Access content directly

Damien Eveillard

111
Documents

Presentation

I try to represent the behavior of living systems on different scales by various modeling approaches based on constraint programming. In my opinion, a living system should be formalized as an hybrid automaton under constraints. My biological studies concern biological systems from molecular to ecological scales, with a special emphasis on marine systems.
I try to represent the behavior of living systems on different scales by various modeling approaches based on constraint programming. In my opinion, a living system should be formalized as an hybrid automaton under constraints. My biological studies concern biological systems from molecular to ecological scales, with a special emphasis on marine systems.

Publications

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⟩
Journal articles hal-04407573v1
Image document

Unveiling abundance-dependent metabolic phenotypes of microbial communities

Natalia E Jiménez , Vicente Acuña , María Paz Cortés , Damien Eveillard , Alejandro Eduardo Maass
Journal articles hal-04198586v1
Image document

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⟩
Journal articles hal-03781901v2
Image document

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⟩
Journal articles hal-04238382v1
Image document

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⟩
Journal articles hal-04184772v1
Image document

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⟩
Journal articles hal-03781935v1
Image document

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⟩
Journal articles hal-03635158v1
Image document

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⟩
Journal articles hal-02399723v2
Image document

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⟩
Journal articles hal-03166895v1
Image document

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⟩
Journal articles hal-03166872v2
Image document

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⟩
Journal articles hal-03389081v1
Image document

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⟩
Journal articles hal-03443359v2

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⟩
Journal articles hal-04394793v1
Image document

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⟩
Journal articles hal-02938656v1
Image document

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⟩
Journal articles hal-03083042v1
Image document

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⟩
Journal articles hal-02938091v1
Image document

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⟩
Journal articles hal-02863761v2

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⟩
Journal articles 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⟩
Journal articles hal-04394809v1
Image document

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⟩
Journal articles hal-02929424v1
Image document

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⟩
Journal articles hal-02539195v1
Image document

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⟩
Journal articles hal-02316446v1
Image document

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⟩
Journal articles 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⟩
Journal articles hal-01996045v1
Image document

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⟩
Journal articles hal-01774624v1
Image document

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⟩
Journal articles hal-01677336v1

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⟩
Journal articles hal-01909434v1

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
Journal articles hal-01478375v1
Image document

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⟩
Journal articles hal-01635688v1

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⟩
Journal articles hal-01658218v1
Image document

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⟩
Journal articles hal-01449100v1
Image document

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⟩
Journal articles hal-01613034v1
Image document

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⟩
Journal articles hal-01290210v1

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⟩
Journal articles hal-01246173v1

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⟩
Journal articles hal-01260866v1
Image document

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⟩
Journal articles hal-01275276v1

Un réseau social chez les planctons

Damien Eveillard , Joanna Jongwane
Interstices, 2016
Journal articles hal-01350462v1

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⟩
Journal articles hal-01157450v1

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⟩
Journal articles hal-01180277v1

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⟩
Journal articles hal-01057153v1

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
Journal articles hal-00951509v1

Marine systems biology.

Thierry Tonon , Damien Eveillard
Frontiers in Genetics, 2014, 6, pp.181
Journal articles hal-01161455v1

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⟩
Journal articles hal-00936195v1

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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles hal-00626708v1

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⟩
Journal articles hal-00626712v1
Image document

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⟩
Journal articles hal-00661751v1

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⟩
Journal articles hal-00626710v1
Image document

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⟩
Journal articles hal-00346588v1

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
Journal articles 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⟩
Journal articles hal-00626711v1

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⟩
Journal articles hal-02352007v1

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⟩
Journal articles 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, pp.10.1016/j.biosystems.2009.05.002. ⟨10.1016/j.biosystems.2009.05.002⟩
Journal articles hal-00423353v1

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⟩
Journal articles 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⟩
Journal articles 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
Journal articles 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⟩
Journal articles inria-00000916v1
Image document

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
Conference papers 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
Conference papers hal-04024046v1

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
Conference papers hal-01576743v1

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
Conference papers hal-04024048v1

