Jérémie Bourdon

Publications

Communication dans un congrès (18)

Modelling Behavior of Microbiota Metabolic Network Subject to Diets Oumarou Abdou Arbi,Jérémie Bourdon,Anne Siegel The African Conference on Research in Computer Science and Applied Mathematics (CARI 2024), Nov 2024, Bejaia, Algeria. pp.341-352, ⟨10.1007/978-3-031-88226-5_24⟩ Communication dans un congrès hal-05591596v1
Inferring Boolean Networks from Single-Cell Human Embryo Datasets Mathieu Bolteau,Jérémie Bourdon,Laurent David,Carito Guziolowski 19th International Symposium on Bioinformatics Research and Applications, ISBRA 2023, Oct 2023, Wrocław, Poland. pp.431-441, ⟨10.1007/978-981-99-7074-2_34⟩ Communication dans un congrès hal-04601243v1
Contributions des entrées sur les sorties pour les réseaux métaboliques sur génomes entiers: performances et utilisation pour des études en nutrition humaine Oumarou Abdou Arbi,Anne Siegel,Jérémie Bourdon CARI 2022 - Colloque Africain sur la Recherche en Informatique et en Mathématiques Appliquées, Oct 2022, Yaoundé, Cameroun. pp.1-12 Communication dans un congrès hal-03689107v2
Regulation and signalization graph assembly through Linked Open Data Marie Lefebvre,Jérémie Bourdon,Carito Guziolowski,Alban Gaignard JOBIM 2017, Jul 2017, Lille, France Communication dans un congrès hal-01768420v1
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks Vincent Picard,Anne Siegel,Jérémie Bourdon IJCAI workshop BAI: Bioinformatics and Artificial Intelligence, 2015, Buenos Aeres, Argentina Communication dans un congrès hal-01196598v1
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
Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applications Vincent Picard,Anne Siegel,Jérémie Bourdon SASB - 5th International Workshop on Static Analysis and Systems Biology, 2014, Munchen, Germany Communication dans un congrès hal-01079768v1
Generating discrete planes with substitutions Valerie Berthe,Jérémie Bourdon,Timo Jolivet,Anne Siegel WORDS - 9th International Conference on Words - 2013, Sep 2013, Turku, Finland Communication dans un congrès hal-00853758v1
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 Groisillieret al. Esil 2012: algal post-genomics, Apr 2012, Roscoff, France Communication dans un congrès hal-00760640v1
Large deviation properties for patterns Jérémie Bourdon,Mireille Regnier LSD&LAW 2012, Simon J. Puglisi and Golnaz Badkobeh, Feb 2012, Londres, United Kingdom Communication dans un congrès hal-00758251v1
Average-case analysis methods dedicated to the study of Biological Networks Jérémie Bourdon Moscow Conference on Computational Molecular Biology (MCCMB) 2011, Jul 2011, Moscou, Russia Communication dans un congrès hal-01176716v1
Complex update strategies for Probabilistic Boolean Networks Théo Merle,Jérémie Bourdon 7th Workshop on Computational Systems Biology, Jun 2010, Luxembourg, France. pp.4 Communication dans un congrès hal-00480366v1
A statistical method for PWM clustering Solenne Carat,Rémi Houlgatte,Jérémie Bourdon Moscow Conference on Computational Molecular Biology, Jul 2009, Moscou, Russia. pp.59-60 Communication dans un congrès hal-00415980v1
La calculette métabolique&quot;: une approche de modélisation biochimique pour explorer les contraintes au sein du métabolisme des mammifères Oumarou Abdou-Arbi,Jérémie Bourdon,Anne Siegel,Jaap J. van Milgen,Sophie Lemosquet 3. Journées d’Animation Scientifique du Département de Physiologie Animale et Systèmes d’Elevage, Oct 2009, Tours, France Communication dans un congrès hal-02758027v1
Distribution of Solutions of Multi-objective Assignment Problem and Links with the Efficiency of Solving Methods. Anthony Przybylski,Jérémie Bourdon,Xavier Gandibleux GOR 2007, Sep 2007, Saarbrücken, Germany Communication dans un congrès hal-00465762v1
Distribution des solutions du problème d'affectation multi-objectif et relation avec l'efficacité des algorithmes de résolution Anthony Przybylski,Jérémie Bourdon,Xavier Gandibleux FRANCORO V / ROADEF 2007, Feb 2007, Grenoble, France Communication dans un congrès hal-00465766v1
Pattern Matching Statistics on Correlated sources Jérémie Bourdon,Brigitte Vallée LATIN 2006, Mar 2006, Chile. pp.224-237 Communication dans un congrès hal-00461975v1
Statistical Properties of Similarity Score Functions Jérémie Bourdon,Alban Mancheron Fourth Colloquium on Mathematics and Computer Science Algorithms, Trees, Combinatorics and Probabilities, 2006, Nancy, France. pp.129-140, ⟨10.46298/dmtcs.3502⟩ Communication dans un congrès hal-01184706v1

