Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets, Bioinformatics, vol.15, issue.3, pp.234-242, 1999. ,
Ligand-dependent responses of the ErbB signaling network: experimental and modeling analysis, Molecular Systems Biology, vol.3, issue.144, 2007. ,
Using hybrid concurrent constraint programming to model dynamic biological systems, Proceedings of ICLP'02, International Conference on Logic Programming, vol.2401, pp.85-99, 2002. ,
URL : https://hal.archives-ouvertes.fr/inria-00100783
A comprehensive modular map of molecular interactions in RB/E2F pathway, Molecular Systems Biology, vol.4, issue.173, 2008. ,
Modeling and querying biochemical interaction networks, Theoretical Computer Science, vol.325, issue.1, pp.25-44, 2004. ,
Deadlock analysis of petri nets using siphons and mathematical programming, IEEE Transactions on Robotics and Automation, vol.13, issue.6, pp.793-804, 1997. ,
Deadlocks in petri nets, Applied Data Research Inc, 1972. ,
A declarative constraintbased method for analyzing discrete genetic regulatory networks, Biosystems, vol.98, issue.2, pp.91-104, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00793012
Characterization of minimal and basis siphons with predicate logic and binary programming, Proceedings of IEEE International Symposium on Computer-Aided Control System Design, pp.193-198, 2002. ,
Some results on the computation of minimal siphons in petri nets, Proceedings of the 42nd IEEE Conference on Decision and Control, 2003. ,
Enumeration algorithms for minimal siphons in petri nets based on place constraints, IEEE transactions on systems, man and cybernetics. Part A, Systems and humans, vol.35, pp.844-854, 2005. ,
The monadic second-order logic of graphs i. recognizable sets of finite graphs. Information and Computation, pp.12-75, 1990. ,
Automata for the verification of monadic second-order graph properties, Journal of Applied Logic, pp.368-409, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00611853
Experimental results on the crossover point in satisfiability problems, Proceedings of the 11th National Conference on Artificial Intelligence, pp.21-27, 1993. ,
Can sugars be produced from fatty acids? a test case for pathway analysis tools, Bioinformatics, vol.25, issue.1, pp.152-158, 2009. ,
Identification of all steady states in large biological systems by logical analysis, Bulletin of Mathematical Biology, vol.65, pp.1025-1051, 2003. ,
Design and implementation of the GNU Prolog system, Journal of Functional and Logic Programming, vol.6, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-00693240
Chemical organisation theory, Bulletin of Mathematical Biology, vol.69, issue.4, pp.1199-1231, 2007. ,
CLPGUI: a generic graphical user interface for constraint logic programming, Journal of Constraints, Special Issue on User-Interaction in Constraint Satisfaction, vol.9, issue.4, pp.241-262, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-01431350
Modeling the molecular network controlling adhesion between human endothelial cells: Inference and simulation using constraint logic programming, CMSB'04: Proceedings of the 20 international conference on Computational Methods in Systems Biology, pp.104-118, 2004. ,
A comparison of structural CSP decomposition methods, Artificial Intelligence, vol.124, 2000. ,
Petriweb: A repository for petri nets, Petri Nets and Other Models of Concurrency -ICATPN, vol.4024, pp.411-420, 2006. ,
Petri nets for systems and synthetic biology, 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, vol.5016, pp.215-264, 2008. ,
Roles of triosephosphate isomerase and aerobic metabolism in trypanosoma brucei, Biochem. J, vol.357, pp.117-125, 2001. ,
Using chemical organization theory for model checking, Bioinformatics, vol.25, issue.15, pp.1915-1922, 2009. ,
Reducibility among combinatorial problems, Proceedings of a Symposium on the Complexity of Computer Computations, pp.85-103, 1972. ,
Generating siphons and traps by petri net representation of logic equations, Proceedings of 2th Conference of the Net Theory SIG-IECE, pp.93-100, 1986. ,
Courcelle's theorem -a game-theoretic approach, Discrete Optimization, vol.8, issue.4, pp.568-594, 2011. ,
Molecular interaction map of the mammalian cell cycle control and DNA repair systems, Molecular Biology of the Cell, vol.10, issue.8, pp.2703-2734, 1999. ,
A new constraint-based description of the steady-state flux cone of metabolic networks, Computational Biology, vol.157, pp.2257-2266, 2009. ,
Linear algebraic calculation of deadlocks and traps, Concurrency and Nets Advances in Petri Nets, pp.315-336, 1987. ,
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems, Nucleic Acid Research, vol.1, issue.34, pp.689-691, 2006. ,
Deadlocks and traps in petri nets as horn-satisfiability solutions and some related polynomially solvable problems, Discrete Applied Mathematics, vol.29, pp.195-210, 1990. ,
Hard and easy distributions of sat problems, Proceedings of the 10th National Conference on Artificial Intelligence, pp.459-465, 1992. ,
Petri nets: properties, analysis and applications, Proceedings of the IEEE, vol.77, pp.541-579, 1989. ,
Finding minimal siphons as a CSP, CP'11: The Seventeenth International Conference on Principles and Practice of Constraint Programming, pp.67-72, 2011. ,
A boolean model for enumerating minimal siphons and traps in petri-nets, Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, vol.7514, pp.798-814, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02308495
Steady-state solution of biochemical systems, beyond S-Systems via T-invariants, CMSB'10: Proceedings of the 8th International Conference on Computational Methods in Systems Biology, pp.14-22, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01779507
New algorithms for deciding the siphon-trap property, PETRI NETS'10 Proceedings of the 31st international conference on Applications and Theory of Petri Nets, pp.267-286, 2010. ,
Petri Net Theory and the Modeling of Systems, 1981. ,
Petri net representations in metabolic pathways, Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB), pp.328-336, 1993. ,
Graph minors. II. Algorithmic aspects of tree-width, Journal of Algorithms, vol.7, issue.3, pp.309-322, 1986. ,
Computational modeling of the dynamics of the map kinase cascade activated by surface and internalized egf receptors, Nature Biotechnology, vol.20, issue.4, pp.370-375, 2002. ,
Invariants and other structural properties of biochemical models as a constraint satisfaction problem, Algorithms for Molecular Biology, vol.7, issue.15, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00784404
, Biochemistry. Freeman, 1995.
Finding minimal siphons in general petri nets, IEICE Trans. on Fundamentals in Electronics, pp.1817-1824, 1996. ,
Metatool 5.0: fast and flexible elementary modes analysis, Bioinformatics, vol.22, issue.15, pp.1930-1931, 2006. ,
Time complexity analysis of the minimal siphon extraction problem of petri nets, EICE Trans. on Fundamentals of Electronics, Communications and Computer Sciences, pp.2558-2565, 1999. ,
Topological analysis of metabolic networks based on petri net theory, In Silico Biology, vol.3, issue.29, 2003. ,