Literature DB >> 14534187

A description of dynamical graphs associated to elementary regulatory circuits.

E Remy1, B Mossé, C Chaouiya, D Thieffry.   

Abstract

The biological and dynamical importance of feedback circuits in regulatory graphs has often been emphasized. The work presented here aims at completely describing the dynamics of isolated elementary regulatory circuits. Our analytical approach is based on a discrete formal framework, built upon the logical approach of R. Thomas. Given a regulatory circuit, we show that the structure of synchronous and asynchronous dynamical graphs depends only on the length of the circuit (number of genes) and on its sign (which depends on the parity of the number of negative interactions). This work constitutes a first step towards the analytical characterisation of discrete dynamical graphs for more complex regulatory networks in terms of contributions corresponding to their embedded elementary circuits.

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Year:  2003        PMID: 14534187     DOI: 10.1093/bioinformatics/btg1075

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  11 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-03       Impact factor: 11.205

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3.  Monotone and near-monotone biochemical networks.

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4.  Discrete time piecewise affine models of genetic regulatory networks.

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Journal:  J Math Biol       Date:  2006-03-06       Impact factor: 2.164

5.  Synthetic biology in the view of European public funding organisations.

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6.  A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks.

Authors:  Johan Kerkhofs; Liesbet Geris
Journal:  PLoS One       Date:  2015-06-11       Impact factor: 3.240

Review 7.  Logical Modeling and Dynamical Analysis of Cellular Networks.

Authors:  Wassim Abou-Jaoudé; Pauline Traynard; Pedro T Monteiro; Julio Saez-Rodriguez; Tomáš Helikar; Denis Thieffry; Claudine Chaouiya
Journal:  Front Genet       Date:  2016-05-31       Impact factor: 4.599

8.  Modular decomposition of protein-protein interaction networks.

Authors:  Julien Gagneur; Roland Krause; Tewis Bouwmeester; Georg Casari
Journal:  Genome Biol       Date:  2004-07-21       Impact factor: 13.583

Review 9.  Why are computational neuroscience and systems biology so separate?

Authors:  Erik De Schutter
Journal:  PLoS Comput Biol       Date:  2008-05-30       Impact factor: 4.475

10.  QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.

Authors:  Ciarán P Fisher; Nicholas J Plant; J Bernadette Moore; Andrzej M Kierzek
Journal:  Bioinformatics       Date:  2013-09-23       Impact factor: 6.937

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