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.
Original language | English |
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Article number | 6216351 |
Pages (from-to) | 1410-1421 |
Number of pages | 12 |
Journal | IEEE/ACM Transactions on Computational Biology and Bioinformatics |
Volume | 9 |
Issue number | 5 |
DOIs | |
State | Published - 17 Aug 2012 |
Keywords
- Boolean network
- SAT
- nested canalyzing function
- periodic attractor
- treewidth
ASJC Scopus subject areas
- Biotechnology
- Genetics
- Applied Mathematics