Finding a periodic attractor of a Boolean network

Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

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 languageEnglish
Article number6216351
Pages (from-to)1410-1421
Number of pages12
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume9
Issue number5
DOIs
StatePublished - 17 Aug 2012

Keywords

  • Boolean network
  • SAT
  • nested canalyzing function
  • periodic attractor
  • treewidth

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