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      Large-scale computation of elementary flux modes with bit pattern trees.

      1 ,
      Bioinformatics (Oxford, England)
      Oxford University Press (OUP)

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          Abstract

          Elementary flux modes (EFMs)--non-decomposable minimal pathways--are commonly accepted tools for metabolic network analysis under steady state conditions. Valid states of the network are linear superpositions of elementary modes shaping a polyhedral cone (the flux cone), which is a well-studied convex set in computational geometry. Computing EFMs is thus basically equivalent to extreme ray enumeration of polyhedral cones. This is a combinatorial problem with poorly scaling algorithms, preventing the large-scale analysis of metabolic networks so far.

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          Author and article information

          Journal
          Bioinformatics
          Bioinformatics (Oxford, England)
          Oxford University Press (OUP)
          1367-4811
          1367-4803
          Oct 01 2008
          : 24
          : 19
          Affiliations
          [1 ] Institute of Computational Science and Swiss Institute of Bioinformatics, ETH Zurich, 8092 Zurich, Switzerland.
          Article
          btn401
          10.1093/bioinformatics/btn401
          18676417
          0ebc4017-57ca-4c5f-a141-d453b046dc97
          History

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