Loïc Paulevé, PhD

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Publications

By chronological order (show by publication type)
[60] conference
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, and Anne Siegel. Learning Boolean controls in regulated metabolic networks: a case-study. In 19th International Conference on Computational Methods in Systems Biology. Bordeaux, France, 2021. Springer.
PDFURLBibtex ]
[59] conference
Loïc Paulevé and Sylvain Sené. Non-deterministic updates of Boolean networks. In AUTOMATA 2021 (27th International Workshop on Cellular Automata and Discrete Complex Systems). Marseille, France, 2021.
PDFURLBibtex ]
[58] journal
Adrien Rougny, Loïc Paulevé, Michéle Teboul, and Franck Delaunay. A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. BMC Bioinformatics, 2021.
DOI:10.1186/s12859-021-04158-9Bibtex ]
[57] journalfr
Loïc Paulevé. Prédire le comportement des cellules avec la modélisation booléenne. Interstices, 2021.
PDFURLBibtex ]
[HDR] thesis
Loïc Paulevé. Réseaux booléens : méthodes formelles et outils pour la modélisation en biologie. Habilitation à diriger des recherches, Université Paris-Saclay, 2020.
PDFURLBibtex ]
[56] journal
Loïc Paulevé, Juraj Kolčák, Thomas Chatain, and Stefan Haar. Reconciling qualitative, abstract, and scalable modeling of biological networks. Nature Communications, 2020.
DOI:10.1038/s41467-020-18112-5Bibtex ]
[55] conference
Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Zinovyev, and Loïc Paulevé. Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision. In CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, volume 12314 of Lecture Notes in Computer Science, 193–209. Cham, 2020. Springer.
DOI:10.1007/978-3-030-60327-4_11PDFBibtex ]
[54] conference
Stefan Haar, Loïc Paulevé, and Stefan Schwoon. Drawing the Line: Basin Boundaries in Safe Petri Nets. In CMSB 2020 - 18th International Conference on Computational Methods in Systems Biology, volume 12314 of Lecture Notes in Computer Science, 321–336. Cham, 2020. Springer.
DOI:10.1007/978-3-030-60327-4_17PDFURLBibtex ]
[53] conference
Gilles Audemard, Loïc Paulevé, and Laurent Simon. SAT Heritage: a community-driven effort for archiving, building and running more than thousand SAT solvers. In Theory and Applications of Satisfiability Testing – SAT 2020, volume 12178 of Lecture Notes in Computer Science, 107–113. Cham, 2020. Springer.
DOI:10.1007/978-3-030-51825-7_8PDFBibtex ]
[MPBNs-TR] report
Thomas Chatain, Stefan Haar, Juraj Kolčák, and Loïc Paulevé. Most Permissive Semantics of Boolean Networks. Technical Report, arXiv, 2020.
arXiv:1808.10240PDFURLBibtex ]
[52] conference
Stéphanie Chevalier, Christine Froidevaux, Loïc Paulevé, and Andrei Zinovyev. Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming. In 2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), 34–41. Portland, Oregon, United States, 2019. IEEE.
DOI:10.1109/ICTAI.2019.00014PDFBibtex ]
[51] conference
Hugues Mandon, Cui Su, Stefan Haar, Jun Pang, and Loïc Paulevé. Sequential Reprogramming of Boolean Networks Made Practical. In CMSB 2019 - 17th International Conference on Computational Methods in Systems Biology, volume 11773 of Lecture Notes in Computer Science, 3–19. Cham, 2019. Springer. Best paper award.
DOI:10.1007/978-3-030-31304-3_1PDFBibtex ]
[50] journal
Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé, and Aalok Thakkar. Concurrency in Boolean networks. Natural Computing, 19(1):91–109, 2020.
DOI:10.1007/s11047-019-09748-4PDFBibtex ]
[49] journal
Hugues Mandon, Cui Su, Jun Pang, Soumya Paul, Stefan Haar, and Loïc Paulevé. Algorithms for the Sequential Reprogramming of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(5):1610–1619, 2019.
DOI:10.1109/TCBB.2019.2914383PDFBibtex ]
[TCS-Issue2019] edition
Jérôme Feret, Loïc Paulevé, and David Šafránek, editors. Formal Verification and Static Analysis of Molecular Devices and Biological Systems, volume 765 of Theoretical Computer Science, Elsevier, 2019.
