Qualitative reasoning: modeling and simulation with incomplete knowledge
Qualitative reasoning: modeling and simulation with incomplete knowledge
Series of Abstractions for Hybrid Automata
HSCC '02 Proceedings of the 5th International Workshop on Hybrid Systems: Computation and Control
Hybrid modeling and simulation of genetic regulatory networks
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE
Electronic Notes in Theoretical Computer Science (ENTCS)
Automatica (Journal of IFAC)
Analysing formal models of genetic regulatory networks with delays
International Journal of Bioinformatics Research and Applications
Brief paper: A mathematical framework for the control of piecewise-affine models of gene networks
Automatica (Journal of IFAC)
Box invariance in biologically-inspired dynamical systems
Automatica (Journal of IFAC)
IJCAI'05 Proceedings of the 19th international joint conference on Artificial intelligence
Hybrid models for gene regulatory networks: the case of lac operon in E. Coli
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
Qualitative analysis of nonlinear biochemical networks with piecewise-affine functions
HSCC'07 Proceedings of the 10th international conference on Hybrid systems: computation and control
Reconstruction of switching thresholds in piecewise-affine models of genetic regulatory networks
HSCC'06 Proceedings of the 9th international conference on Hybrid Systems: computation and control
Compositional reachability analysis of genetic networks
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Delays in biological regulatory networks (BRN)
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
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The switch-like character of the dynamics of genetic regulatory networks has attracted much attention from mathematical biologists and researchers on hybrid systems alike. We extend our previous work on a method for the qualitative analysis of hybrid models of genetic regulatory networks, based on a class of piecewise-affine differential equation (PADE) models, in two directions. First, we present a refinement of the method using a discrete or qualitative abstraction that preserves stronger properties of the dynamics of the PA systems, in particular the sign patterns of the derivatives of the concentration variables. The discrete transition system resulting from the abstraction is a conservative approximation of the dynamics of the PA system and can be computed symbolically. Second, we apply the refined method to a regulatory system whose functioning is not yet well-understood by biologists, the nutritional stress response in the bacterium Escherichia coli.