J. Feret, publications

Static analysis of mobile systems

• Aurélie Kong, Jérôme Feret and Gregor Gössler. A Semantics of Core Erlang with Handling of Signals. In Proceedings of the Twenty second ACM Sigplan Erlang Workshop, ERLANG'23. 2023. Seattle, USA, B.K. Ozkan and K.F. Reyes (Eds). In ACM Digital Library. 2023. © ACM.
• Jérôme Feret. Partitioning the threads of a mobile system. Arxiv. 2008
• Jérôme Feret. Analysis of Mobile Systems by Abstract Interpretation. Thèse de doctorat, École Polytechnique, february 2005.
• Jérôme Feret. Abstract interpretation of mobile systems. Journal of Logic and Algebraic Programming, special issue on pi-calculus, vol. 63(1), pp. 59--130. 2005. © Elsevier Science..
• Jérôme Feret. Dependency analysis of mobile systems. In European Symposium on Programming (ESOP'02), number 2305 in Lecture Notes in Computer Science, pp. 314--330. 2002. © Springer.
• Jérôme Feret. Abstract interpretation-based static analysis of mobile ambients. In Eighth International Static Analysis Symposium (SAS'01), number 2126 in Lecture Notes in Computer Science, pp. 413--431. 2001. © Springer.
• Jérôme Feret. Occurrence counting analysis for the pi-calculus. In Electronic Notes in Theoretical Computer Science, volume 39.(2). Elsevier Science Publishers, 2001. © 2001, Elsevier Science.

• Jérôme Feret. Confidentiality analysis of mobile systems. In Seventh International Static Analysis Symposium (SAS'00), number 1824 in Lecture Notes in Computer Science, pp. 135--154. 2000. © Springer.

• Jérôme Feret. Conception de pi-sa : un analyseur statique générique pour le pi-calcul. Mémoire de dea, SPP, septembre 1999.

Static analysis of biological systems

• Jérôme Feret. Model reduction of infinite rule-based models. In SIGSIM Principles of Advanced Discrete Simulation (PADS'25), To appear in ACM Conference Proceedings 2025. © ACM.

• Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jeremy Bomo, Anne Siegel, Jérôme Feret, and Nathalie Théret. A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. PLoS Computational Biology, volume 20(7). © 2024, Public Library of Science.

• Jérôme Feret. Analyse statique et réduction de modèles pour un langage de réécriture de graphes à sites. HDR. PSL, décembre 2023

• Jérôme Feret. Analyse statique et réduction de modèles de voies de signalisation intracellulaire . Book chapter in Informatique Mathématique. Une photographie en 2023. CNRS Éditions © 2023.

• Jérôme Feret & Albin Salazar. A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation. In Verification, Model Checking, and Abstract Interpretation (VMCAI 2023), In: Lecture Notes in Computer Science, volume 13881. © 2023, Springer.

• Matthieu Bouguéon, Pierre Boutillier, Jérôme Feret, Octave Hazard, & Nathalie Théret The Rule-based model approach. A Kappa model for hepatic stellate cells activation by TGFB1. Book chapter in Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools. Wiley. © 2022.

• Jérôme Feret. Analyses des motifs accessibles dans les modèles Kappa. Book chapter in Approches symboliques de la modélisation et de l'analyse des systèmes biologiques. ISTE. © 2022.

• Sébastien Légaré, Jean Krivine, & Jérôme Feret. Distinguishing Context Dependent Events in Quotients of Causal Stories. In JOBIM 2021 - Journ\'ees Ouvertes en Biologie, Informatique et Math\'ematiques. -- Institut Pasteur © 2021.

• Nathalie Théret, Jérôme Feret, Arran Hodgkinson, Pierre Boutillier, Pierre Vignet, & Ovidiu Radulescu. Integrative models for TGF-β signaling and extracellular matrix. Book chapter in Extracellular Matrix Omics, Biology of Extracellular Matrix, volume 7. © 2020, Springer.

• Pierre Boutillier, Iona Cristescu, & Jérôme Feret. Counters in Kappa: Semantics, Simulation, and Static Analysis. In European Symposium on Programming (ESOP 2019), In: Lecture Notes in Computer Science, volume 11423. © 2019, Springer.

• Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jérôme Feret, Kim Quyên Lý, Nathalie Theret, & Pierre Vignet. KaSa: A Static Analyzer for Kappa In Computational Method in Systems Biology, tools paper track (CMSB 2018), In: Lecture Notes in Computer Sciences / Lecture Notes in BioInformatics, volume 11095. © 2018, Springer.

• Andreea Beica, Jérôme Feret, & Tatjana Petrov. Tropical Abstraction of Biochemical Reaction Networks with Guarantees. In Electronic Notes in Theoretical Computer Science, volume 350. © 2020, Elsevier Science.

• Pierre Boutillier, Aurélie Faure de Pebeyre. Proving the absence of unbounded polymers in rule-based models. In Electronic Notes in Theoretical Computer Science, volume 350. © 2020, Elsevier Science.

• Jérôme Feret & Heinz Koeppl (Eds). Special issue on the best paper of CMSB 2017. IEEE ACM Transactions on Computational Biology and Bioinformatics, Volume 16, issue 5. © 2019, IEEE/ACM.

• Jérôme Feret, Loïc Paulevé, & David Safranek (Eds). Special issue on SASB 2016 and VEMDP 2015. Theoretical Computer Sciences, volume 765. © 2019, Elsevier.

• Pierre Boutillier, Mutaamba Maasha, Xing Li, Héctor F. Medina-Abarca, Jean Krivine, Jérôme Feret, Ioana Cristescu, Angus G. Forbes, & Walter Fontana. The Kappa platform for rule-based modeling. In: Bioinformatics, Volume 34(13). © 2018. Oxford Academic.

• Jérôme Feret & Kim Quyên Lý. Local traces: an over-approximation of the behaviour of the proteins in rule-based models, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. © 2018, IEEE.

• Ferdinanda Camporesi & Jérôme Feret. Using alternated sums to express the occurrence number of extended patterns in site-graphs. In the PostProceedings of the 8th International Workshop on Static Analysis and Systems Biology (SASB 2017). To appear in Electronic Notes in Theoretical Computer Science, Elsevier Science.

• Ferdinanda Camporesi, Jérôme Feret, & Kim Quyên Lý. KaDE: a Tool to Compile Kappa Rules into (Reduced) ODE Models. In Computational Methods in Systems Biology, tools paper track (CMSB 2017), In: Lecture Notes in Computer Sciences / Lecture Notes in BioInformatics, volume 10545. © 2017, Springer.

• Jérôme Feret & Heinz Koeppl (Eds). Proceedings of the 15th Conference on Computational Methods in Systems Biology. In: Lecture Notes in Computer Sciences / Lecture Notes in BioInformatics, volume 10545. © 2017, Springer.

• Wassim Abou-Jaoudé, Denis Thieffry, & Jérôme Feret. Formal derivation of qualitative dynamical models from biochemical networks. In BioSystems. © 2016, Elsevier Science.

• Jérôme Feret & Kim Quyên Lý. Reachability analysis via orthogonal sets of patterns. In the PostProceedings of the 7th International Workshop on Static Analysis and Systems Biology (SASB 2016). In Electronic Notes in Theoretical Computer Science, volume 335. © 2018, Elsevier Science.

• Jérôme Feret & Kim Quyên Lý. Local traces: an over-approximation of the behaviour of the proteins in rule-based models. In the Proceedings of the 14th Conference on Computational Methods in Systems Biology (CMSB 2016), In Lecture Notes in Computer Sciences / Lecture Notes in BioInformatics, volume 9859. © 2016, Springer.

• Wassim Abou-Jaoudé, Jérôme Feret,& Denis Thieffry. Derivation of Qualitative Dynamical Models from Biochemical Networks. In the Proceedings of the 13th Conference on Computational Methods in Systems Biology (CMSB 2015), in Lecture Notes in Computer Sciences / Lecture Notes in BioInformatics, volume 9308, pp:195--207. © 2015, Springer.

