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Damien EVEILLARD

professeur

Professor
HDR

: Damien.Eveillardatls2n.fr

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] I. Deutschmann, E. Delage, C. Giner, M. Sebastián, J. Poulain, J. Arístegui, C. Duarte, S. Acinas, R. Massana, J. Gasol, D. Eveillard, S. Chaffron, R. Logares. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. In Nature Communications ; éd. Nature Publishing Group, 2024, vol. 15, num. 1.
      https://hal.science/hal-04407573v1
    • [2] J. Rolland, R. Boutin, D. Eveillard, B. Delahaye. Datascape: exploring heterogeneous dataspace. In Scientific Reports ; éd. Nature Publishing Group, 2024, vol. 14.
      https://hal.science/hal-04674835v1
    • [3] A. Lambert, M. Budinich, M. Mahé, D. Eveillard, S. Chaffron. Community metabolic modeling of host-microbiota interactions through multi-objective optimization. In iScience ; éd. Elsevier, 2024, vol. 27, num. 6.
      https://hal.science/hal-04674843v1
    • [4] M. Gaudin, D. Eveillard, S. Chaffron. Ecological associations distribution modelling of marine plankton at a global scale. In Philosophical Transactions of the Royal Society B: Biological Sciences ; éd. Royal Society, The, 2024, vol. 379.
      https://hal.science/hal-04674860v1
    • [5] F. Tian, J. Wainaina, C. Howard-Varona, G. Domínguez-Huerta, B. Bolduc, M. Gazitúa, G. Smith, M. Gittrich, O. Zablocki, D. Cronin, D. Eveillard, S. Hallam, M. Sullivan. Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans. In Microbiome ; éd. BioMed Central, 2024, vol. 12, num. 1.
      https://hal.science/hal-04683447v1
    • [6] I. Deutschmann, A. Krabberød, F. Latorre, E. Delage, C. Marrasé, V. Balagué, J. Gasol, R. Massana, D. Eveillard, S. Chaffron, R. Logares. Disentangling temporal associations in marine microbial networks. In Microbiome ; éd. BioMed Central, 2023, vol. 11, num. 83.
      https://hal.science/hal-03781901v2
    • [7] N. Jiménez, V. Acuña, M. Cortés, D. Eveillard, A. Maass. Unveiling abundance-dependent metabolic phenotypes of microbial communities. In mSystems. 2023
      https://hal.science/hal-04198586v1
    • [8] H. Doré, U. Guyet, J. Leconte, G. Farrant, B. Alric, M. Ratin, M. Ostrowski, M. Ferrieux, L. Brillet-Guéguen, M. Hoebeke, J. Siltanen, G. Le Corguillé, E. Corre, P. Wincker, D. Scanlan, D. Eveillard, F. Partensky, L. Garczarek. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies. In The International Society of Microbiologial Ecology Journal ; éd. Nature Publishing Group, 2023, vol. 17, num. 5.
      https://hal.science/hal-04238382v1
    • [9] J. Rigonato, M. Budinich, A. Murillo, M. Brandão, J. Pierella Karlusich, Y. Soviadan, A. Gregory, H. Endo, F. Kokoszka, D. Vik, N. Henry, P. Frémont, K. Labadie, A. Zayed, C. Dimier, M. Picheral, S. Searson, J. Poulain, S. Kandels, S. Pesant, E. Karsenti, C. Bowler, C. de Vargas, D. Eveillard, M. Gehlen, D. Iudicone, F. Lombard, H. Ogata, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, S. Chaffron, O. Jaillon. Ocean-wide comparisons of mesopelagic planktonic community structures. In ISME Communications ; éd. Springer Nature, 2023, vol. 3, num. 1.
      https://hal.science/hal-04184772v1
    • [10] A. Régimbeau, M. Budinich, A. Larhlimi, J. Pierella Karlusich, O. Aumont, L. Mémery, C. Bowler, D. Eveillard. Contribution of genome‐scale metabolic modelling to niche theory. In Ecology Letters ; éd. Wiley, 2022, vol. 25, num. 6.