Article dans une revue (28)

Deep exploration of logical models of cell differentiation in human preimplantation embryos Mathieu Bolteau,Célia Messaoudi,Laurent David,Jérémie Bourdon,Carito Guziolowski npj Systems Biology and Applications, 2025, 11 (1), pp.57. ⟨10.1038/s41540-025-00537-7⟩ Article dans une revue hal-05124943v1
Boolean Network Models of Human Preimplantation Development Mathieu Bolteau,Lokmane Chebouba,Laurent David,Carito Guziolowski,Jérémie Bourdon Journal of Computational Biology, 2024, 31 (6), pp.513-523. ⟨10.1089/cmb.2024.0517⟩ Article dans une revue hal-04673351v1
Exploring the impact of dexamethasone on gene regulation in myeloma cells Victor Bessonneau-Gaborit,Jonathan Cruard,Catherine Guerin-Charbonnel,Jennifer Derrien,Jean-Baptiste Albergeet al. Life Science Alliance, 2023, 6 (9), pp.e202302195. ⟨10.26508/lsa.202302195⟩ Article dans une revue hal-04265700v1
Predicting weighted unobserved nodes in a regulatory network using answer set programming Sophie Le Bars,Carito Guziolowski,Jérémie Bourdon,Mathieu Bolteau BMC Bioinformatics, 2023, 24 (S1), pp.321. ⟨10.1186/s12859-023-05429-3⟩ Article dans une revue hal-04601023v1
Large-scale regulatory and signaling network assembly through linked open data Marie Lefebvre,Alban Gaignard,Maxime Folschette,Jérémie Bourdon,Carito Guziolowski Database - The journal of Biological Databases and Curation, 2021, 2021, pp.baaa113. ⟨10.1093/database/baaa113⟩ Article dans une revue hal-03107317v2
Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks Hanen Mhamdi,Jérémie Bourdon,Abdelhalim Larhlimi,Mourad Elloumi Informatics, 2020, 7 (1), pp.1. ⟨10.3390/informatics7010001⟩ Article dans une revue hal-02458270v1
Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle Damien Eveillard,Nicholas Bouskill,Damien Vintache,Julien Gras,Bess Wardet al. Frontiers in Microbiology, 2019, 9, pp.1-9. ⟨10.3389/fmicb.2018.03298⟩ Article dans une revue hal-01996045v1
Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data Misbah Razzaq,Loïc Paulevé,Anne Siegel,Julio Saez-Rodriguez,Jérémie Bourdonet al. PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩ Article dans une revue hal-01897020v1
Parallel derivation of isogenic human primed and naive induced pluripotent stem cells Stéphanie Kilens,Dimitri Meistermann,Diego Moreno,Caroline Chariau,Anne Gaignerieet al. Nature Communications, 2018, 9 (1), pp.302 - 314. ⟨10.1038/s41467-017-02107-w⟩ Article dans une revue hal-01758726v1
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks Vincent Picard,Anne Siegel,Jérémie Bourdon Journal of Computational Biology, 2017, 24 (8), pp.1--12. ⟨10.1089/cmb.2017.0099⟩ Article dans une revue hal-01552190v1
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. ⟨10.1371/journal.pone.0171744⟩ Article dans une revue hal-01478375v1
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks Sylvain Prigent,Clémence Frioux,Simon M Dittami,Sven Thiele,Abdelhalim Larhlimiet al. PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩ Article dans une revue hal-01449100v1
Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization Vincent Picard,Odile Mulner-Lorillon,Jérémie Bourdon,Julia Morales,Patrick Cormieret al. Molecular Reproduction and Development, 2016, ⟨10.1002/mrd.22746⟩ Article dans une revue hal-01390047v1
