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Number of documents

19

Systems biology, Systems Ecology & Computational Biology


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.


Jérémie Bourdon   

Journal articles9 documents

  • Damien Eveillard, Nicholas Bouskill, Damien Vintache, Julien Gras, Bess Ward, et al.. Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle. Frontiers in Microbiology, Frontiers Media, 2019, 9, pp.1-9. ⟨10.3389/fmicb.2018.03298⟩. ⟨hal-01996045⟩
  • Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.. PLoS ONE, Public Library of Science, 2017, 12 (2), pp.e0171744. ⟨hal-01478375⟩
  • Sylvain Prigent, Clémence Frioux, Simon Dittami, Sven Thiele, Abdelhalim Larhlimi, et al.. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Computational Biology, Public Library of Science, 2017, 13 (1), pp.e1005276. ⟨10.1371/journal.pcbi.1005276⟩. ⟨hal-02937671⟩
  • Sylvain Prigent, Clémence Frioux, Simon M Dittami, Sven Thiele, Abdelhalim Larhlimi, et al.. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Computational Biology, Public Library of Science, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩. ⟨hal-01449100⟩
  • Jérémie Bourdon, Damien Eveillard, Anne Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network.. PLoS Computational Biology, Public Library of Science, 2011, 7 (9), pp.e1002157. ⟨10.1371/journal.pcbi.1002157⟩. ⟨hal-00626708⟩
  • Thierry Tonon, Damien Eveillard, Sylvain Prigent, Jérémie Bourdon, Philippe Potin, et al.. Toward Systems Biology in Brown Algae to Explore Acclimation and Adaptation to the Shore Environment. OMICS, Mary Ann Liebert, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩. ⟨hal-02937721⟩
  • Thierry Tonon, Damien Eveillard, Sylvain Prigent, Jérémie Bourdon, Philippe Potin, et al.. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.. OMICS, Mary Ann Liebert, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩. ⟨hal-00661751⟩
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Temporal constraints of a gene regulatory network: Refining a qualitative simulation.. BioSystems, Elsevier, 2009, 98 (3), pp.149-159. ⟨10.1016/j.biosystems.2009.05.002⟩. ⟨hal-00415921⟩
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Temporal constraints of a gene regulatory network: refining a qualitative simulation. BioSystems, Elsevier, 2009, pp.10.1016/j.biosystems.2009.05.002. ⟨10.1016/j.biosystems.2009.05.002⟩. ⟨hal-00423353⟩

Conference papers2 documents

  • Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard. OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques. 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⟩. ⟨hal-02464859⟩
  • Thierry Tonon, Patricia Bonin, Sylvain Prigent, Z. Shao, Agnès Groisillier, et al.. Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology. Esil 2012: algal post-genomics, Apr 2012, Roscoff, France. ⟨hal-00760640⟩

Book sections3 documents

  • Damien Eveillard, Xavier Raynaud, Jérémie Bourdon, Alain Franc, Frederic Plewniak. Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes. La génomique environnemetale : la révolution du séquençage à haut débit, 2016. ⟨hal-01777358⟩
  • Damien Eveillard, Xavier Raynaud, Jérémie Bourdon, Alain Franc, Frederic Plewniak. XII Des données haut-débit à la modélisation des écosystèmes. Prospective Génomique Environnementale, pp.83-89, 2013. ⟨hal-01176570⟩
  • Jérémie Bourdon, Damien Eveillard. Probabilistic Approaches for Investigating Biological Networks. Mourad Elloumi, Albert Y. Zomaya. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley, pp.1066, 2011. ⟨hal-00531568⟩

Preprints, Working Papers, ...4 documents

  • Marko Budinich, Jérémie Bourdon, Damien Eveillard. Impact of the species compartment definition on quantitative modeling of microbial communities. 2015. ⟨hal-01145858⟩
  • Jamil Ahmad, Jérémie Bourdon, Damien Eveillard, Jonathan Fromentin, Olivier Roux, et al.. Qualitative modelling and analysis of gene regulatory networks: application to the adaptation of Escherichia coli bacterium to carbon availability. 2009. ⟨hal-00359530⟩
  • Jérémie Bourdon, Damien Eveillard. Toll Based Measures for Dynamical Graphs. 2007. ⟨hal-00134078⟩
  • Jérémie Bourdon, Damien Eveillard, Samuel Gabillard, Theo Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach. 2007. ⟨hal-00199362⟩

Reports1 document

  • Marko Budinich, Damien Eveillard, Jérémie Bourdon, Abdelhalim Larhlimi. MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network. 2013. ⟨hal-00839321⟩