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A Computational Method for Reconstructing Gapless Metabolic Networks

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Bioinformatics Research and Development (BIRD 2008)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 13))

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Abstract

We propose a computational method for reconstructing metabolic networks. The method utilizes optimization techniques and graph traversal algorithms to discover a set of biochemical reactions that is most likely catalyzed by the enzymatic genes of the target organism. Unlike most existing computational methods for metabolic reconstruction, our method generates networks that are structurally consistent, or in other terms, gapless. As many analyses of metabolic networks, like flux balance analysis, require gapless networks as inputs, our network offers a more realistic basis for metabolic modelling than the existing automated reconstruction methods. It is easy to incorporate existing information, like knowledge about experimentally discovered metabolic reactions or metabolites into the process. Thus, our method can be used to assist in the manual curation of metabolic network models as it is able to suggest good candidate reactions for filling gaps in the existing network models. However, it is not necessary to assume any prior knowledge on composition of complete biochemical pathways in the network. We argue that this makes the method well-suited to analysis of organisms that might differ considerably from previously known organisms. We demonstrate the viability of our method by analysing the metabolic network of the well-known organism Escherichia coli.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Helsinki, Finland

    Esa Pitkänen, Juho Rousu & Esko Ukkonen

  2. Institute of Molecular Systems Biology, ETH Zürich, Switzerland

    Ari Rantanen

Authors
  1. Esa Pitkänen
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  2. Ari Rantanen
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  3. Juho Rousu
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  4. Esko Ukkonen
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Editor information

Mourad Elloumi Josef Küng Michal Linial Robert F. Murphy Kristan Schneider Cristian Toma

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Pitkänen, E., Rantanen, A., Rousu, J., Ukkonen, E. (2008). A Computational Method for Reconstructing Gapless Metabolic Networks. In: Elloumi, M., Küng, J., Linial, M., Murphy, R.F., Schneider, K., Toma, C. (eds) Bioinformatics Research and Development. BIRD 2008. Communications in Computer and Information Science, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70600-7_22

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  • DOI: https://doi.org/10.1007/978-3-540-70600-7_22

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-70598-7

  • Online ISBN: 978-3-540-70600-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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