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Prédire le comportement des cellules avec la modélisation booléenne

Loïc Paulevé
Interstices, 2021
Journal articles hal-03206126v1
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Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision

Stéphanie Chevalier , Vincent Noël , Laurence Calzone , Andrei Zinovyev , Loïc Paulevé
18th International Conference on Computational Methods in Systems Biology (CMSB), 2020, Online, Germany. pp.193--209, ⟨10.1007/978-3-030-60327-4_11⟩
Conference papers hal-02898849v2
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Identification of Biological Regulatory Networks from Process Hitting models

Maxime Folschette , Loïc Paulevé , Katsumi Inoue , Morgan Magnin , Olivier Roux
Theoretical Computer Science, 2015, 568, pp.39. ⟨10.1016/j.tcs.2014.12.002⟩
Journal articles hal-01094249v1
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Sequential Reprogramming of Boolean Networks Made Practical

Hugues Mandon , Cui Su , Stefan Haar , Jun Pang , Loïc Paulevé
CMSB 2019 - 17th International Conference on Computational Methods in Systems Biology, Sep 2019, Trieste, France. pp.3--19, ⟨10.1007/978-3-030-31304-3_1⟩
Conference papers hal-02178917v2
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Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics

Stefan Haar , Juraj Kolčák , Loïc Paulevé
VMCAI 2019 - 20th International Conference on Verification, Model Checking, and Abstract Interpretation, Jan 2019, Lisbon, Portugal. pp.555-576, ⟨10.1007/978-3-030-11245-5_26⟩
Conference papers hal-01940174v1
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Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming

Louis Fippo Fitime , Olivier F. Roux , Carito Guziolowski , Loïc Paulevé
Algorithms for Molecular Biology, 2017, 12 (1), pp.19. ⟨10.1186/s13015-017-0110-3⟩
Journal articles hal-01566380v1

Journées BIOSS-IA 2017

Loïc Paulevé , Philippe Dague
2017
Other publications hal-01666094v1

Stochastic simulation of process calculi for biology

Andrew Phillips , Matthew R. Lakin , Loïc Paulevé
Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010, Aug 2010, Jena, Germany. ⟨10.4204/EPTCS.40.1⟩
Conference papers hal-00574362v1
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Coarse-grained brownian dynamics simulation of rule-based models

Michael Klann , Loïc Paulevé , Tatjana Petrov , Heinz Koeppl
The 11th Conference on Computational Methods in Systems Biology (CMSB'13), Sep 2013, Klosterneuburg, Austria. pp.64-77, ⟨10.1007/978-3-642-40708-6_6⟩
Conference papers hal-00872963v1
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Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Nicolas Levy , Aurélien Naldi , Céline Hernandez , Gautier Stoll , Denis Thieffry , et al.
Frontiers in Physiology, 2018, 9, pp.787. ⟨10.1101/319780⟩
Journal articles hal-01809081v1
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Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface

Loïc Paulevé
CMSB 2017 - 15th conference on Computational Methods for Systems Biology, Sep 2017, Darmstadt, Germany. pp.370 - 316, ⟨10.1007/978-3-319-67471-1_20⟩
Conference papers hal-01589248v1

Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?

Stefan Janssen , Loïc Paulevé , Yann Ponty , Balaji Raman , Matthias Zytnicki
IWBDA - 4th International Workshop on Bio-Design Automation - 2012, Jun 2012, San Francisco, United States
Conference papers hal-00712557v1
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Cell cycle progression is regulated by intertwined redox oscillators

Jorgelindo da Veiga Moreira , Sabine Pérès , Jean-Marc Steyaert , Erwan Bigan , Loïc Paulevé , et al.
Theoretical Biology and Medical Modelling, 2015, 12 (1), pp.10. ⟨10.1186/s12976-015-0005-2⟩
Journal articles hal-01158514v1
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SAT Heritage: a community-driven effort for archiving, building and running more than thousand SAT solvers

Gilles Audemard , Loïc Paulevé , Laurent Simon
SAT 2020, The 23rd International Conference on Theory and Applications of Satisfiability Testing, 2020, Alghero, Italy. pp.107-113, ⟨10.1007/978-3-030-51825-7_8⟩
Conference papers hal-02704747v1
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Algorithms for the Sequential Reprogramming of Boolean Networks

