Finding a periodic attractor of a Boolean network.
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.
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan. takutsu@kuicr.kyoto-u.ac.jp
Tatsuya
T
Akutsu
Sven
S
Kosub
Avraham A
AA
Melkman
Takeyuki
T
Tamura
D000465:Algorithms; D020869:Gene Expression Profiling; D049490:Systems Biology