Home » Fiche   membre
Fiche   membre Retour à l'annuaire  

Damien EVEILLARD

ENSEIGNANT-CHERCHEUR

Ass. Professor
Responsable d'équipe
Equipe : COMBI.

: Damien.Eveillardatls2n.fr

: +33 (0)2 51 12 59 85

Page pro : http://pagesperso.ls2n.fr/~eveillard-d

Adresse :

Université de Nantes - faculté des Sciences et Techniques ( FST )
Petit Port
2 Chemin de la Houssinière
BP 92208
44322 Nantes Cedex 3

Batiment 34, étage 3, bureau 310



Publications référencées sur HAL

Revues internationales avec comité de lecture (ART_INT)

    • [1] D. Eveillard, N. Bouskill, D. Vintache, J. Gras, B. Ward, J. Bourdon. Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle. In Frontiers in Microbiology ; éd. Frontiers Media, 2019, vol. 9.
      https://hal.archives-ouvertes.fr/hal-01996045
    • [2] S. Thiriet-Rupert, G. Carrier, C. Trottier, D. Eveillard, B. Schoefs, G. Bougaran, J. Cadoret, B. Chénais, B. Saint-Jean. Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea. In Algal Research - Biomass, Biofuels and Bioproducts ; éd. Elsevier, 2018, vol. 30.
      https://hal.archives-ouvertes.fr/hal-01677336
    • [3] D. D'Alelio, D. Eveillard, V. Coles, L. Caputi, M. Ribera d’Alcalà, D. Iudicone. Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline. In Current Opinion in Systems Biology ; éd. Elsevier, 2018.
      https://hal.archives-ouvertes.fr/hal-01909434
    • [4] D. Mandakovic, C. Rojas, J. Maldonado, M. Latorre, D. Travisany, E. Delage, A. Bihouee, G. Jean, F. Diaz, B. Fernández-Gómez, P. Cabrera, A. Gaete, C. Latorre, R. Gutierrez, A. Maass, V. Cambiazo, S. Navarrete, D. Eveillard, M. Gonzalez. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. In Scientific Reports ; éd. Nature Publishing Group, 2018, vol. 8, num. 1.
      https://hal.archives-ouvertes.fr/hal-01774624
    • [5] J. Laniau, C. Frioux, J. Nicolas, C. Baroukh, M. Cortés, J. Got, C. Trottier, D. Eveillard, A. Siegel. Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. In PeerJ ; éd. PeerJ, 2017, vol. 5.
      https://hal.archives-ouvertes.fr/hal-01635688
    • [6] S. Prigent, C. Frioux, S. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. In PLoS Computational Biology ; éd. Public Library of Science, 2017, vol. 13, num. 1.
      https://hal.inria.fr/hal-01449100
    • [7] M. Budinich, J. Bourdon, A. Larhlimi, D. Eveillard. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.. In PLoS ONE ; éd. Public Library of Science, 2017, vol. 12, num. 2.
      https://hal.archives-ouvertes.fr/hal-01478375
    • [8] F. Thomas, P. Bordron, D. Eveillard, G. Michel. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. In Frontiers in Microbiology ; éd. Frontiers Media, 2017, vol. 8.
      https://hal.archives-ouvertes.fr/hal-01613034
    • [10] V. Acuña, A. Aravena, C. Guziolowski, D. Eveillard, A. Siegel, A. Maass. Deciphering transcriptional regulations coordinating the response to environmental changes. In BMC Bioinformatics ; éd. BioMed Central, 2016, vol. 17, num. 1.
      https://hal.archives-ouvertes.fr/hal-01260866
