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Issue 7, 2013
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Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

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Abstract

Mathematical modelling is increasingly becoming an indispensable tool for the study of cellular processes, allowing their analysis in a systematic and comprehensive manner. In the vast majority of the cases, models focus on specific subsystems, and in particular describe either metabolism, gene expression or signal transduction. Integrated models that are able to span and interconnect these layers are, by contrast, rare as their construction and analysis face multiple challenges. Such methods, however, would represent extremely useful tools to understand cell behaviour, with application in distinct fields of biological and medical research. In particular, they could be useful tools to study genotype–phenotype mappings, and the way they are affected by specific conditions or perturbations. Here, we review existing computational approaches that integrate signalling, gene regulation and/or metabolism. We describe existing challenges, available methods and point at potentially useful strategies.

Graphical abstract: Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

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Article information


Submitted
30 Oct 2012
Accepted
28 Feb 2013
First published
01 Mar 2013

This article is Open Access

Mol. BioSyst., 2013,9, 1576-1583
Article type
Review Article

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

E. Gonçalves, J. Bucher, A. Ryll, J. Niklas, K. Mauch, S. Klamt, M. Rocha and J. Saez-Rodriguez, Mol. BioSyst., 2013, 9, 1576
DOI: 10.1039/C3MB25489E

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