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Damien Eveillard

18
Documents

Présentation

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

"jeremie-bourdon"

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

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
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⟩
Article dans une revue hal-01449100v1
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⟩
Article dans une revue hal-00661751v1

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

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

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

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

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

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

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
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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
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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
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Toll Based Measures for Dynamical Graphs

 Jérémie Bourdon , Damien Eveillard
2007
Pré-publication, Document de travail hal-00134078v1
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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
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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