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Intégration de donnéesModélisation de systèmes / problèmes / donnéesOptimisation combinatoire / discrète

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BioinformatiqueBiologie des SystèmesMétagénomiqueModélisation Biologique

Jérémie Bourdon

HDR

Enseignant chercheur / Enseignante chercheuse – Professeur / professeure des universités

Equipe :

Employeur : Nantes Université

Expertises :

Biologie des systèmesModèles probabilistesModèles logiquesOptimisation combinatoireAnalyse intégrative de données omiques

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Publications déposées sur HAL

Nombre de publications retournées : 73

Revues internationales avec comité de lecture

[1] J. Bourdon, A. Mancheron. Statistical Properties of Similarity Score Functions, in Discrete Mathematics and Theoretical Computer Science, vol. DMTCS Proceedings vol. AG, Fourth Colloquium on Mathematics and Computer Science Algorithms, Trees, Combinatorics and Probabilities, pp. 129-140, in Fourth Colloquium on Mathematics and Computer Science Algorithms, Trees, Combinatorics and Probabilities, Nancy, France, DOI

[2] J. Bourdon. On the Khintchine constant for centred continued fraction expansions, in Applied Mathematics E – Notes, vol. 7, pp. 167-174,

[3] 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, vol. 16, no. 7, pp. 1460-7, DOI

[4] 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, vol. 98, no. 3, pp. 149-159, DOI

[5] S. Carat, R. Houlgatte, J. Bourdon. A parallel scheme for comparing transcription factor binding sites matrices, in Journal of Bioinformatics and Computational Biology, vol. 8, no. 3, pp. 18,

[6] J. Bourdon, I. Rusu. Statistical Properties of Factor Oracles, in Journal of Discrete Algorithms, vol. 9, no. 2011, pp. 59-66, DOI

[7] J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network., in PLoS Computational Biology, vol. 7, no. 9, pp. e1002157, DOI

[8] 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, vol. 15, no. 12, pp. 883-892, DOI

[9] M. Regnier, J. Bourdon. Large deviation properties for patterns, in Journal of Discrete Algorithms, DOI

[10] O. Abdou-Arbi, S. Lemosquet, J. van Milgen, A. Siegel, J. Bourdon. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs, in BMC Systems Biology, vol. 8, no. 1, pp. 8, DOI

[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, vol. 5, pp. 117, DOI

[12] 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, vol. 316C, pp. 67-82, DOI

[13] V. Berthé, J. Bourdon, T. Jolivet, A. Siegel. A combinatorial approach to products of Pisot substitutions, in Ergodic Theory and Dynamical Systems, vol. 36, no. 6, pp. 1757-1794, DOI

[14] 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, DOI

[15] S. Prigent, C. Frioux, S. Dittami, S. Thiele, A. Larhlimi, G. Collet, F. Gutknecht, 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, vol. 13, no. 1, pp. 32, DOI

[16] M. Budinich, J. Bourdon, A. Larhlimi, D. Eveillard. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems., in PLoS ONE, vol. 12, no. 2, pp. e0171744, DOI

[17] V. Picard, A. Siegel, J. Bourdon. A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks, in Journal of Computational Biology, vol. 24, no. 8, pp. 1–12, DOI

[18] M. Razzaq, L. Paulevé, A. Siegel, J. Saez-Rodriguez, J. Bourdon, C. Guziolowski. Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data, in PLoS Computational Biology, vol. 14, pp. 1-23, DOI

[19] 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. Le Caignec, C. Pecqueur, R. Redon, P. Barriere, J. Bourdon, V. Pasque, M. Soumillon, T. Mikkelsen, C. Rougeulle, T. Freour, L. David, M. Intérieur Consortium. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells, in Nature Communications, vol. 9, no. 1, pp. 302 – 314, DOI

[20] D. Eveillard, N. Bouskill, D. Vintache, J. Gras, B. Ward, J. Bourdon. Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle, in Frontiers in Microbiology, vol. 9, pp. 1-9, DOI

[21] H. Mhamdi, J. Bourdon, A. Larhlimi, M. Elloumi. Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks, in Informatics, vol. 7, no. 1, pp. 1, DOI

[22] M. Lefebvre, A. Gaignard, M. Folschette, J. Bourdon, C. Guziolowski. Large-scale regulatory and signaling network assembly through linked open data, in Database – The journal of Biological Databases and Curation, vol. 2021, pp. baaa113, DOI

[23] D. Meistermann, A. Bruneau, S. Loubersac, A. Reignier, J. Firmin, V. François-Campion, S. Kilens, Y. Lelièvre, J. Lammers, M. Feyeux, P. Hulin, S. Nedellec, B. Bretin, G. Castel, N. Allègre, S. Covin, A. Bihouée, M. Soumillon, T. Mikkelsen, P. Barrière, C. Chazaud, J. Chappell, V. Pasque, J. Bourdon, T. Fréour, L. David. Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification, in Cell Stem Cell, vol. 28, no. 9, pp. 1625-1640.e6, DOI

[24] V. Bessonneau-Gaborit, J. Cruard, C. Guerin-Charbonnel, J. Derrien, J. Alberge, E. Douillard, M. Devic, S. Deshayes, L. Campion, F. Westermann, P. Moreau, C. Herrmann, J. Bourdon, F. Magrangeas, S. Minvielle. Exploring the impact of dexamethasone on gene regulation in myeloma cells, in Life Science Alliance, vol. 6, no. 9, pp. e202302195, DOI

[25] S. Le Bars, C. Guziolowski, J. Bourdon, M. Bolteau. Predicting weighted unobserved nodes in a regulatory network using answer set programming, in BMC Bioinformatics, vol. 24, no. S1, pp. 321, DOI

[26] M. Bolteau, L. Chebouba, L. David, C. Guziolowski, J. Bourdon. Boolean Network Models of Human Preimplantation Development, in Journal of Computational Biology, vol. 31, no. 6, pp. 513-523, DOI

[27] M. Bolteau, C. Messaoudi, L. David, J. Bourdon, C. Guziolowski. Deep exploration of logical models of cell differentiation in human preimplantation embryos, in npj Systems Biology and Applications, vol. 11, no. 1, pp. 57, DOI

Revues nationales avec comité de lecture

[28] J. Bourdon, M. Nebel, B. Vallée. On The Stack-Size of General Tries, in RAIRO – Theoretical Informatics and Applications (RAIRO: ITA), no. 35, pp. 163–185,

[29] J. Bourdon. Size and Path Length in Patricia Tries: Dynamical Sources Context, in Random Structures and Algorithms, vol. 3-4, no. 19, pp. 289–315,

[30] J. Bourdon, B. Daireaux, B. Vallée. Dynamical Analysis of alpha-Euclidean Algorithms, in Journal of Algorithms in Cognition, Informatics and Logic, vol. 1, no. 44, pp. 246–285,

Conférences internationales avec comité de lecture et actes

[31] J. Bourdon, B. Vallée. Pattern Matching Statistics on Correlated sources, in LATIN 2006, Chili,

[32] S. Carat, R. Houlgatte, J. Bourdon. A statistical method for PWM clustering, in Moscow Conference on Computational Molecular Biology, Moscou, Russie,

[33] O. Abdou-Arbi, J. Bourdon, A. Siegel, J. van Milgen, S. Lemosquet. La calculette métabolique": une approche de modélisation biochimique pour explorer les contraintes au sein du métabolisme des mammifères, in 3. Journées d’Animation Scientifique du Département de Physiologie Animale et Systèmes d’Elevage, Tours, France,

[34] T. Merle, J. Bourdon. Complex update strategies for Probabilistic Boolean Networks, in 7th Workshop on Computational Systems Biology, Luxembourg, France,

[35] J. Bourdon. Average-case analysis methods dedicated to the study of Biological Networks, in Moscow Conference on Computational Molecular Biology (MCCMB) 2011, Moscou, Russie,

[36] J. Bourdon, M. Regnier. Large deviation properties for patterns, in LSD&LAW 2012, Londres, Royaume-Uni,

[37] 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, Roscoff, France,

[38] V. Berthe, J. Bourdon, T. Jolivet, A. Siegel. Generating discrete planes with substitutions, in WORDS – 9th International Conference on Words – 2013, Turku, Finlande,

[39] 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, Munchen, Allemagne,

[40] 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, Buenos Aeres, Argentine,

[41] M. Budinich, J. Bourdon, A. Larhlimi, D. Eveillard. OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques, in 13th International Conference on Computational Methods in Systems Biology CMSB 2015, Nantes, France, DOI

[42] M. Lefebvre, J. Bourdon, C. Guziolowski, A. Gaignard. Regulation and signalization graph assembly through Linked Open Data, in JOBIM 2017, Lille, France,

[43] O. Abdou Arbi, A. Siegel, J. Bourdon. Contributions des entrées sur les sorties pour les réseaux métaboliques sur génomes entiers: performances et utilisation pour des études en nutrition humaine, in CARI 2022 – Colloque Africain sur la Recherche en Informatique et en Mathématiques Appliquées, Yaoundé, Cameroun,

[44] M. Bolteau, J. Bourdon, L. David, C. Guziolowski. Inferring Boolean Networks from Single-Cell Human Embryo Datasets, in 19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023, Wrocław, Pologne, DOI

