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66

Loïc Paulevé


http://loicpauleve.name


Journal articles24 documents

  • Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé, Aalok Thakkar. Concurrency in Boolean networks. Natural Computing, Springer Verlag, 2020, 19 (1), pp.91--109. ⟨10.1007/s11047-019-09748-4⟩. ⟨hal-01893106v2⟩
  • Hugues Mandon, Cui Su, Jun Pang, Soumya Paul, Stefan Haar, et al.. Algorithms for the Sequential Reprogramming of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2019, 16 (5), pp.1610-1619. ⟨10.1109/TCBB.2019.2914383⟩. ⟨hal-02113864⟩
  • Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé. Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. Theoretical Computer Science, Elsevier, 2019, 765, pp.120-144. ⟨10.1016/j.tcs.2018.03.009⟩. ⟨hal-01734805⟩
  • Loïc Paulevé. Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2018, 15 (4), pp.1167-1179. ⟨10.1109/TCBB.2017.2749225⟩. ⟨hal-01580765⟩
  • Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll, Denis Thieffry, et al.. Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). Frontiers in Physiology, Frontiers, 2018, 9, pp.787. ⟨10.1101/319780⟩. ⟨hal-01809081⟩
  • Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro Monteiro, et al.. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology, Frontiers, 2018, 9, pp.n°680:1-13. ⟨10.3389/fphys.2018.00680⟩. ⟨hal-01794294v2⟩
  • Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, et al.. Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data. PLoS Computational Biology, Public Library of Science, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩. ⟨hal-01897020⟩
  • Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé. Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming. Algorithms for Molecular Biology, BioMed Central, 2017, 12 (1), pp.19. ⟨10.1186/s13015-017-0110-3⟩. ⟨hal-01566380⟩
  • Lirong Huang, Loïc Paulevé, Christoph Zechner, Michael Unger, Anders S. Hansen, et al.. Reconstructing dynamic molecular states from single-cell time series. Journal of the Royal Society Interface, the Royal Society, 2016, 13 (122), ⟨10.1098/rsif.2016.0533⟩. ⟨hal-01362502⟩
  • Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski. Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming. BioSystems, Elsevier, 2016, ⟨10.1016/j.biosystems.2016.07.009⟩. ⟨hal-01354075⟩
  • Erwan Bigan, Loïc Paulevé, Jean-Marc Steyaert, Stéphane Douady. Necessary and sufficient conditions for protocell growth. Journal of Mathematical Biology, Springer Verlag (Germany), 2016, ⟨10.1007/s00285-016-0998-0⟩. ⟨hal-01338156⟩
  • Jorgelindo da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine Pérès, et al.. The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect. Metabolites, MDPI, 2016, 6 (4), 12 p. ⟨10.3390/metabo6040033⟩. ⟨hal-01417967⟩
