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Jérémie BOURDON

ENSEIGNANT-CHERCHEUR

HDR

Equipe : COMBI.

: +33 (0)2 51 12 58 25

Adresse :

Université de Nantes - faculté des Sciences et Techniques ( FST )
Petit Port
2 Chemin de la Houssinière
BP 92208
44322 Nantes Cedex 3

Batiment 34, étage 3, bureau 309



Publications référencées sur HAL

Revues internationales avec comité de lecture (ART_INT)

    • [1] T. Consortium, S. Kilens, D. Meistermann, D. Moreno, C. Chariau, A. Gaignerie, A. Reignier, Y. Lelièvre, M. Casanova, C. Vallot, S. Nedellec, L. Flippe, J. Firmin, J. Song, E. Charpentier, J. Lammers, A. Donnart, N. Marec, W. Deb, A. Bihouee, C. Le Caignec, C. Pecqueur, R. Redon, P. Barriere, J. Bourdon, V. Pasque, M. Soumillon, T. Mikkelsen, C. Rougeulle, T. Freour, L. David. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. In Nature Communications ; éd. Nature Publishing Group, 2018, vol. 9, num. 1.
      http://www.hal.inserm.fr/hal-01881146
    • [2] S. Kilens, D. Meistermann, C. Chariau, A. Gaignerie, A. Reignier, Y. Lelièvre, M. Casanova, C. Vallot, S. Nedellec, L. Flippe, J. Firmin, J. Song, E. Charpentier, J. Lammers, A. Donnart, N. Marec, W. Deb, A. Bihouée, M. Intérieur Consortium, C. Le Caignec, C. Pecqueur, R. Redon, P. Barriere, J. Bourdon, V. Pasque, M. Soumillon, T. Mikkelsen, C. Rougeulle, T. Freour, L. David, L. Abel, A. Alcover, P. Bousso, P. Bruhns, A. Cumano, D. Duffy, C. Demangel, L. Deriano, J. Santo, F. Dromer, G. Eberl, J. Enninga, J. Fellay, A. Freitas, O. Gelpi, I. Gomperts Boneca, S. Hercberg, O. Lantz, C. Leclerc, H. Mouquet, E. Patin, S. Pellegrini, S. Pol, L. Rogge, A. Sakuntabhai, O. Schwartz, B. Schwikowski, S. Shorte, V. Soumelis, F. Tangy, E. Tartour, A. Toubert, M. Ungeheuer, L. Quintana-Murci, M. Albert. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. In Nature Communications ; éd. Nature Publishing Group, 2018, vol. 9, num. 1.
      https://hal-pasteur.archives-ouvertes.fr/pasteur-01758726
    • [3] S. Kilens, D. Meistermann, D. Moreno, C. Chariau, A. Gaignerie, A. Reignier, Y. Lelièvre, M. Casanova, C. Vallot, S. Nedellec, L. Flippe, J. Firmin, J. Song, E. Charpentier, J. Lammers, A. Donnart, N. Marec, W. Deb, A. Bihouée, C. The Milieu Interieur, C. Le Caignec, C. Pecqueur, R. Redon, P. Barriere, J. Bourdon, V. Pasque, M. Soumillon, T. Mikkelsen, C. Rougeulle, T. Fréour, L. David. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. In Nature Communications ; éd. Nature Publishing Group, 2018, vol. 9, num. 1.
      http://www.hal.inserm.fr/inserm-01709022
    • [4] S. Prigent, C. Frioux, S. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, 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 ; éd. Public Library of Science, 2017, vol. 13, num. 1.
      https://hal.inria.fr/hal-01449100
    • [5] M. Budinich, J. Bourdon, A. Larhlimi, D. Eveillard. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.. In PLoS ONE ; éd. Public Library of Science, 2017, vol. 12, num. 2.
      https://hal.archives-ouvertes.fr/hal-01478375
    • [6] V. Picard, A. Siegel, J. Bourdon. A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. In Journal of computational biology : a journal of computational molecular cell biology ; éd. Mary Ann Liebert, 2017, vol. 24, num. 8.
      https://hal.archives-ouvertes.fr/hal-01552190
    • [7] V. Berthé, J. Bourdon, T. Jolivet, A. Siegel. A combinatorial approach to products of Pisot substitutions. In Ergodic Theory and Dynamical Systems ; éd. Cambridge University Press (CUP), 2016, vol. 36, num. 6.
      https://hal.inria.fr/hal-01196326
    • [8] V. Picard, O. Mulner-Lorillon, J. Bourdon, J. Morales, P. Cormier, A. Siegel, R. Bellé. Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization. In Molecular Reproduction and Development ; éd. Wiley, 2016.
      https://hal.sorbonne-universite.fr/hal-01390047
    • [9] V. Picard, A. Siegel, J. Bourdon. Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications. In Electronic Notes in Theoretical Computer Science ; éd. Elsevier, 2015, vol. 316C.
      https://hal.inria.fr/hal-01196533
    • [10] O. Abdou-Arbi, S. Lemosquet, J. Milgen, A. Siegel, J. Bourdon. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. In BMC Systems Biology ; éd. BioMed Central, 2014, vol. 8, num. 1.
      https://hal.inria.fr/hal-00947219
    • [11] S. Laurent, A. Richard, O. Mulner-Lorillon, J. Morales, D. Flament, V. Glippa, J. Bourdon, P. Gosselin, A. Siegel, P. Cormier, R. Bellé. Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive. In Frontiers in Genetics ; éd. Frontiers, 2014, vol. 5.
      https://hal.inria.fr/hal-01079758
    • [13] J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network.. In PLoS Computational Biology ; éd. Public Library of Science, 2011, vol. 7, num. 9.
      https://hal.archives-ouvertes.fr/hal-00626708
    • [14] 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 ; éd. Mary Ann Liebert, 2011, vol. 15, num. 12.
      https://hal.archives-ouvertes.fr/hal-00661751
    • [15] S. Carat, R. Houlgatte, J. Bourdon. A parallel scheme for comparing transcription factor binding sites matrices. In Journal of Bioinformatics and Computational Biology ; éd. World Scientific Publishing, 2010, vol. 8, num. 3.
      https://hal.archives-ouvertes.fr/hal-00461973
    • [17] 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 ; éd. Elsevier, 2009, vol. 98, num. 3.
      https://hal.archives-ouvertes.fr/hal-00415921
    • [18] 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, Special Issue on Gene Regulatory Networks. 13-05-2009
      https://hal.archives-ouvertes.fr/hal-00423353
    • [20] S. Küry, B. Buecher, S. Robiou-Du-Pont, C. Scoul, V. Sébille, H. Colman, C. Le Houérou, T. Le Neel, J. Bourdon, R. Faroux, J. Ollivry, B. Lafraise, L. Chupin, S. Bézieau. Combinations of cytochrome P450 gene polymorphisms enhancing the risk for sporadic colorectal cancer related to red meat consumption.. In Cancer Epidemiology, Biomarkers and Prevention ; éd. American Association for Cancer Research, 2007, vol. 16, num. 7.
      https://hal.archives-ouvertes.fr/hal-00415938

