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Finding a Periodic Attractor of a Boolean Network

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4 Author(s)
Akutsu, T. ; Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan ; Kosub, S. ; Melkman, A.A. ; Tamura, T.

In this paper, we study the problem of finding a periodic attractor of a Boolean network (BN), which arises in computational systems biology and is known to be NP-hard. Since a general case is quite hard to solve, we consider special but biologically important subclasses of BNs. For finding an attractor of period 2 of a BN consisting of n OR functions of positive literals, we present a polynomial time algorithm. For finding an attractor of period 2 of a BN consisting of n AND/OR functions of literals, we present an O(1.985n) time algorithm. For finding an attractor of a fixed period of a BN consisting of n nested canalyzing functions and having constant treewidth w, we present an O(n2p(w+1)poly(n)) time algorithm.

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Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:9 ,  Issue: 5 )