URLBibtex ]
[48] conference
Stefan Haar, Juraj Kolčák, and Loïc Paulevé. Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics. In VMCAI 2019 - 20th International Conference on Verification, Model Checking, and Abstract Interpretation, volume 11388 of Lecture Notes in Computer Science, 555–576. Lisbon, Portugal, 2019. Springer.
DOI:10.1007/978-3-030-11245-5_26PDFBibtex ]
[47] journal
Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, and Carito Guziolowski. Computational discovery of dynamic cell line specific boolean networks from multiplex time-course data. PLOS Computational Biology, 14(10):1–23, 2018.
DOI:10.1371/journal.pcbi.1006538Bibtex ]
[46] journal
Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll, Denis Thieffry, Andrei Zinovyev, Laurence Calzone, and Loïc Paulevé. Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial) . Frontiers in Physiology, 9:787, 2018.
DOI:10.3389/fphys.2018.00787Bibtex ]
[45] journal
Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, and Loïc Paulevé. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. Frontiers in Physiology, 9:680, 2018.
DOI:10.3389/fphys.2018.00680Bibtex ]
[44] conference
Thomas Chatain, Stefan Haar, and Loïc Paulevé. Boolean Networks: Beyond Generalized Asynchronicity. In Cellular Automata and Discrete Complex Systems (AUTOMATA 2018), volume 10875 of Lecture Notes in Computer Science, 29–42. Ghent, Belgium, 2018. Springer.
DOI:10.1007/978-3-319-92675-9_3PDFBibtex ]
[43] chapter
Loïc Paulevé and Adrien Richard. Analyse statique des réseaux booléens. In Emmanuel Jeandel and Laurent Vigneron, editors, Informatique Mathématique, Une photographie en 2018. CNRS Éditions, March 2018.
PDFURLBibtex ]
[42] journal
Juraj Kolčák, David Šafránek, Stefan Haar, and Loïc Paulevé. Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. Theoretical Computer Science, 765:120 – 144, 2018.
DOI:10.1016/j.tcs.2018.03.009PDFBibtex ]
[41] journal
Loïc Paulevé. Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4):1167–1179, 2018.
DOI:10.1109/TCBB.2017.2749225PDFBibtex ]
[40] journal
Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, and Loïc Paulevé. Identification of bifurcation transitions in biological regulatory networks using Answer-Set Programming. Algorithms for Molecular Biology, 12(1):19, 2017.
DOI:10.1186/s13015-017-0110-3Bibtex ]
[39] conference
Thomas Chatain and Loïc Paulevé. Goal-Driven Unfolding of Petri Nets. In 28th International Conference on Concurrency Theory (CONCUR 2017), volume 85 of Leibniz International Proceedings in Informatics (LIPIcs), 18:1–18:16. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, 2017.
DOI:10.4230/LIPIcs.CONCUR.2017.18PDFBibtex ]
[38] conference
Hugues Mandon, Stefan Haar, and Loïc Paulevé. Temporal Reprogramming of Boolean Networks. In CMSB 2017 - 15th conference on Computational Methods for Systems Biology, volume 10545 of Lecture Notes in Computer Science, 179–195. Springer International Publishing, 2017.
DOI:10.1007/978-3-319-67471-1_11PDFBibtex ]
[37] conference
Loïc Paulevé. Pint: a static analyzer for transient dynamics of qualitative networks with IPython interface. In CMSB 2017 - 15th conference on Computational Methods for Systems Biology, volume 10545 of Lecture Notes in Computer Science, 309–316. Springer International Publishing, 2017.
DOI:10.1007/978-3-319-67471-1_20PDFBibtex ]
[36] misc
Loïc Paulevé and Philippe Dague. Journées BIOSS-IA 2017. July 2017. Bulletin 97 de l'AFIA - Association française pour l'Intelligence Artificielle.
PDFURLBibtex ]
[35] conference
Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, and Loïc Paulevé. Identification of bifurcations in biological regulatory networks using answer-set programming. In Constraint-Based Methods for Bioinformatics Workshop. 2016.
PDFBibtex ]
[SASB2015] edition
Loïc Paulevé and Nathalie Theret, editors. 6th International Workshop on Static Analysis and Systems Biology (SASB 2015), volume 326 of Electronic Notes in Theoretical Computer Science, Saint-Malo, France, October 2016. Elsevier.
