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A Lattice-Theoretic Framework for Metabolic Pathway Analysis

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Computational Methods in Systems Biology (CMSB 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8130))

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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.

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Authors and Affiliations

  1. DFG Research Center Matheon, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany

    Yaron A. B. Goldstein & Alexander Bockmayr

Authors
  1. Yaron A. B. Goldstein
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  2. Alexander Bockmayr
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Editors and Affiliations

  1. IST Austria, 3400, Klosterneuburg, Austria

    Ashutosh Gupta  & Thomas A. Henzinger  & 

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Goldstein, Y.A.B., Bockmayr, A. (2013). A Lattice-Theoretic Framework for Metabolic Pathway Analysis. In: Gupta, A., Henzinger, T.A. (eds) Computational Methods in Systems Biology. CMSB 2013. Lecture Notes in Computer Science(), vol 8130. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40708-6_14

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  • DOI: https://doi.org/10.1007/978-3-642-40708-6_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-40707-9

  • Online ISBN: 978-3-642-40708-6

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