Hugues Mandon , Cui Su , Jun Pang , Soumya Paul , Stefan Haar , et al.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, 16 (5), pp.1610-1619. ⟨10.1109/TCBB.2019.2914383⟩
Journal articles hal-02113864v1
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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⟩
Journal articles hal-01897020v1
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Unfolding of Parametric Boolean Networks

Juraj Kolčák , David Šafránek , Stefan Haar , Loïc Paulevé
7th International Workshop on Static Analysis and Systems Biology (SASB 2016), Sep 2016, Edimbourg, United Kingdom. pp.67-90, ⟨10.1016/j.entcs.2018.03.009⟩
Conference papers hal-01354109v2
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Qualitative dynamics semantics for SBGN process description

Adrien Rougny , Christine Froidevaux , Laurence Calzone , Loïc Paulevé
BMC Systems Biology, 2016, ⟨10.1186/s12918-016-0285-0⟩
Journal articles hal-01332679v1
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Pint, a static analyzer for dynamics of Automata Networks

Loïc Paulevé
14th International Conference on Computational Methods in Systems Biology (CMSB 2016), Sep 2016, Cambridge, United Kingdom.
Poster communications hal-01366730v1
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The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Aurélien Naldi , Céline Hernandez , Nicolas Levy , Gautier Stoll , Pedro Monteiro , et al.
Frontiers in Physiology, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩
Journal articles hal-01794294v2
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Goal-Oriented Reduction of Automata Networks

Loïc Paulevé
14th International Conference on Computational Methods in Systems Biology (CMSB 2016), Sep 2016, Cambridge, United Kingdom. pp.252-272, ⟨10.1007/978-3-319-45177-0_16⟩
Conference papers hal-01149118v2
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A logic programming exploration of metabolic networks to explain microbial community models

Chabname Ghassemi Nedjad , Loïc Paulevé , Clémence Frioux
GT Bioss 2022 - Journée annuelle du Groupe de Travail sur la Biologie Systémique Symbolique, Nov 2022, Nantes, France
Conference papers hal-03910483v1
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From the Process Hitting to Petri Nets and Back

Loïc Paulevé , Morgan Magnin , Olivier Roux
2012
Reports hal-00744807v1
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Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework

Loïc Paulevé , Morgan Magnin , Olivier Roux
Transactions on Computational Systems Biology, 2011, XIII, pp.171-191. ⟨10.1007/978-3-642-19748-2_8⟩
Journal articles hal-00397235v2

Marginalized Continuous Time Bayesian Networks for Network Reconstruction from Incomplete Observations

Lukas Studer , Loïc Paulevé , Christoph Zechner , Matthias Reumann , Maria Rodriguez Martinez , et al.
AAAI Conference on Artificial Intelligence, Feb 2016, Phoenix, Arizona, United States
Conference papers hal-01305967v1
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Identification of Bifurcations in Biological Regulatory Networks using Answer-Set Programming

Louis Fippo Fitime , Olivier Roux , Carito Guziolowski , Loïc Paulevé
Constraint-Based Methods for Bioinformatics Workshop, Sep 2016, Toulouse, France
Conference papers hal-01361350v1
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BioSimulators: a central registry of simulation engines and services for recommending specific tools

Bilal Shaikh , Lucian Smith , Dan Vasilescu , Gnaneswara Marupilla , Michael Wilson , et al.
2022
Preprints, Working Papers, ... hal-03613651v1
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Concretizing the Process Hitting into Biological Regulatory Networks

Maxime Folschette , Loïc Paulevé , Katsumi Inoue , Morgan Magnin , Olivier Roux
Computational Methods in Systems Biology, Oct 2012, London, United Kingdom. p. 166-186, ⟨10.1007/978-3-642-33636-2_11⟩
Conference papers hal-00704569v2
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Two Qualitative Dynamics Semantics for SBGN Process Description Maps

Adrien Rougny , Christine Froidevaux , Loïc Paulevé
CMSB'15, Sep 2015, Nantes, France. 2015
Poster communications hal-01258943v1
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Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks

Juraj Kolčák , David Šafránek , Stefan Haar , Loïc Paulevé
Theoretical Computer Science, 2019, 765, pp.120-144. ⟨10.1016/j.tcs.2018.03.009⟩
Journal articles hal-01734805v1