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  Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks

Larhlimi, A., Basler, G., Grimbs, S., Selbig, J., & Nikoloski, Z. (2012). Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. In 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB) (pp. I502-I508).

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-1F42-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-1F43-D
Genre: Conference Paper

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Larhlimi-2012-Stoichiometric capac.pdf (Any fulltext), 501KB
 
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 Creators:
Larhlimi, A.1, Author              
Basler, G.2, Author              
Grimbs, S.1, Author              
Selbig, J.1, Author              
Nikoloski, Z.3, Author              
Affiliations:
1BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
2Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753310              
3Mathematical Modelling and Systems Biology, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753341              

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Free keywords: genome-scale reconstruction flux balance analysis escherichia-coli computational approach strain optimization coupling analysis models framework pathways systems
 Abstract: Motivation: Metabolic engineering aims at modulating the capabilities of metabolic networks by changing the activity of biochemical reactions. The existing constraint-based approaches for metabolic engineering have proven useful, but are limited only to reactions catalogued in various pathway databases. Results: We consider the alternative of designing synthetic strategies which can be used not only to characterize the maximum theoretically possible product yield but also to engineer networks with optimal conversion capability by using a suitable biochemically feasible reaction called 'stoichiometric capacitance'. In addition, we provide a theoretical solution for decomposing a given stoichiometric capacitance over a set of known enzymatic reactions. We determine the stoichiometric capacitance for genome-scale metabolic networks of 10 organisms from different kingdoms of life and examine its implications for the alterations in flux variability patterns. Our empirical findings suggest that the theoretical capacity of metabolic networks comes at a cost of dramatic system's changes.

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Language(s): eng - English
 Dates: 2012
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000308532300029
DOI: 10.1093/bioinformatics/bts381
URI: ://000308532300029 http://bioinformatics.oxfordjournals.org/content/28/18/i502.full.pdf
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Title: 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB)
Place of Event: Basel, SWITZERLAND
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Title: 11th European Conference on Computational Biology (ECCB) / Conference of the Intelligent Systems in Molecular Biology (ISMB)
Source Genre: Proceedings
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Pages: - Volume / Issue: - Sequence Number: - Start / End Page: I502 - I508 Identifier: -