Finding a Periodic Attractor of a Boolean Network

Authors:
Tatsuya Akutsu;Sven Kosub;Avraham A. Melkman;Takeyuki Tamura
Affiliations:
Kyoto University, Kyoto;University of Konstanz, Konstanz;Ben-Gurion University of the Negev, Beer-Sheva;Kyoto University, Kyoto
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2012

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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(1.985^n) 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(n^{2p(w+1)} poly(n)) time algorithm.