Loïc Paulevé

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Publications

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Seed2LP: seed inference in metabolic networks for reverse ecology applications

Chabname Ghassemi Nedjad , Mathieu Bolteau , Lucas Bourneuf , Loïc Paulevé , Clémence Frioux

Bioinformatics, 2025, 41 (4), pp.btaf140. ⟨10.1093/bioinformatics/btaf140⟩

Article dans une revue hal-04713829v1
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Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial

Vincent Noël , Aurélien Naldi , Laurence Calzone , Loïc Paulevé , Denis Thieffry

Interface Focus, 2025, 15 (3), ⟨10.1098/rsfs.2025.0002⟩

Article dans une revue hal-04916645v1
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Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming

Stéphanie Chevalier , Julia Becker , Yujuan Gui , Vincent Noël , Cui Su et al.

npj Systems Biology and Applications, 2025, 11, pp.105. ⟨10.1038/s41540-025-00569-z⟩

Article dans une revue hal-04753079v2
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Inference of ecological networks and possibilistic dynamics based on Boolean networks from observations and prior knowledge

Loïc Paulevé , Cédric Gaucherel

Methods in Ecology and Evolution, 2025, 16 (8), pp.1851-1867. ⟨10.1111/2041-210x.70090⟩

Article dans une revue hal-05143187v1
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Bringing memory to Boolean networks: a unifying framework

Maximilien Gadouleau , Loïc Paulevé , Sara Riva

Journal of Computer and System Sciences, 2025, pp.103729. ⟨10.1016/j.jcss.2025.103729⟩

Article dans une revue hal-05342924v1
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scBoolSeq: Linking scRNA-Seq Statistics and Boolean Dynamics

Gustavo Magaña López , Laurence Calzone , Andrei Zinovyev , Loïc Paulevé

PLoS Computational Biology, 2024, 20 (7), pp.1-25. ⟨10.1371/journal.pcbi.1011620⟩

Article dans une revue hal-04294917v2
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Computational Complexity of Minimal Trap Spaces in Boolean Networks

Kyungduk Moon , Kangbok Lee , Loïc Paulevé

SIAM Journal on Discrete Mathematics, 2024, 38 (4), pp.2691-2708. ⟨10.1137/23M1553248⟩

Article dans une revue hal-04309014v1

Towards a qualitative theory of the interruption of eating behavior change

Philippe Dague , Laurent Muller , Loïc Paulevé , Marc Irigoin-Guichandut

Journal of Theoretical Biology, 2024, 581, pp.111731. ⟨10.1016/j.jtbi.2024.111731⟩

Article dans une revue hal-04416553v1
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Phenotype control and elimination of variables in Boolean networks

Elisa Tonello , Loïc Paulevé

Peer Community Journal, 2024, 4, pp.e79. ⟨10.24072/pcjournal.452⟩

Article dans une revue hal-04679930v1
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Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis

Loïc Paulevé

Peer Community Journal, 2023, 3 (e30), ⟨10.24072/pcjournal.255⟩

Article dans une revue hal-03745553v2
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MERRIN: MEtabolic Regulation Rule INference from time series data

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.

Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩

Article dans une revue hal-03701755v2
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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.

Nucleic Acids Research, 2022, pp.1-7. ⟨10.1093/nar/gkac331⟩

Article dans une revue hal-03666382v1
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Prédire le comportement des cellules avec la modélisation booléenne

Loïc Paulevé

Interstices, 2021

Article dans une revue hal-03206126v1
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A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation

Adrien Rougny , Loïc Paulevé , Michèle Teboul , Franck Delaunay

BMC Bioinformatics, 2021, 22 (1), pp.240. ⟨10.1186/s12859-021-04158-9⟩

Article dans une revue inserm-03228503v1
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Concurrency in Boolean networks

Thomas Chatain , Stefan Haar , Juraj Kolčák , Loïc Paulevé , Aalok Thakkar

Natural Computing, 2020, 19 (1), pp.91--109. ⟨10.1007/s11047-019-09748-4⟩

Article dans une revue hal-01893106v2
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Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks

Loïc Paulevé , Juraj Kolčák , Thomas Chatain , Stefan Haar

Nature Communications, 2020, 11, pp.4256. ⟨10.1038/s41467-020-18112-5⟩

Article dans une revue hal-02518582v2
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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⟩

Article dans une revue hal-02113864v1
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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⟩

Article dans une revue hal-01734805v1
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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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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⟩

Article dans une revue hal-01794294v2
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Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis

Loïc Paulevé

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, 15 (4), pp.1167-1179. ⟨10.1109/TCBB.2017.2749225⟩

Article dans une revue hal-01580765v1
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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⟩

Article dans une revue hal-01809081v1
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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⟩

Article dans une revue hal-01566380v1
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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⟩

Article dans une revue hal-01332679v1
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The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect

Jorgelindo da Veiga Moreira , Minoo Hamraz , Mohammad Abolhassani , Erwan Bigan , Sabine Pérès et al.

Metabolites, 2016, 6 (4), 12 p. ⟨10.3390/metabo6040033⟩

Article dans une revue hal-01417967v1
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Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming

Max Ostrowski , Loïc Paulevé , Torsten Schaub , Anne Siegel , Carito Guziolowski Article dans une revue hal-01354075v1
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Necessary and sufficient conditions for protocell growth

Erwan Bigan , Loïc Paulevé , Jean-Marc Steyaert , Stéphane S. Douady

Journal of Mathematical Biology, 2016, ⟨10.1007/s00285-016-0998-0⟩

Article dans une revue hal-01338156v1
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Reconstructing dynamic molecular states from single-cell time series

Lirong Huang , Loïc Paulevé , Christoph Zechner , Michael Unger , Anders S. Hansen et al.

Journal of the Royal Society Interface, 2016, 13 (122), pp.20160533. ⟨10.1098/rsif.2016.0533⟩

Article dans une revue hal-01362502v1
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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⟩

Article dans une revue hal-01094249v1
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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⟩

Article dans une revue hal-01158514v1
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Sufficient Conditions for Reachability in Automata Networks with Priorities

Maxime Folschette , Loïc Paulevé , Morgan Magnin , Olivier F. Roux

Theoretical Computer Science, 2015, ⟨10.1016/j.tcs.2015.08.040⟩

Article dans une revue hal-01202671v1
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Analyses statiques de la dynamique des réseaux d'automates indéterministes

Loïc Paulevé , Maxime Folschette , Morgan Magnin , Olivier Roux

Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 2015, 34 (4), pp.22. ⟨10.3166/TSI.34.463-484⟩

Article dans une revue hal-01070295v2
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Dynamical Properties of Discrete Reaction Networks

Loïc Paulevé , Gheorghe Craciun , Heinz Koeppl

Journal of Mathematical Biology, 2013, pp.Online First, 1-18. ⟨10.1007/s00285-013-0686-2⟩

Article dans une revue hal-00769448v2

Static analysis of Biological Regulatory Networks dynamics using abstract interpretation

Loïc Paulevé , Morgan Magnin , Olivier Roux

Mathematical Structures in Computer Science, 2012, 22 (04), pp 651-685. ⟨10.1017/S0960129511000739⟩

Article dans une revue istex hal-00714481v1

Stochastic simulation of multiple process calculi for biology

Matthew R. Lakin , Loïc Paulevé , Andrew Phillips

Theoretical Computer Science, 2012, 431, pp.181-206. ⟨10.1016/j.tcs.2011.12.057⟩

Article dans une revue hal-00872969v1
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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⟩

Article dans une revue hal-00397235v2
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Tuning Temporal Features within the Stochastic π-Calculus

Loïc Paulevé , Morgan Magnin , Olivier Roux

IEEE Transactions on Software Engineering, 2011, 37 (6), pp.858-871. ⟨10.1109/TSE.2010.95⟩

Article dans une revue hal-00397308v1
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Locality sensitive hashing: a comparison of hash function types and querying mechanisms