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⟩
Conference papers hal-02464859v1

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
Conference papers hal-01176727v1

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
Conference papers hal-00853752v1

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
Conference papers hal-00853762v1

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming

Guillaume Collet , Damien Eveillard , Martin Gebser , Sylvain Prigent , Torsten Schaub
Conference papers hal-02745669v1

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
Conference papers hal-00760640v1
Image document

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
Conference papers 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⟩
Conference papers 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
Conference papers hal-00520054v1

Comparing Bacterial Genomes by Searching Their Common Intervals

Sébastien Angibaud , Damien Eveillard , Guillaume Fertin , Irena Rusu
Bioinformatics and Computational Biology, Apr 2009, New Orleans, United States. pp.102--113, ⟨10.1007/978-3-642-00727-9_12⟩
Conference papers hal-00415955v1
Image document

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
Conference papers hal-00416466v1
Image document

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
Conference papers 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⟩
Conference papers inria-00000917v1
Image document

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
Conference papers inria-00000915v1

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
Conference papers inria-00099705v1

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
Conference papers inria-00099792v1

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
Conference papers inria-00000918v1

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
Book sections 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
Book sections 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
Book sections hal-02389705v1

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
Book sections hal-01777358v1

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
Book sections hal-03823723v1

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
Book sections 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
Book sections 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
Book sections hal-00531568v1

Community metabolic modeling of host-microbiota interactions through multi-objective optimization

Anna Lambert , Marko Budinich , Maxime Mahé , Samuel Chaffron , Damien Eveillard
2023
Preprints, Working Papers, ... hal-04316271v1

Towards modeling genome-scale knowledge in the global ocean

Antoine Régimbeau , Olivier Aumont , Chris Bowler , Lionel Guidi , George Jackson
2023
Preprints, Working Papers, ... 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
Preprints, Working Papers, ... hal-04315997v1

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
Preprints, Working Papers, ... hal-03798651v1
Image document

Insights into biotic and abiotic modulation of ocean mesopelagic communities

Janaina Rigonato , Marko Budinich , Alejandro Murillo , Manoela Brandão , Juan Karlusich
2022
Preprints, Working Papers, ... hal-03166899v1
Image document

Disentangling microbial networks across pelagic zones in the global ocean

Ina M Deutschmann , Erwan Delage , Caterina R Giner , Marta Sebastián , Julie Poulain
2021
Preprints, Working Papers, ... hal-03855706v1

Contribution of genome scale metabolic modeling to niche theory

Antoine Régimbeau , Marko Budinich , Abdelhalim Larhlimi , Juan Jose Pierella Karlusich , Olivier Aumont
2021
Preprints, Working Papers, ... hal-03352833v1
Image document

Ecogenomics of key prokaryotes in the arctic ocean

Marta Royo-Llonch , Pablo Sánchez , Clara Ruiz-González , Guillem Salazar , Carlos Pedrós-Alió
2020
Preprints, Working Papers, ... hal-02946895v1
Image document

Impact of the species compartment definition on quantitative modeling of microbial communities

Marko Budinich , Jérémie Bourdon , Damien Eveillard
2015
Preprints, Working Papers, ... hal-01145858v1
Image document

Combinatorial optimization methods to complete and analyse a metabolic network

Julie Laniau , Anne Siegel , Damien Eveillard
2015
Preprints, Working Papers, ... hal-01244179v1
Image document

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
Preprints, Working Papers, ... hal-00359530v1
Image document

Toll Based Measures for Dynamical Graphs

Jérémie Bourdon , Damien Eveillard
2007
Preprints, Working Papers, ... hal-00134078v1
Image document

Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach

Jérémie Bourdon , Damien Eveillard , Samuel Gabillard , Theo Merle
2007
Preprints, Working Papers, ... hal-00199362v1
Image document

From Systems Biology to Systems Ecology: A Computational Journey Through Biological Scales

Damien Eveillard
Bioinformatics [q-bio.QM]. Université de Nantes, 2020
Habilitation à diriger des recherches tel-04385526v1