title: A SAT-based algorithm for finding attractors in synchronous Boolean networks.
abstract: This paper addresses the problem of finding attractors in synchronous Boolean networks. The existing Boolean decision diagram-based algorithms have limited capacity due to the excessive memory requirements of decision diagrams. The simulation-based algorithms can be applied to larger networks, however, they are incomplete. We present an algorithm, which uses a SAT-based bounded model checking to find all attractors in a Boolean network. The efficiency of the presented algorithm is evaluated by analyzing seven networks models of real biological processes, as well as 150,000 randomly generated Boolean networks of sizes between 100 and 7,000. The results show that our approach has a potential to handle an order of magnitude larger models than currently possible.
authors.affiliation: Department of Electronics, Computer and Software Systems, Royal Institute of Technology, ECS/ICT/KTH, Forum 105, 164 40 Kista, Stockholm, Sweden. dubrova@kth.se
authors.forename: Elena
authors.initials: E
authors.lastname: Dubrova
authors.forename: Maxim
authors.initials: M
authors.lastname: Teslenko
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D008322:Mammals; D008957:Models, Genetic; D015233:Models, Statistical; D015398:Signal Transduction; D015003:Yeasts