Logical modeling and dynamical analysis of cellular networks

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

Research output: Contribution to journalReview article

58 Citations (Scopus)

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

Fingerprint

Biological Phenomena
Helper-Inducer T-Lymphocytes
Cell Cycle Checkpoints
Surveys and Questionnaires

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)

Cite this

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

Logical modeling and dynamical analysis of cellular networks. / Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T.; Saez-Rodriguez, Julio; Helikar, Tomas; Thieffry, Denis; Chaouiya, Claudine.

In: Frontiers in Genetics, Vol. 7, No. MAY, 94, 31.05.2016.

Research output: Contribution to journalReview article

Abou-Jaoudé, W, Traynard, P, Monteiro, PT, Saez-Rodriguez, J, Helikar, T, Thieffry, D & Chaouiya, C 2016, 'Logical modeling and dynamical analysis of cellular networks', Frontiers in Genetics, vol. 7, no. MAY, 94. https://doi.org/10.3389/fgene.2016.00094
Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D et al. Logical modeling and dynamical analysis of cellular networks. Frontiers in Genetics. 2016 May 31;7(MAY). 94. https://doi.org/10.3389/fgene.2016.00094
Abou-Jaoudé, Wassim ; Traynard, Pauline ; Monteiro, Pedro T. ; Saez-Rodriguez, Julio ; Helikar, Tomas ; Thieffry, Denis ; Chaouiya, Claudine. / Logical modeling and dynamical analysis of cellular networks. In: Frontiers in Genetics. 2016 ; Vol. 7, No. MAY.
@article{3b771b64f07a48cfacd8e024816d7f5c,
title = "Logical modeling and dynamical analysis of cellular networks",
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.",
keywords = "Attractors, Cell cycle control, Discrete dynamics, Logical modeling, Reachability analysis, Regulatory and signaling networks, Simulation, T cells activation and differentiation",
author = "Wassim Abou-Jaoud{\'e} and Pauline Traynard and Monteiro, {Pedro T.} and Julio Saez-Rodriguez and Tomas Helikar and Denis Thieffry and Claudine Chaouiya",
year = "2016",
month = "5",
day = "31",
doi = "10.3389/fgene.2016.00094",
language = "English (US)",
volume = "7",
journal = "Frontiers in Genetics",
issn = "1664-8021",
publisher = "Frontiers Media S. A.",
number = "MAY",

}

TY - JOUR

T1 - Logical modeling and dynamical analysis of cellular networks

AU - Abou-Jaoudé, Wassim

AU - Traynard, Pauline

AU - Monteiro, Pedro T.

AU - Saez-Rodriguez, Julio

AU - Helikar, Tomas

AU - Thieffry, Denis

AU - Chaouiya, Claudine

PY - 2016/5/31

Y1 - 2016/5/31

N2 - 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.

AB - 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.

KW - Attractors

KW - Cell cycle control

KW - Discrete dynamics

KW - Logical modeling

KW - Reachability analysis

KW - Regulatory and signaling networks

KW - Simulation

KW - T cells activation and differentiation

UR - http://www.scopus.com/inward/record.url?scp=84975295482&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84975295482&partnerID=8YFLogxK

U2 - 10.3389/fgene.2016.00094

DO - 10.3389/fgene.2016.00094

M3 - Review article

VL - 7

JO - Frontiers in Genetics

JF - Frontiers in Genetics

SN - 1664-8021

IS - MAY

M1 - 94

ER -