Kyungduk Moon, Kangbok Lee, and Loïc Paulevé.
Computational complexity of minimal trap spaces in Boolean networks.
SIAM Journal on Discrete Mathematics, 38(4):2691–2708, 2024.
[ DOI:10.1137/23M1553248
| PDF
| Bibtex ]
Elisa Tonello and Loïc Paulevé.
Phenotype control and elimination of variables in Boolean networks.
Peer Community Journal, 2024.
[ DOI:10.24072/pcjournal.452
| Bibtex ]
Gustavo Magaña López, Laurence Calzone, Andrei Zinovyev, and Loïc Paulevé.
scBoolSeq: Linking scRNA-Seq Statistics and Boolean Dynamics.
PLOS Computational Biology, 20(7):1–25, 07 2024.
[ DOI:10.1371/journal.pcbi.1011620
| Bibtex ]
Philippe Dague, Laurent Muller, Loïc Paulevé, and Marc Irigoin-Guichandut.
Towards a qualitative theory of the interruption of eating behavior change.
Journal of Theoretical Biology, 581:111731, 2024.
[ DOI:10.1016/j.jtbi.2024.111731
| Bibtex ]
Loïc Paulevé.
Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis .
Peer Community Journal, 2023.
[ DOI:10.24072/pcjournal.255
| URL
| Bibtex ]
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, and Anne Siegel.
MERRIN: MEtabolic regulation rule INference from time series data.
Bioinformatics, 38(Supplement_2):ii127–ii133, 2022.
[ DOI:10.1093/bioinformatics/btac479
| PDF
| Bibtex ]
Bilal Shaikh, Lucian P Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S Andrews, Azraf Anwar, Moritz E Beber, Frank T Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G Bard Ermentrout, James R Faeder, Andrew P Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C Ison, Diego Jahn, Henry V Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Rahuman S Malik Sheriff, Synchon Mandal, Robert McDougal, J Kyle Medley, Pedro Mendes, Robert Müller, Chris J Myers, Aurelien Naldi, Tung V N Nguyen, David P Nickerson, Brett G Olivier, Drashti Patoliya, Loïc Paulevé, Linda R Petzold, Ankita Priya, Anand K Rampadarath, Johann M Rohwer, Ali S Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P Goldberg, James C Schaff, Michael L Blinov, Herbert M Sauro, Ion I Moraru, and Jonathan R Karr.
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Research, 50(W1):W108–W114, 2022.
[ DOI:10.1093/nar/gkac331
| Bibtex ]
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/s12859-021-04158-9
| Bibtex ]
Loïc Paulevé, Juraj Kolčák, Thomas Chatain, and Stefan Haar.
Reconciling qualitative, abstract, and scalable modeling of biological networks.
Nature Communications, 2020.
[ DOI:10.1038/s41467-020-18112-5
| Bibtex ]
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/s11047-019-09748-4
| PDF
| Bibtex ]
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.2019.2914383
| PDF
| Bibtex ]
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.1006538
| Bibtex ]
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.2018.00787
| Bibtex ]
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.2018.00680
| Bibtex ]
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.2018.03.009
| PDF
| Bibtex ]
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.2017.2749225
| PDF
| Bibtex ]
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/s13015-017-0110-3
| Bibtex ]
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.2016.0533
| PDF
| Bibtex ]
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.2016.07.009
| PDF
| Bibtex ]
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/s12918-016-0285-0
| PDF
| Bibtex ]
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/metabo6040033
| PDF
| Bibtex ]
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/s00285-016-0998-0
| Bibtex ]
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.2015.08.040
| PDF
| Bibtex ]
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/s12976-015-0005-2
| Bibtex ]
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.2014.12.002
| Bibtex ]
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/s00285-013-0686-2
| arXiv:1302.3363
| Bibtex ]
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/S0960129511000739
| Bibtex ]
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.2011.12.057
| Bibtex ]
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.2010.95
| Bibtex ]
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.2010.07.014
| PDF
| Bibtex ]
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_8
| Corrected PDF
| Bibtex ]
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.2010.04.004
| Bibtex ]
Loïc Paulevé.
