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This article is part of the supplement: Otto Warburg International Summer School and Workshop on Networks and Regulation

Open Access Highly Accessed Review

Current approaches to gene regulatory network modelling

Thomas Schlitt1 and Alvis Brazma2*

Author Affiliations

1 Department of Medical and Molecular Genetics, King's College London School of Medicine, 8th floor Guy's Tower, London SE1 9RT, UK

2 European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

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BMC Bioinformatics 2007, 8(Suppl 6):S9  doi:10.1186/1471-2105-8-S6-S9

Published: 27 September 2007

Abstract

Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model.