Damien Eveillard

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	Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean Ina Deutschmann , Erwan Delage , Caterina Giner , Marta Sebastián , Julie Poulain Nature Communications, 2024, 15 (1), pp.126. ⟨10.1038/s41467-023-44550-y⟩ Article dans une revue hal-04407573v1
	Unveiling abundance-dependent metabolic phenotypes of microbial communities Natalia E Jiménez , Vicente Acuña , María Paz Cortés , Damien Eveillard , Alejandro Eduardo Maass mSystems, In press, ⟨10.1128/msystems.00492-23⟩ Article dans une revue hal-04198586v1
	Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies Hugo Doré , Ulysse Guyet , Jade Leconte , Gregory Farrant , Benjamin Alric The International Society of Microbiologial Ecology Journal, 2023, 17 (5), pp.720-732. ⟨10.1038/s41396-023-01386-0⟩ Article dans une revue hal-04238382v1
	Disentangling temporal associations in marine microbial networks Ina Maria Deutschmann , Anders Krabberød , Francisco Latorre , Erwan Delage , Cèlia Marrasé Microbiome, 2023, 11 (83), https://doi.org/10.1186/s40168-023-01523-z. ⟨10.1101/2021.07.13.452187⟩ Article dans une revue hal-03781901v2
	Ocean-wide comparisons of mesopelagic planktonic community structures Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Pierella Karlusich ISME Communications, 2023, 3 (1), pp.83. ⟨10.1038/s43705-023-00279-9⟩ Article dans une revue hal-04184772v1
	Diversity and ecological footprint of Global Ocean RNA viruses Guillermo Dominguez-Huerta , Ahmed Zayed , James Wainaina , Jiarong Guo , Funing Tian Science, 2022, 376 (6598), pp.1202-1208. ⟨10.1126/science.abn6358⟩ Article dans une revue hal-03781935v1
	Priorities for ocean microbiome research Andre Abreu , Etienne Bourgois , Adam Gristwood , Romain Troublé , Silvia Acinas Nature Microbiology, 2022, 7 (7), pp.937-947. ⟨10.1038/s41564-022-01145-5⟩ Article dans une revue hal-03781942v1
	Contribution of genome‐scale metabolic modelling to niche theory Antoine Régimbeau , Marko Budinich , Abdelhalim Larhlimi , Juan José Pierella Karlusich , Olivier Aumont Ecology Letters, 2022, 25 (6), pp.1352-1364. ⟨10.1111/ele.13954⟩ Article dans une revue hal-03635158v1
	Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems Daniel Richter , Romain Watteaux , Thomas Vannier , Jade Leconte , Paul Frémont eLife, 2022, 11, pp.e78129. ⟨10.7554/eLife.78129⟩ Article dans une revue hal-02399723v2
	A community perspective on the concept of marine holobionts: current status, challenges, and future directions Simon M. Dittami , Enrique Arboleda , J.-C. Auguet , Arite Bigalke , Enora Briand PeerJ, 2021, 9, pp.e10911. ⟨10.7717/peerj.10911⟩ Article dans une revue hal-03166872v2
	Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic Seaver Wang , Weiyi Tang , Erwan Delage , Scott Gifford , Hannah Whitby Scientific Reports, 2021, 11 (1), ⟨10.1038/s41598-021-84969-1⟩ Article dans une revue hal-03166895v1
	Environmental vulnerability of the global ocean epipelagic plankton community interactome Samuel Chaffron , Erwan Delage , Marko Budinich , Damien Vintache , Nicolas Henry Science Advances , 2021, 7 (35), pp.eabg1921. ⟨10.1126/sciadv.abg1921⟩ Article dans une revue hal-03443359v2
	Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula Yajuan Lin , Carly Moreno , Adrian Marchetti , Hugh Ducklow , Oscar Schofield Nature Communications, 2021, 12, pp.4948. ⟨10.1038/s41467-021-25235-w⟩ Article dans une revue hal-03389081v1
	Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió Nature Microbiology, 2021, 6 (12), pp.1561-1574. ⟨10.1038/s41564-021-00979-9⟩ Article dans une revue hal-03781908v1
