Attractor identification in asynchronous Boolean dynamics with network reduction
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Abstract: Identification of attractors, that is, stable states and sustained oscillations, is an important step in the analysis of Boolean models and exploration of potential variants. We describe an approach to the search for asynchronous cyclic attractors of Boolean networks that exploits, in a novel way, the established technique of elimination of components. Computation of attractors of simplified networks allows the identification of a limited number of candidate attractor states, which are then screened with techniques of reachability analysis combined with trap space computation. An implementation that brings together recently developed Boolean network analysis tools, tested on biological models and random benchmark networks, shows the potential to significantly reduce running times.
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Cites work
- A reduction method for Boolean network models proven to conserve attractors
- An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks
- Attractor analysis of asynchronous Boolean models of signal transduction networks
- Attractor separation and signed cycles in asynchronous Boolean networks
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Cited in
(5)- An ASP-based approach for attractor enumeration in synchronous and asynchronous Boolean networks
- Boolean dynamics revisited through feedback interconnections
- SAF: SAT-based attractor finder in asynchronous automata networks
- Reduction for asynchronous Boolean networks: elimination of negatively autoregulated components
- An open problem: why are motif-avoidant attractors so rare in asynchronous Boolean networks?
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