      https://hal.science/hal-03635158v1
    • [11] G. Dominguez-Huerta, A. Zayed, J. Wainaina, J. Guo, F. Tian, A. Pratama, B. Bolduc, M. Mohssen, O. Zablocki, E. Pelletier, E. Delage, A. Alberti, J. Aury, Q. Carradec, C. da Silva, K. Labadie, J. Poulain, C. Bowler, D. Eveillard, L. Guidi, E. Karsenti, J. Kuhn, H. Ogata, P. Wincker, A. Culley, S. Chaffron, M. Sullivan. Diversity and ecological footprint of Global Ocean RNA viruses. In Science ; éd. American Association for the Advancement of Science (AAAS), 2022, vol. 376, num. 6598.
      https://hal.science/hal-03781935v1
    • [12] A. Abreu, E. Bourgois, A. Gristwood, R. Troublé, S. Acinas, P. Bork, E. Boss, C. Bowler, M. Budinich, S. Chaffron, C. de Vargas, T. Delmont, D. Eveillard, L. Guidi, D. Iudicone, S. Kandels, H. Morlon, F. Lombard, R. Pepperkok, J. Karlusich, G. Piganeau, A. Régimbeau, G. Sommeria-Klein, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, O. Zablocki, D. Arendt, J. Bilic, R. Finn, E. Heard, B. Rouse, J. Vamathevan, R. Casotti, I. Cancio, M. Cunliffe, A. Kervella, W. Kooistra, M. Obst, N. Pade, D. Power, I. Santi, T. Tsagaraki, J. Vanaverbeke. Priorities for ocean microbiome research. In Nature Microbiology ; éd. Nature Publishing Group, 2022, vol. 7, num. 7.
      https://hal.science/hal-03781942v1
    • [13] D. Richter, R. Watteaux, T. Vannier, J. Leconte, P. Frémont, G. Reygondeau, N. Maillet, N. Henry, G. Benoit, A. Fernandez-Guerra, S. Suweis, R. Narci, C. Berney, D. Eveillard, F. Gavory, L. Guidi, K. Labadie, E. Mahieu, J. Poulain, S. Romac, S. Roux, C. Dimier, S. Kandels, M. Picheral, S. Searson, S. Pesant, J. Aury, J. Brum, C. Lemaitre, E. Pelletier, P. Bork, S. Sunagawa, L. Karp-Boss, C. Bowler, M. Sullivan, E. Karsenti, M. Mariadassou, I. Probert, P. Peterlongo, P. Wincker, C. de Vargas, M. Ribera d'Alcalà, D. Iudicone, O. Jaillon, T. Delmont. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. In eLife ; éd. eLife Sciences Publication, 2022, vol. 11.
      https://inria.hal.science/hal-02399723v2
    • [14] S. Chaffron, E. Delage, M. Budinich, D. Vintache, N. Henry, C. Nef, M. Ardyna, A. Zayed, P. Junger, P. Galand, C. Lovejoy, A. Murray, H. Sarmento, S. Acinas, M. Babin, D. Iudicone, O. Jaillon, E. Karsenti, P. Wincker, L. Karp-Boss, M. Sullivan, C. Bowler, C. de Vargas, D. Eveillard. Environmental vulnerability of the global ocean epipelagic plankton community interactome. In Science Advances ; éd. American Association for the Advancement of Science (AAAS), 2021, vol. 7, num. 35.
      https://hal.science/hal-03443359v2
    • [15] S. Dittami, E. Arboleda, J. Auguet, A. Bigalke, E. Briand, P. Cárdenas, U. Cardini, J. Decelle, A. Engelen, D. Eveillard, C. Gachon, S. Griffiths, T. Harder, E. Kayal, E. Kazamia, F. Lallier, M. Medina, E. Marzinelli, T. Morganti, L. Núñez Pons, S. Prado, J. Pintado, M. Saha, M. Selosse, D. Skillings, W. Stock, S. Sunagawa, E. Toulza, A. Vorobev, C. Leblanc, F. Not. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. In PeerJ ; éd. PeerJ, 2021, vol. 9.
      https://hal.science/hal-03166872v2
    • [16] Y. Lin, C. Moreno, A. Marchetti, H. Ducklow, O. Schofield, E. Delage, M. Meredith, Z. Li, D. Eveillard, S. Chaffron, N. Cassar. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula. In Nature Communications ; éd. Nature Publishing Group, 2021, vol. 12.
      https://hal.science/hal-03389081v1
