Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IJCAI'05 Proceedings of the 19th international joint conference on Artificial intelligence
Automated symbolic reachability analysis: with application to delta-notch signaling automata
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
AB'07 Proceedings of the 2nd international conference on Algebraic biology
A fast linear-arithmetic solver for DPLL(T)
CAV'06 Proceedings of the 18th international conference on Computer Aided Verification
Which codes have cycle-free Tanner graphs?
IEEE Transactions on Information Theory
Computing Binary Combinatorial Gray Codes Via Exhaustive Search With SAT Solvers
IEEE Transactions on Information Theory
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Glass models are frequently used to model gene regulatory networks. A distinct feature of the Glass model is that its dynamics can be formalized as paths through multi-dimensional binary hypercubes. In this paper, we report a broad range of results about Glass models that have been obtained by computing the binary codes that correspond to the hypercube paths. Specifically, we propose algorithmic methods for the synthesis of specific Glass networks based on these codes. In contrast to existing work, bi-periodic networks and networks possessing both stable equilibria and periodic trajectories are considered. The robustness of the attractor is also addressed, which gives rise to hypercube paths with nondominated nodes and double coils. These paths correspond to novel combinatorial problems, for which initial experimental results are presented. Finally, a classification of Glass networks with respect to their corresponding gene interaction graphs for three genes is presented.