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BioinformatiqueBiologie des SystèmesMétagénomiqueModélisation Biologique

Damien Eveillard

HDR

Enseignant chercheur / Enseignante chercheuse – Professeur / professeure des universités

Equipe :

Employeur : Nantes Université

Expertises :

Modélisation biologiqueBioinformatiqueGénomique EnvironnementaleOcéanographieBiologie des systèmesMétabolisme

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Publications déposées sur HAL

Nombre de publications retournées : 125

Revues internationales avec comité de lecture

[1] 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, vol. 9, no. 10, pp. 2522-2538,

[2] 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, vol. 20, no. 4, pp. 312-20, DOI

[3] G. Mondo, D. Eveillard, I. Rusu. Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions, in Bioinformatics, vol. 25, no. 7, pp. 926-932, DOI

[4] G. Mondo, D. Eveillard, I. Rusu. Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions., in Bioinformatics, vol. 25, no. 7, pp. 926-32, DOI

[5] 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, vol. 98, no. 3, pp. 149-159, DOI

[6] J. Fromentin, D. Eveillard, O. Roux. Hybrid Modeling of Gene Regulatory Networks: Mixing Temporal and Qualitative Biological Properties, in BMC Systems Biology, vol. 4, no. 79, pp. http://www.biomedcentral.com/1752-0509/4/79/abstract, DOI

[7] 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, vol. 92, no. 12, pp. 1832-1838,

[8] 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, vol. 92, no. 12, pp. 1832-8, DOI

[9] 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, vol. 13, no. 4, pp. 872-886, DOI

[10] P. Bordron, D. Eveillard, I. Rusu. Integrated analysis of the gene neighbouring impact on bacterial metabolic networks., in IET Systems Biology, vol. 5, no. 4, pp. 261-268, DOI

[11] 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, vol. 7, no. 8, pp. 2508-2521, DOI

[12] J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network., in PLoS Computational Biology, vol. 7, no. 9, pp. e1002157, DOI

[13] 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, vol. 15, no. 12, pp. 883-892, DOI

[14] 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, vol. 14, no. 3, pp. 714-729, DOI

[15] 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, vol. 83, no. 1, pp. 74-81, DOI

[16] 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, vol. 6, no. 1, pp. 106 – 112, DOI

[17] S. Dittami, D. Eveillard, T. Tonon. A metabolic approach to study algal-bacterial interactions in changing environments., in Molecular Ecology, vol. 23, no. 7, pp. 1656-60, DOI

[18] 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, vol. 80, no. 2, pp. 367-381, DOI

[19] T. Tonon, D. Eveillard. , in Frontiers in Genetics, vol. 6, pp. 181, DOI

[20] 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, vol. 311, pp. 11-19, DOI

[21] N. Mouquet, Y. Lagadeuc, V. Devictor, L. Doyen, A. Duputié, D. Eveillard, D. Faure, É. 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, vol. 52, no. 5, pp. 1293-1310, DOI

[22] 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, vol. 5, no. 1, pp. 106-117, DOI

[23] V. Acuña, A. Aravena, C. Guziolowski, D. Eveillard, A. Siegel, A. Maass. Deciphering transcriptional regulations coordinating the response to environmental changes, in BMC Bioinformatics, vol. 17, no. 1, pp. 129-42, DOI

[24] 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, vol. 532, pp. 465–470, DOI

[25] A. Mas, S. Jamshidi, Y. Lagadeuc, D. Eveillard, P. Vandenkoornhuyse. Beyond the Black Queen Hypothesis., in The International Society of Microbiologial Ecology Journal, vol. 10, no. 9, pp. 2085-2091, DOI

[26] 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, vol. 5, pp. e3860, DOI

[27] S. Prigent, C. Frioux, S. Dittami, S. Thiele, A. Larhlimi, G. Collet, F. Gutknecht, 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, vol. 13, no. 1, pp. 32, DOI

[28] M. Budinich, J. Bourdon, A. Larhlimi, D. Eveillard. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems., in PLoS ONE, vol. 12, no. 2, pp. e0171744, DOI

[29] 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, vol. 8, pp. article 1808, DOI

[30] 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, no. 6, DOI

[31] 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, vol. 30, pp. 59 – 72, DOI

[32] 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, DOI

[33] 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, vol. 8, no. 1, pp. 5875, DOI