	Roadmap for naming uncultivated Archaea and Bacteria Alison Murray , John Freudenstein , Simonetta Gribaldo , Roland Hatzenpichler , Philip Hugenholtz Nature Microbiology, 2020, 5 (8), pp.987-994. ⟨10.1038/s41564-020-0733-x⟩ Article dans une revue hal-02863761v2
	Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area Clarisse Lemonnier , Morgan Perennou , Damien Eveillard , Antonio Fernandez-Guerra , Aude Leynaert Frontiers in Marine Science, 2020, 7, ⟨10.3389/fmars.2020.00376⟩ Article dans une revue hal-03083042v1
	Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area Clarisse Lemonnier , Morgan Perennou , Damien Eveillard , Antonio Fernandez-Guerra , Aude Leynaert Frontiers in Marine Science, 2020, 7, ⟨10.3389/fmars.2020.00376⟩ Article dans une revue hal-02938091v1
	Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions Simon Ramondenc , Damien Eveillard , Lionel Guidi , Fabien Lombard , Benoit Delahaye Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-62357-5⟩ Article dans une revue hal-02539195v1
	Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803 Ulysse Guyet , Ngoc Thanh Nguyen , Hugo Doré , Julie Haguait , Justine Pittera Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01707⟩ Article dans une revue hal-02929424v1
	Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica Alison Murray , Nicole Avalon , Lucas Bishop , Karen Davenport , Erwan Delage Marine drugs, 2020, 18 (6), pp.298. ⟨10.3390/md18060298⟩ Article dans une revue hal-02862365v1
	Tara Oceans: towards global ocean ecosystems biology Shinichi Sunagawa , Silvia Acinas , Peer Bork , Chris Bowler , Silvia Acinas Nature Reviews Microbiology, 2020, 18 (8), pp.428-445. ⟨10.1038/s41579-020-0364-5⟩ Article dans une revue hal-04394809v1
	Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria Hugo Doré , Gregory Farrant , Ulysse Guyet , Julie Haguait , Florian Humily Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.567431⟩ Article dans une revue hal-02938656v1
	Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems Antonietta Capotondi , Michael Jacox , Chris Bowler , Maria Kavanaugh , Patrick Lehodey Frontiers in Marine Science, 2019, 6, pp.623. ⟨10.3389/fmars.2019.00623⟩ Article dans une revue hal-02316446v1
	Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Luigi Caputi , Quentin Carradec , Damien Eveillard , Amos Kirilovsky , Eric Pelletier Global Biogeochemical Cycles, 2019, 33 (3), pp.391-419. ⟨10.1029/2018GB006022⟩ Article dans une revue hal-02999805v1
	Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle Damien Eveillard , Nicholas Bouskill , Damien Vintache , Julien Gras , Bess Ward Frontiers in Microbiology, 2019, 9, pp.1-9. ⟨10.3389/fmicb.2018.03298⟩ Article dans une revue hal-01996045v1
	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 Scientific Reports, 2018, 8 (1), pp.5875. ⟨10.1038/s41598-018-23931-0⟩ Article dans une revue hal-01774624v1
	Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline Domenico d'Alelio , Damien Eveillard , Victoria Coles , Luigi Caputi , Maurizio Ribera D’alcalà Current Opinion in Systems Biology, 2018, ⟨10.1016/j.coisb.2018.10.003⟩ Article dans une revue hal-01909434v1
	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 Algal Research - Biomass, Biofuels and Bioproducts, 2018, 30, pp.59 - 72. ⟨10.1016/j.algal.2017.12.011⟩ Article dans une revue hal-01677336v1
	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 Frontiers in Microbiology, 2017, 8, pp.article 1808. ⟨10.3389/fmicb.2017.01808⟩ Article dans une revue hal-01613034v1
