Finding a periodic attractor of a Boolean network

IEEE/ACM Trans Comput Biol Bioinform. 2012 Sep-Oct;9(5):1410-21. doi: 10.1109/TCBB.2012.87.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Gene Expression Profiling
  • Systems Biology*