An algorithm for identifying dominant-edge metabolic pathways

Ehsan Ullah, Kyongbum Lee, Soha Hassoun

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

5 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationProceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009
Pages144-150
Number of pages7
Publication statusPublished - 1 Dec 2009
Externally publishedYes
Event2009 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2009 - San Jose, CA, United States
Duration: 2 Nov 20095 Nov 2009

Other

Other2009 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2009
CountryUnited States
CitySan Jose, CA
Period2/11/095/11/09

Fingerprint

Stoichiometry
Gibbs free energy
Metabolites
Metabolic Networks and Pathways
Synthetic Biology

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Computer Science Applications
  • Software

Cite this

Ullah, E., Lee, K., & Hassoun, S. (2009). An algorithm for identifying dominant-edge metabolic pathways. In Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009 (pp. 144-150). [5361229]

An algorithm for identifying dominant-edge metabolic pathways. / Ullah, Ehsan; Lee, Kyongbum; Hassoun, Soha.

Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009. 2009. p. 144-150 5361229.

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

Ullah, E, Lee, K & Hassoun, S 2009, An algorithm for identifying dominant-edge metabolic pathways. in Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009., 5361229, pp. 144-150, 2009 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2009, San Jose, CA, United States, 2/11/09.
Ullah E, Lee K, Hassoun S. An algorithm for identifying dominant-edge metabolic pathways. In Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009. 2009. p. 144-150. 5361229
Ullah, Ehsan ; Lee, Kyongbum ; Hassoun, Soha. / An algorithm for identifying dominant-edge metabolic pathways. Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009. 2009. pp. 144-150
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