[45] O. Abdou Arbi, J. Bourdon, A. Siegel. Modelling Behavior of Microbiota Metabolic Network Subject to Diets, in The African Conference on Research in Computer Science and Applied Mathematics (CARI 2024), Bejaia, Algérie, DOI

Conférences nationales avec comité de lecture et actes

[46] 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, Grenoble, France,

[47] 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, Saarbrücken, Allemagne,

Ouvrages – Chapitres d'ouvrages et directions d'ouvrages

[48] 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,

[49] J. Bourdon, D. Eveillard. Probabilistic Approaches for Investigating Biological Networks,

[50] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. XII Des données haut-débit à la modélisation des écosystèmes,

[51] O. Roux, J. Bourdon. Computational Methods in Systems Biology – 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings, DOI

[52] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modeling and predicting behaviors and dynamics of ecosystems,

[53] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes,

[54] M. Razzaq, R. Kaminski, J. Romero, T. Schaub, J. Bourdon, C. Guziolowski. Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data,

[55] M. Razzaq, L. Chebouba, P. Le Jeune, H. Mhamdi, C. Guziolowski, J. Bourdon. Logic and Linear Programs to Understand Cancer Response, DOI

Theses et HDR

[56] J. Bourdon. Sources Probabilistes: des séquences aux systèmes,

Autres publications

[57] E. Giraudet, E. Docet, J. Bourdon. POGG: Integrating qualitative and quantitative data of macromolecular networks. A probabilistic toolbox,

[58] J. Bourdon, D. Eveillard. Toll Based Measures for Dynamical Graphs,

[59] J. Bourdon, D. Eveillard, S. Gabillard, T. Merle. Integrating heterogeneous knowledges for understanding biological behaviors: a probabilistic approach,

[60] J. Bourdon, B. Vallée. Pattern matching statistics on correlated sources,

[61] J. Ahmad, J. Bourdon, D. Eveillard, J. Fromentin, O. Roux, C. Sinoquet. Qualitative modelling and analysis of gene regulatory networks: application to the adaptation of Escherichia coli bacterium to carbon availability,

[62] S. Lemosquet, O. Abdou Arbi, S. 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 7. International Workshop on Modelling Nutrient Digestion and Utilisation in Farm Animals, Paris, France,

[63] M. Budinich, D. Eveillard, J. Bourdon, A. Larhlimi. MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network,

[64] S. Lemosquet, 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, Indianapolis, états-Unis,

[65] M. Budinich, J. Bourdon, D. Eveillard. Impact of the species compartment definition on quantitative modeling of microbial communities, DOI

[66] J. Bourdon, O. Roux. Selected papers from the Computational Methods in Systems Biology 2015 conference, in BioSystems, vol. 149, pp. 1-2, DOI

[67] M. Razzaq, L. Chebouba, P. Le Jeune, H. Mhamdi, C. Guziolowski, J. Bourdon. Logic and Linear programs to understand cancer response,

[68] D. Meistermann, S. Loubersac, A. Reignier, V. François-Campion, T. Fréour, J. Bourdon, L. David. , in JOBIM 2019, Nantes, France,

[69] V. Gaborit, J. Cruard, C. Guérin-Charbonnel, J. Derrien, J. Alberge, E. Douillard, N. Roi, M. Devic, L. Campion, F. Westermann, P. Moreau, C. Herrmann, J. Bourdon, F. Magrangeas, S. Minvielle. Chromatin accessibility combined with enhancer clusters activation mediates heterogeneous response to dexamethasone in myeloma cells, DOI

[70] S. Le Bars, M. Bolteau, J. Bourdon, C. Guziolowski. Predicting weighted unobserved nodes in a regulatory network using Answer Set Programming,

[71] M. Bolteau, J. Bourdon, L. David, C. Guziolowski. Inferring Boolean Networks from Single-Cell Human Embryo Datasets, DOI

[72] M. Bolteau, L. Chebouba, L. David, J. Bourdon, C. Guziolowski. Boolean Network Models of Human Preimplantation Development,

[73] N. Appel, J. Bourdon, N. Bousquet, J. Cohen, A. Genitrini, P. Georgeon, Y. Grandvalet, K. Jaffrès-Runser, A. Legrand, D. Markham, A. Muscholl, A. Paparrizou, L. Paulevé, M. Poss, M. Gradinariu Potop-Butucaru, J. Raymond, R. Rouvoy, Y. Sallent, P. Senellart, T. Seiller, Y. Song, A. Tchana, H. Waeselynck. Section 06 Sciences de l’information : fondements de l’informatique, calculs, algorithmes, représentations, exploitations,

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