    • [17] M. Royo-Llonch, P. Sánchez, C. Ruiz-González, G. Salazar, C. Pedrós-Alió, M. Sebastián, K. Labadie, L. Paoli, F. M. Ibarbalz, L. Zinger, B. Churcheward, S. Chaffron, D. Eveillard, E. Karsenti, S. Sunagawa, P. Wincker, L. Karp-Boss, C. Bowler, S. Acinas. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. In Nature Microbiology ; éd. Nature Publishing Group, 2021, vol. 6, num. 12.
      https://hal.science/hal-03781908v1
    • [18] S. Wang, W. Tang, E. Delage, S. Gifford, H. Whitby, A. Gonzalez, D. Eveillard, H. Planquette, N. Cassar. Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic. In Scientific Reports ; éd. Nature Publishing Group, 2021, vol. 11, num. 1.
      https://hal.science/hal-03166895v1
    • [19] S. Sunagawa, S. Acinas, P. Bork, C. Bowler, S. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, M. Follows, G. Gorsky, N. Grimsley, L. Guidi, P. Hingamp, D. Iudicone, O. Jaillon, S. Kandels, L. Karp-Boss, E. Karsenti, M. Lescot, F. Not, H. Ogata, S. Pesant, N. Poulton, J. Raes, C. Sardet, M. Sieracki, S. Speich, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, D. Eveillard, G. Gorsky, L. Guidi, D. Iudicone, E. Karsenti, F. Lombard, H. Ogata, S. Pesant, M. Sullivan, P. Wincker, C. de Vargas. Tara Oceans: towards global ocean ecosystems biology. In Nature Reviews Microbiology ; éd. Nature Publishing Group, 2020, vol. 18, num. 8.
      https://hal.science/hal-04394809v1
    • [20] A. Murray, N. Avalon, L. Bishop, K. Davenport, E. Delage, A. Dichosa, D. Eveillard, M. Higham, S. Kokkaliari, C. Lo, C. Riesenfeld, R. Young, P. Chain, B. Baker. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica. In Marine drugs ; éd. MDPI, 2020, vol. 18, num. 6.
      https://hal.science/hal-02862365v1
    • [21] C. Lemonnier, M. Perennou, D. Eveillard, A. Fernandez-Guerra, A. Leynaert, L. Marié, H. Morrison, L. Mémery, C. Paillard, L. Maignien. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. In Frontiers in Marine Science ; éd. Frontiers Media, 2020, vol. 7.
      https://hal.science/hal-02938091v1
    • [22] C. Lemonnier, M. Perennou, D. Eveillard, A. Fernandez-Guerra, A. Leynaert, L. Marié, H. Morrison, L. Mémery, C. Paillard, L. Maignien. Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area. In Frontiers in Marine Science ; éd. Frontiers Media, 2020, vol. 7.
      https://hal.science/hal-03083042v1
    • [23] U. Guyet, N. Nguyen, H. Doré, J. Haguait, J. Pittera, M. Conan, M. Ratin, E. Corre, G. Le Corguillé, L. Brillet-Guéguen, M. Hoebeke, C. Six, C. Steglich, A. Siegel, D. Eveillard, F. Partensky, L. Garczarek. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. In Frontiers in Microbiology ; éd. Frontiers Media, 2020, vol. 11.
      https://hal.sorbonne-universite.fr/hal-02929424v1
    • [24] A. Murray, J. Freudenstein, S. Gribaldo, R. Hatzenpichler, P. Hugenholtz, P. Kämpfer, K. Konstantinidis, C. Lane, R. Papke, D. Parks, R. Rossello-Mora, M. Stott, I. Sutcliffe, J. Thrash, S. Venter, W. Whitman, S. Acinas, R. Amann, K. Anantharaman, J. Armengaud, B. Baker, R. Barco, H. Bode, E. Boyd, C. Brady, P. Carini, P. Chain, D. Colman, K. Deangelis, M. de Los Rios, P. Estrada-de Los Santos, C. Dunlap, J. Eisen, D. Emerson, T. Ettema, D. Eveillard, P. Girguis, U. Hentschel, J. Hollibaugh, L. Hug, W. Inskeep, E. Ivanova, H. Klenk, W. Li, K. Lloyd, F. Löffler, T. Makhalanyane, D. Moser, T. Nunoura, M. Palmer, V. Parro, C. Pedrós-Alió, A. Probst, T. Smits, A. Steen, E. Steenkamp, A. Spang, F. Stewart, J. Tiedje, P. Vandamme, M. Wagner, F. Wang, P. Yarza, B. Hedlund, A. Reysenbach. Roadmap for naming uncultivated Archaea and Bacteria. In Nature Microbiology ; éd. Nature Publishing Group, 2020, vol. 5, num. 8.