• Jérôme Feret & Andre Levchenko (Eds.). Proceedings of the 3rd International Workshop on Static Analysis and Systems Biology (SASB 2012). In Electronic Notes in Theoretical Computer Science, volume 313. © 2015, Elsevier Science.

• Jérôme Feret. An algebraic approach for inferring and using symmetries in rule-based models. In the PostProceedings of the 5th International Workshop on Static Analysis and Systems Biology (SASB 2014), in Electronic Notes in Theoretical Computer Science, volume 316. © 2015, Elsevier Science.

• Jérôme Feret, Heinz Koeppl,& Tatjana Petrov. Stochastic fragments: A framework for the exact reduction of the stochastic semantics of rule-based models. In International Journal of Software and Informatics, volume 7(4). © 2013, ISCAS.

• Ferdinanda Camporesi, Jérôme Feret,& Jonathan Hayman. Context-sensitive flow analyses: a hierarchy of model reductions. In Proceedings of the 11th Conference on Computational Methods in Systems Biology (CMSB 2013), in Lecture Notes in BioInformatics, number 8130. © 2013, Springer.

• Jérôme Feret & Andre Levchenko (Eds.). Proceedings of the 2nd International Workshop on Static Analysis and Systems Biology (SASB 2011). In Electronic Notes in Theoretical Computer Science, volume 284. © 2012, Elsevier Science.

• Jérôme Feret, Thomas Henzinger, Heinz Koeppl,& Tatjana Petrov. Lumpability Abstractions of Rule-based Systems. In Theoretical Computer Science, special issue on MeCBIC 2009-2010, vol 431, pp. 137--164. © 2012, Elsevier Inc.

• Eric J. Deeds, Jean Krivine, Jérôme Feret, Vincent Danos,& Walter Fontana. Combinatorial complexity and compositional drift in protein interaction networks. In PLoS ONE, volume 7(3). © 2012, Public Library of Science.

• Tatjana Petrov, Jérôme Feret,& Heinz Koeppl. Reconstructing species-based dynamics from reduced stochastic rule-based models. In Proceedings of the Winter Simulation Conference (WSC 2012).

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh,& Glynn Winskel. Rewriting and Pathway Reconstruction for Rule-Based Models. In Proceedings of the 32nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012), in Leibniz International Proceedings in Informatics, volume 18, pp 276--288. © 2012, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.

• Jérôme Feret & Andre Levchenko (Eds.). Proceedings of the 1st International Workshop on Static Analysis and Systems Biology (SASB 2010). In Electronic Notes in Theoretical Computer Science, volume 272. © 2011, Elsevier Science.

• Ferdinanda Camporesi, Jérôme Feret. Formal reduction of rule-based models. In Mathematical Foundations of Programming Semantics (MFPS XXVII), in Electronic Notes in Theoretical Computer Science, volume 276, pp 31--61. © 2011, Elsevier Science.

• Jérôme Feret. Formal model reduction. In Static Analysis Symposium (SAS 2011), number 6887 in Lecture Notes in Computer Science, p 6. © 2011, Springer.

• Ferdinanda Camporesi, Jérôme Feret, Heinz Koeppl,& Tatjana Petrov. Combining model reductions. In Mathematical Foundations of Programming Semantics (MFPS XXVI), in Electronic Notes in Theoretical Computer Science, volume 265, pp 73--96. © 2010, Elsevier Science.

• Jérôme Feret. Fragments-based model reduction: some case studies. In Interactions between Computer Science and Biology (CS2Bio 2010), in Electronic Notes in Theoretical Computer Science, volume 268, pp 77--96 © 2010, Elsevier Science.

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine. Abstracting the differential semantics of rule-based models: exact and automated model reduction . In Logic in Computer Science (LICS 2010). 2010. © IEEE Computer Society.

• Ferdinanda Camporesi, Jérôme Feret, Heinz Koeppl,& Tatjana Petrov. Automatic reduction of stochastic rules-based models in a nutshell. In International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2010), in American Institute of Physics conference proceedings, numero 1281, pp. 1330--1334. 2010, © American Institute of Physics.