URLBibtex ]
[34] journal
Lirong Huang, Loïc Paulevé, Christoph Zechner, Michael Unger, Anders S. Hansen, and Heinz Koeppl. Reconstructing dynamic molecular states from single-cell time series. Journal of the Royal Society Interface, 2016.
DOI:10.1098/rsif.2016.0533PDFBibtex ]
[33] conference
Hugues Mandon, Stefan Haar, and Loïc Paulevé. Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph. In Hybrid Systems Biology (HSB 2016) Proceedings, volume 9957 of Lecture Notes in Computer Science, 113–127. Springer International Publishing, 2016.
DOI:10.1007/978-3-319-47151-8_8PDFBibtex ]
[32] conference
Loïc Paulevé. Goal-Oriented Reduction of Automata Networks. In CMSB 2016 - 14th conference on Computational Methods for Systems Biology, volume 9859 of Lecture Notes in Bioinformatics. Springer, 2016.
DOI:10.1007/978-3-319-45177-0_16PDFBibtex ]
[31] conference
Juraj Kolčák, David Šafránek, Stefan Haar, and Loïc Paulevé. Unfolding of Parametric Boolean Networks. In 7th International Workshop on Static Analysis and Systems Biology (SASB 2016), volume 335 of Electronic Notes in Theoretical Computer Science, 67 – 90. Edinburgh, United Kingdom, 2016. Elsevier.
DOI:10.1016/j.entcs.2018.03.009PDFURLBibtex ]
[30] journal
Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, and Carito Guziolowski. Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming. Biosystems, 149:139 – 153, 2016.
DOI:10.1016/j.biosystems.2016.07.009PDFBibtex ]
[29] journal
Adrien Rougny, Christine Froidevaux, Laurence Calzone, and Loïc Paulevé. Qualitative dynamics semantics for SBGN process description. BMC Systems Biology, 10(1):1–24, 2016.
DOI:10.1186/s12918-016-0285-0PDFBibtex ]
[28] conference
Lukas Studer, Loïc Paulevé, Christoph Zechner, Matthias Reumann, Maria Rodriguez Martinez, and Heinz Koeppl. Marginalized continuous time bayesian networks for network reconstruction from incomplete observations. In AAAI Conference on Artificial Intelligence. 2016.
PDFURLBibtex ]
[27] journal
Jorgelindo Da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine Pérès, Loïc Paulevé, Marcel Levy Nogueira, Jean-Marc Steyaert, and Laurent Schwartz. The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect. Metabolites, 2016.
DOI:10.3390/metabo6040033PDFBibtex ]
[26] journal
Erwan Bigan, Loïc Paulevé, Jean-Marc Steyaert, and Stéphane Douady. Necessary and sufficient conditions for protocell growth. Journal of Mathematical Biology, pages 1–38, 2016.
DOI:10.1007/s00285-016-0998-0Bibtex ]
[25] conference
Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, and Carito Guziolowski. Boolean Network Identification from Multiplex Time Series Data. In CMSB 2015 - 13th conference on Computational Methods for Systems Biology, volume 9308 of Lecture Notes in Computer Science, 170–181. Springer International Publishing, 2015.
DOI:10.1007/978-3-319-23401-4_15PDFBibtex ]
[24] journal
Maxime Folschette, Loïc Paulevé, Morgan Magnin, and Olivier Roux. Sufficient conditions for reachability in automata networks with priorities. Theoretical Computer Science, 608, Part 1, From Computer Science to Biology and Back:66 – 83, 2015.
DOI:10.1016/j.tcs.2015.08.040PDFBibtex ]
[23] journalfr
Loïc Paulevé, Maxime Folschette, Morgan Magnin, and Olivier Roux. Analyses statiques de la dynamique des réseaux d'automates indéterministes. Technique et Science Informatiques (TSI), 34(4):463–484, 2015.
DOI:10.3166/TSI.34.463-484PDFBibtex ]
[22] journal
Jorgelindo da Vega Moreira, Sabine Peres, Jean-Marc Steyaert, Erwan Bigan, Loïc Paulevé, Marcel Levy Nogeira, and Laurent Schwartz. Cell cycle progression is regulated by intertwined redox oscillators. Theoretical Biology and Medical Modelling, 12(1):10, 2015.
