Determining a singleton attractor of a Boolean network with nested canalyzing functions

Tatsuya Akutsu, Avraham A. Melkman, Takeyuki Tamura, Masaki Yamamoto

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

In this article, we study the problem of finding a singleton attractor for several biologically important subclasses of Boolean networks (BNs). The problem of finding a singleton attractor in a BN is known to be NP-hard in general. For BNs consisting of n nested canalyzing functions, we present an O(1.799 n) time algorithm. The core part of this development is an O(min(2 k/2•2 m/2, 2 k)•poly(k, m)) time algorithm for the satisfiability problem for m nested canalyzing functions over k variables. For BNs consisting of chain functions, a subclass of nested canalyzing functions, we present an O(1.619 n) time algorithm and show that the problem remains NP-hard, even though the satisfiability problem for m chain functions over k variables is solvable in polynomial time. Finally, we present an o(2 n) time algorithm for bounded degree BNs consisting of canalyzing functions.

Original languageEnglish
Pages (from-to)1275-1290
Number of pages16
JournalJournal of Computational Biology
Volume18
Issue number10
DOIs
StatePublished - 1 Oct 2011

Keywords

  • Boolean network
  • SAT
  • nested canalyzing function
  • singleton attractor

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