A combinatorial approach to products of Pisot substitutions Valérie Berthé,Jérémie Bourdon,Timo Jolivet,Anne Siegel Ergodic Theory and Dynamical Systems, 2016, 36 (6), pp.1757-1794. ⟨10.1017/etds.2014.141⟩ Article dans une revue hal-01196326v1
Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications Vincent Picard,Anne Siegel,Jérémie Bourdon Electronic Notes in Theoretical Computer Science, 2015, 316C, pp.67-82. ⟨10.1016/j.entcs.2015.06.011⟩ Article dans une revue hal-01196533v1
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 Sébastien Laurent,Adrien Richard,Odile Mulner-Lorillon,Julia Morales,Didier Flamentet al. Frontiers in Genetics, 2014, 5, pp.117. ⟨10.3389/fgene.2014.00117⟩ Article dans une revue hal-01079758v1
Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs Oumarou Abdou-Arbi,Sophie Lemosquet,Jaap J. van Milgen,Anne Siegel,Jérémie Bourdon BMC Systems Biology, 2014, 8 (1), pp.8. ⟨10.1186/1752-0509-8-8⟩ Article dans une revue hal-00947219v1
Large deviation properties for patterns Mireille Regnier,Jérémie Bourdon Journal of Discrete Algorithms, 2013, ⟨10.1016/j.jda.2013.09.004⟩ Article dans une revue hal-00868462v1
Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. Thierry Tonon,Damien Eveillard,Sylvain Prigent,Jérémie Bourdon,Philippe Potinet al. 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
Statistical Properties of Factor Oracles Jérémie Bourdon,Irena Rusu Journal of Discrete Algorithms, 2010, LNCS, 9 (2011), pp.59-66. ⟨10.1007/978-3-642-02441-2⟩ Article dans une revue hal-00415952v1
A parallel scheme for comparing transcription factor binding sites matrices Solenne Carat,Rémi Houlgatte,Jérémie Bourdon Journal of Bioinformatics and Computational Biology, 2010, 8 (3), pp.18 Article dans une revue hal-00461973v1
Temporal constraints of a gene regulatory network: Refining a qualitative simulation. Jamil Ahmad,Jérémie Bourdon,Damien Eveillard,Jonathan Fromentin,Olivier Rouxet al. BioSystems, 2009, 98 (3), pp.149-159. ⟨10.1016/j.biosystems.2009.05.002⟩ Article dans une revue istex hal-00415921v1
On the Khintchine constant for centred continued fraction expansions Jérémie Bourdon Applied Mathematics E - Notes, 2007, 7, pp.167-174 Article dans une revue hal-00461985v1
Combinations of cytochrome P450 gene polymorphisms enhancing the risk for sporadic colorectal cancer related to red meat consumption. Sébastien Küry,Bruno Buecher,Sébastien Robiou-Du-Pont,Catherine Scoul,Véronique Sébilleet al. Cancer Epidemiology, Biomarkers and Prevention, 2007, 16 (7), pp.1460-7. ⟨10.1158/1055-9965.EPI-07-0236⟩ Article dans une revue hal-00415938v1
Dynamical Analysis of alpha-Euclidean Algorithms Jérémie Bourdon,Benoît Daireaux,Brigitte Vallée Journal of Algorithms in Cognition, Informatics and Logic, 2002, 1 (44), pp.246--285 Article dans une revue hal-00442421v1
On The Stack-Size of General Tries Jérémie Bourdon,Markus Nebel,Brigitte Vallée RAIRO - Theoretical Informatics and Applications (RAIRO: ITA), 2001, 35, pp.163--185 Article dans une revue hal-00442422v1
Size and Path Length in Patricia Tries: Dynamical Sources Context Jérémie Bourdon Random Structures and Algorithms, 2001, 3-4 (19), pp.289--315 Article dans une revue hal-00442432v1

