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Jérôme Feret
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Publications
- 2020
- [c38]Andreea Beica, Jérôme Feret, Tatjana Petrov:
Tropical Abstraction of Biochemical Reaction Networks with Guarantees. SASB 2020: 3-32 - [c37]Pierre Boutillier, Aurélie Faure de Pebeyre, Jérôme Feret:
Proving the Absence of Unbounded Polymers in Rule-based Models. SASB 2020: 33-56 - 2019
- [j15]Jérôme Feret, Heinz Koeppl:
Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 16(5): 1561 (2019) - [j14]Jérôme Feret, Loïc Paulevé, David Safránek:
Preface. Theor. Comput. Sci. 765: 1-2 (2019) - [c35]Pierre Boutillier, Ioana Cristescu, Jérôme Feret:
Counters in Kappa: Semantics, Simulation, and Static Analysis. ESOP 2019: 176-204 - 2018
- [j13]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. Bioinform. 34(13): i583-i592 (2018) - [j12]Jérôme Feret, Kim Quyen Ly:
Local Traces: An Over-Approximation of the Behavior of the Proteins in Rule-Based Models. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1124-1137 (2018) - [c34]Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jérôme Feret, Kim Quyên Lý, Nathalie Théret, Pierre Vignet:
KaSa: A Static Analyzer for Kappa. CMSB 2018: 285-291 - [c33]Jérôme Feret, Kim Quyên Lý:
Reachability Analysis via Orthogonal Sets of Patterns. SASB 2018: 27-48 - 2017
- [c32]Ferdinanda Camporesi, Jérôme Feret, Kim Quyên Lý:
KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models. CMSB 2017: 291-299 - [e4]Jérôme Feret, Heinz Koeppl:
Computational Methods in Systems Biology - 15th International Conference, CMSB 2017, Darmstadt, Germany, September 27-29, 2017, Proceedings. Lecture Notes in Computer Science 10545, Springer 2017, ISBN 978-3-319-67470-4 [contents] - 2016
- [c31]Jérôme Feret, Kim Quyên Lý:
Local Traces: An Over-Approximation of the Behaviour of the Proteins in Rule-Based Models. CMSB 2016: 116-131 - 2013
- [j8]Jérôme Feret, Heinz Koeppl, Tatjana Petrov:
Stochastic Fragments: A Framework for the Exact Reduction of the Stochastic Semantics of Rule-Based Models. Int. J. Softw. Informatics 7(4): 527-604 (2013) - [c28]Ferdinanda Camporesi, Jérôme Feret, Jonathan Hayman:
Context-Sensitive Flow Analyses: A Hierarchy of Model Reductions. CMSB 2013: 220-233 - 2012
- [j7]Jérôme Feret, Thomas A. Henzinger, Heinz Koeppl, Tatjana Petrov:
Lumpability abstractions of rule-based systems. Theor. Comput. Sci. 431: 137-164 (2012) - [c27]Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Christopher D. Thompson-Walsh, Glynn Winskel:
Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models. FSTTCS 2012: 276-288 - [c26]Tatjana Petrov, Jérôme Feret, Heinz Koeppl:
Reconstructing species-based dynamics from reduced stochastic rule-based models. WSC 2012: 225:1-225:15 - 2011
- [c22]Ferdinanda Camporesi, Jérôme Feret:
Formal Reduction for Rule-based Models. MFPS 2011: 29-59 - 2010
- [c21]Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine:
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction. LICS 2010: 362-381 - [c20]Jérôme Feret, Thomas A. Henzinger, Heinz Koeppl, Tatjana Petrov:
Lumpability Abstractions of Rule-based Systems. MeCBIC 2010: 142-161 - [c18]Ferdinanda Camporesi, Jérôme Feret, Heinz Koeppl, Tatjana Petrov:
Combining Model Reductions. MFPS 2010: 73-96 - 2009
- [j4]Jérôme Feret, Vincent Danos, Jean Krivine, Russ Harmer, Walter Fontana:
Internal coarse-graining of molecular systems. Proc. Natl. Acad. Sci. USA 106(16): 6453-6458 (2009) - [j2]Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine:
Rule-Based Modelling and Model Perturbation. Trans. Comp. Sys. Biology 11: 116-137 (2009) - 2008
- [c16]Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine:
Rule-Based Modelling, Symmetries, Refinements. FMSB 2008: 103-122 - [c15]Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine:
Investigation of a Biological Repair Scheme. Workshop on Membrane Computing 2008: 1-12 - [c14]Vincent Danos, Jérôme Feret, Walter Fontana, Jean Krivine:
Abstract Interpretation of Cellular Signalling Networks. VMCAI 2008: 83-97 - 2007
- [c13]Vincent Danos, Jérôme Feret, Walter Fontana, Jean Krivine:
Scalable Simulation of Cellular Signaling Networks. APLAS 2007: 139-157 - [c12]Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine:
Rule-Based Modelling of Cellular Signalling. CONCUR 2007: 17-41
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