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Jean Krivine

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Presentation

I am interested in fundamental aspects of computer science, mainly models for concurrency (non interleaving semantics, event structures), quantitative simulation (stochastic semantics), formal languages including bigraphs, kappa-calculus and process algebras. I am investigating applications of these concepts to highly distributed systems such as self assembling or transactional systems and molecular interaction networks.
I am interested in fundamental aspects of computer science, mainly models for concurrency (non interleaving semantics, event structures), quantitative simulation (stochastic semantics), formal languages including bigraphs, kappa-calculus and process algebras. I am investigating applications of these concepts to highly distributed systems such as self assembling or transactional systems and molecular interaction networks.

Publications

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Fundamentals of Compositional Rewriting Theory

Nicolas Behr , Russ Harmer , Jean Krivine
Journal of Logical and Algebraic Methods in Programming, 2023, 135, pp.100893. ⟨10.1016/j.jlamp.2023.100893⟩
Journal articles hal-03739405v1
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Rewriting theory for the life sciences: A unifying theory of CTMC semantics

Nicolas Behr , Jean Krivine , Jakob Andersen , Daniel Merkle
Theoretical Computer Science, 2021, 884, pp.68-115. ⟨10.1016/j.tcs.2021.07.026⟩
Journal articles hal-03835365v1

Compositionality of Rewriting Rules with Conditions

Nicolas Behr , Jean Krivine
Compositionality, 2021, 3, pp.2. ⟨10.32408/compositionality-3-2⟩
Journal articles hal-03835375v1
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A calculus of branching processes

Thomas Ehrhard , Jean Krivine , Ying Jiang
Theoretical Computer Science, 2019, ⟨10.1016/j.tcs.2019.06.028⟩
Journal articles hal-02357975v1
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The Kappa platform for rule-based modeling

Pierre Boutillier , Mutaamba Maasha , Xing Li , Héctor F Medina-Abarca , Jean Krivine
Bioinformatics, 2018, Bioinformatics, 34 (13), pp.i583-i592. ⟨10.1093/bioinformatics/bty272⟩
Journal articles hal-01962663v1
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Dynamic Influence Networks for Rule-Based Models

Angus G. Forbes , Andrew Burks , Kristine Lee , Xing Li , Pierre Boutillier
IEEE Transactions on Visualization and Computer Graphics, 2018, 24 (1), pp.184-194. ⟨10.1109/TVCG.2017.2745280⟩
Journal articles hal-02399102v1
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Combinatorial complexity and compositional drift in protein interaction networks.

Eric J. Deeds , Jean Krivine , Jérôme Feret , Vincent Danos , Walter Fontana
PLoS ONE, 2012, 7 (3), ⟨10.1371/journal.pone.0032032⟩
Journal articles hal-00677889v1
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Intrinsic Information carriers in combinatorial dynamical systems

Russ Harmer , Vincent Danos , Jérôme Feret , Jean Krivine , Walter Fontana
Chaos: An Interdisciplinary Journal of Nonlinear Science, 2010, 20 (3), pp.037108. ⟨10.1063/1.3491100⟩
Journal articles hal-00520128v1
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Internal coarse-graining of molecular systems

Jérôme Feret , Vincent Danos , Jean Krivine , Russ Harmer , Walter Fontana
Proceedings of the National Academy of Sciences of the United States of America, 2009, 106 (16), ⟨10.1073/pnas.0809908106⟩
Journal articles inria-00528330v1

Rule-Based Modelling and Model Perturbation

Vincent Danos , Jérôme Feret , Walter Fontana , Russ Harmer , Jean Krivine
Transactions on Computational Systems Biology, 2009, Transactions on Computational Systems Biology XI, 5750, pp.116-137. ⟨10.1007/978-3-642-04186-0_6⟩
Journal articles inria-00528364v1
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Computational self-assembly

Pierre-Louis Curien , Vincent Danos , Jean Krivine , Min Zhang
Theoretical Computer Science, 2008, 404 ((1-2)), pp.61-75
Journal articles hal-00155297v1

Clustering and thermodynamics in the lattice-gas model

Xavier Campi , Hubert Krivine , Jean Krivine
Physica A: Statistical Mechanics and its Applications, 2003, 320, pp.41-50. ⟨10.1016/S0378-4371(02)01514-5⟩
Journal articles hal-00012310v1
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Concurrency Theorems for Non-linear Rewriting Theories