[34] 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, vol. 6, pp. 623, DOI

[35] 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, vol. 9, pp. 1-9, DOI

[36] L. Caputi, Q. Carradec, D. Eveillard, A. Kirilovsky, É. 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, vol. 33, no. 3, pp. 391-419, DOI

[37] 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, vol. 18, no. 8, pp. 428-445, DOI

[38] 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, vol. 18, no. 6, pp. 298, DOI

[39] 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, vol. 7, DOI

[40] 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, vol. 11, pp. e01707, DOI

[41] 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, vol. 5, no. 8, pp. 987-994, DOI

[42] 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, vol. 11, pp. e567431, DOI

[43] S. Ramondenc, D. Eveillard, L. Guidi, F. Lombard, B. Delahaye. Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions, in Scientific Reports, vol. 10, no. 1, pp. e6074, DOI

[44] 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, vol. 7, no. 35, pp. eabg1921, DOI

[45] 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, vol. 9, pp. e10911, DOI

[46] 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, vol. 12, pp. 4948, DOI

[47] 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, vol. 6, no. 12, pp. 1561-1574, DOI

[48] 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, vol. 11, no. 1, DOI

[49] 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, vol. 25, no. 6, pp. 1352-1364, DOI

[50] S. Schroeter, D. Eveillard, S. Chaffron, J. Zoppi, B. Kampe, P. Lohmann, N. Jehmlich, M. von Bergen, C. Sanchez-Arcos, G. Pohnert, M. Taubert, K. Küsel, G. Gleixner. Microbial community functioning during plant litter decomposition, in Scientific Reports, vol. 12, no. 1, pp. 7451, DOI

[51] 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, vol. 376, no. 6598, pp. 1202-1208, DOI

[52] 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, vol. 7, no. 7, pp. 937-947, DOI

[53] 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, vol. 11, pp. e78129, DOI

[54] 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, vol. 11, no. 83, pp. https://doi.org/10.1186/s40168-023-01523-z, DOI

[55] N. Jiménez, V. Acuña, M. Cortés, D. Eveillard, A. Maass. Unveiling abundance-dependent metabolic phenotypes of microbial communities, in mSystems, DOI

[56] 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, vol. 17, no. 5, pp. 720-732, DOI

[57] 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, vol. 3, no. 1, pp. 83, DOI

[58] 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, vol. 15, no. 1, pp. 126, DOI

[59] J. Rolland, R. Boutin, D. Eveillard, B. Delahaye. Datascape: exploring heterogeneous dataspace, in Scientific Reports, vol. 14, pp. 7041, DOI

[60] A. Lambert, M. Budinich, M. Mahé, S. Chaffron, D. Eveillard. Community metabolic modeling of host-microbiota interactions through multi-objective optimization, in iScience, vol. 27, no. 6, pp. 110092, DOI

[61] 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, vol. 379, DOI

[62] 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, vol. 12, no. 1, pp. 159, DOI

[63] S. Ramondenc, D. Eveillard, K. Metfies, M. Iversen, E. Nöthig, D. Piepenburg, C. Hasemann, T. Soltwedel. Unveiling pelagic-benthic coupling associated with the biological carbon pump in the Fram Strait (Arctic Ocean), in Nature Communications, vol. 16, no. 1, pp. 840, DOI

[64] A. Régimbeau, O. Aumont, C. Bowler, L. Guidi, G. Jackson, E. Karsenti, L. Mémery, A. Tagliabue, D. Eveillard. Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling, in Science Advances, vol. 11, no. 23, DOI

[65] L. Paré, P. Bordron, L. David, M. Mahé, A. Bihouée, D. Eveillard. HUMESS: integrating quantitative transcriptomic analysis and metabolic modeling to unveil condition-specific gene signatures, in Bioinformatics, vol. 41, no. 8, pp. btaf448, DOI

[66] O. Esteban-Cantillo, A. Abreu, S. Bourgeois-Gironde, E. Wanek, U. Gurchani, D. Eveillard, R. Casati. Six key policy recommendations to advocate for marine conservation that matches the ocean’s dynamism, in npj Ocean Sustainability, vol. 4, DOI

