Model checking
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Completely Derandomized Self-Adaptation in Evolution Strategies
Evolutionary Computation
On temporal logic constraint solving for analyzing numerical data time series
Theoretical Computer Science
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
From model-checking to temporal logic constraint solving
CP'09 Proceedings of the 15th international conference on Principles and practice of constraint programming
Temporal logic constraints in the biochemical abstract machine BIOCHAM
LOPSTR'05 Proceedings of the 15th international conference on Logic Based Program Synthesis and Transformation
Probabilistic model checking of complex biological pathways
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Algorithmic algebraic model checking i: challenges from systems biology
CAV'05 Proceedings of the 17th international conference on Computer Aided Verification
Temporal Logics for Phylogenetic Analysis via Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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In systems biology, the number of available models of cellular processes has increased rapidly, but re-using models in different contexts or for different questions remains a challenging issue. In this paper, we study the coupling of different models playing a role in the mammalian cell cycle and in cancer therapies. We show how the formalization of experimental observations in temporal logic with numerical constraints can be used to compute the unknown coupling kinetics parameter values agreeing with experimental data. This constraint-based approach to computing with partial information is illustrated through the design of a complex model of the mammalian cell cycle, the circadian clock, the p53/Mdm2 DNA-damage repair system, the metabolism of irinotecan and the control of cell exposure to it. We discuss the use of this model for cancer chronotherapies and evaluate its predictive power with respect to circadian core gene knock-outs.