  • Adrien Rougny, Christine Froidevaux, Laurence Calzone, Loïc Paulevé. Qualitative dynamics semantics for SBGN process description. BMC Systems Biology, BioMed Central, 2016, ⟨10.1186/s12918-016-0285-0⟩. ⟨hal-01332679⟩
  • Loïc Paulevé, Maxime Folschette, Morgan Magnin, Olivier Roux. Analyses statiques de la dynamique des réseaux d'automates indéterministes. Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, Lavoisier, 2015, 34 (4), pp.22. ⟨10.3166/TSI.34.463-484⟩. ⟨hal-01070295v2⟩
  • Maxime Folschette, Loïc Paulevé, Morgan Magnin, Olivier Roux. Sufficient Conditions for Reachability in Automata Networks with Priorities. Theoretical Computer Science, Elsevier, 2015, ⟨10.1016/j.tcs.2015.08.040⟩. ⟨hal-01202671⟩
  • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, Olivier Roux. Identification of Biological Regulatory Networks from Process Hitting models. Theoretical Computer Science, Elsevier, 2015, 568, pp.39. ⟨10.1016/j.tcs.2014.12.002⟩. ⟨hal-01094249⟩
  • Jorgelindo da Veiga Moreira, Sabine Pérès, Jean-Marc Steyaert, Erwan Bigan, Loïc Paulevé, et al.. Cell cycle progression is regulated by intertwined redox oscillators. Theoretical Biology and Medical Modelling, BioMed Central, 2015, 12 (1), pp.10. ⟨10.1186/s12976-015-0005-2⟩. ⟨hal-01158514⟩
  • Loïc Paulevé, Gheorghe Craciun, Heinz Koeppl. Dynamical Properties of Discrete Reaction Networks. Journal of Mathematical Biology, Springer Verlag (Germany), 2013, pp.Online First, 1-18. ⟨10.1007/s00285-013-0686-2⟩. ⟨hal-00769448v2⟩
  • Loïc Paulevé, Morgan Magnin, Olivier Roux. Static analysis of Biological Regulatory Networks dynamics using abstract interpretation. Mathematical Structures in Computer Science, Cambridge University Press (CUP), 2012, 22 (04), pp 651-685. ⟨10.1017/S0960129511000739⟩. ⟨hal-00714481⟩
  • Matthew Lakin, Loïc Paulevé, Andrew Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science, Elsevier, 2012, 431, pp.181-206. ⟨10.1016/j.tcs.2011.12.057⟩. ⟨hal-00872969⟩
  • Loïc Paulevé, Morgan Magnin, Olivier Roux. Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework. Transactions on Computational Systems Biology, Springer, 2011, XIII, pp.171-191. ⟨10.1007/978-3-642-19748-2_8⟩. ⟨hal-00397235v2⟩
  • Loïc Paulevé, Morgan Magnin, Olivier Roux. Tuning Temporal Features within the Stochastic π-Calculus. IEEE Transactions on Software Engineering, Institute of Electrical and Electronics Engineers, 2011, 37 (6), pp.858-871. ⟨10.1109/TSE.2010.95⟩. ⟨hal-00397308⟩
  • Loïc Paulevé, Adrien Richard. Topological fixed points in Boolean networks. Comptes rendus de l'Académie des sciences. Série I, Mathématique, Elsevier, 2010, 348 (15-16), pp.825-828. ⟨10.1016/j.crma.2010.07.014⟩. ⟨hal-00510892⟩
  • Loïc Paulevé, Hervé Jégou, Laurent Amsaleg. Locality sensitive hashing: a comparison of hash function types and querying mechanisms. Pattern Recognition Letters, Elsevier, 2010, 31 (11), pp.1348-1358. ⟨10.1016/j.patrec.2010.04.004⟩. ⟨inria-00567191⟩