Revues nationales avec comité de lecture (ART_NAT)

    • [21] J. Bourdon, B. Daireaux, B. Vallée. Dynamical Analysis of alpha-Euclidean Algorithms. In Journal of Algorithms in Cognition, Informatics and Logic ; éd. Elsevier, 2002, vol. 1, num. 44.
      https://hal.archives-ouvertes.fr/hal-00442421

Conférences internationales avec comité de lecture et actes (COMM_INT)

    • [26] V. Picard, A. Siegel, J. Bourdon. A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. In IJCAI workshop BAI: Bioinformatics and Artificial Intelligence, 2015, Buenos Aeres, Argentine.
      https://hal.inria.fr/hal-01196598
    • [27] V. Picard, A. Siegel, J. Bourdon. Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applications. In SASB - 5th International Workshop on Static Analysis and Systems Biology, 2014, Munchen, Allemagne.
      https://hal.inria.fr/hal-01079768
    • [28] V. Berthe, J. Bourdon, T. Jolivet, A. Siegel. Generating discrete planes with substitutions. In WORDS - 9th International Conference on Words - 2013, septembre 2013, Turku, Finlande.
      https://hal.inria.fr/hal-00853758
    • [29] 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, avril 2012, Roscoff, France.
      https://hal.inria.fr/hal-00760640
    • [30] J. Bourdon, M. Regnier. Large deviation properties for patterns. In LSD&LAW 2012, février 2012, Londres, Royaume-Uni.In Thierry Lecroq (éds.), . , 2012.
      https://hal.inria.fr/hal-00758251
    • [31] J. Bourdon. Average-case analysis methods dedicated to the study of Biological Networks. In Moscow Conference on Computational Molecular Biology (MCCMB) 2011, juillet 2011, Moscou, Russie.
      https://hal.archives-ouvertes.fr/hal-01176716
    • [32] T. Merle, J. Bourdon. Complex update strategies for Probabilistic Boolean Networks. In 7th Workshop on Computational Systems Biology, juin 2010, Luxembourg, France.In TISCP (éds.), Proceedings of WSCB 2010. , 2010.
      https://hal.archives-ouvertes.fr/hal-00480366
    • [34] S. Lemosquet, J. Bourdon, J. Guinard-Flament, A. Siegel, J. Van Milgen. A Generic Stochiometric Model to Analyse the Metabolic Flexibility of the Mammary Gland in Lactating Dairy Cows. In 7th Workshop Modelling Nutrient Digestion and Utilization in Farm Animals, septembre 2009, Paris, France.In INRA (éds.), Proceedings of 7th Workshop Modelling Nutrient Digestion and Utilization in Farm Animals. , 2009.
      https://hal.archives-ouvertes.fr/hal-00416396
    • [36] J. Bourdon, A. Mancheron. Statistical Properties of Similarity Score Functions. In Fourth Colloquium on Mathematics and Computer Science Algorithms, Trees, Combinatorics and Probabilities, 2006, Nancy, France.In Discrete Mathematics and Theoretical Computer Science ; éd. DMTCS, 2006, vol. DMTCS Proceedings vol. AG, Fourth Colloquium on Mathematics and Computer Science Algorithms, Trees, Combinatorics and Probabilities.In Chassaing, Philippe and others (éds.), . Discrete Mathematics and Theoretical Computer Science, 2006.
      https://hal.inria.fr/hal-01184706

Conférences nationales avec comité de lecture et actes (COMM_NAT)

    • [37] A. Przybylski, J. Bourdon, X. Gandibleux. Distribution des solutions du problème d'affectation multi-objectif et relation avec l'efficacité des algorithmes de résolution. In FRANCORO V / ROADEF 2007, février 2007, Grenoble, France.
      https://hal.archives-ouvertes.fr/hal-00465766
    • [38] A. Przybylski, J. Bourdon, X. Gandibleux. Distribution of Solutions of Multi-objective Assignment Problem and Links with the Efficiency of Solving Methods.. In GOR 2007, septembre 2007, Saarbrücken, Allemagne.
      https://hal.archives-ouvertes.fr/hal-00465762

Ouvrages - Chapitres d‘ouvrages et directions d‘ouvrages (OUV)

    • [39] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes. In La génomique environnemetale : la révolution du séquençage à haut débit. 01-07-2016
      https://hal.archives-ouvertes.fr/hal-01777358
    • [41] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. XII Des données haut-débit à la modélisation des écosystèmes. In Prospective Génomique Environnementale. 2013
      https://hal.archives-ouvertes.fr/hal-01176570
    • [42] J. Bourdon, D. Eveillard. Probabilistic Approaches for Investigating Biological Networks. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications. 05-01-2011
      https://hal.archives-ouvertes.fr/hal-00531568
    • [43] S. Lemosquet, O. Abdou-Arbi, A. Siegel, J. Guinard-Flament, J. Van Milgen, J. Bourdon. A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cows. In Modelling nutrient digestion and utilization in farm animals. 2010
      https://hal.inria.fr/inria-00538138

Theses et HDR (THESE)

Autres publications (AUTRES)

    • [45] M. Budinich, D. Eveillard, J. Bourdon, A. Larhlimi. MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network. Rapport technique, 2013 ; .
      https://hal.archives-ouvertes.fr/hal-00839321
    • [46] S. Lemosquet-Simon, O. Abdou Arbi, J. Van Milgen, A. Siegel, J. Bourdon. Exploring the metabolic flexibility of the mammary gland of dairy cows through flux-balance analysis. In Meeting of the Animal Science Modelling Group, juillet 2013, Indianapolis, états-Unis.In Canadian Journal of Animal Science, vol. 93, num. 4. 07-07-2013
      https://hal.archives-ouvertes.fr/hal-01210552
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