Jérémie Bourdon

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Publications

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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
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Exploring the impact of dexamethasone on gene regulation in myeloma cells

Victor Bessonneau-Gaborit , Jonathan Cruard , Catherine Guerin-Charbonnel , Jennifer Derrien , Jean-Baptiste Alberge et al.

Life Science Alliance, 2023, 6 (9), pp.e202302195. ⟨10.26508/lsa.202302195⟩

Article dans une revue hal-04265700v1
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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 Ward et al.

Frontiers in Microbiology, 2019, 9, pp.1-9. ⟨10.3389/fmicb.2018.03298⟩

Article dans une revue hal-01996045v1
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Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data

Misbah Razzaq , Loïc Paulevé , Anne Siegel , Julio Saez-Rodriguez , Jérémie Bourdon et al.

PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩

Article dans une revue hal-01897020v1
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Parallel derivation of isogenic human primed and naive induced pluripotent stem cells

Stéphanie Kilens , Dimitri Meistermann , Diego Moreno , Caroline Chariau , Anne Gaignerie et 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
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Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Sylvain Prigent , Clémence Frioux , Simon M Dittami , Sven Thiele , Abdelhalim Larhlimi et al.

PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩

Article dans une revue hal-01449100v1
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Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization

Vincent Picard , Odile Mulner-Lorillon , Jérémie Bourdon , Julia Morales , Patrick Cormier et al.

Molecular Reproduction and Development, 2016, ⟨10.1002/mrd.22746⟩

Article dans une revue hal-01390047v1
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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 Flament et al.

Frontiers in Genetics, 2014, 5, pp.117. ⟨10.3389/fgene.2014.00117⟩

Article dans une revue hal-01079758v1
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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

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
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Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.

Thierry Tonon , Damien Eveillard , Sylvain Prigent , Jérémie Bourdon , Philippe Potin et al.

OMICS, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩

Article dans une revue hal-00661751v1

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
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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

Temporal constraints of a gene regulatory network: Refining a qualitative simulation.

Jamil Ahmad , Jérémie Bourdon , Damien Eveillard , Jonathan Fromentin , Olivier Roux et 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 Sébille et 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
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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
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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
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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 Alberge et al.

2021

Pré-publication, Document de travail inserm-03364330v1
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Logic and Linear programs to understand cancer response

Misbah Razzaq , Lokmane Chebouba , Pierre Le Jeune , Hanen Mhamdi , Carito Guziolowski et al.

2018

Pré-publication, Document de travail hal-01897036v1
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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
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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 Roux et al.

2009

Pré-publication, Document de travail hal-00359530v1
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Pattern matching statistics on correlated sources

Jérémie Bourdon , Brigitte Vallée

2008

Pré-publication, Document de travail hal-00210348v1
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Toll Based Measures for Dynamical Graphs

Jérémie Bourdon , Damien Eveillard

2007

Pré-publication, Document de travail hal-00134078v1
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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

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
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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
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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
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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
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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 Groisillier et al.

Esil 2012: algal post-genomics, Apr 2012, Roscoff, France

Communication dans un congrès hal-00760640v1
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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": 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 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

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

Pattern Matching Statistics on Correlated sources

Jérémie Bourdon , Brigitte Vallée

LATIN 2006, Mar 2006, Chile. pp.224-237

Communication dans un congrès hal-00461975v1
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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
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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 Fréour et 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 Milgen et 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

Logic and Linear Programs to Understand Cancer Response

Misbah Razzaq , Lokmane Chebouba , Pierre Le Jeune , Hanen Mhamdi , Carito Guziolowski et 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

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

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

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 Milgen et 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
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Sources Probabilistes: des séquences aux systèmes

Jérémie Bourdon

Bio-informatique [q-bio.QM]. Université de Nantes, 2012

HDR tel-00776681v1