Russ Harmer , Nicolas Behr , Jean Krivine
ICGT 2021 - 14th International Conference on Graph Transformation, Jun 2021, Bergen, Norway. pp.3-21, ⟨10.1007/978-3-030-78946-6_1⟩
Conference papers hal-03358036v1
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Distinguishing Context Dependent Events in Quotients of Causal Stories

Sébastien Légaré , Jean Krivine , Jérôme Feret
JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Sophie Schbath; Denis Thieffry, Jul 2021, Virtuel, France. pp.54-61
Conference papers hal-03389052v1
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Rewriting Theory for the Life Sciences

Nicolas Behr , Jean Krivine
International Conference on Graph Transformation 2020, Jun 2020, Bergen, Norway. pp.185-202, ⟨10.1007/978-3-030-51372-6_11⟩
Conference papers hal-02920023v1

A Tractable Logic for Molecular Biology

Adrien Husson , Jean Krivine
International Conference on Logic Programming, Sep 2019, Las Cruces, United States. pp.101-113, ⟨10.4204/EPTCS.306.17⟩
Conference papers hal-02399098v1

Interactions between Causal Structures in Graph Rewriting Systems

Ioana Cristescu , Walter Fontana , Jean Krivine
International Workshop on Formal reasoning about Causation, Responsibility, and Explanations in Science and Technology, Apr 2018, Thessalonique, Greece. pp.65-78, ⟨10.4204/EPTCS.286.6⟩
Conference papers hal-02922069v1

Incremental Update for Graph Rewriting

Thomas Ehrhard , Pierre Boutillier , Jean Krivine
European Symposium on Programming (ESOP), Apr 2017, Uppsala, Sweden. ⟨10.1007/978-3-662-54434-1_8⟩
Conference papers hal-02357978v1
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Rigid Families for CCS and the π-calculus

Ioana Cristescu , Jean Krivine , Daniele Varacca
12th International Colloquium on Theoretical Aspects of Computing (ICTAC 2015), Oct 2015, Cali, Colombia
Conference papers hal-01189062v1
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A compositional semantics for the reversible pi-calculus

Ioana Domnina Cristescu , Jean Krivine , Daniele Varacca
Logic in Computer Science, 2013, New Orleans, United States. pp.388-397, ⟨10.1109/LICS.2013.45⟩
Conference papers hal-00840156v1
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A verification technique for reversible process algebra

Jean Krivine
Fourth international workshop on reversible computation (RC 2012), 2012, Copenhagen, Denmark
Conference papers hal-00697549v3
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Models of Tet-On System with Epigenetic Effects

Russ Harmer , Jean Krivine , Élise Laruelle , Cédric Lhoussaine , Guillaume Madelaine
Computational Methods in Systems Biology 2012 (CMSB 2012, Flashposter), Oct 2012, London, United Kingdom. pp.378
Conference papers hal-00725553v1
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Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models

Vincent Danos , Jérôme Feret , Walter Fontana , Russell Harmer , Jonathan Hayman
FSTTCS 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⟩
Conference papers hal-00809065v1
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Formal Cellular Machinery

Troels C. Damgaard , Espen Hojsgaard , Jean Krivine
SASB 2011, 2011, Venice, Italy. pp.55-74, ⟨10.1016/j.entcs.2012.05.015⟩
Conference papers hal-00692416v1
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Abstracting the differential semantics of rule-based models: exact and automated model reduction

Vincent Danos , Jérôme Feret , Walter Fontana , Russell Harmer , Jean Krivine
Logic in Computer Science, 2010, Edinburgh, United Kingdom. pp.362-381
Conference papers hal-00520112v1
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Modelling epigenetic information maintenance a Kappa tutorial

Jean Krivine , Vincent Danos , Arndt Benecke
Computer Aided Verification, 2009, Grenoble, France. pp.17-32
Conference papers hal-00692430v1
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Investigation of a biological repair scheme

Vincent Danos , Jérôme Feret , Walter Fontana , Russell Harmer , Jean Krivine
the 9th Workshop on Membrane Computing - WMC9, Paun, G., Jul 2008, Edinburgh, United Kingdom. pp.1-12, ⟨10.1007/978-3-540-95885-7_1⟩
Conference papers inria-00528319v1
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Rule-based modelling, symmetries, refinements

