Institut National de Recherche en Informatique et en Automatique, France

Research Fellow

Email: [email protected]

Qualifications

2005 Ph.D., Computer Science, Laboratoire d'informatique de l'École normale supérieure, France

2000 M.Sc, Pure and Applied Mathématics and Computer Science,École normale supérieure, France

Publications (Selected)

1. Chaouiya, C., Feret, J., Tenera Roxo, P. (2025, August). On Model Reductions of Boolean Networks. In International Conference on Computational Methods in Systems Biology (pp. 42-60). Cham: Springer Nature Switzerland.
2. Feret, J., Ghidini, R. (2025, August). Reachability Analysis for Parametric Rule-Based Models. In International Conference on Computational Methods in Systems Biology (pp. 153-173). Cham: Springer Nature Switzerland.
3. Feret, J. (2025, June). Model reduction of infinite rule-based models. In 39th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (pp. 46-55).
4. Boillot, J., Feret, J. (2025, May). Abstraction of memory block manipulations by symbolic loop folding. In European Symposium on Programming (pp. 117-143). Cham: Springer Nature Switzerland.
5. Bougueon, M., Legagneux, V., Hazard, O., Bomo, J., Siegel, A., Feret, J., Théret, N. (2024). A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. PLoS Computational Biology, 20(7), e1011858.
6. Bougueon, M., Legagneux, V., Hazard, O., Bomo, J., Siegel, A., Féret, J., Theret, N. (2024). OS-102 A rule-based multiscale model of hepatic stellate cell plasticity: critical role of the inactivation loop in fibrosis progression. Journal of Hepatology, 80, S64.
7. Boillot, J., Feret, J. (2023, October). Symbolic transformation of expressions in modular arithmetic. In International Static Analysis Symposium (pp. 84-113). Cham: Springer Nature Switzerland.
8. Kong Win Chang, A., Feret, J., Gössler, G. (2023, August). A semantics of core Erlang with handling of signals. In Proceedings of the 22nd ACM SIGPLAN International Workshop on Erlang (pp. 31-38).
9. Castro, R., Denil, J., Feret, J., Matkovic, K., Popper, N., Sanchez, S., Sloot, P. (2023). 4.2 Policy by simulation: seeing is believing for interactive model co-creation and effective intervention. Computer Science Methods for Effective and Sustainable Simulation Studies, 47.
10. Feret, J., Salazar, A. (2023, January). A generic framework to coarse-grain stochastic reaction networks by abstract interpretation. In International Conference on Verification, Model Checking, and Abstract Interpretation (pp. 228-251). Cham: Springer Nature Switzerland.
11. Bouguéon, M., Boutillier, P., Feret, J., Hazard, O., Théret, N. (2022). The Rule‐Based Model Approach: A Kappa Model for Hepatic Stellate Cells Activation by TGFB1. Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools, 69-126.
12. FERET, J. (2022). Chapitre 9-Analyses des motifs accessibles dans les modèles Kappa. ISTE Group.
13. Bouguéon, M., Boutillier, P., Feret, J., Hazard, O., Theret, N. (2021, November). A Kappa model for hepatic stellate cells activation by TGFB1. In CompSysBio 2021-Advanced Lecture Course on Computational Systems Biology (pp. 1-1).
14. Légaré, S., Krivine, J., Feret, J. (2021, July). Distinguishing Context Dependent Events in Quotients of Causal Stories. In JOBIM 2021-Journées Ouvertes en Biologie, Informatique et Mathématiques (pp. 54-61).
15. Theret, N., Feret, J., Hodgkinson, A., Boutillier, P., Vignet, P., Radulescu, O. (2020). Integrative models for TGF-β signaling and extracellular matrix. In Extracellular matrix omics (pp. 209-225). Cham: Springer International Publishing.
16. Beica, A., Feret, J., Petrov, T. (2020). Tropical abstraction of biochemical reaction networks with guarantees. Electronic Notes in Theoretical Computer Science, 350, 3-32.
17. Boutillier, P., de Pebeyre, A. F., Feret, J. (2020). Proving the absence of unbounded polymers in rule-based models. Electronic Notes in Theoretical Computer Science, 350, 33-56.
18. Chevalier, M., Feret, J. (2020, January). Sharing ghost variables in a collection of abstract domains. In International Conference on Verification, Model Checking, and Abstract Interpretation (pp. 158-179). Cham: Springer International Publishing.
19. Boutillier, P., Cristescu, I., Feret, J. (2019, April). Counters in Kappa: Semantics, Simulation, and Static Analysis. In ESOP (pp. 176-204).
20. Boutillier, P., Camporesi, F., Coquet, J., Feret, J., Lý, K. Q., Théret, N., Vignet, P. (2018, August). Kasa: A static analyzer for kappa. In International Conference on Computational Methods in Systems Biology (pp. 285-291). Cham: Springer International Publishing.
21. Boutillier, P., Maasha, M., Li, X., Medina-Abarca, H. F., Krivine, J., Feret, J.,Fontana, W. (2018). The Kappa platform for rule-based modeling. Bioinformatics, 34(13), i583-i592.
22. Feret, J., Lý, K. Q. (2018). Reachability analysis via orthogonal sets of patterns. Electronic Notes in Theoretical Computer Science, 335, 27-48.
23. Feret, J., Lý, K. Q. (2018). Local traces: An over-approximation of the behavior of the proteins in rule-based models. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4), 1124-1137.
24. Camporesi, F., Feret, J., Lý, K. Q. (2017, September). Kade: A tool to compile kappa rules into (reduced) ODE models. In International Conference on Computational Methods in Systems Biology (pp. 291-299). Cham: Springer International Publishing.
25. Abou-Jaoudé, W., Thieffry, D., Feret, J. (2016). Formal derivation of qualitative dynamical models from biochemical networks. Biosystems, 149, 70-112.
26. Miné, A., Mauborgne, L., Rival, X., Feret, J., Cousot, P., Kästner, D.,Ferdinand, C. (2016, January). Taking static analysis to the next level: proving the absence of run-time errors and data races with Astrée. In 8th European Congress on Embedded Real Time Software and Systems (ERTS 2016).

Profile Details

https://scholar.google.com/citations?user=oWsrtiUAAAAJ&hl=fr

https://www.researchgate.net/profile/Jerome-Feret

https://cv.hal.science/jerome-feret

WoS Researcher ID: GBY-1601-2022