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

Gonçalves, E., Bucher, J., Ryll, A., Niklas, J., Mauch, K., Klamt, S., et al. (2013). Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Molecular BioSystems, 9(7), 1576-1583. doi:10.1039/c3mb25489e.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-4E40-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-9030-E
Genre: Journal Article

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1801321_ryll.pdf (Publisher version), 2MB
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This publication is with persmission of the rights owner freely accessible on MPG.PuRe (s. email SG/RSC vom 17.4.2015)
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 Creators:
Gonçalves, Emanuel1, Author
Bucher, Joachim2, Author
Ryll, Anke3, Author              
Niklas, Jens2, Author
Mauch, Klaus2, Author
Klamt, Steffen3, Author              
Rocha, Miguel4, Author
Saez-Rodriguez, Julio1, Author              
Affiliations:
1EMBL-EBI Bioinformatics Institut, Cambridge, UK , escidoc:persistent22              
2Insilico Biotechnology, Stuttgart, escidoc:persistent22              
3Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society, escidoc:1738139              
4Computer Science and Technology Centre - CCTC, School of Engineering, University of Minho, Portugal , escidoc:1753325              

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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. © Royal Society of Chemistry 2013 [accessed 2013 September 9th]

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Language(s): eng - English
 Dates: 2013
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1039/c3mb25489e
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Title: Molecular BioSystems
Source Genre: Journal
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Pages: - Volume / Issue: 9 (7) Sequence Number: - Start / End Page: 1576 - 1583 Identifier: ISSN: 1742-206X
CoNE: http://pubman.mpdl.mpg.de/cone/journals/resource/1000000000023020