    • [11] L. Guidi, S. Chaffron, L. Bittner, D. Eveillard, A. Larhlimi, S. Roux, Y. Darzi, S. Audic, L. Berline, J. Brum, L. Coelho, J. Espinoza, S. Malviya, S. Sunagawa, C. Dimier, S. Kandels-Lewis, M. Picheral, J. Poulain, S. Searson, L. Stemmann, F. Not, P. Hingamp, S. Speich, M. Follows, L. Karp-Boss, E. Boss, H. Ogata, S. Pesant, J. Weissenbach, P. Wincker, S. Acinas, P. Bork, D. Iudicone, M. Sullivan, J. Raes, E. Karsenti, C. Bowler, G. Gorsky. Plankton networks driving carbon export in the oligotrophic ocean. In Nature ; éd. Nature Publishing Group, 2016, vol. 532.
      https://hal.sorbonne-universite.fr/hal-01275276
    • [12] A. Mas, S. Jamshidi, Y. Lagadeuc, D. Eveillard, P. Vandenkoornhuyse. Beyond the Black Queen Hypothesis.. In ISME Journal ; éd. Nature Publishing Group, 2016, vol. 10, num. 9.
      https://hal.archives-ouvertes.fr/hal-01290210
    • [13] N. Mouquet, Y. Lagadeuc, V. Devictor, L. Doyen, A. Duputié, D. Eveillard, D. Faure, E. Garnier, O. Gimenez, P. Huneman, F. Jabot, P. Jarne, D. Joly, R. Julliard, S. Kéfi, G. Kergoat, S. Lavorel, L. Le Gall, L. Meslin, S. Morand, X. Morin, H. Morlon, G. Pinay, R. Pradel, F. Schurr, W. Thuiller, M. Loreau. Predictive ecology in a changing world. In Journal of Applied Ecology ; éd. Wiley, 2015, vol. 52, num. 5.
      https://hal.archives-ouvertes.fr/hal-01180277
    • [14] P. Bordron, M. Latorre, M. Cortés, M. Gonzales, S. Thiele, A. Siegel, A. Maass, D. Eveillard. Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. In MicrobiologyOpen ; éd. Wiley, 2015, vol. 5, num. 1.
      https://hal.inria.fr/hal-01246173
    • [15] S. Jamshidi, J. Behm, D. Eveillard, E. Kiers, P. Vandenkoornhuyse. Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism. In Ecological Modelling ; éd. Elsevier, 2015, vol. 311.
      https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158560
    • [16] S. Jamshidi, J. Behm, D. Eveillard, E. Kiers, P. Vandenkoornhuyse. Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism. In Ecological Modelling ; éd. Elsevier, 2015, vol. 311.
      https://hal.archives-ouvertes.fr/hal-01157450
    • [17] S. E. Newell, D. Eveillard, M. J. Mccarthy, W. S. Gardner, Z. Liu, B. B. Ward. A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico. In Environmental Microbiology Reports ; éd. Wiley, 2014, vol. 6, num. 1.
      https://hal.archives-ouvertes.fr/hal-00951509
    • [18] S. Dittami, D. Eveillard, T. Tonon. A metabolic approach to study algal-bacterial interactions in changing environments.. In Molecular Ecology ; éd. Wiley, 2014, vol. 23, num. 7.
      https://hal.archives-ouvertes.fr/hal-00936195
    • [19] S. Prigent, G. Collet, S. Dittami, L. Delage, F. Ethis de Corny, O. Dameron, D. Eveillard, S. Thiele, J. Cambefort, C. Boyen, A. Siegel, T. Tonon. The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.. In Plant Journal ; éd. Wiley, 2014, vol. 80, num. 2.
      https://hal.archives-ouvertes.fr/hal-01057153
    • [21] R. Long, D. Eveillard, S. Franco, E. Reeves, J. Pinckney. Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats.. In FEMS Microbiology Ecology ; éd. Wiley-Blackwell, 2013, vol. 83, num. 1.
      https://hal.archives-ouvertes.fr/hal-00752749
    • [22] N. Bouskill, D. Eveillard, D. Chien, A. Jayakumar, B. Ward. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.. In Environmental Microbiology ; éd. Wiley-Blackwell, 2012, vol. 14, num. 3.
      https://hal.archives-ouvertes.fr/hal-00661746