DOI:10.1186/s12976-015-0005-2Bibtex ]
[SASB2014] edition
Loïc Paulevé and Heinz Koeppl, editors. 5th International Workshop on Static Analysis and Systems Biology (SASB 2014), volume 316 of Electronic Notes in Theoretical Computer Science, Munich, Germany, September 2015. Elsevier.
URLBibtex ]
[21] journal
Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Identification of Biological Regulatory Networks from Process Hitting models. Theoretical Computer Science, 568(0):49 – 71, 2015.
DOI:10.1016/j.tcs.2014.12.002Bibtex ]
[20] chapter
Loïc Paulevé, Courtney Chancellor, Maxime Folschette, Morgan Magnin, and Olivier Roux. Logical Modeling of Biological Systems, chapter Analyzing Large Network Dynamics with Process Hitting, pages 125 – 166. Wiley, 2014.
PDFURLBibtex ]
[19] conference
Thomas Chatain, Stefan Haar, Loïg Jezequel, Loïc Paulevé, and Stefan Schwoon. Characterization of reachable attractors using Petri net unfoldings. In Computational Methods in Systems Biology, volume 8859 of Lecture Notes in Computer Science, pages 129–142. Springer Berlin Heidelberg, Cham, 2014.
DOI:10.1007/978-3-319-12982-2_10PDFBibtex ]
[18] conference
Michael Klann, Loïc Paulevé, Tatjana Petrov, and Heinz Koeppl. Coarse-grained brownian dynamics simulation of rule-based models. In Ashutosh Gupta and Thomas Henzinger, editors, The 11th Conference on Computational Methods in Systems Biology (CMSB'13), volume 8130 of Lecture Notes in Computer Science, pages 64–77. Springer Berlin Heidelberg, 2013.
DOI:10.1007/978-3-642-40708-6_6PDFURLBibtex ]
[17] journal
Loïc Paulevé, Gheorghe Craciun, and Heinz Koeppl. Dynamical Properties of Discrete Reaction Networks. Journal of Mathematical Biology, 69(1):55–72, 2014.
DOI:10.1007/s00285-013-0686-2arXiv:1302.3363Bibtex ]
[16] conference
Loïc Paulevé, Geoffroy Andrieux, and Heinz Koeppl. Under-approximating cut sets for reachability in large scale automata networks. In Computer Aided Verification (CAV), volume 8044 of Lecture Notes in Computer Science, pages 69–84. Springer Berlin Heidelberg, Berlin, Heidelberg, 2013.
DOI:10.1007/978-3-642-39799-8_4PDFBibtex ]
[15] conference
Maxime Folschette, Loïc Paulevé, Morgan Magnin, and Olivier Roux. Under-approximation of reachability in multivalued asynchronous networks. Electronic Notes in Theoretical Computer Science, 299:33 – 51, 2013. 4th International Workshop on Interactions between Computer Science and Biology (CS2Bio'13).
DOI:10.1016/j.entcs.2013.11.004PDFBibtex ]
[TR-TMP-12] report
Araks Martirosyan, Loïc Paulevé, Clair Poignard, Mireille Régnier, Jean-Marc Steyaert, and Laurent Schwartz. A Dynamical Model for the Transmembrane Potential Regulation by pH. Technical Report hal-00769446, Inria Saclay-Île-de-France, September 2012.
URLBibtex ]
[TR-PHvsPN-12] report
Loïc Paulevé, Morgan Magnin, and Olivier Roux. From the Process Hitting to Petri Nets and Back. Technical Report hal-00744807, ETH Zürich, October 2012.
URLBibtex ]
[14] conference
Patrick Amar and Loïc Paulevé. Hsim: a hybrid stochastic simulation system for systems biology. Electronic Notes in Theoretical Computer Science, 313(0):3 – 21, 2012. 3rd International Workshop on Static Analysis and Systems Biology (SASB 2012).
DOI:10.1016/j.entcs.2015.04.016Bibtex ]
[13] conference
Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Concretizing the process hitting into biological regulatory networks. In David Gilbert and Monika Heiner, editors, Computational Methods in Systems Biology, Lecture Notes in Computer Science, pages 166–186. Springer Berlin Heidelberg, 2012.
