Jérôme Feret
Chargé de recherche
79
Documents
Présentation
Jérôme Feret est Chargé de Recherche INRIA dans l'équipe projet Antique.
Il s'intéresse à l'analyse statique, notamment, à ses applications dans la certification des systèmes critiques embarqués et dans l'étude des modèles en biologie des systèmes.
Jérôme Feret est coauteur des logiciels [ASTREE](https://www.astreea.ens.fr/) et [Kappa](https://www.kappalanguage.org/).
Jérôme Feret is a research fellow at INRIA in the project team Antique.
He is interested in Static Analysis.
He is focussing on application to the certification of critical embedded systems and the studies of models in Systems Biology.
Jérôme Feret is coautor of the following software: [ASTREE](https://www.astreea.ens.fr/) and [Kappa](https://www.kappalanguage.org/).
Domaines de recherche
Bio-Informatique, Biologie Systémique [q-bio.QM]
Informatique et langage [cs.CL]
Publications
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The Kappa platform for rule-based modelingBioinformatics, 2018, Bioinformatics, 34 (13), pp.i583-i592. ⟨10.1093/bioinformatics/bty272⟩
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Local Traces: An Over-Approximation of the Behavior of the Proteins in Rule-Based ModelsIEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, 15 (4), pp.1124-1137. ⟨10.1109/TCBB.2018.2812195⟩
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Formal Derivation of Qualitative Dynamical Models from Biochemical NetworksBioSystems, 2016, pp.100. ⟨10.1016/j.biosystems.2016.09.001⟩
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Static Analysis and Verification of Aerospace Software by Abstract InterpretationFoundations and Trends in Programming Languages, 2015, 2 (2-3), pp.171-291. ⟨10.1561/2500000002⟩
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hal-01312241v1
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Stochastic FragmentsInternational Journal of Software and Informatics (IJSI), 2014, Special Issue on DCM09, 7 (4), pp.527-604
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Stochastic fragments: A framework for the exact reduction of the stochastic semantics of rule-based modelsInternational Journal of Software and Informatics (IJSI), 2014, Special issue of DCM'09, 7 (4), pp.527-604
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Lumpability Abstractions of Rule-based SystemsTheoretical Computer Science, 2012, Modelling and Analysis of Biological Systems -- Based on papers presented at the Workshop on Membrane Computing and Bio-logically Inspired Process Calculi (MeCBIC) held in 2008 (Iasi), 2009 (Bologna) and 2010 (Jena), 431, pp.137-164. ⟨10.1016/j.tcs.2011.12.059⟩
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Combinatorial complexity and compositional drift in protein interaction networks.PLoS ONE, 2012, 7 (3), ⟨10.1371/journal.pone.0032032⟩
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Intrinsic Information carriers in combinatorial dynamical systemsChaos: An Interdisciplinary Journal of Nonlinear Science, 2010, 20 (3), pp.037108. ⟨10.1063/1.3491100⟩
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Rule-Based Modelling and Model PerturbationTransactions on Computational Systems Biology, 2009, Transactions on Computational Systems Biology XI, 5750, pp.116-137. ⟨10.1007/978-3-642-04186-0_6⟩
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inria-00528364v1
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Why does Astrée scale up?Formal Methods in System Design, 2009, Special issue on Numerical Software Verification, 35 (3), pp.229-264. ⟨10.1007/s10703-009-0089-6⟩
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inria-00528582v1
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Internal coarse-graining of molecular systemsProceedings of the National Academy of Sciences of the United States of America, 2009, 106 (16), ⟨10.1073/pnas.0809908106⟩
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inria-00528330v1
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Abstract Interpretation of Mobile SystemsJournal of Logic and Algebraic Programming, 2004, special issue on the pi-calcucus, 63 (1), pp.59--130. ⟨10.1016/j.jlap.2004.01.005⟩
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inria-00527910v1
