Publications HAL des membres

Damien Eveillard

      2018

    • [1] Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
      Dinka Mandakovic, Claudia Rojas, Jonathan Maldonado, Mauricio Latorre, Dante Travisany, Erwan Delage, Audrey Bihouee, Géraldine Jean, Francisca Diaz, Beatriz Fernández-Gómez, Pablo Cabrera, Alexis Gaete, Claudio Latorre, Rodrigo Gutierrez, Alejandro Maass, Veronica Cambiazo, Sergio Navarrete, Damien Eveillard, Mauricio Gonzalez.
      https://hal.archives-ouvertes.fr/hal-01774624
    • [2] Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea
      S. Thiriet-Rupert, Gregory Carrier, C. Trottier, Damien Eveillard, B. Schoefs, G. Bougaran, J.-P. Cadoret, B. Chénais, B. Saint-Jean.
      https://hal.archives-ouvertes.fr/hal-01677336
    • [4] Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses
      François Thomas, Philippe Bordron, Damien Eveillard, Gurvan Michel.
      https://hal.archives-ouvertes.fr/hal-01613034
    • [5] Toward a better understanding of the plant microbiota
      Victoria Potdevin, Marie Chevallier, Ruben Garrido Oter, Anne Siegel, Stéphane Hacquard, Damien Eveillard, Philippe Vandenkoornhuyse.
      https://hal.inria.fr/hal-01576743
    • [7] Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
      Sylvain Prigent, Clémence Frioux, Simon M Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Gutknecht Fabien, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel.
      https://hal.inria.fr/hal-01449100
    • [9] Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks
      Julie Laniau, Clémence Frioux, Jacques Nicolas, Caroline Baroukh, María Paz Cortés, Jeanne Got, Camille Trottier, Damien Eveillard, Anne Siegel.
      https://hal.archives-ouvertes.fr/hal-01635688
    • [13] Plankton networks driving carbon export in the oligotrophic ocean
      Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, Simon Roux, Youssef Darzi, Stéphane Audic, Léo Berline, Jennifer R. Brum, Luis Pedro Coelho, Julio Cesar Ignacio Espinoza, Shruti Malviya, Shinichi Sunagawa, Céline Dimier, Stefanie Kandels-Lewis, Marc Picheral, Julie Poulain, Sarah Searson, Lars Stemmann, Fabrice Not, Pascal Hingamp, Sabrina Speich, Mick Follows, Lee Karp-Boss, Emmanuel Boss, Hiroyuki Ogata, Stephane Pesant, Jean Weissenbach, Patrick Wincker, Silvia G. Acinas, Peer Bork, Daniele Iudicone, Matthew B. Sullivan, Jeroen Raes, Eric Karsenti, Chris Bowler, Gabriel Gorsky.
      https://hal.sorbonne-universite.fr/hal-01275276
    • [14] Deciphering transcriptional regulations coordinating the response to environmental changes
      Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass.
      https://hal.archives-ouvertes.fr/hal-01260866

      2015

    • [15] Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism
      Shahrad Jamshidi, Jocelyn E. Behm, Damien Eveillard, E. Toby Kiers, Philippe Vandenkoornhuyse.
      https://hal.archives-ouvertes.fr/hal-01157450
    • [18] Revealing and analyzing networks of marine microbial ecosystems
      Damien Eveillard, Lionel Guidi, Lucie Bittner, Samuel Chaffron, Jeroen Raes, Eric Karsenti, Chris Bowler, Gaby Gorsky.
      https://hal.archives-ouvertes.fr/hal-01176727
    • [19] Predictive ecology in a changing world
      Nicolas Mouquet, Yvan Lagadeuc, Vincent Devictor, Luc Doyen, Anne Duputié, Damien Eveillard, Denis Faure, Eric Garnier, Olivier Gimenez, Philippe Huneman, Franck Jabot, Philippe Jarne, Dominique Joly, Romain Julliard, Gael Kergoat, Sandra Lavorel, Line Le Gall, Laurence Meslin, Serge Morand, Xavier Morin, Hélène Morlon, Gilles Pinay, Roger Pradel, F. M. Schurr, Wilfried Thuiller, Michel Loreau.
      https://hal.archives-ouvertes.fr/hal-01180277
    • [20] Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach
      Philippe Bordron, Mauricio Latorre, María Paz Cortés, Mauricio Gonzales, Sven Thiele, Anne Siegel, Alejandro Maass, Damien Eveillard.
      https://hal.inria.fr/hal-01246173
    • [22] The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.
      Sylvain Prigent, Guillaume Collet, Simon M Dittami, Ludovic Delage, Floriane Ethis de Corny, Olivier Dameron, Damien Eveillard, Sven Thiele, Jeanne Cambefort, Catherine Boyen, Anne Siegel, Thierry Tonon.
      https://hal.archives-ouvertes.fr/hal-01057153
    • [24] A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico
      Silvia E. Newell, Damien Eveillard, Mark J. Mccarthy, Wayne S. Gardner, Zhanfei Liu, Bess B. Ward.
      https://hal.archives-ouvertes.fr/hal-00951509