Prédire le comportement des cellules avec la modélisation booléenne.
Interstices, 2021.
[ PDF
| URL
| Bibtex ]
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.34.463-484
| PDF
| Bibtex ]
Stéphanie Chevalier, Déborah Boyenval, Gustavo Magaña López, Théo Roncalli, Athénaïs Vaginay, and Loïc Paulevé.
BoNesis: a Python-based declarative environment for the verification, reprogramming, and synthesis of Most Permissive Boolean networks.
In 22th International Conference on Computational Methods in Systems Biology (CMSB 2024), LNCS. Pisa, Italy, 2024. Springer.
[ DOI:10.1007/978-3-031-71671-3_6
| PDF
| Bibtex ]
Kerian Thuillier, Anne Siegel, and Loïc Paulevé.
CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems.
In AAAI 2024 - The 38th Annual AAAI Conference on Artificial Intelligence, 1–8. Vancouver, Canada, 2024.
[ DOI:10.1609/aaai.v38i8.28654
| PDF
| Supplement
| Bibtex ]
Sara Riva, Jean-Marie Lagniez, Gustavo Magaña López, and Loïc Paulevé.
Tackling universal properties of minimal trap spaces of Boolean networks.
In Computational Methods in Systems Biology, 157–174. Cham, 2023. Springer Nature Switzerland.
[ DOI:10.1007/978-3-031-42697-1_11
| arXiv:2305.02442
| Bibtex ]
Elisa Tonello and Loïc Paulevé.
Attractor identification in asynchronous Boolean dynamics with network reduction.
In Computational Methods in Systems Biology, 202–219. Cham, 2023. Springer Nature Switzerland.
[ DOI:10.1007/978-3-031-42697-1_14
| arXiv:2305.01327
| Bibtex ]
Giann Karlo Aguirre-Samboní, Stefan Haar, Loïc Paulevé, Stefan Schwoon, and Nick Würdemann.
Avoid One's Doom: Finding Cliff-Edge Configurations in Petri Nets.
In GandALF 2022: Games, Automata, Logics, and Formal Verification. Madrid, Spain, 2022.
[ DOI:10.4204/EPTCS.370.12
| PDF
| Bibtex ]
Théo Roncalli and Loïc Paulevé.
Variable-Depth Simulation of Most Permissive Boolean Networks.
In 20th International Conference on Computational Methods in Systems Biology (CMSB 2022), LNCS. Bucharest, Romania, 2022. Springer.
[ DOI:10.1007/978-3-031-15034-0_7
| PDF
| Bibtex ]
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, volume 12881 of Lecture Notes in Computer Science, 159–180. Bordeaux, France, 2021. Springer.
[ DOI:10.1007/978-3-030-85633-5_10
| PDF
| URL
| Bibtex ]
Loïc Paulevé and Sylvain Sené.
Non-deterministic updates of Boolean networks.
In 27th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems (AUTOMATA 2021), volume 90 of Open Access Series in Informatics (OASIcs), 10:1–10:16. Dagstuhl, Germany, 2021. Schloss Dagstuhl – Leibniz-Zentrum für Informatik.
[ DOI:10.4230/OASIcs.AUTOMATA.2021.10
| PDF
| Bibtex ]
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_11
| PDF
| Bibtex ]
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_17
| PDF
| URL
| Bibtex ]
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_8
| PDF
| Bibtex ]
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.2019.00014
| PDF
| Bibtex ]
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_1
| PDF
| Bibtex ]
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_26
| PDF
| Bibtex ]
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_3
| PDF
| Bibtex ]
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.2017.18
| PDF
| Bibtex ]
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_11
| PDF
| Bibtex ]
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_20
| PDF
| Bibtex ]
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.
