Computing maximal and minimal trap spaces of Boolean networks
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Abstract: Asymptotic behaviors are often of particular interest when analyzing Boolean networks that represent biological systems such as signal trans- duction or gene regulatory networks. Methods based on a generalization of the steady state notion, the so-called trap spaces, can be exploited to investigate attractor properties as well as for model reduction techniques. In this paper, we propose a novel optimization-based method for com- puting all minimal and maximal trap spaces and motivate their use. In particular, we add a new result yielding a lower bound for the number of cyclic attractors and illustrate the methods with a study of a MAPK pathway model. To test the efficiency and scalability of the method, we compare the performance of the ILP solver gurobi with the ASP solver potassco in a benchmark of random networks.
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(18)- Modeling multi-valued biological interaction networks using fuzzy answer set programming
- Variable stabilisation in Boolean monotonic model pools
- Minimal trap spaces of logical models are maximal siphons of their Petri net encoding
- Attractor separation and signed cycles in asynchronous Boolean networks
- Correspondence of Trap Spaces in Different Models of Bioregulatory Networks
- CONTROLLING THE CELL CYCLE RESTRICTION SWITCH ACROSS THE INFORMATION GRADIENT
- Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding
- Tackling universal properties of minimal trap spaces of Boolean networks
- Linear cuts in Boolean networks
- Reduction for asynchronous Boolean networks: elimination of negatively autoregulated components
- Computational complexity of minimal trap spaces in Boolean networks
- A semantics for Boolean networks consistent with regulatory threshold constraints
- Modular control of Boolean network models
- An open problem: why are motif-avoidant attractors so rare in asynchronous Boolean networks?
- An integer programming framework for identifying stable components in asynchronous Boolean networks
- An ASP-based approach for Boolean networks representation and attractor detection
- Trapping and commutative Boolean networks
- Computing bottom SCCs symbolically using transition guided reduction
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