Logical Modeling and Dynamical Analysis of Cellular Networks

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

http://hdl.handle.net/10400.7/656

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Authors

Abou-Jaoudé, Wassim

Traynard, Pauline

Monteiro, Pedro T.

Saez-Rodriguez, Julio

Helikar, Tomáš

Thieffry, Denis

Chaouiya, Claudine

Abstract(s)

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.

Keywords

regulatory and signaling networks logical modeling discrete dynamics attractors reachability analysis simulation T cells activation and differentiation cell cycle control

URI

http://hdl.handle.net/10400.7/656

Citation

Abou-JaoudéW,TraynardP, Monteiro PT,Saez-RodriguezJ, HelikarT,ThieffryDandChaouiyaC (2016) LogicalModelingand DynamicalAnalysisofCellular Networks.Front.Genet.7:94. doi: 10.3389/fgene.2016.00094