-021-25235-w⟩. ⟨hal-03389081⟩
  • Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, et al.. Environmental vulnerability of the global ocean epipelagic plankton community interactome. Science Advances , American Association for the Advancement of Science (AAAS), 2021, 7 (35), pp.eabg1921. ⟨10.1126/sciadv.abg1921⟩. ⟨hal-03443359⟩
  • Alison Murray, John Freudenstein, Simonetta Gribaldo, Roland Hatzenpichler, Philip Hugenholtz, et al.. Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, Nature Publishing Group, 2020, 5 (8), pp.987-994. ⟨10.1038/s41564-020-0733-x⟩. ⟨hal-02863761⟩
  • Hugo Doré, Gregory Farrant, Ulysse Guyet, Julie Haguait, Florian Humily, et al.. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. Frontiers in Microbiology, Frontiers Media, 2020, 11, ⟨10.3389/fmicb.2020.567431⟩. ⟨hal-02938656⟩
  • Alison Murray, Nicole Avalon, Lucas Bishop, Karen Davenport, Erwan Delage, et al.. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica. Marine drugs, MDPI, 2020, 18 (6), pp.298. ⟨10.3390/md18060298⟩. ⟨hal-02862365⟩
  • Shinichi Sunagawa, Silvia G. Acinas, Peer Bork, Chris Bowler, Damien Eveillard, et al.. Tara Oceans: towards global ocean ecosystems biology. Nature Reviews Microbiology, Nature Publishing Group, 2020, 18, pp.428-445. ⟨10.1038/s41579-020-0364-5⟩. ⟨hal-02862376⟩
  • Clarisse Lemonnier, Morgan Perennou, Damien Eveillard, Antonio Fernandez-Guerra, Aude Leynaert, et al.. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. Frontiers in Marine Science, Frontiers Media, 2020, 7, ⟨10.3389/fmars.2020.00376⟩. ⟨hal-03083042⟩
  • Clarisse Lemonnier, Morgan Perennou, Damien Eveillard, Antonio Fernandez-Guerra, Aude Leynaert, et al.. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. Frontiers in Marine Science, Frontiers Media, 2020, 7, ⟨10.3389/fmars.2020.00376⟩. ⟨hal-02938091⟩
  • Ulysse Guyet, Ngoc Thanh Nguyen, Hugo Doré, Julie Haguait, Justine Pittera, et al.. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. Frontiers in Microbiology, Frontiers Media, 2020, 11, ⟨10.3389/fmicb.2020.01707⟩. ⟨hal-02929424⟩
  • Simon Ramondenc, Damien Eveillard, Lionel Guidi, Fabien Lombard, Benoit Delahaye. Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions. Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-62357-5⟩. ⟨hal-02539195⟩
  • Luigi Caputi, Quentin Carradec, Damien Eveillard, Amos Kirilovsky, Eric Pelletier, et al.. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems. Global Biogeochemical Cycles, American Geophysical Union, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩. ⟨hal-02999805⟩
  • Antonietta Capotondi, Michael Jacox, Chris Bowler, Maria Kavanaugh, Patrick Lehodey, et al.. Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems. Frontiers in Marine Science, Frontiers Media, 2019, 6, pp.623. ⟨10.3389/fmars.2019.00623⟩. ⟨hal-02316446⟩
  • Simon Dittami, Enrique Arboleda, J.-C. Auguet, Arite Bigalke, Enora Briand, et al.. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions. PeerJ Preprints, Computer Science Preprints., 2019, 7, pp.e27519v1. ⟨10.7287/peerj.preprints.27519v1⟩. ⟨hal-02169877⟩
  • Damien Eveillard, Nicholas Bouskill, Damien Vintache, Julien Gras, Bess Ward, et al.. Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle. Frontiers in Microbiology, Frontiers Media, 2019, 9, pp.1-9. ⟨10.3389/fmicb.2018.03298⟩. ⟨hal-01996045⟩
  • 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⟩
  • 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⟩
  • Domenico d'Alelio, Damien Eveillard, Victoria Coles, Luigi Caputi, Maurizio Ribera D’alcalà, et al.. Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline. Current Opinion in Systems Biology, Elsevier, 2018, ⟨10.1016/j.coisb.2018.10.003⟩. ⟨hal-01909434⟩
  • 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, 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⟩
  • 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⟩
  • Philippe Bordron, Mauricio Latorre, Maria-Paz Cortés, Mauricio Gonzales, Sven Thiele, et al.. Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. MicrobiologyOpen, Wiley, 2016, 5 (1), pp.106-117. ⟨10.1002/mbo3.315⟩. ⟨hal-01246173⟩
  • 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⟩
  • 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⟩
  • 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. ⟨10.1186/s12859-016-0885-0⟩. ⟨hal-01260866⟩
  • Damien Eveillard, Joanna Jongwane. Un réseau social chez les planctons. Interstices, INRIA, 2016. ⟨hal-01350462⟩
  • 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 L. 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⟩
  • 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⟩
  • 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⟩
  • 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, Society for Applied Microbiology and 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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, Society for Applied Microbiology and Wiley-Blackwell, 2011, 13 (4), pp.872-886. ⟨10.1111/j.1462-2920.2010.02362.x⟩. ⟨hal-00626710⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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.926-932. ⟨10.1093/bioinformatics/btp083⟩. ⟨hal-02352007⟩
  • 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, pp.10.1016/j.biosystems.2009.05.002. ⟨10.1016/j.biosystems.2009.05.002⟩. ⟨hal-00423353⟩
  • 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 Nutritional Biochemistry, Elsevier, 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, 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, Society for Applied Microbiology and 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⟩