Rapport (2)

Section 06 Sciences de l’information : fondements de l’informatique, calculs, algorithmes, représentations, exploitations Nathalie Appel,Jérémie Bourdon,Nicolas Bousquet,Johanne Cohen,Antoine Genitriniet al. CNRS. 2025, pp.1-20 Rapport hal-05238890v1
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

Pré-publication, Document de travail (10)

Boolean Network Models of Human Preimplantation Development Mathieu Bolteau,Lokmane Chebouba,Laurent David,Jérémie Bourdon,Carito Guziolowski 2024 Pré-publication, Document de travail hal-04579386v1
Inferring Boolean Networks from Single-Cell Human Embryo Datasets Mathieu Bolteau,Jérémie Bourdon,Laurent David,Carito Guziolowski 2023 Pré-publication, Document de travail hal-04206397v1
Predicting weighted unobserved nodes in a regulatory network using Answer Set Programming Sophie Le Bars,Mathieu Bolteau,Jérémie Bourdon,Carito Guziolowski 2023 Pré-publication, Document de travail hal-04047587v1
Chromatin accessibility combined with enhancer clusters activation mediates heterogeneous response to dexamethasone in myeloma cells Victor Gaborit,Jonathan Cruard,Catherine Guérin-Charbonnel,Jennifer Derrien,Jean-Baptiste Albergeet al. 2021 Pré-publication, Document de travail inserm-03364330v1
Logic and Linear programs to understand cancer response Misbah Razzaq,Lokmane Chebouba,Pierre Le Jeune,Hanen Mhamdi,Carito Guziolowskiet al. 2018 Pré-publication, Document de travail hal-01897036v1
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
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 Rouxet al. 2009 Pré-publication, Document de travail hal-00359530v1
Pattern matching statistics on correlated sources Jérémie Bourdon,Brigitte Vallée 2008 Pré-publication, Document de travail hal-00210348v1
Toll Based Measures for Dynamical Graphs Jérémie Bourdon,Damien Eveillard 2007 Pré-publication, Document de travail hal-00134078v1
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

Poster de conférence (3)

The limit of cell specification concept: a lesson from scRNA-Seq on early human development Dimitri Meistermann,Sophie Loubersac,Arnaud Reignier,Valentin François-Campion,Thomas Fréouret al. JOBIM 2019, Jul 2019, Nantes, France Poster de conférence inserm-02164425v1
Exploring the metabolic flexibility of the mammary gland of dairy cows through flux-balance analysis Sophie Lemosquet,O. Abdou Arbi,Jaap J. van Milgen,Anne Siegel,J. Bourdon Meeting of the Animal Science Modelling Group, Jul 2013, Indianapolis, United States. , Canadian Journal of Animal Science, 93 (4), 2013, Canadian Journal of Animal Science Poster de conférence hal-01210552v1
A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cows Sophie Lemosquet,Oumarou Abdou Arbi,S. Siegel,Jocelyne Guinard-Flament,Jaap J. van Milgenet al. INRA. 7. International Workshop on Modelling Nutrient Digestion and Utilisation in Farm Animals, Sep 2009, Paris, France. Wageningen Academic Publishers, pp.279-288, 2010, Modelling nutrient digestion and utilisation in farm animals Poster de conférence hal-02758319v1

Chapitre d'ouvrage (6)

Logic and Linear Programs to Understand Cancer Response Misbah Razzaq,Lokmane Chebouba,Pierre Le Jeune,Hanen Mhamdi,Carito Guziolowskiet al. Liò P., Zuliani P. (eds) Automated Reasoning for Systems Biology and Medicine. Computational Biology, vol 30. Springer, Cham, pp.191-213, 2019, ⟨10.1007/978-3-030-17297-8_7⟩ Chapitre d'ouvrage hal-02467018v1
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
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
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
A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cows Sophie Lemosquet,Oumarou Abdou-Arbi,Anne Siegel,Jocelyne Guinard-Flament,Jaap J. van Milgenet al. D. Sauvant, J. Van Milgen, P. Faverdin and N. Friggens. Modelling nutrient digestion and utilization in farm animals, Wageningen Academic Publishers, 2010, 978-90-8686-156-9 Chapitre d'ouvrage inria-00538138v1

Ouvrages (2)

Computing Diverse Boolean Networks from Phosphoproteomic Time Series Data Misbah Razzaq,Roland Kaminski,Javier J Romero,Torsten Schaub,Jérémie Bourdonet al. pp.59-74, 2018 Ouvrages hal-01988432v1
Computational Methods in Systems Biology - 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings Olivier F. Roux,Jérémie Bourdon Olivier F. Roux and Jérémie Bourdon. Springer, 9308, 2015, Lecture Notes in Computer Science, 978-3-319-23400-7. ⟨10.1007/978-3-319-23401-4⟩ Ouvrages hal-01371899v1

N°spécial de revue/special issue (1)

Selected papers from the Computational Methods in Systems Biology 2015 conference Jérémie Bourdon,Olivier Roux BioSystems, 149, pp.1-2, 2016, ⟨10.1016/j.biosystems.2016.10.006⟩ N°spécial de revue/special issue hal-02469955v1

HDR (1)

Sources Probabilistes: des séquences aux systèmes Jérémie Bourdon Bio-informatique [q-bio.QM]. Université de Nantes, 2012 HDR tel-00776681v1

Autre publication scientifique (1)

POGG: Integrating qualitative and quantitative data of macromolecular networks. A probabilistic toolbox Etienne Giraudet,Eric Docet,Jérémie Bourdon 2007 Autre publication scientifique hal-00445610v1