Incorporating time delays into the logical analysis of gene regulatory networks
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Action-based analysis of discrete regulatory networks with short-term stimuli
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
Stochasticity in reactions: a probabilistic Boolean modeling approach
Proceedings of the 8th International Conference on Computational Methods in Systems Biology
On the use of temporal formal logic to model gene regulatory networks
CIBB'09 Proceedings of the 6th international conference on Computational intelligence methods for bioinformatics and biostatistics
Formal Analysis of Oscillatory Behaviors in Biological Regulatory Networks: An Alternative Approach
Electronic Notes in Theoretical Computer Science (ENTCS)
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Starting from the logical description of gene regulatory networks developed by R. Thomas, we introduce an enhanced modeling approach based on timed automata. We obtain a refined qualitative description of the dynamical behavior by exploiting not only information on ratios of kinetic parameters related to synthesis and decay, but also constraints on the time delays associated with the operations of the system. We develop a formal framework for handling such temporal constraints using timed automata, discuss the relationship with the original Thomas formalism, and demonstrate the potential of our approach by analyzing an illustrative gene regulatory network of bacteriophage @l.