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Jérémie BOURDON

ENSEIGNANT-CHERCHEUR

HDR

: Jeremie.Bourdonatls2n.fr

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] 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 ; éd. Life Science Alliance LLC, 2023, vol. 6, num. 9.
      https://hal.science/hal-04265700v1
    • [2] 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 ; éd. Oxford University Press, 2021, vol. 2021.
      https://hal.science/hal-03107317v2
    • [3] H. Mhamdi, J. Bourdon, A. Larhlimi, M. Elloumi. Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks. In Informatics ; éd. MDPI, 2020, vol. 7, num. 1.
      https://hal.science/hal-02458270v1
    • [4] 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 ; éd. Frontiers Media, 2019, vol. 9.
      https://hal.science/hal-01996045v1
    • [5] 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 ; éd. PLOS, 2018, vol. 14.
      https://hal.science/hal-01897020v1
    • [6] 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 ; éd. Nature Publishing Group, 2018, vol. 9, num. 1.
      https://pasteur.hal.science/pasteur-01758726v1
    • [7] 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. PLOS, 2017, vol. 13, num. 1.
      https://inria.hal.science/hal-01449100v1
    • [8] 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.science/hal-01478375v1
    • [9] V. Picard, A. Siegel, J. Bourdon. A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. In Journal of Computational Biology ; éd. Mary Ann Liebert, 2017, vol. 24, num. 8.
      https://hal.science/hal-01552190v1
    • [10] 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://inria.hal.science/hal-01196326v1
    • [11] 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-01390047v1
    • [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 ; éd. Elsevier, 2015, vol. 316C.
      https://inria.hal.science/hal-01196533v1
    • [13] 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 ; éd. BioMed Central, 2014, vol. 8, num. 1.
      https://inria.hal.science/hal-00947219v1
    • [14] 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 Media, 2014, vol. 5.
      https://inria.hal.science/hal-01079758v1
    • [16] J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gene regulatory network.. In PLoS Computational Biology ; éd. PLOS, 2011, vol. 7, num. 9.
      https://hal.science/hal-00626708v1
    • [17] 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.science/hal-00661751v1
    • [18] 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.science/hal-00461973v1
    • [19] J. Bourdon, I. Rusu. Statistical Properties of Factor Oracles. In Journal of Discrete Algorithms ; éd. Elsevier, 2010, vol. 9, num. 2011.
      https://hal.science/hal-00415952v1
    • [20] 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.science/hal-00415921v1
    • [21] 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.
      https://hal.science/hal-00423353v1
    • [22] J. Bourdon. On the Khintchine constant for centred continued fraction expansions. In Applied Mathematics E - Notes ; éd. Tsing Hua University, 2007, vol. 7.
      https://hal.science/hal-00461985v1
    • [23] 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.science/hal-00415938v1

Revues nationales avec comité de lecture (ART_NAT)

    • [24] 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.science/hal-00442421v1
    • [25] J. Bourdon, M. Nebel, B. Vallée. On The Stack-Size of General Tries. In RAIRO - Theoretical Informatics and Applications (RAIRO: ITA) ; éd. EDP Sciences, 2001, num. 35.
      https://hal.science/hal-00442422v1
    • [26] J. Bourdon. Size and Path Length in Patricia Tries: Dynamical Sources Context. In Random Structures and Algorithms ; éd. Wiley, 2001, vol. 3-4, num. 19.
      https://hal.science/hal-00442432v1

Conférences internationales avec comité de lecture et actes (COMM_INT)

    • [27] 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, octobre 2023, Wrocław, Pologne.
      https://hal.science/hal-04601243v1
    • [28] 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, octobre 2022, Yaoundé, Cameroun.
      https://inria.hal.science/hal-03689107v2
    • [29] M. Lefebvre, J. Bourdon, C. Guziolowski, A. Gaignard. Regulation and signalization graph assembly through Linked Open Data. In JOBIM 2017, juillet 2017, Lille, France.
      https://hal.science/hal-01768420v1
    • [30] 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://inria.hal.science/hal-01196598v1
    • [31] 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, septembre 2015, Nantes, France.In Olivier Roux (éds.), . Springer International Publishing, 2015.
      https://hal.science/hal-02464859v1
    • [32] 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://inria.hal.science/hal-01079768v1
    • [33] 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://inria.hal.science/hal-00853758v1
    • [34] 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://inria.hal.science/hal-00760640v1
    • [35] J. Bourdon, M. Regnier. Large deviation properties for patterns. In LSD&LAW 2012, février 2012, Londres, Royaume-Uni.In Thierry Lecroq (éds.), . , 2012.
      https://inria.hal.science/hal-00758251v1
    • [36] 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.science/hal-01176716v1
    • [37] 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.science/hal-00480366v1
    • [38] S. Carat, R. Houlgatte, J. Bourdon. A statistical method for PWM clustering. In Moscow Conference on Computational Molecular Biology, juillet 2009, Moscou, Russie.
      https://hal.science/hal-00415980v1
    • [39] 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, octobre 2009, Tours, France.
      https://hal.inrae.fr/hal-02758027v1
    • [41] 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://inria.hal.science/hal-01184706v1

Conférences nationales avec comité de lecture et actes (COMM_NAT)

    • [42] 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.science/hal-00465766v1
    • [43] 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.science/hal-00465762v1

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

    • [44] M. Razzaq, L. Chebouba, P. Le Jeune, H. Mhamdi, C. Guziolowski, J. Bourdon. Logic and Linear Programs to Understand Cancer Response. In Liò P., Zuliani P. (eds) Automated Reasoning for Systems Biology and Medicine. Computational Biology, vol 30. Springer, Cham. 12-06-2019
      https://hal.science/hal-02467018v1
    • [45] M. Razzaq, R. Kaminski, J. Romero, T. Schaub, J. Bourdon, C. Guziolowski. Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data. 24-08-2018
      https://hal.science/hal-01988432v1
    • [46] D. Eveillard, X. Raynaud, J. Bourdon, A. Franc, F. Plewniak. Modeling and predicting behaviors and dynamics of ecosystems. In Insight on environmental genomics, the high-throughput sequencing revolution. 2016
      https://hal.science/hal-03823723v1
    • [47] 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.science/hal-01777358v1
    • [48] O. Roux, J. Bourdon. Computational Methods in Systems Biology - 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings. 2015
      https://hal.science/hal-01371899v1
    • [49] 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.science/hal-01176570v1
    • [50] 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.science/hal-00531568v1
    • [51] 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://inria.hal.science/inria-00538138v1

Theses et HDR (THESE)

Autres publications (AUTRES)

    • [53] D. Meistermann, S. Loubersac, A. Reignier, V. François-Campion, T. Fréour, J. Bourdon, L. David. The limit of cell specification concept: a lesson from scRNA-Seq on early human development. In JOBIM 2019, juillet 2019, Nantes, France.
      https://inserm.hal.science/inserm-02164425v1
    • [54] 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.science/hal-00839321v1
    • [55] 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, juillet 2013, Indianapolis, états-Unis.
      https://hal.science/hal-01210552v1
    • [56] 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, septembre 2009, Paris, France.In INRA (éds.), Proceedings of 7th Workshop Modelling Nutrient Digestion and Utilization in Farm Animals. Wageningen Academic Publishers, 2009.
      https://hal.inrae.fr/hal-02758319v1
    • [57] E. Giraudet, E. Docet, J. Bourdon. POGG: Integrating qualitative and quantitative data of macromolecular networks. A probabilistic toolbox.
      https://hal.science/hal-00445610v1
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