    • [23] N. Bouskill, D. Eveillard, G. O'Mullan, G. Jackson, B. Ward. Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.. In Environmental Microbiology ; éd. Wiley-Blackwell, 2011, vol. 13, num. 4.
      https://hal.archives-ouvertes.fr/hal-00626710
    • [24] P. Bordron, D. Eveillard, I. Rusu. Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.. In IET Systems Biology ; éd. Institution of Engineering and Technology, 2011, vol. 5, num. 4.
      https://hal.archives-ouvertes.fr/hal-00626709
    • [25] E. Gnimpieba, D. Eveillard, J. Guéant, A. Chango. Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes.. In Molecular BioSystems ; éd. Royal Society of Chemistry, 2011, vol. 7, num. 8.
      https://hal.archives-ouvertes.fr/hal-00626712
    • [26] J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network.. In PLoS Computational Biology ; éd. Public Library of Science, 2011, vol. 7, num. 9.
      https://hal.archives-ouvertes.fr/hal-00626708
    • [27] T. Tonon, D. Eveillard, S. Prigent, J. Bourdon, P. Potin, C. Boyen, A. Siegel. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.. In OMICS ; éd. Mary Ann Liebert, 2011, vol. 15, num. 12.
      https://hal.archives-ouvertes.fr/hal-00661751
    • [28] J. Fromentin, D. Eveillard, O. Roux. Hybrid Modeling of Gene Regulatory Networks: Mixing Temporal and Qualitative Biological Properties. In BMC Systems Biology ; éd. BioMed Central, 2010, vol. 4, num. 79.
      https://hal.archives-ouvertes.fr/hal-00346588
    • [29] S. Martinez, A. Renodon-Cornière, J. Nomme, D. Eveillard, F. Fleury, M. Takahashi, P. Weigel. Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination. In Biochimie ; éd. Elsevier, 2010, vol. 92, num. 12.
      https://hal.archives-ouvertes.fr/hal-00549787
    • [30] S. Martinez, A. Renodon-Cornière, J. Nomme, D. Eveillard, F. Fleury, M. Takahashi, P. Weigel. Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination.. In Biochimie ; éd. Elsevier, 2010, vol. 92, num. 12.
      https://hal.archives-ouvertes.fr/hal-00626711
    • [31] A. Chango, A. Nour, S. Bousserouel, D. Eveillard, P. Anton, J. Guéant. Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium.. In Journal of Nutrition Biochemistry, vol. 20, num. 4. 04-2009
      https://hal.archives-ouvertes.fr/hal-00415914
    • [32] G. Del Mondo, D. Eveillard, I. Rusu. Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions.. In Bioinformatics ; éd. Oxford University Press (OUP), 2009, vol. 25, num. 7.
      https://hal.archives-ouvertes.fr/hal-00415905
    • [33] J. Ahmad, J. Bourdon, D. Eveillard, J. Fromentin, O. Roux, C. Sinoquet. Temporal constraints of a gene regulatory network: Refining a qualitative simulation.. In BioSystems ; éd. Elsevier, 2009, vol. 98, num. 3.
      https://hal.archives-ouvertes.fr/hal-00415921
    • [34] J. Ahmad, J. Bourdon, D. Eveillard, J. Fromentin, O. Roux, C. Sinoquet. Temporal constraints of a gene regulatory network: refining a qualitative simulation. In BioSystems, Special Issue on Gene Regulatory Networks. 13-05-2009
      https://hal.archives-ouvertes.fr/hal-00423353
    • [35] B. Ward, D. Eveillard, J. D. Kirshtein, J. D. Nelson, M. A. Voytek, G. Jackson. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray. In Environmental Microbiology ; éd. Wiley-Blackwell, 2007, vol. 9, num. 10.
      https://hal.archives-ouvertes.fr/hal-00346599

