An information theoretic approach to constructing robust boolean gene regulatory networks

Bane Vasić, Vida Ravanmehr, Anantha Raman Krishnan

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

We introduce a class of finite systems models of gene regulatory networks exhibiting behavior of the cell cycle. The network is an extension of a Boolean network model. The system spontaneously cycles through a finite set of internal states, tracking the increase of an external factor such as cell mass, and also exhibits checkpoints in which errors in gene expression levels due to cellular noise are automatically corrected. We present a 7-gene network based on Projective Geometry codes, which can correct, at every given time, one gene expression error. The topology of a network is highly symmetric and requires using only simple Boolean functions that can be synthesized using genes of various organisms. The attractor structure of the Boolean network contains a single cycle attractor. It is the smallest nontrivial network with such high robustness. The methodology allows construction of artificial gene regulatory networks with the number of phases larger than in natural cell cycle.

Original languageEnglish (US)
Article number5740844
Pages (from-to)52-65
Number of pages14
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume9
Issue number1
DOIs
StatePublished - Jan 1 2012

Keywords

  • Boolean networks
  • Gene regulatory networks
  • cell cycle
  • error correction
  • error correction coding

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics

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