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Symbolic transformation of expressions in modular arithmeticStatic Analysis: 30th International Symposium, SAS 2023, Oct 2023, Cascais, Portugal
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A Semantics of Core Erlang with Handling of SignalsErlang 2023 - 22nd ACM SIGPLAN International Workshop on Erlang, Sep 2023, Seattle WA, United States. pp.31-38, ⟨10.1145/3609022.3609417⟩
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Distinguishing Context Dependent Events in Quotients of Causal StoriesJOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Sophie Schbath; Denis Thieffry, Jul 2021, Virtuel, France. pp.54-61
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Sharing Ghost Variables in a Collection of Abstract DomainsVMCAI 2020 - 21st International Conference on Verification, Model Checking, and Abstract Interpretation, Jan 2020, New Orleans, LA, United States
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Counters in Kappa: Semantics, Simulation, and Static AnalysisESOP 2019 - 28th European Symposium on Programming, Apr 2019, Prague, Czech Republic. pp.176-204, ⟨10.1007/978-3-030-17184-1_7⟩
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Proving the absence of unbounded polymers in rule-based modelsStatic Analysis and Systems Biology 2018, Aug 2018, Freiburg im Breisgau, Germany
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KaSa: A Static Analyzer for KappaCMSB 2018 - 16th International Conference on Computational Methods in Systems Biology, Sep 2018, Brno, Czech Republic. pp.285-291, ⟨10.1007/978-3-319-99429-1_17⟩
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Tropical Abstraction of Biochemical Reaction Networks with GuaranteesSASB'18 - Static Analysis in Systems Biology, affiliated with Static Analysis Symposium, Aug 2018, Freiburg, Germany
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KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models CMSB 2017 - 15th Conference on Computational Methods in Systems Biology, Heinz Koeppl, Sep 2017, Darmstadt, Germany. pp.291-299, ⟨10.1007/978-3-319-67471-1_18⟩
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Using alternated sums to express the occurrence number of extended patterns in site-graphsSASB 2017 - The Eighth International Workshop on Static Analysis for Systems Biology, Aug 2017, New York, United States. pp.18
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Finding All Potential Run-Time Errors and Data Races in Automotive SoftwareWCX™ 2017 - SAE World Congress Experience, Apr 2017, Detroit United States. pp.1-9, ⟨10.4271/2017-01-0054⟩
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Local traces: an over-approximation of the behaviour of the proteins in rule-based modelsCMSB 2016 - Fourteenth Conference on Computational Method in Systems Biology, Sep 2016, Cambridge, United Kingdom. pp.116-131, ⟨10.1007/978-3-319-45177-0_8⟩
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Reachability analysis via orthogonal sets of patterns7th International Workshop on Static Analysis and Systems Biology, (SASB 2016), David Safranek; Guido Sanguinetti, Sep 2016, Edinburgh, United Kingdom
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Taking Static Analysis to the Next Level: Proving the Absence of Run-Time Errors and Data Races with Astrée8th European Congress on Embedded Real Time Software and Systems (ERTS 2016), Jan 2016, Toulouse, France
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Derivation of Qualitative Dynamical Models from Biochemical NetworksCMSB 2015 : Computational Methods in Systems Biology, Olivier Roux; Jérémie Bourdon, Sep 2015, Nantes, France. pp.195-207, ⟨10.1007/978-3-319-23401-4_17⟩
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Le suivi de la contamination des écosystèmes par les pesticides OPA-C : un dispositif de bassins versants instrumentés aux Antilles44. Congrès du Groupe Français des Pesticides : "Protection des cultures et santé environmentale : héritages et conceptions nouvelles", Groupe Français des Pesticides (GFP). FRA.; Université des Antilles et de la Guyane (UAG). Schoelcher, FRA.; Institut de Recherche pour le Développement (IRD). FRA., 2014, Schoelcher, Martinique, France
Communication dans un congrès
