Skip Navigation



Bioinformatics Advance Access published online on February 27, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl069
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/10/1198    most recent
btl069v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Rantanen, A.
Right arrow Articles by Ukkonen, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rantanen, A.
Right arrow Articles by Ukkonen, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 30, 2005
Revised February 21, 2006
Accepted February 21, 2006

Article

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes*

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.
Ari Rantanen, E-mail: ajrantan{at}cs.helsinki.fi


  Abstract

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 S. cerevisiae.

*Preliminary version of this article appeared in the proceedings of German Conference on Bioinformatics 2005. Lecture Notes in Informatics Vol. P-71 (2005), pp. 177-191.

Thomas Lengauer


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.