AUTHOR=Abou-Jaoudé Wassim , Traynard Pauline , Monteiro Pedro T. , Saez-Rodriguez Julio , Helikar Tomáš , Thieffry Denis , Chaouiya Claudine TITLE=Logical Modeling and Dynamical Analysis of Cellular Networks JOURNAL=Frontiers in Genetics VOLUME=7 YEAR=2016 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2016.00094 DOI=10.3389/fgene.2016.00094 ISSN=1664-8021 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.