      https://hal.science/hal-02863761v2
    • [25] H. Doré, G. Farrant, U. Guyet, J. Haguait, F. Humily, M. Ratin, F. Pitt, M. Ostrowski, C. Six, L. Brillet-Guéguen, M. Hoebeke, A. Bisch, G. Le Corguillé, E. Corre, K. Labadie, J. Aury, P. Wincker, D. Choi, J. Noh, D. Eveillard, D. Scanlan, F. Partensky, L. Garczarek. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. In Frontiers in Microbiology ; éd. Frontiers Media, 2020, vol. 11.
      https://hal.science/hal-02938656v1
    • [26] S. Ramondenc, D. Eveillard, L. Guidi, F. Lombard, B. Delahaye. Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions. In Scientific Reports ; éd. Nature Publishing Group, 2020, vol. 10, num. 1.
      https://hal.science/hal-02539195v1
    • [27] A. Capotondi, M. Jacox, C. Bowler, M. Kavanaugh, P. Lehodey, D. Barrie, S. Brodie, S. Chaffron, W. Cheng, D. Dias, D. Eveillard, L. Guidi, D. Iudicone, N. Lovenduski, J. Nye, I. Ortiz, D. Pirhalla, M. Pozo Buil, V. Saba, S. Sheridan, S. Siedlecki, A. Subramanian, C. de Vargas, E. Di Lorenzo, S. Doney, A. Hermann, T. Joyce, M. Merrifield, A. Miller, F. Not, S. Pesant. Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems. In Frontiers in Marine Science ; éd. Frontiers Media, 2019, vol. 6.
      https://hal.science/hal-02316446v1
    • [28] 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.science/hal-01996045v1
    • [29] L. Caputi, Q. Carradec, D. Eveillard, A. Kirilovsky, E. Pelletier, J. Pierella Karlusich, F. Rocha Jimenez Vieira, E. Villar, S. Chaffron, S. Malviya, E. Scalco, S. Acinas, A. Alberti, J. Aury, A. Benoiston, A. Bertrand, T. Biard, L. Bittner, M. Boccara, J. Brum, C. Brunet, G. Busseni, A. Carratalà, H. Claustre, L. Coelho, S. Colin, S. d'Aniello, C. da Silva, M. del Core, H. Doré, S. Gasparini, F. Kokoszka, J. Jamet, C. Lejeusne, C. Lepoivre, M. Lescot, G. Lima-Mendez, F. Lombard, J. Lukeš, N. Maillet, M. Madoui, E. Martinez, M. Mazzocchi, M. Néou, J. Paz-Yepes, J. Poulain, S. Ramondenc, J. Romagnan, S. Roux, D. Salvagio Manta, R. Sanges, S. Speich, M. Sprovieri, S. Sunagawa, V. Taillandier, A. Tanaka, L. Tirichine, C. Trottier, J. Uitz, A. Veluchamy, J. Veselá, F. Vincent, S. Yau, S. Kandels-Lewis, S. Searson, C. Dimier, M. Picheral, P. Bork, E. Boss, C. de Vargas, M. Follows, N. Grimsley, L. Guidi, P. Hingamp, E. Karsenti, P. Sordino, L. Stemmann, M. Sullivan, A. Tagliabue, A. Zingone, L. Garczarek, F. d'Ortenzio, P. Testor, F. Not, M. d'Alcalà, P. Wincker, G. Gorsky, O. Jaillon, L. Karp-Boss, U. Krzic, H. Ogata, S. Pesant, J. Raes, E. Reynaud, C. Sardet, M. Sieracki, D. Velayoudon, J. Weissenbach, C. Bowler, D. Iudicone. Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems. In Global Biogeochemical Cycles ; éd. American Geophysical Union, 2019, vol. 33, num. 3.
      https://hal.science/hal-02999805v1
    • [30] 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.science/hal-01677336v1
    • [31] 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.science/hal-01909434v1
    • [32] D. Mandakovic, C. Rojas, J. Maldonado, M. Latorre, D. Travisany, E. Delage, A. Bihouée, 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.science/hal-01774624v1
    • [33] 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.science/hal-01635688v1
