EURASIP Journal on Bioinformatics and Systems Biology 
Volume 2008 (2008), Article ID 521407, 16 pages
doi:10.1155/2008/521407
Research Article

Algorithms and Complexity Analyses for Control of Singleton Attractors in Boolean Networks

Morihiro Hayashida,1 Takeyuki Tamura,1 Tatsuya Akutsu,1 Shu-Qin Zhang,2 and Wai-Ki Ching3

 1Bioinformatics Center, Laboratory of Biological Information Networks, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
2School of Mathematical Sciences, Fudan University, Shanghai 200433, China
3Advanced Modeling and Applied Computing Laboratory, Department of Mathematics, The University of Hong Kong, Pokfulam Road, Hong Kong
Received 12 January 2008; Revised 4 April 2008; Accepted 2 June 2008

Recommended by Ilya Shmulevich

Abstract

A Boolean network (BN) is a mathematical model of genetic networks. We propose several algorithms for control of singleton attractors in BN. We theoretically estimate the average-case time complexities of the proposed algorithms, and confirm them by computer experiments. The results suggest the importance of gene ordering. Especially, setting internal nodes ahead yields shorter computational time than setting external nodes ahead in various types of algorithms. We also present a heuristic algorithm which does not look for the optimal solution but for the solution whose computational time is shorter than that of the exact algorithms.