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An Algebraic Approach for Inferring and Using Symmetries in Rule-based ModelsStatic Analysis and Systems Biology, Heinz Koeppl; Loïc Paulevé, Sep 2014, Munich, Germany. pp.20, ⟨10.1016/j.entcs.2015.06.010⟩
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Context-sensitive flow analyses: a hierarchy of model reductionsCMSB - 11th Conference on Computational Methods in Systems Biology - 2013, Ashutosh Gupta and Thomas A. Henzinger, Sep 2013, Klosterneuburg, Austria. pp.220-233, ⟨10.1007/978-3-642-40708-6_17⟩
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Reconstructing Species-Based Dynamics from Reduced Stochastic Rule-Based Models.WSC - Winter Simulation Conference - 2012, Dec 2012, Berlin, Germany
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Graphs, Rewriting and Pathway Reconstruction for Rule-Based ModelsFSTTCS 2012 - IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Dec 2012, Hyderabad, India. pp.276-288, ⟨10.4230/LIPIcs.FSTTCS.2012.276⟩
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Formal reduction for rule-based modelsthe 27th Conference on the Mathematical Foundations of Programming Semantics - MFPS 2011, May 2011, Pittsburgh, United States. pp.29-59, ⟨10.1016/j.entcs.2011.09.014⟩
Communication dans un congrès
inria-00636850v1
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Formal Model ReductionStatic Analysis Symposium, Sep 2011, Venice, Italy. pp.6, ⟨10.1007/978-3-642-23702-7_5⟩
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inria-00626640v1
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Static Analysis and Verification of Aerospace Software by Abstract InterpretationAmerican Institute of Aeronautics and Astronautics - AIAA Infotech@Aerospace 2010, Apr 2010, Atlanta, United States
Communication dans un congrès
inria-00528611v1
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Lumpability Abstractions of Rule-based SystemsThe 4th Workshop on Membrane Computing and Biologically Inspired Process Calculi - MeCBIC 2010, Ciobanu, G. and Koutny, M., Aug 2010, Jena, Germany
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inria-00527971v1
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Automatic reduction of stochastic rules-based models in a nutshellInternational Conference of Numerical Analysis and Applied Mathematics - ICNAAM 2010, Sep 2010, Rhodos, Greece. pp.1330-1334, ⟨10.1063/1.3497965⟩
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Abstracting the differential semantics of rule-based models: exact and automated model reductionLogic in Computer Science, 2010, Edinburgh, United Kingdom. pp.362-381
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Combining Model Reductionsthe 26th Conference on the Mathematical Foundations of Programming Semantics - MFPS 2010, May 2010, Ottawa, Canada. pp.73--96, ⟨10.1016/j.entcs.2010.08.006⟩
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Astree: Proving the Absence of Runtime ErrorsEmbedded real time software and systems - ERTS2 2010, AAAF, SEE, SIA, May 2010, Toulouse, France
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Fragments-based model reduction: some case studiesFirst International Workshop on Interactions between Computer Science and Biology - CS2Bio 2010, Jun 2010, Amsterdam, Netherlands
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Static Analysis by Abstract Interpretation of Embedded Critical Softwarethe 3rd IEEE International workshop UML and Formal Methods, Nov 2010, Shangai, China
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Space Software Validation using Abstract InterpretationThe International Space System Engineering Conference : Data Systems in Aerospace - DASIA 2009, EUROSPACE, May 2009, Istambul, Turkey. pp.1-7
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Astrée: Nachweis der Abwesenheit von Laufzeitfehlern.Workshop "Entwicklung zuverlässiger Software-Systeme", Jun 2009, Regensburg, Germany
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Investigation of a biological repair schemethe 9th Workshop on Membrane Computing - WMC9, Paun, G., Jul 2008, Edinburgh, United Kingdom. pp.1-12, ⟨10.1007/978-3-540-95885-7_1⟩
