Modelling gene and protein regulatory networks with Answer Set Programming

: 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 to model specific networks with little effort. ASP provides a rich and flexible toolbox that allows to expand 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. Obtained steady states of these networks correspond to those of the boolean networks.

• Type: Journal
• Year: 2011
• Where: IJDMB
• Authors: Timur Fayruzov, Jeroen Janssen, Dirk Vermeir, Chris Cornelis, Martine De Cock
• Keywords: Budding Yeast, IJDMB 2011, Model Interaction, Yeast Cell Cycle