
Jérôme Feret
Chargé de recherche
82
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.
Domaines de recherche
Bio-Informatique, Biologie Systémique [q-bio.QM]
Informatique et langage [cs.CL]
Publications
Publications
Model reduction of infinite rule-based modelsPADS 25 - 39th ACM SIGPLAN Principle of Advanced Discrete Simulation, Adelinde Uhrmacher, Jun 2025, Santa Fe (NM), United States
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hal-05002272
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Abstraction of memory block manipulations by symbolic loop foldingESOP 2025 - 34th European Symposium on Programming, Viktor Vafeiadis, May 2025, Hamilton, Canada
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hal-04853849
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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⟩
Communication dans un congrès
hal-04222884
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Symbolic transformation of expressions in modular arithmeticStatic Analysis: 30th International Symposium, SAS 2023, Oct 2023, Cascais, Portugal. pp.84-113, ⟨10.1007/978-3-031-44245-2_6⟩
Communication dans un congrès
hal-04187086
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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
Communication dans un congrès
hal-03389052
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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
Communication dans un congrès
hal-02378809
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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⟩
Communication dans un congrès
hal-02397876
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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
Communication dans un congrès
hal-01962674
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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
Communication dans un congrès
hal-01967632
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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⟩
Communication dans un congrès
hal-01888951
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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⟩
Communication dans un congrès
hal-01613600
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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⟩
Communication dans un congrès
hal-01674831
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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
Communication dans un congrès
hal-01613603
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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
Communication dans un congrès
hal-01271552
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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
Communication dans un congrès
hal-01379902
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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⟩
Communication dans un congrès
hal-01379897
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Derivation of Qualitative Dynamical Models from Biochemical NetworksComputational Methods in Systems Biology - CMSB 2015, Olivier Roux; Jérémie Bourdon, Sep 2015, Nantes, France. pp.195-207, ⟨10.1007/978-3-319-23401-4_17⟩
Communication dans un congrès
hal-01199243
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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⟩
Communication dans un congrès
hal-01098556
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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⟩
Communication dans un congrès
istex
hal-00846893
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Reconstructing Species-Based Dynamics from Reduced Stochastic Rule-Based Models.WSC - Winter Simulation Conference - 2012, Dec 2012, Berlin, Germany
Communication dans un congrès
hal-00734483
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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⟩
Communication dans un congrès
hal-00809065
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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-00636850
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Formal Model ReductionStatic Analysis Symposium, Sep 2011, Venice, Italy. pp.6, ⟨10.1007/978-3-642-23702-7_5⟩
Communication dans un congrès
istex
inria-00626640
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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
Communication dans un congrès
inria-00527971
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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⟩
Communication dans un congrès
inria-00527548
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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-00528611
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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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inria-00527960
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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⟩
Communication dans un congrès
inria-00527536
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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
Communication dans un congrès
inria-00528600
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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
Communication dans un congrès
hal-00520112
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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
Communication dans un congrès
inria-00528632
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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
Communication dans un congrès
inria-00528590
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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⟩
Communication dans un congrès
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inria-00528319
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Astrée: Nachweis der Abwesenheit von Laufzeitfehlern.Workshop "Entwicklung zuverlässiger Software-Systeme", Jun 2009, Regensburg, Germany
Communication dans un congrès
hal-00753732
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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⟩
Communication dans un congrès
inria-00528352
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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⟩
Communication dans un congrès
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inria-00528339
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Rule-based modelling of cellular signallingInternational Conference on Concurrency Theory (CONCUR'07), Sep 2007, Lisbon, Portugal
Communication dans un congrès
hal-00164297
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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⟩
Communication dans un congrès
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inria-00528409
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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⟩
Communication dans un congrès
inria-00528358
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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⟩
Communication dans un congrès
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inria-00528571
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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⟩
Communication dans un congrès
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inria-00528450
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Numerical Abstract Domains for Digital FiltersNSAD 2005, Radhia Cousot, 2005, London, United Kingdom
Communication dans un congrès
hal-04951006
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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⟩
Communication dans un congrès
inria-00528447
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A Static Analyzer for Large Safety-Critical Software2003, pp.196 - 207, ⟨10.1145/781131.781153⟩
Communication dans un congrès
hal-00128135
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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⟩
Communication dans un congrès
istex
inria-00527924
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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⟩
Communication dans un congrès
istex
inria-00527929
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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⟩
Communication dans un congrès
inria-00527933
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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⟩
Communication dans un congrès
istex
inria-00527941
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A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progressionPLoS Computational Biology, 2024, 20 (7), pp.e1011858. ⟨10.1371/journal.pcbi.1011858⟩
Article dans une revue
hal-04689199
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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⟩
Article dans une revue
hal-01967635
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The Kappa platform for rule-based modelingBioinformatics, 2018, Bioinformatics, 34 (13), pp.i583-i592. ⟨10.1093/bioinformatics/bty272⟩
Article dans une revue
hal-01962663
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Formal Derivation of Qualitative Dynamical Models from Biochemical NetworksBioSystems, 2016, pp.100. ⟨10.1016/j.biosystems.2016.09.001⟩
Article dans une revue
hal-01379733
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Static Analysis and Verification of Aerospace Software by Abstract InterpretationFoundations and Trends in Programming Languages, 2015, 2 (2-3), pp.71-190. ⟨10.1561/2500000002⟩
Article dans une revue
hal-01312241
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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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hal-00975861
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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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hal-01098561
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Combinatorial complexity and compositional drift in protein interaction networks.PLoS ONE, 2012, 7 (3), ⟨10.1371/journal.pone.0032032⟩
Article dans une revue
hal-00677889
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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⟩
Article dans une revue
hal-00677894
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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⟩
Article dans une revue
hal-00520128
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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⟩
Article dans une revue
istex
inria-00528582
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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-00528330
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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⟩
Article dans une revue
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inria-00528364
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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⟩
Article dans une revue
istex
hal-04947676
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Analyse statique et réduction de modèles pour un langage de réécriture de graphes à sitesInformatique [cs]. ENS-PSL, 2023
HDR
tel-04326091
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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
hal-04144668
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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
hal-03088539
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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
hal-03388100
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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-02458073
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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
inria-00636877
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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⟩
Chapitre d'ouvrage
inria-00527981
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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
istex
hal-00350299
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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
istex
inria-00528442
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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
hal-03545135
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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
hal-03545256
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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
hal-03357485
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Modelling hepatic stellate cells activation by TGFB1 using Kappa language2021, pp.1-23
Autre publication scientifique
hal-03545569
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Special issue "Formal Method for Biological Systems ModellingCedric Lhoussaine; Jérôme Feret. MDPI, 9, 2021, Section Computational Biology, 2079-3197
Ouvrages
hal-03542053
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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
hal-01613596
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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
hal-00722482
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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
hal-00722483
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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
hal-02962679
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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
hal-01147670
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Analyse des systèmes mobiles par interprétation abstraite.Informatique mobile. Ecole Polytechnique X, 2005. Français. ⟨NNT : ⟩
Thèse
pastel-00001303
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