Loïc Paulevé , Hervé Jégou , Laurent Amsaleg

Pattern Recognition Letters, 2010, 31 (11), pp.1348-1358. ⟨10.1016/j.patrec.2010.04.004⟩

Article dans une revue inria-00567191v1
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Topological fixed points in Boolean networks

Loïc Paulevé , Adrien Richard

Comptes rendus de l'Académie des sciences. Série I, Mathématique, 2010, 348 (15-16), pp.825-828. ⟨10.1016/j.crma.2010.07.014⟩

Article dans une revue hal-00510892v1
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Seed Inference in Interacting Microbial Communities Using Combinatorial Optimization

Chabname Ghassemi Nedjad , Sebastián Nelson Mendoza , Clémence Frioux , Loïc Paulevé

CMSB 2025 - 23rd International Conference on Computational Methods in Systems Biology, François Fages, Inria Saclay, co-PC chair; Sabine Peres, Univ. Lyon, co-PC chair, Sep 2025, Villeurbanne - Lyon, France. pp.370-387, ⟨10.1007/978-3-032-01436-8_20⟩

Communication dans un congrès hal-05230510v1
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CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems

Kerian Thuillier , Anne Siegel , Loïc Paulevé

AAAI 2024 - The 38th Annual AAAI Conference on Artificial Intelligence, Feb 2024, Vancouver, Canada. pp.1-8

Communication dans un congrès hal-04420454v1
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BoNesis: a Python-based declarative environment for the verification, reprogramming, and synthesis of Most Permissive Boolean networks

Stéphanie Chevalier , Déborah Boyenval , Gustavo Magaña-López , Théo Roncalli , Athénaïs Vaginay et al.

CMSB 2024: 22nd International Conference on Computational Methods in Systems Biology, Sep 2024, Pisa, Italy. ⟨10.1007/978-3-031-71671-3_6⟩

Communication dans un congrès hal-04629083v1
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Attractor Identification in Asynchronous Boolean Dynamics with Network Reduction

Elisa Tonello , Loïc Paulevé

Computational Methods in Systems Biology (CMSB 2023), 2023, Luxembourg, Luxembourg. pp.202-219, ⟨10.1007/978-3-031-42697-1_14⟩

Communication dans un congrès hal-04601061v1

Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks

Sara Riva , Jean-Marie Lagniez , Gustavo Magaña López , Loïc Paulevé

Computational Methods in Systems Biology, Sep 2023, Luxembourg, Luxembourg. pp.157-174, ⟨10.1007/978-3-031-42697-1_11⟩

Communication dans un congrès hal-04325368v1
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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

Communication dans un congrès hal-03910483v1
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Avoid One's Doom: Finding Cliff-Edge Configurations in Petri Nets

Giann Karlo Aguirre-Samboní , Stefan Haar , Loïc Paulevé , Stefan Schwoon , Nick Würdemann

GandALF 2022 - Games, Automata, Logics, and Formal Verification, Sep 2022, Madrid, Spain. ⟨10.4204/EPTCS.370.12⟩

Communication dans un congrès hal-03773855v1
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Variable-Depth Simulation of Most Permissive Boolean Networks

Théo Roncalli , Loïc Paulevé

20th International Conference on Computational Methods in Systems Biology (CMSB 2022), 2022, Bucharest, Romania. ⟨10.1007/978-3-031-15034-0_7⟩

Communication dans un congrès hal-03704761v1
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Non-deterministic updates of Boolean networks

Loïc Paulevé , Sylvain Sené

27th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2021), Jul 2021, Marseille, France. pp.10:1-10:16, ⟨10.4230/OASIcs.AUTOMATA.2021.10⟩

Communication dans un congrès hal-03210805v2
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Learning Boolean controls in regulated metabolic networks: a case-study

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.

CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, 2021, Bordeaux, France. pp.159-180, ⟨10.1007/978-3-030-85633-5_10⟩

Communication dans un congrès hal-03207589v3
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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⟩

Communication dans un congrès hal-02898849v2
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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⟩

Communication dans un congrès hal-02704747v1
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Drawing the Line: Basin Boundaries in Safe Petri Nets

Stefan Haar , Loïc Paulevé , Stefan Schwoon

CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, Sep 2020, Konstanz / Online, Germany. ⟨10.1007/978-3-030-60327-4_17⟩

Communication dans un congrès hal-02898841v1
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Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming

Stéphanie Chevalier , Christine Froidevaux , Loïc Paulevé , Andrei Zinovyev

2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), 2019, Portland, Oregon, United States. ⟨10.1109/ICTAI.2019.00014⟩

Communication dans un congrès hal-02276921v2
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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⟩

Communication dans un congrès hal-01940174v1
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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⟩

Communication dans un congrès hal-02178917v2
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Boolean Networks: Beyond Generalized Asynchronicity

Thomas Chatain , Stefan Haar , Loïc Paulevé

AUTOMATA 2018 - 24th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems, Jun 2018, Ghent, Belgium. pp.29-42, ⟨10.1007/978-3-319-92675-9_3⟩

Communication dans un congrès hal-01768359v2
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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⟩

Communication dans un congrès hal-01354109v2
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Temporal Reprogramming of Boolean Networks

Hugues Mandon , Stefan Haar , Loïc Paulevé

CMSB 2017 - 15th conference on Computational Methods for Systems Biology, Sep 2017, Darmstadt, Germany. pp.179 - 195, ⟨10.1007/978-3-319-67471-1_11⟩

Communication dans un congrès hal-01589251v1
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Goal-Driven Unfolding of Petri Nets

Thomas Chatain , Loïc Paulevé

28th International Conference on Concurrency Theory (CONCUR 2017), Sep 2017, Berlin, Germany. ⟨10.4230/LIPIcs.CONCUR.2017.14⟩

Communication dans un congrès hal-01392203v2
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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⟩

Communication dans un congrès hal-01589248v1
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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⟩

Communication dans un congrès hal-01149118v2
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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

Communication dans un congrès hal-01361350v1

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

Communication dans un congrès hal-01305967v1
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Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph

Hugues Mandon , Stefan Haar , Loïc Paulevé

Fifth International Workshop on Hybrid Systems Biology (HSB 2016), Oct 2016, Grenoble, France. pp.113-127, ⟨10.1007/978-3-319-47151-8_8⟩

Communication dans un congrès hal-01354079v1
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Boolean Network Identification from Multiplex Time Series Data

Max Ostrowski , Loïc Paulevé , Torsten Schaub , Anne Siegel , Carito Guziolowski

CMSB 2015 - 13th conference on Computational Methods for Systems Biology, Sep 2015, Nantes, France. pp.170-181, ⟨10.1007/978-3-319-23401-4_15⟩

Communication dans un congrès hal-01164751v1
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Characterization of Reachable Attractors Using Petri Net Unfoldings

Thomas Chatain , Stefan Haar , Loïg Jezequel , Loïc Paulevé , Stefan Schwoon

CMSB 2014, Nov 2014, Manchester, United Kingdom. pp.14, ⟨10.1007/978-3-319-12982-2_10⟩

Communication dans un congrès hal-01060450v1
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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⟩

Communication dans un congrès hal-00872963v1
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Under-approximating Cut Sets for Reachability in Large Scale Automata Networks

Loïc Paulevé , Geoffroy Andrieux , Heinz Koeppl

25th International Conference, CAV 2013, Saint Petersburg, Russia, July 13-19, 2013. Proceedings, Jul 2013, Saint Petersburg, Russia. pp.69-84, ⟨10.1007/978-3-642-39799-8_4⟩

Communication dans un congrès hal-00769447v3
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Under-approximation of Reachability in Multivalued Asynchronous Networks

Maxime Folschette , Loïc Paulevé , Morgan Magnin , Olivier Roux

fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13), Jun 2013, Florence, Italy. pp.33--51, ⟨10.1016/j.entcs.2013.11.004⟩

Communication dans un congrès hal-00873000v1
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Static Analysis of Boolean Networks Based on Interaction Graphs: A Survey