    • [34] 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. PLOS, 2017, vol. 13, num. 1.
      https://inria.hal.science/hal-01449100v1
    • [35] 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.science/hal-01478375v1
    • [36] 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.science/hal-01613034v1
    • [37] B. Delahaye, D. Eveillard, N. Bouskill. On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore. In mSystems, vol. 2, num. 6. 05-12-2017
      https://hal.science/hal-01658218v1
    • [38] 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, 2016, vol. 5, num. 1.
      https://inria.hal.science/hal-01246173v1
    • [39] 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.science/hal-01260866v1
    • [40] 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-01275276v1
    • [41] A. Mas, S. Jamshidi, Y. Lagadeuc, D. Eveillard, P. Vandenkoornhuyse. Beyond the Black Queen Hypothesis.. In The International Society of Microbiologial Ecology Journal ; éd. Nature Publishing Group, 2016, vol. 10, num. 9.
      https://hal.science/hal-01290210v1
    • [42] 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.science/hal-01180277v1
    • [43] 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.science/hal-01157450v1
    • [44] 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.science/hal-00951509v1
    • [45] 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.science/hal-00936195v1
    • [46] 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 The Plant Journal ; éd. Wiley, 2014, vol. 80, num. 2.
      https://hal.science/hal-01057153v1
    • [48] 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.science/hal-00752749v1
    • [49] 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. Society for Applied Microbiology and Wiley-Blackwell, 2012, vol. 14, num. 3.
      https://hal.science/hal-00661746v1
    • [50] 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. Society for Applied Microbiology and Wiley-Blackwell, 2011, vol. 13, num. 4.
      https://hal.science/hal-00626710v1
    • [51] 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.science/hal-00626709v1
    • [52] 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.science/hal-00626712v1
    • [53] J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network.. In PLoS Computational Biology ; éd. PLOS, 2011, vol. 7, num. 9.
      https://hal.science/hal-00626708v1
    • [54] 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.science/hal-00661751v1
    • [55] 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.science/hal-00346588v1
    • [56] 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.science/hal-00549787v1
    • [57] 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.science/hal-00626711v1
    • [58] 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 Nutritional Biochemistry ; éd. Elsevier, 2009, vol. 20, num. 4.
      https://hal.science/hal-00415914v1
    • [59] 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.science/hal-02352007v1
    • [60] 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.science/hal-00415905v1
    • [61] 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.science/hal-00415921v1
    • [62] 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.
      https://hal.science/hal-00423353v1
    • [63] 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. Society for Applied Microbiology and Wiley-Blackwell, 2007, vol. 9, num. 10.
      https://hal.science/hal-00346599v1