Conference papers19 documents

  • Nayat Sanchez-Pi, Luis Marti, André Abreu, Olivier Bernard, Colomban de Vargas, et al.. Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change. NeurIPS 2020 Workshop - Tackling Climate Change with Machine Learning, Dec 2020, Santiago / Virtual, Chile. ⟨hal-03138712⟩
  • 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, GDR Génomique Environnementale, Sep 2017, Marseille, France. ⟨hal-01576743⟩
  • Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard. OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques. 13th International Conference on Computational Methods in Systems Biology CMSB 2015, Sep 2015, Nantes, France. pp.279-281, ⟨10.1007/978-3-319-23401-4_23⟩. ⟨hal-02464859⟩
  • 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⟩
  • 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. ⟨hal-00853752⟩
  • 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. ⟨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, 2013, ⟨10.1007/978-3-642-40564-8_25⟩. ⟨hal-02745669⟩
  • Thierry Tonon, Patricia 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. ⟨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, ⟨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. 1st International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011), 2011, Singapore, Singapore. pp.101-105. ⟨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. pp.221--235. ⟨hal-00520054⟩
  • Sébastien Angibaud, Damien Eveillard, Guillaume Fertin, Irena Rusu. Comparing Bacterial Genomes by Searching their Common Intervals. 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), 2009, New Orleans, United States. pp.102-113. ⟨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. pp.102--113, ⟨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. ⟨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. ⟨inria-00000915⟩
  • Alexander Bockmayr, Arnaud Courtois, Damien Eveillard, Myriam Vezain. Building and analysing an integrative model of HIV-1 RNA alternative splicing. International Conference on Computational Methods in Systems Biology - CMSB 2004, May 2004, Paris/France, pp.43--57, ⟨10.1007/b107287⟩. ⟨inria-00000917⟩
  • 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. ⟨inria-00099705⟩
  • Damien Eveillard, Delphine Ropers, Hidde de Jong, Christiane Branlant, Alexander Bockmayr. Multiscale modeling of alternative splicing regulation. International Workshop on Computational Methods in Systems Biology - CMSB'03, 2003, Rovereto, Italie, pp.75-87. ⟨inria-00099792⟩
  • Damien Eveillard, yann Guermeur. Traitement statistique des résultats SELEX. Journées Ouvertes en Biologie Informatiques et Mathématiques - JOBIM 2002, Jacques Nicolas & Claude Thermes, Jun 2002, Saint Malo - France, pp.277--283. ⟨inria-00000918⟩

Books1 document

  • Nayat Sanchez-Pi, Luis Marti, Julien Salomon, Jacques Sainte-Marie, Olivier Bernard, et al.. OcéanIA: AI, Data, and Models for Understanding the Ocean and Climate Change. pp.1-64, 2021. ⟨hal-03274323v2⟩

Book sections7 documents

  • Lucie Bittner, Lionel Guidi, Samuel Chaffron, Damien Eveillard. Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique. Laurent Palka. Microbiodiversité : un nouveau regard, 161 - 185, editions matériologiques, 2018. ⟨hal-01996304⟩
  • 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, Anne Siegel, Philippe Vandenkoornhuyse. L’écologie des systèmes. CNRS éditions. Les big data à découvert, Mokrane Bouzeghoub et Rémy Mosseri, 2017, 978-2-271-11464-8. ⟨hal-02389705⟩
  • Damien Eveillard, Xavier Raynaud, Jérémie Bourdon, Alain A. 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⟩
  • Frédéric Austerlitz, Michael Blum, Sarah Calba, Jérôme Chave, Marc Choisy, et al.. Ecologie prédictive & changement planétaire. Thiébault; Stéphanie and Hadi; Halima. Prospective de l'Institut écologie & environnement du CNRS, hors s\'rie, Institut écologie & environnement du CNRS, pp.9-44, 2013. ⟨hal-01911607⟩
  • Damien Eveillard, Xavier Raynaud, Jérémie Bourdon, Alain A 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⟩

Preprints, Working Papers, ...9 documents

  • Janaina Rigonato, Marko Budinich, Alejandro Murillo, Manoela Brandão, Juan Karlusich, et al.. Insights into biotic and abiotic modulation of ocean mesopelagic communities. 2021. ⟨hal-03166899⟩
  • Samuel Chaffron, Erwan Delage, M. Budinich, N. Henry, C. Nef, et al.. Environmental vulnerability of the global ocean plankton community interactome. 2021. ⟨hal-03097196⟩
  • Antoine Régimbeau, Marko Budinich, Abdelhalim Larhlimi, Juan Jose Pierella Karlusich, Olivier Aumont, et al.. Contribution of genome scale metabolic modeling to niche theory. 2021. ⟨hal-03352833⟩
  • Marta Royo-Llonch, Pablo Sánchez, Clara Ruiz-González, Guillem Salazar, Carlos Pedrós-Alió, et al.. Ecogenomics of key prokaryotes in the arctic ocean. 2020. ⟨hal-02946895⟩
  • Julie Laniau, Anne Siegel, Damien Eveillard. Combinatorial optimization methods to complete and analyse a metabolic network. 2015. ⟨hal-01244179⟩
  • Marko Budinich, Jérémie Bourdon, Damien Eveillard. Impact of the species compartment definition on quantitative modeling of microbial communities. 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. 2009. ⟨hal-00359530⟩
  • Jérémie Bourdon, Damien Eveillard. Toll Based Measures for Dynamical Graphs. 2007. ⟨hal-00134078⟩
  • Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach. 2007. ⟨hal-00199362⟩

Reports3 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⟩

Theses1 document

  • Damien Eveillard. Modélisation statistique et formelle de la régulation de l'épissage alternatif. Biologie moléculaire. Université Henri Poincaré - Nancy 1, 2004. Français. ⟨NNT : 2004NAN10037⟩. ⟨tel-01754419⟩