Literature DB >> 20868697

Mapping multivalued onto Boolean dynamics.

Gilles Didier1, Elisabeth Remy, Claudine Chaouiya.   

Abstract

This paper deals with the generalized logical framework defined by René Thomas in the 70's to qualitatively represent the dynamics of regulatory networks. In this formalism, a regulatory network is represented as a graph, where nodes denote regulatory components (basically genes) and edges denote regulations between these components. Discrete variables are associated to regulatory components accounting for their levels of expression. In most cases, Boolean variables are enough, but some situations may require further values. Despite this fact, the majority of tools dedicated to the analysis of logical models are restricted to the Boolean case. A formal Boolean mapping of multivalued logical models is a natural way of extending the applicability of these tools. Three decades ago, a multivalued to Boolean variable mapping was proposed by P. Van Ham. Since then, all works related to multivalued logical models and using a Boolean representation rely on this particular mapping. We formally show in this paper that this mapping is actually the sole, up to cosmetic changes, that could preserve the regulatory structures of the underlying graphs as well as their dynamical behaviours. Copyright Â
© 2010 Elsevier Ltd. All rights reserved.

Mesh:

Substances:

Year:  2010        PMID: 20868697     DOI: 10.1016/j.jtbi.2010.09.017

Source DB:  PubMed          Journal:  J Theor Biol        ISSN: 0022-5193            Impact factor:   2.691


  8 in total

1.  Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

Authors:  Samuel Collombet; Chris van Oevelen; Jose Luis Sardina Ortega; Wassim Abou-Jaoudé; Bruno Di Stefano; Morgane Thomas-Chollier; Thomas Graf; Denis Thieffry
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-06       Impact factor: 11.205

2.  Control of Intracellular Molecular Networks Using Algebraic Methods.

Authors:  Luis Sordo Vieira; Reinhard C Laubenbacher; David Murrugarra
Journal:  Bull Math Biol       Date:  2019-12-23       Impact factor: 1.758

3.  Dynamic network-based epistasis analysis: boolean examples.

Authors:  Eugenio Azpeitia; Mariana Benítez; Pablo Padilla-Longoria; Carlos Espinosa-Soto; Elena R Alvarez-Buylla
Journal:  Front Plant Sci       Date:  2011-12-15       Impact factor: 5.753

4.  BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks.

Authors:  Aurélien Naldi
Journal:  Front Physiol       Date:  2018-11-19       Impact factor: 4.566

5.  Repairing Boolean logical models from time-series data using Answer Set Programming.

Authors:  Alexandre Lemos; Inês Lynce; Pedro T Monteiro
Journal:  Algorithms Mol Biol       Date:  2019-03-25       Impact factor: 1.405

6.  Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation.

Authors:  Xiao Gan; Réka Albert
Journal:  BMC Syst Biol       Date:  2016-08-19

7.  Identification of control targets in Boolean molecular network models via computational algebra.

Authors:  David Murrugarra; Alan Veliz-Cuba; Boris Aguilar; Reinhard Laubenbacher
Journal:  BMC Syst Biol       Date:  2016-09-23

8.  Reconciling qualitative, abstract, and scalable modeling of biological networks.

Authors:  Loïc Paulevé; Juraj Kolčák; Thomas Chatain; Stefan Haar
Journal:  Nat Commun       Date:  2020-08-26       Impact factor: 14.919

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.