Vincent Danos , Jérôme Feret , Walter Fontana , Russell Harmer , Jean Krivine
the 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⟩
Conference papers inria-00528339v1
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Stochastic Bigraphs

Jean Krivine , Robin Milner , Angelo Troina
Mathematical foundation of programming semantics 2008, 2008, United States. pp.73-96
Conference papers hal-00530712v1
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Abstract Interpretation of Cellular Signalling Networks

Vincent Danos , Jérôme Feret , Walter Fontana , Jean Krivine
the 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⟩
Conference papers inria-00528352v1

Self-assembling Trees

Vincent Danos , Fabien Tarissan , Jean Krivine
May 2007, pp.19-32
Conference papers hal-00155303v1

Rule-based modelling of cellular signalling

Vincent Danos , Jerome Feret , Walter Fontana , Russell Harmer , Jean Krivine
International Conference on Concurrency Theory (CONCUR'07), Sep 2007, Portugal
Conference papers hal-00164297v1

General Reversibility

Vincent Danos , Jean Krivine , Pawel Sobocinski
Jun 2007, pp.75-86
Conference papers hal-00156389v1
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Scalable Simulation of Cellular Signaling Networks

Vincent Danos , Jérôme Feret , Walter Fontana , Jean Krivine
the 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⟩
Conference papers inria-00528409v1

Transactions in RCCS

Vincent Danos , Jean Krivine
Sixteenth International Conference on Concurrency Theory (CONCUR'05), 2005, United Kingdom. pp.398-412
Conference papers hal-00164585v1
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Reversible Communicating Systems

Vincent Danos , Jean Krivine
CONCUR, 2004, Londres, United Kingdom. pp.292-307
Conference papers hal-00784051v1

Formal Molecular Biology done in CCS

Vincent Danos , Jean Krivine
BIO-CONCUR'03, Sep 2003, France. pp.31-49
Conference papers hal-00164586v1
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Modelling Systems Biology Wide and Deep

Sébastien Légaré , Jean Krivine , Russ Harmer , Jérôme Feret
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. CMSB
Conference poster hal-03357485v1
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Rule Based Modeling and Model Refinement

Elaine Murphy , Vincent Danos , Jérôme Feret , Jean Krivine , Russell Harmer
H. 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⟩
Book sections inria-00527981v1
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Rule-based modelling and model perturbations

Vincent Danos , Jérôme Feret , Walter Fontana , Russ Harmer , Jean Krivine
Corrado 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⟩
Book sections hal-00350299v1
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Algèbres de Processus Réversibles

Jean Krivine
Réseaux et télécommunications [cs.NI]. Université Pierre et Marie Curie - Paris VI, 2006. Français. ⟨NNT : ⟩
Theses tel-00519528v1

Revisiting the Liquidity/Risk Trade-Off with Smart Contracts (Short Paper)

Vincent Danos , Jean Krivine , Julien Prat
2nd International Conference on Blockchain Economics, Security and Protocols (Tokenomics 2020), Open Access Series in Informatics, No. 10, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 10:1-10:5, 2021, ⟨10.4230/OASIcs.Tokenomics.2020.10⟩
Proceedings hal-04336736v1

Reversible Computation

Jean Krivine , Jean-Bernard Stefani
Krivine, Jean; Stefani, Jean-Bernard. Reversible Computation, Jul 2015, Grenoble, France. 9138, Springer, 2015, Lecture Notes in Computer Science, 978-3-319-20859-6. ⟨10.1007/978-3-319-20860-2⟩
Proceedings hal-01246644v1
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A Rule-Based Model of Base Excision Repair

Agnes Köhler , Jean Krivine , Jakob Vidmar
Computational Methods in Systems Biology, 8859, Springer International Publishing; Springer, pp.173 - 195, 2014, Computational Methods in Systems Biology, ⟨10.1007/978-3-319-12982-2_13⟩
Proceedings hal-01107691v1

A Rule-Based Model of Base Excision Repair

Agnes Köhler , Jean Krivine , Jakob Vidmar
Computational Methods in Systems Biology. CMSB 2014, 8859, Springer International Publishing, pp.173-195, 2014, Lecture Notes in Computer Science, ⟨10.1007/978-3-319-12982-2_13⟩
Proceedings hal-04620127v1