[67] H. Sarmento, P. Huber, C. Santos-Júnior, A. Abreu, T. Makhalanyane, N. Karenyi, E. Rocke, S. Acinas, L. Amaral-Zettler, M. Araujo, C. Arboleda-Baena, G. Bachi, D. Bănaru, É. Becker, M. Bellacicco, F. Benedetti, C. Bowler, B. Buongiorno Nardelli, L. Campese, D. Canu, U. Cardini, R. Casotti, S. Chaffron, D. Couet, H. Cruz de Carvalho, D. D’alelio, G. Dall’olmo, N. Dames, C. de Vargas, C. Delgado, C. Dimier, D. Eveillard, S. Faye, M. Flores, P. Galand, L. Gammage, J. Gasol, M. Gehlen, A. Green Koettker, V. Guinder, T. Heggeset, L. Heimbürger-Boavida, A. Hidas, C. Hörstmann, F. Ibarbalz, O. Jaillon, D. Johns, F. Jordán, P. Junger, K. Labadie, R. Laxenaire, S. Libralato, C. Longo, R. Lopes, M. Loschi, S. Mafwila, L. Maiorano, M. Meredith, E. Muxagata, G. Nguyen, S. Nicolau, P. Oliveira, L. Olivier, R. Palmela de Oliveira, N. Patin, P. Pita, G. Pohnert, A. Ruggiero, A. S. Freire, M. Saraceno, R. Schwamborn, A. Soccodato, C. Solidoro, D. Sousa, S. Speich, S. Sunagawa, A. Tagliabue, L. Thompson, R. Troublé, L. Veado, F. Vincent, M. Vogt, S. Zunino, S. Pesant, D. Iudicone. The southern gap in ocean microbiome science, in Ocean Microbiology, vol. 1, no. 1, pp. 6, DOI

[68] D. Talmy, C. Howard-Varona, D. Eveillard, M. Covert, M. Sullivan. Viruses in multi-scale ocean models: challenges and opportunities, in Frontiers in Marine Science, vol. 12, DOI

[69] R. Casati, A. Portier, C. Delor, B. Baird-Zars, C. Cerino, O. Esteban-Cantillo, D. Eveillard, S. Malatesta, M. Di Friedberg. Sea level rise: A plea for taking the viewpoint of the ocean, in Marine Policy, vol. 185, pp. 106972, DOI

Revues nationales avec comité de lecture

[70] 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, vol. 325, no. 1, pp. 3-24, DOI

[71] D. Eveillard, J. Jongwane. Un réseau social chez les planctons, in Interstices,

Conférences internationales avec comité de lecture et actes

[72] 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, Paris, France,

[73] 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, Rovereto, Italie,

[74] D. Eveillard, J. Fromentin, O. Roux. Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches, in Workshop on Constraint Based Methods for Bioinformatics (WCB08), Paris, France,

[75] 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), New Orleans, états-Unis, DOI

[76] 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, St Andrews, Royaume-Uni,

[77] 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), Singapore, Singapour,

[78] 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, Orlando, états-Unis, DOI

[79] 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, Roscoff, France,

[80] G. Collet, D. Eveillard, M. Gebser, S. Prigent, T. Schaub, A. Siegel, S. Thiele. Extending the Metabolic Network of <em>Ectocarpus Siliculosus</em> Using Answer Set Programming, in LPNMR, DOI

[81] 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, Corunna, Espagne,

[82] 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, Corunna, Espagne,

[83] 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, Roscoff, France,

[84] 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, Nantes, France, DOI

[85] 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 réseaux, GDR génomique environnementale, Nantes, France,

[86] 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, Nancy, France,

[87] 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, Santiago / Virtual, Chili,

Conférences nationales avec comité de lecture et actes

[88] D. Eveillard, Y. Guermeur. Traitement statistique des résultats SELEX, in Journées Ouvertes en Biologie Informatiques et Mathématiques – JOBIM 2002, Saint Malo – France,

[89] 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, Paris/France, DOI

[90] 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, Montréal, Canada,

[91] 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, Marseille, France,

Ouvrages – Chapitres d'ouvrages et directions d'ouvrages

[92] J. Bourdon, D. Eveillard. Probabilistic Approaches for Investigating Biological Networks,

[93] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. XII Des données haut-débit à la modélisation des écosystèmes,

[94] 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, É. 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,

[95] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modeling and predicting behaviors and dynamics of ecosystems,

[96] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes,

[97] D. Eveillard, A. Siegel, P. Vandenkoornhuyse. L'écologie des systèmes,

[98] D. Eveillard, A. Siegel, P. Vandenkoornhuyse. L’écologie des systèmes,

[99] L. Bittner, L. Guidi, S. Chaffron, D. Eveillard. Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique,

[100] 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,

Theses et HDR

[101] D. Eveillard. Modélisation statistique et formelle de la régulation de l'épissage alternatif,

