Dynamical properties of a boolean model of gene regulatory network with memory

J Comput Biol. 2011 Oct;18(10):1291-303. doi: 10.1089/cmb.2010.0069. Epub 2011 Jan 7.

Abstract

Classical random Boolean networks (RBN) are not well suited to describe experimental data from time-course microarray, mainly because of the strict assumptions about the synchronicity of the regulatory mechanisms. In order to overcome this setback, a generalization of the RBN model is described and analyzed. Gene products (e.g., regulatory proteins) are introduced, with each one characterized by a specific decay time, thereby introducing a form of memory in the system. The dynamics of these networks is analyzed, and it is shown that the distribution of the decay times has a strong effect that can be adequately described and understood. The implications for the dynamical criticality of the networks are also discussed.

MeSH terms

  • Algorithms*
  • Computational Biology
  • Computer Simulation
  • Gene Expression Regulation
  • Gene Regulatory Networks*
  • Models, Genetic*
  • Molecular Dynamics Simulation*
  • Time