International Conference on Computational Methods in Systems Biology

CMSB 2007: Computational Methods in Systems Biology pp 217-232

Reconstructing Metabolic Pathways by Bidirectional Chemical Search

  • Liliana Félix
  • Francesc Rosselló
  • Gabriel Valiente
Conference paper

DOI: 10.1007/978-3-540-75140-3_15

Volume 4695 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Félix L., Rosselló F., Valiente G. (2007) Reconstructing Metabolic Pathways by Bidirectional Chemical Search. In: Calder M., Gilmore S. (eds) Computational Methods in Systems Biology. CMSB 2007. Lecture Notes in Computer Science, vol 4695. Springer, Berlin, Heidelberg

Abstract

One of the main challenges in systems biology is the establishment of the metabolome: a catalogue of the metabolites and biochemical reactions present in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical reactions. In this paper, we present an efficient method to build a substantial portion of the artificial chemistry defined by the metabolites and biochemical reactions in a given metabolic pathway, which is based on bidirectional chemical search. Computational results on the pathways stored in KEGG reveal novel biochemical pathways.

Keywords

Artificial chemistry biochemical reaction metabolic pathway 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Liliana Félix
    • 1
  • Francesc Rosselló
    • 2
  • Gabriel Valiente
    • 1
  1. 1.Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034 BarcelonaSpain
  2. 2.Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma de Mallorca