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Issue No. 05 - Sept.-Oct. (2012 vol. 9)
ISSN: 1545-5963
pp: 1410-1421
Avraham A. Melkman , Dept. of Comput. Sci., Ben-Gurion Univ. of the Negev, Beer-Sheva, Israel
Sven Kosub , Dept. of Comput. & Inf. Sci., Univ. of Konstanz, Konstanz, Germany
Tatsuya Akutsu , Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan
Takeyuki Tamura , Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan
ABSTRACT
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.
INDEX TERMS
polynomials, biology computing, Boolean functions, genetic algorithms, time algorithm, periodic attractor, Boolean network, computational systems biology, positive literals, polynomial time algorithm, AND-OR functions, nested canalyzing functions, constant treewidth, Boolean functions, Computational systems biology, Polynomials, treewidth., Boolean network, periodic attractor, SAT, nested canalyzing function
CITATION
Avraham A. Melkman, Sven Kosub, Tatsuya Akutsu, Takeyuki Tamura, "Finding a Periodic Attractor of a Boolean Network", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. , pp. 1410-1421, Sept.-Oct. 2012, doi:10.1109/TCBB.2012.87
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