Comparing Flux Balance Analysis to Network Expansion: Producibility,Sustainability and the Scope of Compounds

K. Kruse, Oliver Ebenhoeh

Research output: Chapter in Book/Report/Conference proceedingConference contribution

11 Citations (Scopus)

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.
Original languageEnglish
Title of host publicationGenome Informatics 2008
Subtitle of host publicationProceedings of the 8th International Workshop on Bioinformatics and Systems Biology
EditorsErnst-Walter Knapp, Gary Benson, Herman-Georg Holzhutter
Place of PublicationLondon, United Kingdom
PublisherImperial College Press
Pages91-101
Volume20
ISBN (Print)1848162995, 978-1848162990
Publication statusPublished - 6 Dec 2008
Event8th International Workshop on Bioinformatics and Systems Biology (IBSB 2008) - Berlin, Germany
Duration: 9 Jun 200711 Jun 2007

Publication series

NameGenome Informatics Series (GIS)
Publisher Japanese Society for Bioinformatics
Volume20
ISSN (Print)0919-9454

Conference

Conference8th International Workshop on Bioinformatics and Systems Biology (IBSB 2008)
CountryGermany
CityBerlin
Period9/06/0711/06/07

Fingerprint

metabolite
sustainability
heuristics
genome
analysis
resource

Cite this

Kruse, K., & Ebenhoeh, O. (2008). Comparing Flux Balance Analysis to Network Expansion: Producibility,Sustainability and the Scope of Compounds. In E-W. Knapp, G. Benson, & H-G. Holzhutter (Eds.), Genome Informatics 2008: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology (Vol. 20, pp. 91-101). (Genome Informatics Series (GIS); Vol. 20). London, United Kingdom: Imperial College Press.

Comparing Flux Balance Analysis to Network Expansion : Producibility,Sustainability and the Scope of Compounds. / Kruse, K.; Ebenhoeh, Oliver.

Genome Informatics 2008: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology. ed. / Ernst-Walter Knapp; Gary Benson; Herman-Georg Holzhutter. Vol. 20 London, United Kingdom : Imperial College Press, 2008. p. 91-101 (Genome Informatics Series (GIS); Vol. 20).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kruse, K & Ebenhoeh, O 2008, Comparing Flux Balance Analysis to Network Expansion: Producibility,Sustainability and the Scope of Compounds. in E-W Knapp, G Benson & H-G Holzhutter (eds), Genome Informatics 2008: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology. vol. 20, Genome Informatics Series (GIS), vol. 20, Imperial College Press, London, United Kingdom, pp. 91-101, 8th International Workshop on Bioinformatics and Systems Biology (IBSB 2008), Berlin, Germany, 9/06/07.
Kruse K, Ebenhoeh O. Comparing Flux Balance Analysis to Network Expansion: Producibility,Sustainability and the Scope of Compounds. In Knapp E-W, Benson G, Holzhutter H-G, editors, Genome Informatics 2008: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology. Vol. 20. London, United Kingdom: Imperial College Press. 2008. p. 91-101. (Genome Informatics Series (GIS)).
Kruse, K. ; Ebenhoeh, Oliver. / Comparing Flux Balance Analysis to Network Expansion : Producibility,Sustainability and the Scope of Compounds. Genome Informatics 2008: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology. editor / Ernst-Walter Knapp ; Gary Benson ; Herman-Georg Holzhutter. Vol. 20 London, United Kingdom : Imperial College Press, 2008. pp. 91-101 (Genome Informatics Series (GIS)).
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