Conference papers28 documents

  • Gilles Audemard, Loïc Paulevé, Laurent Simon. SAT Heritage: a community-driven effort for archiving, building and running more than thousand SAT solvers. 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⟩. ⟨hal-02704747⟩
  • Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Zinovyev, Loïc Paulevé. Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. 18th International Conference on Computational Methods in Systems Biology (CMSB), 2020, Online, Germany. ⟨hal-02898849⟩
  • Stefan Haar, Loïc Paulevé, Stefan Schwoon. Drawing the Line: Basin Boundaries in Safe Petri Nets. 18th International Conference on Computational Methods in Systems Biology (CMSB), Sep 2020, Online, Germany. ⟨hal-02898841⟩
  • Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, Andrei Zinovyev. Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. 2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), 2019, Portland, Oregon, United States. ⟨10.1109/ICTAI.2019.00014⟩. ⟨hal-02276921v2⟩
  • Stefan Haar, Juraj Kolčák, Loïc Paulevé. Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics. 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⟩. ⟨hal-01940174⟩
  • Hugues Mandon, Cui Su, Stefan Haar, Jun Pang, Loïc Paulevé. Sequential Reprogramming of Boolean Networks Made Practical. 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⟩. ⟨hal-02178917v2⟩
  • Thomas Chatain, Stefan Haar, Loïc Paulevé. Boolean Networks: Beyond Generalized Asynchronicity. 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⟩. ⟨hal-01768359v2⟩
  • Thomas Chatain, Loïc Paulevé. Goal-Driven Unfolding of Petri Nets. 28th International Conference on Concurrency Theory (CONCUR 2017), Sep 2017, Berlin, Germany. ⟨10.4230/LIPIcs.CONCUR.2017.14⟩. ⟨hal-01392203v2⟩
  • Hugues Mandon, Stefan Haar, Loïc Paulevé. Temporal Reprogramming of Boolean Networks. 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⟩. ⟨hal-01589251⟩
  • Loïc Paulevé. Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface. 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⟩. ⟨hal-01589248⟩
  • Hugues Mandon, Stefan Haar, Loïc Paulevé. Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph. Fifth International Workshop on Hybrid Systems Biology (HSB 2016), Oct 2016, Grenoble, France. pp.113-127, ⟨10.1007/978-3-319-47151-8_8⟩. ⟨hal-01354079⟩
  • Lukas Studer, Loïc Paulevé, Christoph Zechner, Matthias Reumann, Maria Rodriguez Martinez, et al.. Marginalized Continuous Time Bayesian Networks for Network Reconstruction from Incomplete Observations. AAAI Conference on Artificial Intelligence, Feb 2016, Phoenix, Arizona, United States. ⟨hal-01305967⟩
  • Loïc Paulevé. Goal-Oriented Reduction of Automata Networks. 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⟩. ⟨hal-01149118v2⟩
  • Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé. Unfolding of Parametric Boolean Networks. 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⟩. ⟨hal-01354109v2⟩
  • Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé. Identification of Bifurcations in Biological Regulatory Networks using Answer-Set Programming. Constraint-Based Methods for Bioinformatics Workshop, Sep 2016, Toulouse, France. ⟨hal-01361350⟩
  • Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski. Boolean Network Identification from Multiplex Time Series Data. 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⟩. ⟨hal-01164751⟩
  • Thomas Chatain, Stefan Haar, Loïg Jezequel, Loïc Paulevé, Stefan Schwoon. Characterization of Reachable Attractors Using Petri Net Unfoldings. CMSB 2014, Nov 2014, Manchester, United Kingdom. pp.14, ⟨10.1007/978-3-319-12982-2_10⟩. ⟨hal-01060450⟩
  • Michael Klann, Loïc Paulevé, Tatjana Petrov, Heinz Koeppl. Coarse-grained brownian dynamics simulation of rule-based models. 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⟩. ⟨hal-00872963⟩
  • Loïc Paulevé, Geoffroy Andrieux, Heinz Koeppl. Under-approximating Cut Sets for Reachability in Large Scale Automata Networks. 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⟩. ⟨hal-00769447v3⟩
  • Maxime Folschette, Loïc Paulevé, Morgan Magnin, Olivier Roux. Under-approximation of Reachability in Multivalued Asynchronous Networks. 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⟩. ⟨hal-00873000⟩
  • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, Olivier Roux. Abducing Biological Regulatory Networks from Process Hitting models. ECML-PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology, Sep 2012, Bristol, United Kingdom. ⟨hal-01314470⟩
  • Stefan Janssen, Loïc Paulevé, Yann Ponty, Balaji Raman, Matthias Zytnicki. Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?. IWBDA - 4th International Workshop on Bio-Design Automation - 2012, Jun 2012, San Francisco, United States. ⟨hal-00712557⟩
  • Patrick Amar, Loïc Paulevé. HSIM: an hybrid stochastic simulation system for systems biology. 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⟩. ⟨hal-00758168⟩
  • Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, Olivier Roux. Concretizing the Process Hitting into Biological Regulatory Networks. Computational Methods in Systems Biology, Oct 2012, London, United Kingdom. p. 166-186, ⟨10.1007/978-3-642-33636-2_11⟩. ⟨hal-00704569v2⟩
  • Loïc Paulevé, Adrien Richard. Static Analysis of Boolean Networks Based on Interaction Graphs: A Survey. 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⟩. ⟨hal-00714476⟩
  • Loïc Paulevé, Simon Youssef, Matthew Lakin, Andrew Phillips. A generic abstract machine for stochastic process calculi. CMSB '10: The 8th International Conference on Computational Methods in Systems Biology, Sep 2010, Trento, Italy. pp.43--54, ⟨10.1145/1839764.1839771⟩. ⟨hal-00525503⟩
  • Loïc Paulevé, Morgan Magnin, Olivier Roux. Abstract Interpretation of Dynamics of Biological Regulatory Networks. 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⟩. ⟨hal-00601118⟩
  • Andrew Phillips, Matthew Lakin, Loïc Paulevé. Stochastic simulation of process calculi for biology. Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010, Aug 2010, Jena, Germany. ⟨10.4204/EPTCS.40.1⟩. ⟨hal-00574362⟩

