Gene ontology: tool for the unification of biology, Nature Genetics, vol.25, pp.25-29, 2000. ,
Complex intracellular calcium oscillations A theoretical exploration of possible mechanisms, Biophysical Chemistry, vol.66, issue.1, pp.25-41, 1997. ,
DOI : 10.1016/S0301-4622(97)00010-0
Machine Learning Biochemical Networks from Temporal Logic Properties, Transactions on Computational Systems Biology VI, pp.68-94 ,
DOI : 10.1007/11880646_4
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.75.5250
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, issue.14, pp.1805-1807, 2006. ,
DOI : 10.1093/bioinformatics/btl172
URL : https://hal.archives-ouvertes.fr/hal-01431364
Typeful programming, Formal Description of Programming Concepts, pp.431-507, 1991. ,
Brane calculi -interactions of biological membranes, Proceedings of the second international workshop on Computational Methods in Systems Biology, pp.257-280, 2004. ,
Symbolic Model Checking of Biochemical Networks, CMSB'03: Proceedings of the first workshop on Computational Methods in Systems Biology, pp.149-162, 2003. ,
DOI : 10.1007/3-540-36481-1_13
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.66.2355
Modeling and querying biomolecular interaction networks, Theoretical Computer Science, vol.325, issue.1, pp.25-44, 2004. ,
DOI : 10.1016/j.tcs.2004.03.063
URL : http://doi.org/10.1016/j.tcs.2004.03.063
Petri net modelling of biological networks, Briefings in Bioinformatics, vol.8, issue.4, 2007. ,
DOI : 10.1093/bib/bbm029
Steady States and Oscillations in the p53/Mdm2 Network, Cell Cycle, vol.4, issue.3, pp.488-493, 2005. ,
DOI : 10.4161/cc.4.3.1548
Subtyping Constraints in Quasi-lattices, Proceedings of the 23rd conference on foundations of software technology and theoretical computer science, FSTTCS'2003, pp.136-148, 2003. ,
DOI : 10.1007/978-3-540-24597-1_12
URL : https://hal.archives-ouvertes.fr/inria-00071653
Abstract interpretation and application to logic programs, The Journal of Logic Programming, vol.13, issue.2-3, pp.103-179, 1992. ,
DOI : 10.1016/0743-1066(92)90030-7
Types as abstract interpretation (invited paper), POPL'97: Proceedings of the 24th ACM Symposium on Principles of Programming Languages, pp.316-331, 1997. ,
Constructive design of a hierarchy of semantics of a transition system by abstract interpretation, Theoretical Computer Science, vol.277, issue.1-2, pp.47-103, 2002. ,
DOI : 10.1016/S0304-3975(00)00313-3
Abstract interpretation, Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on Principles of programming languages , POPL '77, pp.238-252, 1977. ,
DOI : 10.1145/512950.512973
URL : https://hal.archives-ouvertes.fr/hal-01108790
PATHWAY LOGIC: SYMBOLIC ANALYSIS OF BIOLOGICAL SIGNALING, Biocomputing 2002, pp.400-412, 2002. ,
DOI : 10.1142/9789812799623_0038
From Syntax to Semantics in Systems Biology Towards Automated Reasoning Tools, Transactions on Computational Systems Biology IV, vol.3939, pp.68-70, 2006. ,
DOI : 10.1007/11732488_6
Typing constraint logic programs, Theory and Practice of Logic Programming, vol.1, issue.06, pp.751-777, 2001. ,
DOI : 10.1017/S1471068401001120
Type Inference in Systems Biology, Proceedings of the fourth international conference on Computational Methods in Systems Biology, 2006. ,
DOI : 10.1007/11885191_4
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM, Journal of Biological Physics and Chemistry, vol.4, issue.2, pp.64-73, 2004. ,
DOI : 10.4024/2040402.jbpc.04.02
URL : https://hal.archives-ouvertes.fr/hal-01431345
Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model, Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control, HSCC'01, pp.232-246, 2001. ,
DOI : 10.1007/3-540-45351-2_21
A probabilistic model of a prokaryotic gene and its regulation, Computational Methods in Molecular Biology: From Genotype to Phenotype, 2000. ,
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets, CMSB'07: Proceedings of the fifth international conference on Computational Methods in Systems Biology, 2007. ,
DOI : 10.1007/978-3-540-75140-3_14
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.122.7585
General method for numerically simulating stochastic time evolution of coupled chemical-reactions, Journal of Computational Physics, vol.22, pp.403-434, 1976. ,
Exact stochastic simulation of coupled chemical reactions, Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977. ,
Rules for Modeling Signal-Transduction Systems, Science Signaling, vol.2006, issue.344, p.6, 2006. ,
DOI : 10.1126/stke.3442006re6
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.83.1561
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003. ,
DOI : 10.1093/bioinformatics/btg015
: Systems Biology, Annual Review of Genomics and Human Genetics, vol.2, issue.1, pp.343-372, 2001. ,
DOI : 10.1146/annurev.genom.2.1.343
KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000. ,
DOI : 10.1093/nar/28.1.27
Private communication, 2006. ,
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. ,
DOI : 10.1091/mbc.10.8.2703
Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties, Proceedings of the National Academy of Sciences, vol.97, issue.11, pp.975818-5823, 2000. ,
DOI : 10.1073/pnas.97.11.5818
Complex calcium oscillations and the role of mitochondria and cytosolic proteins, Biosystems, vol.57, issue.2, pp.75-86, 2000. ,
DOI : 10.1016/S0303-2647(00)00090-3
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades, The Journal of Cell Biology, vol.71, issue.3, pp.353-359, 2005. ,
DOI : 10.1074/jbc.M103369200
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2172246
Bistability and oscillations in the huang-ferrell model of mapk signaling, PLoS Computational Biology, vol.3, issue.9, pp.1819-1826, 2007. ,
Petri net representations in metabolic pathways ,
Application of petri net based analysis techniques to signal transduction pathways, BMC Bioinformatics, vol.7, issue.482, 2006. ,
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae, Bioinformatics, vol.18, issue.2, pp.51-61, 2002. ,
DOI : 10.1093/bioinformatics/18.2.351
Modeling dynamic phenomena in molecular and cellular biology, 1984. ,
CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems, CMSB'04: Proceedings of the second international workshop on Computational Methods in Systems Biology, pp.231-235, 2004. ,
DOI : 10.1093/nar/28.1.27
Graphic Requirements for Multistationarity, Complexus, vol.1, issue.3, pp.123-133, 2003. ,
DOI : 10.1159/000076100
A Complex Control Circuit. Regulation of Immunity in Temperate Bacteriophages, European Journal of Biochemistry, vol.54, issue.1, pp.211-227, 1976. ,
DOI : 10.1016/0022-5193(72)90062-8
Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.170-195, 2001. ,
DOI : 10.1063/1.1350439
A Hidden Feedback in Signaling Cascades Is Revealed, PLoS Computational Biology, vol.164, issue.3, 2008. ,
DOI : 10.1371/journal.pcbi.1000041.s007
URL : https://hal.archives-ouvertes.fr/hal-00267106
Topological analysis of metabolic networks based on petri net theory, In Silico Biology, vol.3, issue.29, 2003. ,