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J Comput Biol. 2011 Oct;18(10):1275-90. doi: 10.1089/cmb.2010.0281. Epub 2011 May 9.

Determining a singleton attractor of a boolean network with nested canalyzing functions.

Author information

1
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyot, Japan. takutsu@kuicr.kyoto-u.ac.jp

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.

PMID:
21554129
DOI:
10.1089/cmb.2010.0281
[Indexed for MEDLINE]

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