Revues nationales avec comité de lecture (ART_NAT)

    • [37] D. Eveillard, D. Ropers, H. De Jong, C. Branlant, A. Bockmayr. A multi-scale constraint programming model of alternative splicing regulation. In Theoretical Computer Science ; éd. Elsevier, 2004, vol. 325, num. 1.
      https://hal.inria.fr/inria-00000916

Conférences internationales avec comité de lecture et actes (COMM_INT)

    • [38] D. Eveillard, L. Guidi, L. Bittner, S. Chaffron, J. Raes, E. Karsenti, C. Bowler, G. Gorsky. Revealing and analyzing networks of marine microbial ecosystems. In Conférence Jacques Monod - Marine Ecosystems Biology, 2015, Roscoff, France.
      https://hal.archives-ouvertes.fr/hal-01176727
    • [39] G. Collet, D. Eveillard, M. Gebser, S. Prigent, T. Schaub, A. Siegel, S. Thiele. Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming. In LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, septembre 2013, Corunna, Espagne.
      https://hal.inria.fr/hal-00853752
    • [40] P. Bordron, D. Eveillard, A. Maass, A. Siegel, S. Thiele. An ASP application in integrative biology: identification of functional gene units. In LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, septembre 2013, Corunna, Espagne.
      https://hal.inria.fr/hal-00853762
    • [41] T. Tonon, P. Bonin, S. Prigent, Z. Shao, A. Groisillier, S. Rousvoal, S. Goulitquer, J. Bourdon, D. Eveillard, C. Boyen, A. Siegel. Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology. In Esil 2012: algal post-genomics, avril 2012, Roscoff, France.
      https://hal.inria.fr/hal-00760640
    • [42] P. Bordron, D. Eveillard, I. Rusu. SIPPER: A flexible method to integrate heterogeneous data into a metabolic network. In Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on, février 2011, Orlando, états-Unis.
      https://hal.archives-ouvertes.fr/hal-00585102
    • [43] S. Angibaud, P. Bordron, D. Eveillard, G. Fertin, I. Rusu. Integration of omics data to investigate common intervals. In 1st International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011), 2011, Singapore, Singapour.In IEEE (éds.), Proc. 1st International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011). , 2011.
      https://hal.archives-ouvertes.fr/hal-00606226
    • [44] A. Goldsztejn, O. Mullier, D. Eveillard, H. Hosobe. Including Ordinary Differential Equations Based Constraints in the Standard CP Framework. In Principles and Practice of Constraint Programming, CP2010, septembre 2010, St Andrews, Royaume-Uni.
      http://hal.univ-nantes.fr/hal-00520054
    • [45] S. Angibaud, D. Eveillard, G. Fertin, I. Rusu. Comparing Bacterial Genomes by Searching Their Common Intervals. In Bioinformatics and Computational Biology, avril 2009, New Orleans, états-Unis.
      https://hal.archives-ouvertes.fr/hal-00415955
    • [46] S. Angibaud, D. Eveillard, G. Fertin, I. Rusu. Comparing Bacterial Genomes by Searching their Common Intervals. In 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), 2009, New Orleans, états-Unis.In Springer-Verlag (éds.), In Proc. 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009). Springer-Verlag, 2009.
      https://hal.archives-ouvertes.fr/hal-00416466
    • [47] D. Eveillard, J. Fromentin, O. Roux. Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches. In Workshop on Constraint Based Methods for Bioinformatics (WCB08), 2008, Paris, France.
      https://hal.archives-ouvertes.fr/hal-00277104
    • [48] D. Eveillard, A. Courtois, A. Bockmayr. Hybrid concurrent constraint programming: A well-suited formalism for modelling alternative splicing regulation (Abstract). In Modeling and Simulation of Biological Regulatory Processes - ECCB Satellite Meeting, 2003, Paris, France.
      https://hal.inria.fr/inria-00099705
    • [49] D. Eveillard, D. Ropers, H. De Jong, C. Branlant, A. Bockmayr. Multiscale modeling of alternative splicing regulation. In International Workshop on Computational Methods in Systems Biology - CMSB'03, 2003, Rovereto, Italie.In Corrado Priami (éds.), . Springer-Verlag, 2003.
      https://hal.inria.fr/inria-00099792

Conférences nationales avec comité de lecture et actes (COMM_NAT)