• Jérôme Feret, Thomas Henzinger, Heinz Koeppl,& Tatjana Petrov. Lumpability Abstractions of Rule-based Systems. In The 4th Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2010), in Electronic Proceedings in Theoretical Computer Science, volume 40, pp 142--161. © 2010, Elsevier Science.

• Russell Harmer, Vincent Danos, Jérôme Feret, Jean Krivine,& Walter Fontana. Intrinsic Information Carriers in Combinatorial Dynamics Systems. In Chaos, volume 20(3), 2010. © American Institute of Physics.

• Elaine Murphy, Vincent Danos, Jérôme Feret, Jean Krivine,& Russell Harmer. Rule Based Modelling and Model Refinement. In Elements of Computational Systems Biology , Wiley Book Series on Bioinformatics, 2010. © John Wiley & Sons, Inc.

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine. Investigation of a biological repair scheme. In Membrane Computing (WMC9), number 5391 in Lecture Notes in Computer Sciences. 2009. © Springer.

• Jérôme Feret, Vincent Danos, Jean Krivine, Russell Harmer,& Walter Fontana. Internal coarse-graining of molecular systems. Proceedings of National Academy of Sciences of the United States of America (PNAS), volume 106.(16). 2009. © National Academy of Sciences.

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine. Rule-based modelling and model perturbation. Accepted to Transactions on Computational Systems Biology XI, 2009, number 5740 in Lecture Notes in Computer Science. 2009. © Springer.

• Vincent Danos, Jérôme Feret, Walter Fontana,& Jean Krivine. Abstract interpretation of cellular signalling networks. In Verification, Model Checking, and Abstract Interpretation, VMCAI 2008, number 4905 in Lecture Notes in Computer Sciences. 2008. © Springer.

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine. Rule-based modelling, symmetries, refinements. In Formal Modelling Systems Biology (FMSB 2008), number 5054 in Lecture Notes in Bioinformatics. 2008. © Springer.

• Jérôme Feret. Reachability analysis of biological signalling pathways by abstract interpretation. In International Conference of Computational Methods in Sciences and Engineering (ICCMSE'07), numero 963(2) in American Institute of Physics conference proceedings. 2007. © American Institute of Physics.

• Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer,& Jean Krivine. Rule-based modelling of cellular signalling. Invited in International Conference on Concurrency Theory (CONCUR 2007), number 4703 in Lecture Notes in Computer Science. 2007. © Springer.

• Vincent Danos, Jérôme Feret, Walter Fontana,& Jean Krivine. Scalable modelling of biological pathways. Invited in Asian Symposium on Programming Systems (APLAS 2007), number 4807 in Lecture Notes in Computer Science. 2007. © Springer.

Static analysis of embedded critical software

• Jérôme Boillot and Jérôme Feret. Abstraction of memory block manipulations by symbolic loop folding. In European Symposium on Programming (ESOP'25), To appear in Lecture Notes in Computer Science. 2025. © Springer.

• Jérôme Boillot and Jérôme Feret. Symbolic transformation of expressions in modular arithmetic. In Static Analysis Symposium (SAS'23), number 14284 in Lecture Notes in Computer Science. 2023. © Springer.

• Marc Chevalier and Jérôme Feret. Sharing ghost variables in a collection of abstract domains. In Verification, Model Checking and Abstract Interpretation (VMCAI'20), number 11990 in Lecture Notes in Computer Science. 2020. © Springer.

• Daniel Kästner, Antoine Miné, André Schmidt, Heinz Hille, Laurent Mauborgne, Stephan Wilhelm, Xavier Rival, Jérôme Feret, Patrick Cousot, and Christian Ferdinand. Finding All Potential Run-Time Errors and Data Races in Automotive Software. In SAE wold Congress 2017 (SAE 2017).

• Antoine Miné, Laurent Mauborgne, Xavier Rival, Jérôme Feret, Patrick Cousot, Daniel Kästner, Stephan Wilhelm, and Christian Ferdinand. Taking Static Analysis to the Next Level: Proving the Absence of Run-Time Errors and Data Races with Astrée. In Embedded Real Time Software and Systems (ERTSS 2016).

