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A Lattice-Theoretic Framework for Metabolic Pathway Analysis

  • Yaron A. B. Goldstein
  • Alexander Bockmayr
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8130)

Abstract

Constraint-based analysis of metabolic networks has become a widely used approach in computational systems biology. In the simplest form, a metabolic network is represented by a stoichiometric matrix and thermodynamic information on the irreversibility of certain reactions. Then one studies the set of all steady-state flux vectors satisfying these stoichiometric and thermodynamic constraints.

We introduce a new lattice-theoretic framework for the computational analysis of metabolic networks, which focuses on the support of the flux vectors, i.e., we consider only the qualitative information whether or not a certain reaction is active, but not its specific flux rate. Our lattice-theoretic view includes classical metabolic pathway analysis as a special case, but turns out to be much more flexible and general, with a wide range of possible applications.

We show how important concepts from metabolic pathway analysis, such as blocked reactions, flux coupling, or elementary modes, can be generalized to arbitrary lattice-based models. We develop corresponding general algorithms and present a number of computational results.

Keywords

metabolic networks constraint-based analysis lattices 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Yaron A. B. Goldstein
    • 1
  • Alexander Bockmayr
    • 1
  1. 1.DFG Research Center MatheonFreie Universität BerlinBerlinGermany

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