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Finding Minimal Reaction Sets in Large Metabolic Pathways

15 pagesPublished: May 15, 2012


In systems biology, identifying vital functions like glycolysis from a given metabolic pathway is important to understand living organisms. In this paper, we particularly focus on the problem of finding minimal sub-pathways producing target metabolites from source metabolites. We represent laws of biochemical reactions in propositional formulas and use a state-of-the-art SAT solver as a minimal model generator to solve the problem efficiently. An advantage of our method is that it can treat reversible reactions represented by cycles. Moreover recent advances of SAT technologies enables us to obtain solutions for large pathways. We have applied our method to a whole Escherichia coli pathway. As a result, we found 5 sets of reactions including the conventional glycolysis sub-pathway described in a biological database EcoCyc.

Keyphrases: metabolic pathways, minimal model generation, propositional formulas, SAT solver, systems biology

In: Agostino Dovier, Alessandro Dal Palù and Sebastian Will (editors). WCB10. Workshop on Constraint Based Methods for Bioinformatics, vol 4, pages 38--52

BibTeX entry
  author    = {Takehide Soh and Katsumi Inoue},
  title     = {Finding Minimal Reaction Sets in Large Metabolic Pathways},
  booktitle = {WCB10. Workshop on Constraint Based Methods for Bioinformatics},
  editor    = {Agostino Dovier and Alessandro Dal Pal\textbackslash{}`u and Sebastian Will},
  series    = {EPiC Series in Computing},
  volume    = {4},
  pages     = {38--52},
  year      = {2012},
  publisher = {EasyChair},
  bibsource = {EasyChair,},
  issn      = {2398-7340},
  url       = {},
  doi       = {10.29007/xp2k}}
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