	On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore Benoît Delahaye , Damien Eveillard , Nicholas Bouskill mSystems, 2017, 2 (6), ⟨10.1128/mSystems.00169-17⟩ Article dans une revue hal-01658218v1
	Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks Julie Laniau , Clémence Frioux , Jacques Nicolas , Caroline Baroukh , Maria-Paz Cortés PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩ Article dans une revue hal-01635688v1
	A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. Marko Budinich , Jérémie Bourdon , Abdelhalim Larhlimi , Damien Eveillard PLoS ONE, 2017, 12 (2), pp.e0171744 Article dans une revue hal-01478375v1
	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 PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩ Article dans une revue hal-01449100v1
	Beyond the Black Queen Hypothesis. Alix Mas , Shahrad Jamshidi , Yvan Lagadeuc , Damien Eveillard , Philippe Vandenkoornhuyse The International Society of Microbiologial Ecology Journal, 2016, 10 (9), pp.2085-2091. ⟨10.1038/ismej.2016.22⟩ Article dans une revue hal-01290210v1
	Deciphering transcriptional regulations coordinating the response to environmental changes Vicente Acuña , Andrés Aravena , Carito Guziolowski , Damien Eveillard , Anne Siegel BMC Bioinformatics, 2016, 17 (1), pp.129-42. ⟨10.1186/s12859-016-0885-0⟩ Article dans une revue hal-01260866v1
	Plankton networks driving carbon export in the oligotrophic ocean Lionel Guidi , Samuel Chaffron , Lucie Bittner , Damien Eveillard , Abdelhalim Larhlimi Nature, 2016, 532, pp.465-470. ⟨10.1038/nature16942⟩ Article dans une revue hal-01275276v1
	Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach Philippe Bordron , Mauricio Latorre , Maria-Paz Cortés , Mauricio Gonzales , Sven Thiele MicrobiologyOpen, 2016, 5 (1), pp.106-117. ⟨10.1002/mbo3.315⟩ Article dans une revue hal-01246173v1
	Un réseau social chez les planctons Damien Eveillard , Joanna Jongwane Interstices, 2016 Article dans une revue hal-01350462v1
	Predictive ecology in a changing world Nicolas Mouquet , Yvan Lagadeuc , Vincent Devictor , Luc L. Doyen , Anne Duputié Journal of Applied Ecology, 2015, 52 (5), pp.1293-1310. ⟨10.1111/1365-2664.12482⟩ Article dans une revue hal-01180277v1
	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 Ecological Modelling, 2015, 311, pp.11-19. ⟨10.1016/j.ecolmodel.2015.04.021⟩ Article dans une revue hal-01157450v1
	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 Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩ Article dans une revue hal-01057153v1
	A metabolic approach to study algal-bacterial interactions in changing environments. Simon M. Dittami , Damien Eveillard , Thierry Tonon Molecular Ecology, 2014, 23 (7), pp.1656-60. ⟨10.1111/mec.12670⟩ Article dans une revue hal-00936195v1
	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 Environmental Microbiology Reports, 2014, 6 (1), pp.106 - 112 Article dans une revue hal-00951509v1
	Marine systems biology. Thierry Tonon , Damien Eveillard Frontiers in Genetics, 2014, 6, pp.181 Article dans une revue hal-01161455v1
	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 FEMS Microbiology Ecology, 2013, 83 (1), pp.74-81. ⟨10.1111/j.1574-6941.2012.01457.x⟩ Article dans une revue hal-00752749v1
	Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments. Nicholas J Bouskill , Damien Eveillard , Diana Chien , Amal Jayakumar , Bess B Ward Environmental Microbiology, 2012, 14 (3), pp.714-729. ⟨10.1111/j.1462-2920.2011.02623.x⟩ Article dans une revue hal-00661746v1
