Loïc Paulevé's HomePage

Publications

By publication type (show by chronological order)

International Journals

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, 2018. In press.
DOI:10.3389/fphys.2018.00787Bibtex ]

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, 2018.
DOI:10.3389/fphys.2018.00680PDFBibtex ]

Juraj Kolčák, David Šafránek, Stefan Haar, and Loïc Paulevé. Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks. Theoretical Computer Science, 2018. In press.
PDFBibtex ]

Loïc Paulevé. Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017. In press.
DOI:10.1109/TCBB.2017.2749225PDFBibtex ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

French-speaking Journals

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 ]

International Conferences and Workshops (full-paper selection)

Thomas Chatain, Stefan Haar, and Loïc Paulevé. Boolean Networks: Beyond Generalized Asynchronicity. In AUTOMATA 2018, Lecture notes in computer science. Ghent, Belgium, 2018. Springer.
PDFURLBibtex ]

Thomas Chatain and Loïc Paulevé. Goal-Driven Unfolding of Petri Nets. In Roland Meyer and Uwe Nestmann, editors, 28th International Conference on Concurrency Theory (CONCUR 2017), volume 85 of Leibniz International Proceedings in Informatics (LIPIcs), 18:1–18:16. Dagstuhl, Germany, 2017. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik.
DOI:10.4230/LIPIcs.CONCUR.2017.18PDFURLBibtex ]

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_11PDFURLBibtex ]

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_20PDFURLBibtex ]

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 ]

Hugues Mandon, Stefan Haar, and Loïc Paulevé. Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph. In Eugenio Cinquemani and Alexandre Donzé, editors, Hybrid Systems Biology: 5th International Workshop, HSB 2016, Grenoble, France, October 20-21, 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 ]

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 ]

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 ]

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 ]

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. Nantes, France, September 2015. Springer International Publishing.
DOI:10.1007/978-3-319-23401-4_15PDFBibtex ]

Thomas Chatain, Stefan Haar, Loïg Jezequel, Loïc Paulevé, and Stefan Schwoon. Characterization of reachable attractors using Petri net unfoldings. In Pedro Mendes, Joseph Dada, and Kieran Smallbone, editors, 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 ]

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 ]

Loïc Paulevé, Geoffroy Andrieux, and Heinz Koeppl. Under-approximating cut sets for reachability in large scale automata networks. In Natasha Sharygina and Helmut Veith, editors, Computer Aided Verification, 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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

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 ]

Book chapters

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 ]

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 ]

Edited Proceedings

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 ]

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 ]

Workshops (abstract selection)

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 ]

Posters (abstract selection)

Loïc Paulevé. Pint, a static analyzer for dynamics of Automata Networks. 14th International Conference on Computational Methods in Systems Biology (CMSB 2016), September 2016. \url http://loicpauleve.name/pint.
PDFBibtex ]

Adrien Rougny, Christine Froidevaux, and Loïc Paulevé. Two Qualitative Dynamics Semantics for SBGN Process Description Maps. CMSB'15, September 2015. Poster.
PDFBibtex ]

Araks Martirosyan, Loïc Paulevé, Clair Poignard, Frédéric Campion, Mireille Régnier, Jean-Marc Steyaert, and Laurent Schwartz. A dynamical model for the transmembrane potential regulation by pH. RECOMB Conference on Regulatory and Systems Genomics, 2012. poster.
Bibtex ]

Invited Papers

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 ]

Other publications

Loïc Paulevé and Philippe Dague. Journées BIOSS-IA 2017. July 2017. Bulletin 97 de l'AFIA - Association française pour l'Intelligence Artificielle.
PDFURLBibtex ]

Reports

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 ]

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 ]

Loïc Paulevé. Modélisation, Simulation et Vérification des Grands Réseaux de Régulation Biologique. PhD thesis, École Centrale de Nantes, 2011.
URLBibtex ]

Loïc Paulevé. Euclidean lattices for high dimensional indexing and searching. Research Report, IRISA, 2008.
URLBibtex ]

Co-authors

(by date/name)