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Bioinformatics Advance Access originally published online on February 27, 2006
Bioinformatics 2006 22(10):1198-1206; doi:10.1093/bioinformatics/btl069
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes{dagger}

Ari Rantanen 1,*, Taneli Mielikäinen 1, Juho Rousu 1, Hannu Maaheimo 2 and Esko Ukkonen 1

1 Department of Computer Science P.O. Box 68 (Gustaf Hällströmin katu 2b) 00014 University of Helsinki Finland
2 NMR Laboratory, VTT Technical Research Centre of Finland P.O. Box 65, 00014 Helsinki, Finland

*To whom correspondence should be addressed.

Motivation: Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the development of isotopomer measurement techniques for intermediate metabolites is a demanding task. Careful planning of isotopomer measurements is thus needed to maximize the available flux information while minimizing the experimental effort.

Results: In this paper we study the question of finding the smallest subset of metabolites to measure that ensure the same level of isotopomer information as the measurement of every metabolite in the metabolic network. We study the computational complexity of this optimization problem in the case of the so-called positional enrichment data, give methods for obtaining exact and fast approximate solutions, and evaluate empirically the efficacy of the proposed methods by analyzing a metabolic network that models the central carbon metabolism of Saccharomyces cerevisiae.

Contact: ajrantan{at}cs.helsinki.fi

Received on November 30, 2005; revised on February 21, 2006; accepted on February 21, 2006

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