Application of formal methods to biological regulatory networks: extending Thomas??? asynchronous logical approach with temporal logic, Journal of Theoretical Biology, vol.229, issue.3, pp.339-347, 2004. ,
DOI : 10.1016/j.jtbi.2004.04.003
Analysis of signalling pathways using the continuous time markow chains, Transactions on Computational Systems Biology VI CM- SB'05 Special Issue, pp.44-67, 2006. ,
Machine Learning Biochemical Networks from Temporal Logic Properties, Transactions on Computational Systems Biology VI CMSB'05 Special Issue, pp.68-94, 2006. ,
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
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
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
Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle, Molecular Biology of the Cell, vol.11, issue.1, pp.396-391, 2000. ,
DOI : 10.1091/mbc.11.1.369
Model Checking [12] Vincent Danos and Cosimo Laneve. Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 1999. ,
PATHWAY LOGIC: SYMBOLIC ANALYSIS OF BIOLOGICAL SIGNALING, Biocomputing 2002, pp.400-412, 2002. ,
DOI : 10.1142/9789812799623_0038
Temporal logic constraints in the biochemical abstract machine biocham (invited talk), Proceedings of Logic Based Program Synthesis and Transformation , LOPSTR'05, number 3901 in Lecture Notes in Computer Science, 2005. ,
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
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
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
Probabilistic Model Checking of Complex Biological Pathways, Proc. Computational Methods in Systems Biology (CM- SB'06), pp.32-47, 2006. ,
DOI : 10.1007/11885191_3
Inferring quantitative models of regulatory networks from expression data, Bioinformatics, vol.20, issue.Suppl 1, pp.248-256, 2004. ,
DOI : 10.1093/bioinformatics/bth941
AMT: A Property-Based Monitoring Tool for Analog Systems, Proceedings of 5th International Conference on Formal Modelling and Analysis of Times Systems, FORMATS'07, 2007. ,
DOI : 10.1007/978-3-540-75454-1_22
A correct abstract machine for the stochastic pi-calculus ,
Petri net representations in metabolic pathways, Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB), pp.328-336, 1993. ,
BioAmbients: an abstraction for biological compartments, Theoretical Computer Science, vol.325, issue.1, pp.141-167, 2004. ,
DOI : 10.1016/j.tcs.2004.03.061
Representation and simulation of biochemical processes using the pi-calculus process algebra, Proceedings of the sixth Pacific Symposium of Biocomputing, pp.459-470, 2001. ,
Inference of genetic regulatory networks from time series gene expression data, JCNN, pp.1215-1220, 2004. ,