Graph-Based Algorithms for Boolean Function Manipulation
IEEE Transactions on Computers
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Transactions on Computational Systems Biology VII
Local Structure and Behavior of Boolean Bioregulatory Networks
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Proving stabilization of biological systems
VMCAI'11 Proceedings of the 12th international conference on Verification, model checking, and abstract interpretation
Dynamically consistent reduction of logical regulatory graphs
Theoretical Computer Science
Petri net representation of multi-valued logical regulatory graphs
Natural Computing: an international journal
Static Analysis of Boolean Networks Based on Interaction Graphs: A Survey
Electronic Notes in Theoretical Computer Science (ENTCS)
Concretizing the process hitting into biological regulatory networks
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Efficient handling of large signalling-regulatory networks by focusing on their core control
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Model-Checking signal transduction networks through decreasing reachability sets
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
Algebraic Representation of Asynchronous Multiple-Valued Networks and Its Dynamics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The complexity of biological regulatory networks calls for the development of proper mathematical methods to model their structures and to obtain insight in their dynamical behaviours. One qualitative approach consists in modelling regulatory networks in terms of logical equations (using either Boolean or multi-valued discretisation). In this paper, we propose a novel implementation of the generalised logical formalism by means of Multi-valued Decision Diagrams. We show that the use of this representation enables the development of efficient algorithms for the analysis of specific dynamical properties of the regulatory graphs. In particular, we address the question of determining conditions insuring the functionality of feedback circuits, as well as the identification of stable states. Finally, we apply these algorithms to logical models of T cell activation and differentiation.