Logical modeling and dynamical analysis of cellular networks

Wassim Abou-Jaoudé, Pauline Traynard, Pedro T. Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, Claudine Chaouiya

Research output: Contribution to journalReview article

76 Scopus citations

Abstract

The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle.

Original languageEnglish (US)
Article number94
JournalFrontiers in Genetics
Volume7
Issue numberMAY
DOIs
StatePublished - May 31 2016

Keywords

  • Attractors
  • Cell cycle control
  • Discrete dynamics
  • Logical modeling
  • Reachability analysis
  • Regulatory and signaling networks
  • Simulation
  • T cells activation and differentiation

ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Genetics(clinical)

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    Abou-Jaoudé, W., Traynard, P., Monteiro, P. T., Saez-Rodriguez, J., Helikar, T., Thieffry, D., & Chaouiya, C. (2016). Logical modeling and dynamical analysis of cellular networks. Frontiers in Genetics, 7(MAY), [94]. https://doi.org/10.3389/fgene.2016.00094