	Integrated analysis of the gene neighbouring impact on bacterial metabolic networks. P. Bordron , D. Eveillard , I. Rusu IET Systems Biology, 2011, 5 (4), pp.261-268. ⟨10.1049/iet-syb.2010.0070⟩ Article dans une revue hal-00626709v1
	Integrating quantitative knowledge into a qualitative gene regulatory network. Jérémie Bourdon , Damien Eveillard , Anne Siegel PLoS Computational Biology, 2011, 7 (9), pp.e1002157. ⟨10.1371/journal.pcbi.1002157⟩ Article dans une revue hal-00626708v1
	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 Environmental Microbiology, 2011, 13 (4), pp.872-886. ⟨10.1111/j.1462-2920.2010.02362.x⟩ Article dans une revue hal-00626710v1
	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 OMICS, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩ Article dans une revue hal-00661751v1
	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 Molecular BioSystems, 2011, 7 (8), pp.2508-2521. ⟨10.1039/c1mb05102d⟩ Article dans une revue hal-00626712v1
	Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination Sf Martinez , A. Renodon-Cornière , J. Nomme , D. Eveillard , F. Fleury Biochimie, 2010, 92 (12), pp.1832-1838 Article dans une revue hal-00549787v1
	Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination. Susan F Martinez , Axelle Renodon-Cornière , Julian Nomme , Damien Eveillard , Fabrice Fleury Biochimie, 2010, 92 (12), pp.1832-8. ⟨10.1016/j.biochi.2010.08.006⟩ Article dans une revue hal-00626711v1
	Hybrid Modeling of Gene Regulatory Networks: Mixing Temporal and Qualitative Biological Properties Jonathan Fromentin , Damien Eveillard , Olivier Roux BMC Systems Biology, 2010, 4 (79), http://www.biomedcentral.com/1752-0509/4/79/abstract. ⟨10.1186/1752-0509-4-79⟩ Article dans une revue hal-00346588v1
	Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions Géraldine del Mondo , Damien Eveillard , Irena Rusu Bioinformatics, 2009, 25 (7), pp.926-932. ⟨10.1093/bioinformatics/btp083⟩ Article dans une revue hal-02352007v1
	Temporal constraints of a gene regulatory network: refining a qualitative simulation Jamil Ahmad , Jérémie Bourdon , Damien Eveillard , Jonathan Fromentin , Olivier Roux BioSystems, 2009, pp.10.1016/j.biosystems.2009.05.002. ⟨10.1016/j.biosystems.2009.05.002⟩ Article dans une revue hal-00423353v1
	Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions. Géraldine del Mondo , Damien Eveillard , Irena Rusu Bioinformatics, 2009, 25 (7), pp.926-32. ⟨10.1093/bioinformatics/btp083⟩ Article dans une revue hal-00415905v1
	Temporal constraints of a gene regulatory network: Refining a qualitative simulation. Jamil Ahmad , Jérémie Bourdon , Damien Eveillard , Jonathan Fromentin , Olivier Roux BioSystems, 2009, 98 (3), pp.149-159. ⟨10.1016/j.biosystems.2009.05.002⟩ Article dans une revue hal-00415921v1
	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 Journal of Nutritional Biochemistry, 2009, 20 (4), pp.312-20. ⟨10.1016/j.jnutbio.2008.04.004⟩ Article dans une revue hal-00415914v1
	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 Environmental Microbiology, 2007, 9 (10), pp.2522-2538 Article dans une revue hal-00346599v1
	A multi-scale constraint programming model of alternative splicing regulation Damien Eveillard , Delphine Ropers , Hidde de Jong , Christiane Branlant , Alexander Bockmayr Theoretical Computer Science, 2004, Special issue: computational systems biology, 325 (1), pp.3-24. ⟨10.1016/j.tcs.2004.03.062⟩ Article dans une revue inria-00000916v1

	Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change Nayat Sanchez-Pi , Luis Marti , André Abreu , Olivier Bernard , Colomban de Vargas NeurIPS 2020 Workshop - Tackling Climate Change with Machine Learning, Dec 2020, Santiago / Virtual, Chile Communication dans un congrès hal-03138712v1
	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 Sakina-Dorothée Ayata , E. Faure , A.-S. Benoiston , Fabrice Not , Olivier Aumont Functional Ecology Conference, 2018, Nancy, France Communication dans un congrès hal-04024046v1
	Plankton networks correlated to the biological carbon pump in the global ocean A.S. Benoiston , L. Bittner , Lionel Guidi , S. Chaffron , D. Eveillard Journée analyse des réseau, GDR génomique environnementale, 2017, Nantes, France Communication dans un congrès hal-04024048v1
	Toward a better understanding of the plant microbiota Victoria Potdevin , Marie Chevallier , Ruben Garrido Oter , Anne Siegel , Stéphane Hacquard 4ème colloque de Génomique Environnementale, GDR Génomique Environnementale, Sep 2017, Marseille, France Communication dans un congrès hal-01576743v1
	Revealing and analyzing networks of marine microbial ecosystems Damien Eveillard , Lionel Guidi , Lucie Bittner , Samuel Chaffron , Jeroen Raes Conférence Jacques Monod - Marine Ecosystems Biology, 2015, Roscoff, France Communication dans un congrès hal-01176727v1
	OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques Marko Budinich , Jérémie Bourdon , Abdelhalim Larhlimi , Damien Eveillard 13th International Conference on Computational Methods in Systems Biology CMSB 2015, Sep 2015, Nantes, France. pp.279-281, ⟨10.1007/978-3-319-23401-4_23⟩ Communication dans un congrès hal-02464859v1
	Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming Guillaume Collet , Damien Eveillard , Martin Gebser , Sylvain Prigent , Torsten Schaub LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain Communication dans un congrès hal-00853752v1
	Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming Guillaume Collet , Damien Eveillard , Martin Gebser , Sylvain Prigent , Torsten Schaub LPNMR, 2013, ⟨10.1007/978-3-642-40564-8_25⟩ Communication dans un congrès hal-02745669v1
	An ASP application in integrative biology: identification of functional gene units Philippe Bordron , Damien Eveillard , Alejandro Maass , Anne Siegel , Sven Thiele LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain Communication dans un congrès hal-00853762v1
	Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology Thierry Tonon , Patricia Bonin , Sylvain Prigent , Z. Shao , Agnès Groisillier Esil 2012: algal post-genomics, Apr 2012, Roscoff, France Communication dans un congrès hal-00760640v1
	Integration of omics data to investigate common intervals Sébastien Angibaud , Philippe Bordron , Damien Eveillard , Guillaume Fertin , Irena Rusu 1st International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2011), 2011, Singapore, Singapore. pp.101-105 Communication dans un congrès hal-00606226v1
	SIPPER: A flexible method to integrate heterogeneous data into a metabolic network Philippe Bordron , Damien Eveillard , Irena Rusu Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on, Feb 2011, Orlando, United States. pp.40 - 45, ⟨10.1109/ICCABS.2011.5729937⟩ Communication dans un congrès hal-00585102v1
	Including Ordinary Differential Equations Based Constraints in the Standard CP Framework Alexandre Goldsztejn , Olivier Mullier , Damien Eveillard , Hiroshi Hosobe Principles and Practice of Constraint Programming, CP2010, Sep 2010, St Andrews, United Kingdom. pp.221--235 Communication dans un congrès hal-00520054v1
	Comparing Bacterial Genomes by Searching their Common Intervals Sébastien Angibaud , Damien Eveillard , Guillaume Fertin , Irena Rusu 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), 2009, New Orleans, United States. pp.102-113, ⟨10.1007/978-3-642-00727-9_12⟩ Communication dans un congrès hal-00416466v1
	Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches Damien Eveillard , Jonathan Fromentin , Olivier Roux Workshop on Constraint Based Methods for Bioinformatics (WCB08), 2008, Paris, France. pp.10 Communication dans un congrès hal-00277104v1
	Building and analysing an integrative model of HIV-1 RNA alternative splicing Alexander Bockmayr , Arnaud Courtois , Damien Eveillard , Myriam Vezain International Conference on Computational Methods in Systems Biology - CMSB 2004, May 2004, Paris/France, pp.43--57, ⟨10.1007/b107287⟩ Communication dans un congrès inria-00000917v1
	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 5èmes Journées Ouvertes Biologie Informatique Mathématiques - JOBIM 2004, Jun 2004, Montréal, Canada Communication dans un congrès inria-00000915v1
	Multiscale modeling of alternative splicing regulation Damien Eveillard , Delphine Ropers , Hidde de Jong , Christiane Branlant , Alexander Bockmayr International Workshop on Computational Methods in Systems Biology - CMSB'03, 2003, Rovereto, Italie, pp.75-87 Communication dans un congrès inria-00099792v1
	Hybrid concurrent constraint programming: A well-suited formalism for modelling alternative splicing regulation (Abstract) Damien Eveillard , Arnaud Courtois , Alexander Bockmayr Modeling and Simulation of Biological Regulatory Processes - ECCB Satellite Meeting, 2003, Paris, France Communication dans un congrès inria-00099705v1
	Traitement statistique des résultats SELEX Damien Eveillard , Yann Guermeur Journées Ouvertes en Biologie Informatiques et Mathématiques - JOBIM 2002, Jacques Nicolas & Claude Thermes, Jun 2002, Saint Malo - France, pp.277--283 Communication dans un congrès inria-00000918v1

	PhotoEukStein opens doors to the metabolism of eukaryotic-algae Marie Burel , Antoine Régimbeau , Damien Eveillard , Eric Pelletier ISME18, Aug 2022, Lausanne, Switzerland Poster de conférence hal-04384915v1
	Assessing functional diversity of plankton communities from high throughput –omics data Sakina-Dorothée Ayata , E. Faure , A.-S. Benoiston , O. Silva , V. Sonnet Colloque de Bilan et de Prospective du programme LEFE, Mar 2018, Clermont-Ferrand, France. 2018 Poster de conférence hal-04021818v1

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

	Les microbiomes de l'océan : une démarche à haut débit pour une compréhension globale et systémique Lucie Bittner , Lionel Guidi , Samuel Chaffron , Damien Eveillard Laurent Palka. Microbiodiversité : un nouveau regard, 161 - 185, editions matériologiques, 2018 Chapitre d'ouvrage hal-01996304v1
	L'écologie des systèmes Damien Eveillard , Anne Siegel , Philippe Vandenkoornhuyse Mokrane Bouzeghoub et Rémy Mosseri. Les Big Data à Découvert, CNRS éditions, 2017, 978-2-271-11464-8 Chapitre d'ouvrage hal-01575603v1
	L’écologie des systèmes Damien Eveillard , Anne Siegel , Philippe Vandenkoornhuyse CNRS éditions. Les big data à découvert, Mokrane Bouzeghoub et Rémy Mosseri, 2017, 978-2-271-11464-8 Chapitre d'ouvrage hal-02389705v1
	Modeling and predicting behaviors and dynamics of ecosystems Damien Eveillard , Xavier Raynaud , Jérémie Bourdon , Alain Franc , Frédéric Plewniak Insight on environmental genomics, the high-throughput sequencing revolution, 2016 Chapitre d'ouvrage hal-03823723v1
	Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes Damien Eveillard , Xavier Raynaud , Jérémie Bourdon , Alain Franc , Frederic Plewniak La génomique environnemetale : la révolution du séquençage à haut débit, 2016 Chapitre d'ouvrage hal-01777358v1
	XII Des données haut-débit à la modélisation des écosystèmes Damien Eveillard , Xavier Raynaud , Jérémie Bourdon , Alain Franc , Frederic Plewniak Prospective Génomique Environnementale, , pp.83-89, 2013 Chapitre d'ouvrage hal-01176570v1
	Ecologie prédictive & changement planétaire Frédéric Austerlitz , Michael Blum , Sarah Calba , Jérôme Chave , Marc Choisy Thiébault; Stéphanie and Hadi; Halima. Prospective de l'Institut écologie & environnement du CNRS, hors s\'{e}rie, Institut écologie & environnement du CNRS, pp.9-44, 2013 Chapitre d'ouvrage hal-01911607v1
	Probabilistic Approaches for Investigating Biological Networks Jérémie Bourdon , Damien Eveillard Mourad Elloumi, Albert Y. Zomaya. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley, pp.1066, 2011 Chapitre d'ouvrage hal-00531568v1

	Contribution of the jellyfish Pelagia Noctiluca to carbon export in the Mediterranean Sea S. Ramondenc , F. Delahaye , D. Eveillard , L. Stemmann , L. Guidi 2017 Autre publication scientifique hal-04023034v1

	Towards modeling genome-scale knowledge in the global ocean Antoine Régimbeau , Olivier Aumont , Chris Bowler , Lionel Guidi , George Jackson 2023 Pré-publication, Document de travail hal-04316033v1
	PhotoEukStein: Towards an omics-based definition of unicellular eukaryote phototrophs functional traits via metabolic modelling Marie Burel , Antoine Régimbeau , Samuel Chaffron , Damien Eveillard , Eric Pelletier 2023 Pré-publication, Document de travail hal-04315997v1
	Community metabolic modeling of host-microbiota interactions through multi-objective optimization Anna Lambert , Marko Budinich , Maxime Mahé , Samuel Chaffron , Damien Eveillard 2023 Pré-publication, Document de travail hal-04316271v1
	Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies Hugo Doré , Ulysse Guyet , Jade Leconte , Gregory Farrant , Benjamin Alric 2022 Pré-publication, Document de travail hal-03798651v1
	Insights into biotic and abiotic modulation of ocean mesopelagic communities Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Karlusich 2022 Pré-publication, Document de travail hal-03166899v1
	Disentangling microbial networks across pelagic zones in the global ocean Ina M Deutschmann , Erwan Delage , Caterina R Giner , Marta Sebastián , Julie Poulain 2021 Pré-publication, Document de travail hal-03855706v1
	Contribution of genome scale metabolic modeling to niche theory Antoine Régimbeau , Marko Budinich , Abdelhalim Larhlimi , Juan Jose Pierella Karlusich , Olivier Aumont 2021 Pré-publication, Document de travail hal-03352833v1
	Ecogenomics of key prokaryotes in the arctic ocean Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió 2020 Pré-publication, Document de travail hal-02946895v1
	Impact of the species compartment definition on quantitative modeling of microbial communities Marko Budinich , Jérémie Bourdon , Damien Eveillard 2015 Pré-publication, Document de travail hal-01145858v1
	Combinatorial optimization methods to complete and analyse a metabolic network Julie Laniau , Anne Siegel , Damien Eveillard 2015 Pré-publication, Document de travail hal-01244179v1
	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 2009 Pré-publication, Document de travail hal-00359530v1
	Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach Jérémie Bourdon , Damien Eveillard , Samuel Gabillard , Theo Merle 2007 Pré-publication, Document de travail hal-00199362v1
	Toll Based Measures for Dynamical Graphs Jérémie Bourdon , Damien Eveillard 2007 Pré-publication, Document de travail hal-00134078v1

	MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network Marko Budinich , Damien Eveillard , Jérémie Bourdon , Abdelhalim Larhlimi 2013 Rapport hal-00839321v1
	A Multi-Site Constraint Programming Model of Alternative Splicing Regulation Damien Eveillard , Delphine Ropers , Hidde de Jong , Christiane Branlant , Alexander Bockmayr [Research Report] RR-4830, INRIA. 2003 Rapport inria-00071756v1
	Modeling the effects of SR proteins on alternative splicing Damien Eveillard , Delphine Ropers , Hidde de Jong , Christiane Branlant , Alexander Bockmayr [Intern report] A02-R-117 \|\| eveillard02b, 2002, 8 p Rapport inria-00101060v1

	Modélisation statistique et formelle de la régulation de l'épissage alternatif Damien Eveillard Biologie moléculaire. Université Henri Poincaré - Nancy 1, 2004. Français. ⟨NNT : 2004NAN10037⟩ Thèse tel-01754419v1

	From Systems Biology to Systems Ecology: A Computational Journey Through Biological Scales Damien Eveillard Bioinformatics [q-bio.QM]. Université de Nantes, 2020 HDR tel-04385526v1

Damien Eveillard

Présentation

Publications

Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean

Unveiling abundance-dependent metabolic phenotypes of microbial communities

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Disentangling temporal associations in marine microbial networks

Ocean-wide comparisons of mesopelagic planktonic community structures

Diversity and ecological footprint of Global Ocean RNA viruses

Priorities for ocean microbiome research

Contribution of genome‐scale metabolic modelling to niche theory

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic

Environmental vulnerability of the global ocean epipelagic plankton community interactome

Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Roadmap for naming uncultivated Archaea and Bacteria

Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area

Linking Spatial and Temporal Dynamic of Bacterioplankton Communities With Ecological Strategies Across a Coastal Frontal Area

Probabilistic modeling to estimate jellyfish ecophysiological properties and size distributions

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803

Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Tara Oceans: towards global ocean ecosystems biology

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Observational Needs Supporting Marine Ecosystems Modeling and Forecasting: From the Global Ocean to Regional and Coastal Systems

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline

Identification of transcription factors involved in the phenotype of a domesticated oleaginous microalgae strain of Tisochrysis lutea

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Beyond the Black Queen Hypothesis.

Deciphering transcriptional regulations coordinating the response to environmental changes

Plankton networks driving carbon export in the oligotrophic ocean

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

Un réseau social chez les planctons

Predictive ecology in a changing world

Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.

A metabolic approach to study algal-bacterial interactions in changing environments.

A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico

Marine systems biology.

Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats.

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.

Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.

Integrating quantitative knowledge into a qualitative gene regulatory network.

Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.

Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes.

Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination

Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination.

Hybrid Modeling of Gene Regulatory Networks: Mixing Temporal and Qualitative Biological Properties

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions

Temporal constraints of a gene regulatory network: refining a qualitative simulation

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions.

Temporal constraints of a gene regulatory network: Refining a qualitative simulation.

Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium.

Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

A multi-scale constraint programming model of alternative splicing regulation

Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change

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

Plankton networks correlated to the biological carbon pump in the global ocean

Toward a better understanding of the plant microbiota

Revealing and analyzing networks of marine microbial ecosystems

OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques

Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

An ASP application in integrative biology: identification of functional gene units

Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology

Integration of omics data to investigate common intervals

SIPPER: A flexible method to integrate heterogeneous data into a metabolic network

Including Ordinary Differential Equations Based Constraints in the Standard CP Framework

Comparing Bacterial Genomes by Searching their Common Intervals

Constraints Programming for Unifying Gene Regulatory Networks Modeling Approaches

Building and analysing an integrative model of HIV-1 RNA alternative splicing