A New Approach to Obtain EFMs Using Graph Methods Based on the Shortest Path between End Nodes

Céspedes, Jose Francisco Hidalgo; Asensio, Francisco De Asís Guil; Carrasco, José Manuel García

doi:10.1007/978-3-319-16483-0_62

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Cited by 3 publications

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“…The method of [20] explores the shortest pathways in the AND/OR graph of the network. The authors did not take into account the stoichiometry coefficients.…”

Section: Discussionmentioning

confidence: 99%

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A graph-based approach to analyze flux-balanced pathways in metabolic networks

et al. 2018

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An elementary flux mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to find a subset of EFMs is proposed based on a graph data model. The given metabolic network is mapped to the graph model and decisions for reaction inclusion can be made based on metabolites and their associated reactions. This notion makes the approach more convenient to categorize the output pathways. Implications of the proposed method on metabolic networks are discussed.

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“…The method of [20] explores the shortest pathways in the AND/OR graph of the network. The authors did not take into account the stoichiometry coefficients.…”

Section: Discussionmentioning

confidence: 99%

“…Besides, methods based on linear programming have been proposed that explore a set of EFMs with specific properties, such as K-shortest EFMs [18], or EFMs with a given set of target reactions [19]. A new set of methods based on graph-theory, [20,21] tries to overcome the scalability problem of the double-description-based techniques.…”

Section: Introductionmentioning

confidence: 99%