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Rule-based modelling, symmetries, refinementsthe 1st International Workshop, Formal Methods in Systems Biology - FMSB 2008, Jasmin Fisher, Jun 2008, Cambridge, United Kingdom. pp.103-122, ⟨10.1007/978-3-540-68413-8_8⟩
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Abstract Interpretation of Cellular Signalling Networksthe 9th International Conference on Verification, Model Checking and Abstract Interpretation - VMCAI'08, Jan 2008, San Francisco, United States. pp.83-97, ⟨10.1007/978-3-540-78163-9_11⟩
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inria-00528352v1
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Scalable Simulation of Cellular Signaling Networksthe 5th Asian Symposium on Programming Languages and Systems - APLAS'07, Shao, Z., Nov 2007, Singapore, Singapore. pp.139-157, ⟨10.1007/978-3-540-76637-7_10⟩
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inria-00528409v1
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Reachability analysis of biological signalling pathways by abstract interpretationthe International Conference of Computational Methods in Sciences and Engineerin - ICCMSE2007, T.E. Simos, Sep 2007, Corfu, Greece. pp.619 - 622, ⟨10.1063/1.2836158⟩
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Rule-based modelling of cellular signallingInternational Conference on Concurrency Theory (CONCUR'07), Sep 2007, Portugal
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Combination of Abstractions in the ASTRÉE Static Analyzerthe 11th Annual Asian Computing Science Conference - ASIAN'06, Okada, Mitsu and Satoh, Ichir, Dec 2006, Tokyo, Japan. pp.272-300, ⟨10.1007/978-3-540-77505-8_23⟩
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inria-00528571v1
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The Arithmetic-Geometric Progression Abstract Domainthe 6th International Conference on Verification, Model Checking and Abstract Interpretation - VMCAI 2005, Radhia Cousot, Jan 2005, Paris, France. pp.42-58, ⟨10.1007/978-3-540-30579-8_3⟩
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Static Analysis of Digital Filtersthe 13th European Symposium on Programming - ESOP 2004, David A. Schmidt, Mar 2004, Barcelona, Spain. pp.33-48, ⟨10.1007/978-3-540-24725-8_4⟩
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A Static Analyzer for Large Safety-Critical Software2003, pp.196 - 207, ⟨10.1145/781131.781153⟩
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Dependency analysis of Mobile Systemsthe European Symposium on Programming (ESOP'02), Apr 2002, Grenoble, France. pp.314--330, ⟨10.1007/3-540-45927-8_22⟩
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Abstract Interpretation-Based Static Analysis of Mobile Ambientsthe 8th International Symposium on Static Analysis (SAS'01), Jul 2001, Paris, France. pp.413--431, ⟨10.1007/3-540-47764-0_24⟩
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Occurrence counting analysis for the pi-calculusGEometry and Topology in COncurrency theory (Satellite Workshop from CONCUR 2000), Eric Goubault, Aug 2000, University Park, United States. pp.1--18, ⟨10.1016/S1571-0661(05)01155-2⟩
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Confidentiality Analysis of Mobile Systemshe 7th International Symposium on Static Analysis (SAS'00), J. Palsberg, Jun 2000, Santa Barbara, United States. pp.135--154, ⟨10.1007/978-3-540-45099-3_8⟩
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Modelling hepatic stellate cells activation by TGFB1 using Kappa language2021, pp.1-23
Autre publication scientifique
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Analyse statique et réduction de modèles de voies de signalisation intracellulaireInformatique Mathématique Une photographie en 2023, CNRS, pp.67, 2023
Chapitre d'ouvrage
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The rule-based model approach. A Kappa model for hepatic stellate cells activation by TGFB1Elisabetta De Maria. Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools, Wiley, pp.1-76, 2022, 978-1-119-71653-2
Chapitre d'ouvrage
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Analyses des motifs accessibles dans les modèles KappaCédric Lhoussaine et Élisabeth Remy. Approches symboliques de la modélisation et de l’analyse des systèmes biologiques, ISTE, 2022, 9781789480290
Chapitre d'ouvrage