    • [50] V. Potdevin, M. Chevallier, R. Garrido Oter, A. Siegel, S. Hacquard, D. Eveillard, P. Vandenkoornhuyse. Toward a better understanding of the plant microbiota. In 4ème colloque de Génomique Environnementale, septembre 2017, Marseille, France.
      https://hal.inria.fr/hal-01576743
    • [51] D. Eveillard, A. Larhlimi, D. Ropers, S. Billaut, S. Peyrefitte. KOALAB: A new method for regulatory motif search. Illustration on alternative splicing regulation in HIV-1. In 5èmes Journées Ouvertes Biologie Informatique Mathématiques - JOBIM 2004, juin 2004, Montréal, Canada.
      https://hal.inria.fr/inria-00000915
    • [52] A. Bockmayr, A. Courtois, D. Eveillard, M. Vezain. Building and analysing an integrative model of HIV-1 RNA alternative splicing. In International Conference on Computational Methods in Systems Biology - CMSB 2004, mai 2004, Paris/France.In Vincent Danos & Vincent Schachter (éds.), . Springer-Verlag, 2004.
      https://hal.inria.fr/inria-00000917
    • [53] D. Eveillard, Y. Guermeur. Traitement statistique des résultats SELEX. In Journées Ouvertes en Biologie Informatiques et Mathématiques - JOBIM 2002, juin 2002, Saint Malo - France.
      https://hal.inria.fr/inria-00000918

Ouvrages - Chapitres d‘ouvrages et directions d‘ouvrages (OUV)

    • [54] L. Bittner, L. Guidi, S. Chaffron, D. Eveillard. Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique. In Microbiodiversité : un nouveau regard. 01-12-2018
      https://hal.archives-ouvertes.fr/hal-01996304
    • [56] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes. In La génomique environnemetale : la révolution du séquençage à haut débit. 01-07-2016
      https://hal.archives-ouvertes.fr/hal-01777358
    • [57] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. XII Des données haut-débit à la modélisation des écosystèmes. In Prospective Génomique Environnementale. 2013
      https://hal.archives-ouvertes.fr/hal-01176570
    • [58] F. Austerlitz, M. Blum, S. Calba, J. Chave, M. Choisy, A. Coreau, V. Devictor, L. Doyen, S. Dray, A. Duputié, D. Eveillard, D. Faure, C. Favier, O. Gaggiotti, N. Galtier, E. Garnier, O. Gimenez, H. Guis, V. Herbreteau, P. Huneman, F. Jabot, P. Jarne, D. Joly, R. Julliard, S. Kéfi, G. Kergoat, G. Lacroix, Y. Lagadeuc, S. Lavorel, J. Le Gaillard, L. Le Gall, M. Loreau, V. Maris, S. Morand, X. Morin, H. Morlon, N. Mouquet, G. Pinay, J. Pottier, R. Pradel, O. Ronce, F. Schurr, P. Simonet, C. Teplitsky, W. Thuiller, A. Tran, S. Venner. Ecologie prédictive & changement planétaire. In Prospective de l'Institut écologie & environnement du CNRS. 2013
      https://hal.archives-ouvertes.fr/hal-01911607
    • [59] J. Bourdon, D. Eveillard. Probabilistic Approaches for Investigating Biological Networks. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications. 05-01-2011
      https://hal.archives-ouvertes.fr/hal-00531568

Autres publications (AUTRES)

    • [60] M. Budinich, D. Eveillard, J. Bourdon, A. Larhlimi. MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network. Rapport technique, 2013 ; .
      https://hal.archives-ouvertes.fr/hal-00839321
    • [61] D. Eveillard, D. Ropers, H. De Jong, C. Branlant, A. Bockmayr. A Multi-Site Constraint Programming Model of Alternative Splicing Regulation. Rapport technique, 2003 ; INRIA.
      https://hal.inria.fr/inria-00071756
    • [62] D. Eveillard, D. Ropers, H. De Jong, C. Branlant, A. Bockmayr. Modeling the effects of SR proteins on alternative splicing. Rapport technique, 2002 ; .
      https://hal.inria.fr/inria-00101060
Copyright : LS2N 2017 - Mentions Légales - 
 -