Scientific activities

Programming

As part of the Kappa project, I am developing KaSim, an efficient stochastic simulator for rule-based models in Kappa. Binaries, source code and other useful resources are available here

Ongoing grants

2019-2023: ANR  DCORE - Causality in concurrent systems (with INRIA & ENS Paris)

2019-2021: Bourse de la chaire blockchain de l’École Polytechnique (LIX/INRIA/Capgemini)

Some talks

From Molecules to Systems: the problem of knowledge representation in molecular biology. Collège de France seminar (in French!) from Chaire Informatique et Sciences de l’Information, Walter Fontana (2019).


Physical systems, composite explanations and diagrams. Invited talk at SYCO5, 2019.


Jobbers, sentient buildings and lions: a short walk into Robin Milner’s tower. In memoriam of Robin Milner, talk at the Milner Symposium in Edinburgh (2012).

Publications

My complete list of publication can be found here

Otherwise, you can check what google believes my publications are here.

Some selected publications

Concurrency theory / Graph Rewriting

Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics. Nicolas Behr, Jean Krivine. Proceedings of the International Conference on Graph Transformation. ICGT 2020, pp.185-202, 2020, 

A calculus of branching processes. Thomas Ehrhard, Ying Jiang and Jean Krivine. Slides of OPCT19. To appear in  Theoretical Comp. Sci. 2019.

Incremental Update for Graph Rewriting . Pierre Boutillier, Thomas Ehrhard and Jean Krivine. ESOP2017 :201-228 . Lecture Notes in Computer Science 10201

Rigid Families for the Reversible pi-calculus. Ioana D. Cristescu, Jean Krivine and Daniele Varacca. Proceedings of RC 2016 . To appear in LNCS 9720.

Rigid families for CCS and the pi-calculus . Ioana D. Cristescu, Jean Krivine and Daniele Varacca. Proceedings of ICTAC 2015 . LNCS volume 9399, pp 223-240 2015.

A compositional semantics for the reversible pi-calculus . Ioana D. Cristescu , Jean Krivine and Daniele Varacca . Proceedings of LICS 2013 . IEEE Computer Society, pp. 388-397

Formal methods for Systems Biology

A tractable logic for Molecular Biology . Adrien Husson and Jean Krivine. ICLP 2019 .

The Kappa platform for rule-based modeling . Pierre Boutillier, Mutaamba Maasha, Xing Li, Hector Medina, Jean Krivine, Jerome Feret, Ioana Cristescu, Angus Forbes and Walter Fontana. Presented at ISMB 2018 .  Bioinformatics,  34(13), i583–i592,.

Dynamic Influence Networks for Rule-based Models . Forbes AG,Burks A,Lee K,Li X,Boutillier P,Krivine J,Fontana W. IEEE Trans Vis Comput Graph.2017.

Semantics column on Systems biology . Jean Krivine. ACM Siglog news. Vol 4(3) p. 43-61. 2017

A rule-based model of base excision repair . Agnes Köhler, Jean Krivine and Jakob Vidmar. Proceedings of CMSB 2014 . Lecture Notes in Computer Science Volume 8859, 2014, pp. 173-195.

Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models . Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Christopher D. Thompson-Walsh, Glynn Winskel. FSTTCS 2012 : 276-288

Formal Cellular Machinery Troels C. Damgaard, Espen Hojsgaard and Jean Krivine. Proceedings of SASB 2011, to appear in ENTCS. (Keynote talk)

Combinatorial Complexity and Compositional Drift in Protein Interaction Networks Eric J. Deeds, Jean Krivine, Jérôme Feret, Vincent Danos and Walter Fontana. PLoS ONE 7(3): e32032. doi:10.1371/journal.pone.0032032, published 08 Mar 2012.

Abstracting the differential semantics of rule-based models: exact and automated model reduction . Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer et Jean Krivine. Proceedings of LICS 2010, p. 362-381 IEEE Computer Society (Invited paper)

Intrinsic Information carriers in combinatorial dynamical systems. Russell Harmer, Vincent Danos, Jerome Feret, Jean Krivine, Walter Fontana, Chaos. 2010 Sep;20(3):037108.

Internal coarse-graining of Molecular Systems . Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer and Jean Krivine. Vol. 106(16), Proceedings of the National Academy of Science ( PNAS ), p. 6453-6458, 2009.