2016
DOI: 10.1186/s13015-016-0087-3
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Enumeration of minimal stoichiometric precursor sets in metabolic networks

Abstract: BackgroundWhat an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flu… Show more

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Cited by 18 publications
(22 citation statements)
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“…We show that minimal functional routes (MFRs), and thus elementary signaling modes (ESMs), are special cases of topological factories previously described [5,1] once graphs with composite nodes are translated into a hypergraph structure. In particular, the concept of topological factories extends the concept of MFRs.…”
Section: Capturing Signaling Via Topological Factoriesmentioning
confidence: 94%
See 3 more Smart Citations
“…We show that minimal functional routes (MFRs), and thus elementary signaling modes (ESMs), are special cases of topological factories previously described [5,1] once graphs with composite nodes are translated into a hypergraph structure. In particular, the concept of topological factories extends the concept of MFRs.…”
Section: Capturing Signaling Via Topological Factoriesmentioning
confidence: 94%
“…We will assume hereinafter that our input layer is equal to the source layer. We will be using some concepts from metabolic network analysis, which we briefly introduce in the appendix, and refer the reader to [82,5,1] for the full treatment.…”
Section: The Basics Of Hypergraphsmentioning
confidence: 99%
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“…We detail below the main results obtained on each of the above activities. Other subjects that were addressed as a part of this project were metabolic communication between the different species in a community (Milreu et al 2014;Andrade et al 2016) and modeling dynamic metabolic networks for potential application in strain optimization (Costa et al 2014;Hartmann et al 2015aHartmann et al , b, 2016Costa et al 2016).…”
Section: Bioinformatics and Modellingmentioning
confidence: 99%