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Integrative models for TGF-$\beta$ signaling and extracellular matrixSylvie Ricard-Blum. Extracellular Matrix Omics, 7, Springer, pp.17, 2020, Biology of Extracellular Matrix, 978-3-030-58329-3. ⟨10.1007/978-3-030-58330-9_10⟩
Chapitre d'ouvrage
hal-02458073v1
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L'analyseur statique AstréeJean-Louis Boulanger. Utilisations industrielles des techniques formelles : interprétation abstraite, Hermes-Lavoisier, pp.67--114, 2011, Informatique et systèmes d'information, 2-7462-3206-5
Chapitre d'ouvrage
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Rule Based Modeling and Model RefinementH. Lodhi and S. Muggleton. Elements of Computational Systems Biology, John Wiley & Sons, pp.83--114, 2010, Wiley Book Series on Bioinformatics, 978-0470180938. ⟨10.1002/9780470556757.ch4⟩
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Rule-based modelling and model perturbationsCorrado Priami ; Ralph-Johan Back ; Ion Petre. Transactions on Computational Systems Biology XI, Springer, pp.116-137, 2008, Lecture Notes in Computer Science, 978-3-642-04186-0. ⟨10.1007/978-3-642-04186-0_6⟩
Chapitre d'ouvrage
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Design and Implementation of a Special-Purpose Static Program Analyzer for Safety-Critical Real-Time Embedded SoftwareMogensen, T. and Schmidt, D.A. and Sudborough, I.H. The Essence of Computation: Complexity, Analysis, Transformation. Essays Dedicated to Neil D. Jones, 2566, Springer, pp.85-108, 2002, Lecture Notes in Computer Science, ⟨10.1007/3-540-36377-7_5⟩
Chapitre d'ouvrage
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Special issue "Formal Method for Biological Systems Modelling"Cedric Lhoussaine; Jérôme Feret. MDPI, 9, 2021, Section Computational Biology, 2079-3197
Ouvrages
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Computational Methods in Systems BiologySpringer, 10545, pp.332, 2017, Lecture Notes in Bioinformatics, 978-3-319-67470-4. ⟨10.1007/978-3-319-67471-1⟩
Ouvrages
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Proceedings of the 2nd International Workshop on Static Analysis and Systems Biology (SASB 2011)Jérôme Feret and Andre Levchenko. Elsevier, 284, pp.137, 2012, Electronic Notes in Theoretical Computer Science
Ouvrages
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Proceedings of the 1st International Workshop on Static Analysis and Systems Biology (SASB 2010)Jérôme Feret and Andre Levchenko. Elsevier, 272, pp.56, 2011, Electronic Notes in Theoretical Computer Science
Ouvrages
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Analyse des systèmes mobiles par interprétation abstraite.Informatique mobile. Ecole Polytechnique X, 2005. Français. ⟨NNT : ⟩
Thèse
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Formal Verification and Static Analysis of Molecular Devices and Biological SystemsJérôme Feret; Loïc Paulevé; David Šafránek. Theoretical Computer Science, 765, 2019
N°spécial de revue/special issue
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Proceedings of the 3rd International Workshop on Static Analysis and Systems Biology (SASB 2012)Jérôme Feret and Andre Levchenko. 3rd International Workshop on Static Analysis and Systems Biology (SASB 2012), Sep 2012, Deauville, France. 313, Elsevier, pp.78, 2015, Electronic Notes in Theoretical Computer Science
Proceedings/Recueil des communications
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A Kappa model for hepatic stellate cells activation by TGFB1CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux / Virtual, France. pp.1-6
Poster de conférence
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A Kappa model for hepatic stellate cells activation by TGFB1CompSysBio 2021 - Advanced Lecture Course on Computational Systems Biology, Nov 2021, Aussois, France. pp.1-1
Poster de conférence
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Modelling Systems Biology Wide and DeepCMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. CMSB
Poster de conférence
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Analyse statique et réduction de modèles pour un langage de réécriture de graphes à sitesInformatique [cs]. ENS-PSL, 2023
HDR
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