By Topic

An algorithm for identifying dominant-edge metabolic pathways

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$33 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

3 Author(s)
Ehsan Ullah ; Department of Computer Science, Tufts University ; Kyongbum Lee ; Soha Hassoun

Metabolic pathway analysis seeks to identify critical reactions in living organisms and plays an important role in synthetic biology. We present in this paper an algorithm, DOMINANT-EDGE PATHWAY, for identifying a thermodynamically favored dominant-edge pathway forming a particular metabolite product from a particular reactant in a metabolic reaction network. The metabolic network is represented as a graph based on the stoichiometry of the reactions. The problem is formulated to first identify the path between the reactant and product with a limiting reaction based on Gibbs free energy changes, and then to augment this path with supplementary pathways with the goal of balancing the overall stoichiometry. Results of three representative test cases show that our algorithm efficiently finds potentially preferred reaction routes, offering a substantial run-time advantage over commonly used enumeration-based approaches.

Published in:

2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers

Date of Conference:

2-5 Nov. 2009