Chaff: engineering an efficient SAT solver
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SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
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Periodic orbits and equilibria in glass models for gene regulatory networks
IEEE Transactions on Information Theory - Special issue on information theory in molecular biology and neuroscience
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Genetic Networks and Soft Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Theoretical Computer Science
Inference of Biological S-System Using the Separable Estimation Method and the Genetic Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Analysis of the attractors of a genetic regulatory network gives a good indication of the possible functional modes of the system. In this paper we are concerned with the problem of finding all steady states of genetic regulatory networks described by piecewise-linear differential equation (PLDE) models. We show that the problem is NP-hard and translate it into a propositional satisfiability (SAT) problem. This allows the use of existing, efficient SAT solvers and has enabled the development of a steady state search module of the computer tool Genetic Network Analyzer (GNA). The practical use of this module is demonstrated by means of the analysis of a number of relatively small bacterial regulatory networks as well as randomly generated networks of several hundreds of genes.