Book sections2 documents

  • Loïc Paulevé, Adrien Richard. Analyse statique des réseaux booléens. Emmanuel Jeandel; Laurent Vigneron. Informatique Mathématique, Une photographie en 2018, CNRS Éditions, pp.157-194, 2018, 78-2-271-11974-2. ⟨hal-01753101⟩
  • Loïc Paulevé, Courtney Chancellor, Maxime Folschette, Morgan Magnin, Olivier Roux. Analyzing Large Network Dynamics with Process Hitting. Luis Fariñas del Cerro; Katsumi Inoue. Logical Modeling of Biological Systems, Wiley, pp.125 - 166, 2014, 978-1-84821-680-8. ⟨hal-01060490⟩

Poster communications2 documents

  • Loïc Paulevé. Pint, a static analyzer for dynamics of Automata Networks. 14th International Conference on Computational Methods in Systems Biology (CMSB 2016), Sep 2016, Cambridge, United Kingdom. ⟨hal-01366730⟩
  • Adrien Rougny, Christine Froidevaux, Loïc Paulevé. Two Qualitative Dynamics Semantics for SBGN Process Description Maps. CMSB'15, Sep 2015, Nantes, France. 2015. ⟨hal-01258943⟩

Directions of work or proceedings2 documents

  • Loïc Paulevé, Nathalie Théret. 6th International Workshop on Static Analysis and Systems Biology (SASB 2015) . Loïc Paulevé; Nathalie Theret. SASB, Sep 2015, Saint-Malo, France. 326, Elsevier, pp.88, 2016, Electronic Notes in Theoretical Computer Science. ⟨hal-01385704⟩
  • Loïc Paulevé, Heinz Koeppl. 5th International Workshop on Static Analysis and Systems Biology (SASB 2014). Loïc Paulevé; Heinz Koeppl. SASB, Sep 2014, Munich, Germany. 316, Elsevier, pp.97, 2015, Electronic Notes in Theoretical Computer Science. ⟨hal-01197269⟩

Other publications1 document

Preprints, Working Papers, ...1 document

  • Loïc Paulevé, Juraj Kolčák, Thomas Chatain, Stefan Haar. Reconciling Qualitative, Abstract, and Scalable Modeling of Biological Networks. 2020. ⟨hal-02518582⟩

Reports5 documents

  • Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé. Most Permissive Semantics of Boolean Networks. [Research Report] Univ. Bordeaux, Bordeaux INP, CNRS, LaBRI, UMR5800, F-33400 Talence, France; LSV, ENS Cachan, CNRS, INRIA, Université Paris-Saclay, Cachan (France). 2020. ⟨hal-01864693v2⟩
  • Loïc Paulevé, Morgan Magnin, Olivier Roux. From the Process Hitting to Petri Nets and Back. 2012. ⟨hal-00744807⟩
  • Araks Martirosyan, Loïc Paulevé, Clair Poignard, Mireille Régnier, Jean-Marc Steyaert, et al.. A Dynamical Model for the Transmembrane Potential Regulation by pH. [Research Report] LIX, Ecole polytechnique. 2012. ⟨hal-00769446⟩
  • Loïc Paulevé, Morgan Magnin, Olivier Roux. Static Analysis by Abstract Interpretation of Biological Regulatory Networks Dynamics. 2011. ⟨hal-00574353v2⟩
  • Loïc Paulevé. Euclidean lattices for high dimensional indexing and searching. [Research Report] PI 1903, 2008, pp.57. ⟨inria-00326262⟩

Theses1 document

  • Loïc Paulevé. Modélisation, Simulation et Vérification des Grands Réseaux de Régulation Biologique. Réseaux et télécommunications [cs.NI]. Ecole Centrale de Nantes (ECN), 2011. Français. ⟨tel-00635750v2⟩