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  Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds

Kruse, K., & Ebenhoeh, O. (2008). Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds. Genome Informatics, 20, 91-101. doi:10.1142/9781848163003_0008.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2740-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2741-3
Genre: Journal Article

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Comparing flux balance analysis to network expansion producibility, sustainability and the scope of compounds.pdf (Any fulltext), 628KB
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Comparing flux balance analysis to network expansion producibility, sustainability and the scope of compounds.pdf
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Kruse, K.1, Author
Ebenhoeh, O.2, Author              
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1External Organizations, ou_persistent22              
2Mathematical Modelling and Systems Biology, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753341              

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Free keywords: Adenosine Triphosphate/metabolism Escherichia coli/genetics/metabolism *Genome, Bacterial Kinetics Methanosarcina barkeri/genetics/metabolism *Models, Genetic NAD/metabolism NADP/metabolism Organisms, Genetically Modified/genetics/metabolism Predictive Value of Tests Probability Reproducibility of Results
 Abstract: The producibility of metabolites from available resources is investigated systematically using flux balance analysis (FBA) and network expansion. Calculations are performed for the genome-scale metabolic networks of Escherichia coli and Methanosarcina barkeri. Strict biological interpretation of the results obtained with FBA leads to the concept of sustainability, which reduces the set of producible metabolites by assuming a growing and dividing cell. A systematic comparison showed that applying network expansion in many cases results in exactly the set of all sustainable metabolites. The purely heuristic approach of allowing for certain cofactors to facilitate reactions during the process of network expansion dramatically helps to improve agreement of the results from the two different approaches. In conclusion, we state that network expansion, due to its enormous advantages in computational speed, is a valuable alternative to determining producible metabolites with FBA.

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Language(s): eng - English
 Dates: 2008-01-012008
 Publication Status: Published in print
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Title: Genome Informatics
Source Genre: Journal
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Pages: - Volume / Issue: 20 Sequence Number: - Start / End Page: 91 - 101 Identifier: -