Loïc Paulevé , Adrien Richard

2nd International Workshop on Static Analysis and Systems Biology (SASB 2011), Sep 2011, Venice, Italy. pp.93-104, ⟨10.1016/j.entcs.2012.05.017⟩

Communication dans un congrès hal-00714476v2
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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⟩

Communication dans un congrès hal-00704569v2

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

Communication dans un congrès hal-00712557v1
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Abducing Biological Regulatory Networks from Process Hitting models

Maxime Folschette , Loïc Paulevé , Katsumi Inoue , Morgan Magnin , Olivier F. Roux

ECML-PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology, Sep 2012, Bristol, United Kingdom

Communication dans un congrès hal-01314470v1

HSIM: an hybrid stochastic simulation system for systems biology

Patrick Amar , Loïc Paulevé

The Third International Workshop on Static Analysis and Systems Biology (SASB 2012), Sep 2012, Deauville, France. pp.3 -- 21, ⟨10.1016/j.entcs.2015.04.016⟩

Communication dans un congrès hal-00758168v1

Abstract Interpretation of Dynamics of Biological Regulatory Networks

Loïc Paulevé , Morgan Magnin , Olivier Roux

1st International Workshop on Static Analysis and Systems Biology (SASB 2010), Sep 2010, Perpignan, France. pp.43-56, ⟨10.1016/j.entcs.2011.04.004⟩

Communication dans un congrès hal-00601118v1

A generic abstract machine for stochastic process calculi

Loïc Paulevé , Simon Youssef , Matthew R. Lakin , Andrew Phillips

CMSB '10: The 8th International Conference on Computational Methods in Systems Biology, Sep 2010, Trento, Italy. pp.43--54, ⟨10.1145/1839764.1839771⟩

Communication dans un congrès hal-00525503v1

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⟩

Communication dans un congrès hal-00574362v1
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Réseaux booléens : formalisme, sémantiques, et complexité

Loïc Paulevé

Cédric Lhoussaine; Élisabeth Remy. Approches symboliques de la modélisation et de l'analyse des systèmes biologiques, ISTE Editions, 2022, 9781789490299

Chapitre d'ouvrage hal-03612593v1
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Boolean networks and their dynamics: the impact of updates

Loïc Paulevé , Sylvain Sené

Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools, Wiley, pp.173-250, 2022, 978-1-119-71658-7. ⟨10.1002/9781119716600.ch6⟩

Chapitre d'ouvrage hal-03736899v1
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Analyse statique des réseaux booléens

Loïc Paulevé , Adrien Richard

Emmanuel Jeandel; Laurent Vigneron. Informatique Mathématique, Une photographie en 2018, CNRS Éditions, pp.157-194, 2018, 978-2-271-11974-2

Chapitre d'ouvrage hal-01753101v1
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Analyzing Large Network Dynamics with Process Hitting

Loïc Paulevé , Courtney Chancellor , Maxime Folschette , Morgan Magnin , Olivier Roux

Luis Fariñas del Cerro; Katsumi Inoue. Logical Modeling of Biological Systems, Wiley, pp.125 - 166, 2014, 978-1-84821-680-8. ⟨10.1002/9781119005223.ch4⟩

Chapitre d'ouvrage hal-01060490v1
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Seed2LP: seed inference in metabolic networks for reverse ecology applications

Chabname Ghassemi Nedjad , Clémence Frioux , Loïc Paulevé

JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France

Poster de conférence hal-05446736v1
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Logic and linear programming for seed identification in metabolic networks

Chabname Ghassemi Nedjad , Clémence Frioux , Loïc Paulevé

Biorégul 2023 - Modélisation Formelle de Réseaux de Régulation Biologique, Jun 2023, Porquerolles (Hyères), France. pp.1-1, 2023

Poster de conférence hal-04328778v1
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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 de conférence hal-01366730v1
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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 de conférence hal-01258943v1
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Modélisation, Simulation et Vérification des Grands Réseaux de Régulation Biologique

Loïc Paulevé

Réseaux et télécommunications [cs.NI]. Ecole Centrale de Nantes (ECN), 2011. Français. ⟨NNT : ⟩

Thèse tel-00635750v2