title: Modelling gene and protein regulatory networks with answer set programming.
abstract: Recently, many approaches to model regulatory networks have been proposed in the systems biology domain. However, the task is far from being solved. In this paper, we propose an Answer Set Programming (ASP)-based approach to model interaction networks. We build a general ASP framework that describes the network semantics and allows modelling specific networks with little effort. ASP provides a rich and flexible toolbox that allows expanding the framework with desired features. In this paper, we tune our framework to mimic Boolean network behaviour and apply it to model the Budding Yeast and Fission Yeast cell cycle networks. The obtained steady states of these networks correspond to those of the Boolean networks.
authors.affiliation: Department of Applied Mathematics and Computer Science, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Belgium. timur.fayruzov@ugent.be
authors.forename: Timur
authors.initials: T
authors.lastname: Fayruzov
authors.forename: Jeroen
authors.initials: J
authors.lastname: Janssen
authors.forename: Dirk
authors.initials: D
authors.lastname: Vermeir
authors.forename: Chris
authors.initials: C
authors.lastname: Cornelis
authors.forename: Martine
authors.initials: M
authors.lastname: De Cock
mesh_terms: D000465:Algorithms; D002453:Cell Cycle / Q000235:genetics; D019295:Computational Biology; D003198:Computer Simulation; D057225:Data Mining; D053263:Gene Regulatory Networks; D008954:Models, Biological; D008957:Models, Genetic; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D004718:Saccharomycetales / Q000166:cytology / Q000235:genetics; D012568:Schizosaccharomyces / Q000166:cytology / Q000235:genetics; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics; D012984:Software; D049490:Systems Biology
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins