Logical Modeling and Dynamical Analysis of Cellular Networks

Authors

Wassim Abou-Jaoudé, Institut de Biologie de l’Ecole Normale Supérieure
Pauline Traynard, Institut de Biologie de l’Ecole Normale Supérieure
Pedro T. Monteiro, University of Lisbon
Julio Saez-Rodriguez, European Bioinformatics Institute (EMBL-EBI)Follow
Tomáš Helikar, University of Nebraska-LincolnFollow
Denis Thieffry, Institut de Biologie de l’Ecole Normale Supérieure
Claudine Chaouiya, Instituto Gulbenkian de CiênciaFollow

Document Type

Article

Date of this Version

2016

Citation

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D and Chaouiya C (2016) Logical Modeling and Dynamical Analysis of Cellular Networks. Front. Genet. 7:94. doi: 10.3389/fgene.2016.00094

Comments

Copyright © 2016 Abou-Jaoudé, Traynard, Monteiro, Saez-Rodriguez, Helikar, Thieffry and Chaouiya. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CCBY).

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.