An integrative approach towards completing genome-scale metabolic networks

Nils Christian, Patrick May, Stefan Kempa, Thomas Handorf, Oliver Ebenhoeh (Corresponding Author)

Research output: Contribution to journalArticle

41 Citations (Scopus)

Abstract

Genome-scale metabolic networks which have been automatically derived through sequence comparison techniques are necessarily incomplete. We propose a strategy that incorporates genomic sequence data and metabolite profiles into modeling approaches to arrive at improved gene annotations and more complete genome-scale metabolic networks. The core of our strategy is an algorithm that computes minimal sets of reactions by which a draft network has to be extended in order to be consistent with experimental observations. A particular strength of our approach is that alternative possibilities are suggested and thus experimentally testable hypotheses are produced. We carefully evaluate our strategy on the well-studied metabolic network of Escherichia coli, demonstrating how the predictions can be improved by incorporating sequence data. Subsequently, we apply our method to the recently sequenced green alga Chlamydomonas reinhardtii. We suggest specific genes in the genome of Chlamydomonas which are the strongest candidates for coding the responsible enzymes.
Original languageEnglish
Pages (from-to)1889-1903
Number of pages15
JournalMolecular BioSystems
Volume5
Issue number12
Early online date10 Sep 2009
DOIs
Publication statusPublished - 1 Dec 2009

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Metabolic Networks and Pathways
Genome
Chlamydomonas
Chlamydomonas reinhardtii
Chlorophyta
Enzymes

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Christian, N., May, P., Kempa, S., Handorf, T., & Ebenhoeh, O. (2009). An integrative approach towards completing genome-scale metabolic networks. Molecular BioSystems, 5(12), 1889-1903. https://doi.org/10.1039/B915913b

An integrative approach towards completing genome-scale metabolic networks. / Christian, Nils; May, Patrick; Kempa, Stefan; Handorf, Thomas; Ebenhoeh, Oliver (Corresponding Author).

In: Molecular BioSystems, Vol. 5, No. 12, 01.12.2009, p. 1889-1903.

Research output: Contribution to journalArticle

Christian, N, May, P, Kempa, S, Handorf, T & Ebenhoeh, O 2009, 'An integrative approach towards completing genome-scale metabolic networks', Molecular BioSystems, vol. 5, no. 12, pp. 1889-1903. https://doi.org/10.1039/B915913b
Christian N, May P, Kempa S, Handorf T, Ebenhoeh O. An integrative approach towards completing genome-scale metabolic networks. Molecular BioSystems. 2009 Dec 1;5(12):1889-1903. https://doi.org/10.1039/B915913b
Christian, Nils ; May, Patrick ; Kempa, Stefan ; Handorf, Thomas ; Ebenhoeh, Oliver. / An integrative approach towards completing genome-scale metabolic networks. In: Molecular BioSystems. 2009 ; Vol. 5, No. 12. pp. 1889-1903.
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