      2013

    • [25] An ASP application in integrative biology: identification of functional gene units
      Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, Sven Thiele.
      https://hal.inria.fr/hal-00853762
    • [26] Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming
      Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel, Sven Thiele.
      https://hal.inria.fr/hal-00853752
    • [28] Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats.
      Richard A Long, Damien Eveillard, Shelli L M Franco, Eric Reeves, James L Pinckney.
      https://hal.archives-ouvertes.fr/hal-00752749

      2012

    • [30] Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology
      Thierry Tonon, P. Bonin, Sylvain Prigent, Z. Shao, Agnès Groisillier, Sylvie Rousvoal, Sophie Goulitquer, Jérémie Bourdon, Damien Eveillard, Catherine Boyen, Anne Siegel.
      https://hal.inria.fr/hal-00760640
    • [31] Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.
      Nicholas J Bouskill, Damien Eveillard, Diana Chien, Amal Jayakumar, Bess B Ward.
      https://hal.archives-ouvertes.fr/hal-00661746

      2011

    • [32] Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.
      Thierry Tonon, Damien Eveillard, Sylvain Prigent, Jérémie Bourdon, Philippe Potin, Catherine Boyen, Anne Siegel.
      https://hal.archives-ouvertes.fr/hal-00661751
    • [34] Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes.
      Etienne Z Gnimpieba, Damien Eveillard, Jean-Louis Guéant, Abalo Chango.
      https://hal.archives-ouvertes.fr/hal-00626712
    • [35] Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.
      Nicholas J Bouskill, Damien Eveillard, Gregory O'Mullan, George A Jackson, Bess B Ward.
      https://hal.archives-ouvertes.fr/hal-00626710

      2010

    • [39] Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination.
      Susan F Martinez, Axelle Renodon-Cornière, Julian Nomme, Damien Eveillard, Fabrice Fleury, Masayuki Takahashi, Pierre Weigel.
      https://hal.archives-ouvertes.fr/hal-00626711
    • [40] Including Ordinary Differential Equations Based Constraints in the Standard CP Framework
      Alexandre Goldsztejn, Olivier Mullier, Damien Eveillard, Hiroshi Hosobe.
      http://hal.univ-nantes.fr/hal-00520054

      2009

    • [42] Temporal constraints of a gene regulatory network: refining a qualitative simulation
      Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, Christine Sinoquet.
      https://hal.archives-ouvertes.fr/hal-00423353
    • [43] Temporal constraints of a gene regulatory network: Refining a qualitative simulation.
      Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, Christine Sinoquet.
      https://hal.archives-ouvertes.fr/hal-00415921
    • [45] Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium.
      Abalo Chango, Afif Abdel Nour, Souad Bousserouel, Damien Eveillard, Pauline M Anton, Jean-Louis Guéant.
      https://hal.archives-ouvertes.fr/hal-00415914
    • [47] Qualitative modelling and analysis of gene regulatory networks: application to the adaptation of Escherichia coli bacterium to carbon availability
      Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, Christine Sinoquet.
      https://hal.archives-ouvertes.fr/hal-00359530
    • [51] Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray
      Bess B. Ward, Damien Eveillard, Julie D. Kirshtein, Joshua D. Nelson, Mary A. Voytek, George A. Jackson.
      https://hal.archives-ouvertes.fr/hal-00346599

      2004

    • [53] KOALAB: A new method for regulatory motif search. Illustration on alternative splicing regulation in HIV-1
      Damien Eveillard, Abdelhalim Larhlimi, Delphine Ropers, Stéphanie Billaut, Sandrine Peyrefitte.
      https://hal.inria.fr/inria-00000915
    • [55] Building and analysing an integrative model of HIV-1 RNA alternative splicing
      Alexander Bockmayr, Arnaud Courtois, Damien Eveillard, Myriam Vezain.
      https://hal.inria.fr/inria-00000917
    • [56] A multi-scale constraint programming model of alternative splicing regulation
      Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr.
      https://hal.inria.fr/inria-00000916

      2003

    • [57] A Multi-Site Constraint Programming Model of Alternative Splicing Regulation
      Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr.
      https://hal.inria.fr/inria-00071756
    • [58] Multiscale modeling of alternative splicing regulation
      Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr.
      https://hal.inria.fr/inria-00099792
    • [59] Hybrid concurrent constraint programming: A well-suited formalism for modelling alternative splicing regulation (Abstract)
      Damien Eveillard, Arnaud Courtois, Alexander Bockmayr.
      https://hal.inria.fr/inria-00099705
    • [61] Modeling the effects of SR proteins on alternative splicing
      Damien Eveillard, Delphine Ropers, Hidde De Jong, Christiane Branlant, Alexander Bockmayr.
      https://hal.inria.fr/inria-00101060
page

Groupement de Recherche en Intégration de données Omics à Très grande Echelle