[ PDF
| Bibtex ]
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_8
| PDF
| Bibtex ]
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_16
| PDF
| Bibtex ]
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.2018.03.009
| PDF
| URL
| Bibtex ]
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.
[ PDF
| URL
| Bibtex ]
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_15
| PDF
| Bibtex ]
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_10
| PDF
| Bibtex ]
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_6
| PDF
| URL
| Bibtex ]
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_4
| PDF
| Bibtex ]
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.2013.11.004
| PDF
| Bibtex ]
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.2015.04.016
| Bibtex ]
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_11
| Bibtex ]
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.
[ URL
| Bibtex ]
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.2012.05.017
| Corrected PDF
| Bibtex ]
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.2011.04.004
| Bibtex ]
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:10.1145/1839764.1839771
| Bibtex ]
Loïc Paulevé and Sylvain Sené.
Boolean networks and their dynamics: the impact of updates.
In Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools.
Wiley, 2022.
[ PDF
| URL
| Bibtex ]
Loïc Paulevé.
Réseaux booléens : formalisme, sémantiques, et complexité.
In Approches symboliques de la modélisation et de l'analyse des systèmes biologiques.
ISTE Editions, 2022.
[ URL
| Bibtex ]
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.
[ PDF
| URL
| Bibtex ]
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.
[ PDF
| URL
| Bibtex ]
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.
[ URL
| Bibtex ]
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.
[ URL
| Bibtex ]
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.
[ URL
| Bibtex ]
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.
[ URL
| Bibtex ]
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.40.1
| Bibtex ]
Loïc Paulevé and Philippe Dague.
Journées BIOSS-IA 2017.
July 2017.
Bulletin 97 de l'AFIA - Association française pour l'Intelligence Artificielle.
[ PDF
| URL
| Bibtex ]
Stéphanie Chevalier, Julia Becker, Yujuan Gui, Vincent Noël, Cui Su, Sascha Jung, Laurence Calzone, Andrei Zinovyev, Antonio del Sol, Jun Pang, Lasse Sinkkonen, Thomas Sauter, and Loïc Paulevé.
Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming.
bioRxiv, 2024.
[ DOI:10.1101/2024.10.21.618706
| Bibtex ]
Loïc Paulevé and Cedric Gaucherel.
Inference of ecological networks and possibilistic dynamics based on Boolean networks from observations and prior knowledge.
bioRxiv, 2024.
[ DOI:10.1101/2024.07.01.601264
| Bibtex ]
Maximilien Gadouleau, Loïc Paulevé, and Sara Riva.
Bringing memory to Boolean networks: a unifying framework.
arXiv, 2024.
[ arXiv:2404.03553
| Bibtex ]
Van-Giang Trinh, Belaid Benhamou, and Loïc Paulevé.
mpbn: a simple tool for efficient edition and analysis of elementary properties of Boolean networks.
arXiv, 2024.
[ arXiv:2403.06255
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Thomas Chatain, Stefan Haar, Juraj Kolčák, and Loïc Paulevé.
Most Permissive Semantics of Boolean Networks.
Technical Report, arXiv, 2020.
[ arXiv:1808.10240
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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.
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Loïc Paulevé, Morgan Magnin, and Olivier Roux.
From the Process Hitting to Petri Nets and Back.
Technical Report hal-00744807, ETH Zürich, October 2012.
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Loïc Paulevé.
Réseaux booléens : méthodes formelles et outils pour la modélisation en biologie.
Habilitation à diriger des recherches, Université Paris-Saclay, 2020.
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Loïc Paulevé.
Modélisation, Simulation et Vérification des Grands Réseaux de Régulation Biologique.
PhD thesis, École Centrale de Nantes, 2011.
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Loïc Paulevé.
Euclidean lattices for high dimensional indexing and searching.
Research Report, IRISA, 2008.
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