Revues nationales avec comité de lecture (ART_NAT)

    • [65] 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://inria.hal.science/inria-00000916v1

Conférences internationales avec comité de lecture et actes (COMM_INT)

    • [66] N. Sanchez-Pi, L. Marti, A. Abreu, O. Bernard, C. de Vargas, D. Eveillard, A. Maass, P. Marquet, J. Sainte-Marie, J. Salomon, M. Schoenauer, M. Sebag. Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change. In NeurIPS 2020 Workshop - Tackling Climate Change with Machine Learning, décembre 2020, Santiago / Virtual, Chili.
      https://hal.science/hal-03138712v1
    • [67] S. Ayata, E. Faure, A. Benoiston, F. Not, O. Aumont, L. Guidi, S. Chaffron, D. Eveillard, L. Bittner. From plankton functional traits to marine ecosystem functions: Assessing functional diversity of plankton communities from high throughput -omics data and its impact on oceanic biogeochemical cycles. In Functional Ecology Conference, 2018, Nancy, France.
      https://hal.science/hal-04024046v1
    • [68] A. Benoiston, L. Bittner, L. Guidi, S. Chaffron, D. Eveillard, S. Ayata, G. Jean, E. Pelletier, S. Pesant, C. de Vargas, E. Karsenti, C. Bowler, G. Gorsky, T. Consortium. Plankton networks correlated to the biological carbon pump in the global ocean. In Journée analyse des réseau, GDR génomique environnementale, 2017, Nantes, France.
      https://hal.science/hal-04024048v1
    • [69] 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.science/hal-01176727v1
    • [70] M. Budinich, J. Bourdon, A. Larhlimi, D. Eveillard. OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques. In 13th International Conference on Computational Methods in Systems Biology CMSB 2015, septembre 2015, Nantes, France.In Olivier Roux (éds.), . Springer International Publishing, 2015.
      https://hal.science/hal-02464859v1
    • [71] 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, 2013, .
      https://hal.inrae.fr/hal-02745669v1
    • [72] 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://inria.hal.science/hal-00853752v1
    • [73] 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://inria.hal.science/hal-00853762v1
    • [74] 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://inria.hal.science/hal-00760640v1
    • [75] 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.science/hal-00585102v1
    • [76] 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.science/hal-00606226v1
    • [77] 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.
      https://nantes-universite.hal.science/hal-00520054v1
    • [78] 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.), . Springer-Verlag, 2009.
      https://hal.science/hal-00416466v1
    • [79] 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.science/hal-00277104v1
    • [80] 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://inria.hal.science/inria-00099705v1
    • [81] 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://inria.hal.science/inria-00099792v1

Conférences nationales avec comité de lecture et actes (COMM_NAT)

    • [82] 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://inria.hal.science/hal-01576743v1
    • [83] 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://inria.hal.science/inria-00000915v1
    • [84] 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://inria.hal.science/inria-00000917v1
    • [85] 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://inria.hal.science/inria-00000918v1

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

    • [86] N. Sanchez-Pi, L. Marti, J. Salomon, J. Sainte-Marie, O. Bernard, M. Sebag, M. Schoenauer, A. Maass, D. Eveillard, A. Abreu, C. de Vargas, P. Marquet. OcéanIA: AI, Data, and Models for Understanding the Ocean and Climate Change. 01-07-2021
      https://hal.science/hal-03274323v2
    • [87] 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.science/hal-01996304v1
    • [90] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modeling and predicting behaviors and dynamics of ecosystems. In Insight on environmental genomics, the high-throughput sequencing revolution. 2016
      https://hal.science/hal-03823723v1
    • [91] 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.science/hal-01777358v1
    • [92] 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.science/hal-01176570v1
    • [93] 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.science/hal-01911607v1
    • [94] 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.science/hal-00531568v1

Theses et HDR (THESE)

Autres publications (AUTRES)

    • [97] M. Burel, A. Régimbeau, D. Eveillard, E. Pelletier. PhotoEukStein opens doors to the metabolism of eukaryotic-algae. In ISME18, août 2022, Lausanne, Suisse.
      https://hal.science/hal-04384915v1
    • [98] S. Ayata, E. Faure, A. Benoiston, O. Silva, V. Sonnet, F. Benedetti, F. Not, O. Aumont, L. Guidi, S. Chaffron, D. Eveillard, L. Bittner. Assessing functional diversity of plankton communities from high throughput –omics data. In Colloque de Bilan et de Prospective du programme LEFE, mars 2018, Clermont-Ferrand, France.
      https://hal.science/hal-04021818v1
    • [99] S. Ramondenc, F. Delahaye, D. Eveillard, L. Stemmann, L. Guidi, F. Lombard. Contribution of the jellyfish Pelagia Noctiluca to carbon export in the Mediterranean Sea.
      https://hal.science/hal-04023034v1
    • [100] 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.science/hal-00839321v1
    • [101] 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://inria.hal.science/inria-00071756v1
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