Logical modeling and dynamical analysis of cellular networks

• Main Authors: Wassim eAbou-Jaoudé, Pauline eTraynard, Pedro Tiago Monteiro, Julio eSaez Rodriguez, Tomáš eHelikar, Denis eThieffry, Claudine eChaouiya
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2016-05-01
• Series: Frontiers in Genetics
• Subjects: attractors; simulation; cell cycle control; Logical modeling; Reachability analysis; discrete dynamics
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fgene.2016.00094/full

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.