• Julien Bertrane, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné,& Xavier Rival. Static Analysis and Verification of Aerospace Software by Abstract Interpretation. In Foundations and Trends in Programming Languages Vol. 2: No. 2-3, pp 71-190. © now publishers inc.

• Julien Bertrane, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné,& Xavier Rival. L'analyseur statique Astrée, In Utilisations industrielles des techniques formelles : interprétation abstraite, J.-L. Boulanger (Editor) in Hermes Science - Lavoisier, 2010. © Hermes-Lavoisier.

• Daniel Kästner, Stephan Wilhelm, Stefana Nenova, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné,& Xavier Rival. Astrée: Proving the Absence of Runtime Errors. In Embedded Real Time Software and Systems (ERTSS 2010).

• Julien Bertrane, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné,& Xavier Rival. Static Analysis by Abstract Interpretation of Embedded Critical Software. In Third IEEE International workshop UML and Formal Methods. © ACM.

• Julien Bertrane, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné,& Xavier Rival. Static Analysis and Verification of Aerospace Software by Abstract Interpretation. In American Institute of Aeronautics and Astronautics (AIAA 2010). © AIAA.
  This paper received the "Best Paper Award" from the AIAA Infotech@Aerospace Conference.

• Olivier Bouissou, Eric Conquet, Patrick Cousot, Radhia Cousot, Jérôme Feret, Khalil Ghorbal, Eric Goubault, David Lesens, Laurent Mauborgne, Antoine Miné, Sylvie Putot, Xavier Rival,& Michel Turin. Space Software Validation using Abstract Interpretation. In DAta System In Aerospace (DASIA 2009). © ESA 2009.

• Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné,& Xavier Rival. Why does ASTRÉE scale up? In Formal Methods in System Design. 2009.

• Daniel Késtner, Christian Ferdinand, Stephan Wilhelm, Stefana Nenova, Olha Honcharova, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné, Xavier Rival, and Élodie-Jane Sims. Astree: Nachweis der Abwesenheit von Laufzeitfehlern. In Workshop ``Entwicklung zuverlässiger Software-Systeme'', Regensburg, German, 18 June 2009.

• Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné, David Monniaux,& Xavier Rival. Varieties of Static Analyzers: A Comparison with Astrée. Invited in Theoretical Aspects of Software Engineering (TASE'07). © IEEE Computer Society.

• Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné, David Monniaux,& Xavier Rival. Combination of Abstractions in the Astrée Static Analyzer. Invited in Asian Computing Science Conference (ASIAN'06), number 4435 in Lecture Notes in Computer Science. 2006. © Springer.

• Jérôme Feret. The Arithmetic-Geometric Progression Abstract Domain. In Verification, Model Checking and Abstract Interpretation (VMCAI'05), number 3385 in Lecture Notes in Computer Science. 2005. © Springer.
  This paper received the "Best Paper Award" at VMCAI'05.

• Jérôme Feret. Numerical Abstract Domains for Digital Filters. Accepted in Numerical & Symbolic Abstract Domains (NSAD'05).

• Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné, David Monniaux & Xavier Rival. The Astrée Analyzer. In European Symposium on Programming (ESOP 2005), number 3444 in Lecture Notes in Computer Science. 2005. © Springer.

• Jérôme Feret. Static Analysis of Digital Filters. In European Symposium on Programming (ESOP 2004), number 2986 in Lecture Notes in Computer Science. 2004. © Springer.

• Bruno Blanchet, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné, David Monniaux & Xavier Rival. A Static Analyzer for Large Safety-Critical Software. In Programming Language Design and Implementation (PLDI 2003). 2003. © ACM.

• Bruno Blanchet, Patrick Cousot, Radhia Cousot, Jérôme Feret, Laurent Mauborgne, Antoine Miné, David Monniaux & Xavier Rival. Design and Implementation of a Special-Purpose Static Program Analyzer for Safety-Critical Real-Time Embedded Software, invited chapter. In The Essence of Computation: Complexity, Analysis, Transformation. Essays Dedicated to Neil D. Jones, T. Mogensen and D.A. Schmidt and I.H. Sudborough (Editors), number 2566 in Lecture Notes in Computer Science, 2002. © Springer.