DOI:10.1007/978-3-642-33636-2_11Bibtex ]
[12] conference
Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin, and Olivier Roux. Abducing biological regulatory networks from process hitting models. In ECML-PKDD 2012 Workshop on Learning and Discovery in Symbolic Systems Biology. Bristol, United Kingdom, 2012.
URLBibtex ]
[11] workshop
Stefan Janssen, Loïc Paulevé, Yann Ponty, Balaji Raman, and Matthias Zytnicki. Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space? In IWBDA - 4th International Workshop on Bio-Design Automation - 2012. San Francisco, États-Unis, 2012.
URLBibtex ]
[10] journal
Loïc Paulevé, Morgan Magnin, and Olivier Roux. Static analysis of biological regulatory networks dynamics using abstract interpretation. Mathematical Structures in Computer Science, 22(04):651–685, 2012.
DOI:10.1017/S0960129511000739Bibtex ]
[9] journal
Matthew R. Lakin, Loïc Paulevé, and Andrew Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science, 431:181 – 206, 2012.
DOI:10.1016/j.tcs.2011.12.057Bibtex ]
[PhD] thesis
Loïc Paulevé. Modélisation, Simulation et Vérification des Grands Réseaux de Régulation Biologique. PhD thesis, École Centrale de Nantes, 2011.
URLBibtex ]
[8] conference
Loïc Paulevé and Adrien Richard. Static analysis of boolean networks based on interaction graphs: a survey. Electronic Notes in Theoretical Computer Science, 284:93 – 104, 2011. Proceedings of The Second International Workshop on Static Analysis and Systems Biology (SASB 2011).
DOI:10.1016/j.entcs.2012.05.017Corrected PDFBibtex ]
[7] journal
Loïc Paulevé, Morgan Magnin, and Olivier Roux. Tuning Temporal Features within the Stochastic π-Calculus. IEEE Transactions on Software Engineering, 37(6):858–871, 2011.
DOI:10.1109/TSE.2010.95Bibtex ]
[6] invited
Andrew Phillips, Matthew Lakin, and Loïc Paulevé. Stochastic simulation of process calculi for biology. In Gabriel Ciobanu and Maciej Koutny, editors, Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi 2010, volume 40 of EPTCS, 1 – 5. 2010. invited paper.
DOI:10.4204/EPTCS.40.1Bibtex ]
[5] conference
Loïc Paulevé, Morgan Magnin, and Olivier Roux. Abstract Interpretation of Dynamics of Biological Regulatory Networks. Electronic Notes in Theoretical Computer Science, 272:43–56, 2011. Proceedings of The First International Workshop on Static Analysis and Systems Biology (SASB 2010).
DOI:10.1016/j.entcs.2011.04.004Bibtex ]
[4] journal
Loïc Paulevé and Adrien Richard. Topological Fixed Points in Boolean Networks. Comptes Rendus de l'Académie des Sciences - Series I - Mathematics, 348(15-16):825 – 828, 2010.
DOI:10.1016/j.crma.2010.07.014PDFBibtex ]
[3] conference
Loïc Paulevé, Simon Youssef, Matthew R. Lakin, and Andrew Phillips. A generic abstract machine for stochastic process calculi. In CMSB '10: Proceedings of the 8th International Conference on Computational Methods in Systems Biology, 43–54. New York, NY, USA, 2010. ACM.
DOI:10.1145/1839764.1839771Bibtex ]
[2] journal
Loïc Paulevé, Morgan Magnin, and Olivier Roux. Refining dynamics of gene regulatory networks in a stochastic π-calculus framework. In Transactions on Computational Systems Biology XIII, volume 6575 of Lecture Notes in Comp Sci, pages 171–191. Springer, 2011.
DOI:10.1007/978-3-642-19748-2_8Corrected PDFBibtex ]
[1] journal
Loïc Paulevé, Hervé Jégou, and Laurent Amsaleg. Locality sensitive hashing: a comparison of hash function types and querying mechanisms. Pattern Recognition Letters, 31(11):1348 – 1358, 2010.
DOI:10.1016/j.patrec.2010.04.004Bibtex ]
[Master] thesis
Loïc Paulevé. Euclidean lattices for high dimensional indexing and searching. Research Report, IRISA, 2008.
URLBibtex ]

Co-authors

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