[102] D. Eveillard. De la biologie systémique à l'écologie systémique : un voyage informatique à travers les échelles biologiques,

Autres publications

[103] D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr. Modeling the effects of SR proteins on alternative splicing,

[104] D. Eveillard, D. Ropers, H. de Jong, C. Branlant, A. Bockmayr. A Multi-Site Constraint Programming Model of Alternative Splicing Regulation,

[105] J. Bourdon, D. Eveillard. Toll Based Measures for Dynamical Graphs,

[106] J. Bourdon, D. Eveillard, S. Gabillard, T. Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach,

[107] J. Ahmad, J. Bourdon, D. Eveillard, J. Fromentin, O. Roux, C. Sinoquet. Qualitative modelling and analysis of gene regulatory networks: application to the adaptation of Escherichia coli bacterium to carbon availability,

[108] M. Budinich, D. Eveillard, J. Bourdon, A. Larhlimi. MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network,

[109] M. Budinich, J. Bourdon, D. Eveillard. Impact of the species compartment definition on quantitative modeling of microbial communities, DOI

[110] J. Laniau, A. Siegel, D. Eveillard. Combinatorial optimization methods to complete and analyse a metabolic network,

[111] 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,

[112] 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, Clermont-Ferrand, France,

[113] 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 plankton community interactome, DOI

[114] M. Royo-Llonch, P. Sánchez, C. Ruiz-González, G. Salazar, C. Pedrós-Alió, K. Labadie, L. Paoli, S. Chaffron, D. Eveillard, E. Karsenti, S. Sunagawa, P. Wincker, L. Karp-Boss, C. Bowler, S. Acinas. Ecogenomics of key prokaryotes in the arctic ocean, DOI

[115] 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 global ocean, DOI

[116] A. Régimbeau, M. Budinich, A. Larhlimi, J. Karlusich, O. Aumont, L. Mémery, C. Bowler, D. Eveillard. Contribution of genome scale metabolic modeling to niche theory, DOI

[117] M. Burel, A. Régimbeau, D. Eveillard, E. Pelletier. PhotoEukStein opens doors to the metabolism of eukaryotic-algae, in ISME18, Lausanne, Suisse,

[118] J. Rigonato, M. Budinich, A. Murillo, M. Brandão, J. 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, P. Bork, C. Bowler, S. Chaffron, C. de Vargas, D. Eveillard, M. Gehlen, D. Iudicone, F. Lombard, H. Ogata, L. Stemmann, M. Sullivan, S. Sunagawa, P. Wincker, O. Jaillon. Insights into biotic and abiotic modulation of ocean mesopelagic communities, DOI

[119] A. Régimbeau, O. Aumont, C. Bowler, L. Guidi, G. Jackson, E. Karsenti, L. Mémery, A. Tagliabue, D. Eveillard. Towards modeling genome-scale knowledge in the global ocean, DOI

[120] A. Lambert, M. Budinich, M. Mahé, S. Chaffron, D. Eveillard. Community metabolic modeling of host-microbiota interactions through multi-objective optimization, DOI

[121] M. Burel, A. Régimbeau, S. Chaffron, D. Eveillard, E. Pelletier. PhotoEukStein: Towards an omics-based definition of unicellular eukaryote phototrophs functional traits via metabolic modelling, DOI

[122] O. Julian Esteban-Cantillo, A. Abreu, S. Bourgeois-Gironde, E. Wanek, U. Gurchani, D. Eveillard, R. Casati. Dynamic Oceans, Dynamic Solutions,

[123] A. Régimbeau, F. Tian, G. Smith, V. Riddell, C. Andreani, P. Bordron, M. Budinich, C. Howard-Varona, A. Larhlimi, E. Ser-Giacomi, C. Trottier, L. Guidi, S. Hallam, D. Iudicone, E. Karsenti, A. Maass, M. Sullivan, D. Eveillard. Planetary-scale heterotrophic microbial community modeling assesses metabolic synergy and viral impacts, DOI

[124] L. Paré, P. Bordron, L. David, M. Mahé, A. Bihouée, D. Eveillard. HUMESS: Integrating Quantitative Transcriptomic Analysis and Metabolic Modeling to Unveil Condition-Specific Gene Signatures, DOI

[125] A. Lambert, S. Chaffron, D. Eveillard. MIMEco: Multi-objective metabolic modeling to predict and explain pairwise interactions, DOI

Pas de plateformes référencées pour l’instant

Pas de logiciels de référencés pour l’instant