Computing Weakly Reversible Deficiency Zero Network Translations Using Elementary Flux Modes
نویسندگان
چکیده
منابع مشابه
Computing Elementary Flux Modes in Genome-scale Metabolic Networks
Elementary flux mode analysis (EFM analysis) is an important method in the study of biochemical pathways. However, the computation of EFMs is limited to small and medium size metabolic networks due to a combinatorial explosion in their number in larger networks. Additionally, the existing tools to compute EFMs require to enumerate all EFMs before selecting those of interest. The method presente...
متن کاملtEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks
UNLABELLED : Elementary flux modes (EFMs) are important structural tools for the analysis of metabolic networks. It is known that many topologically feasible EFMs are biologically irrelevant. Therefore, tools are needed to find the relevant ones. We present thermodynamic tEFM analysis (tEFMA) which uses the cellular metabolome to avoid the enumeration of thermodynamically infeasible EFMs. Speci...
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Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising fro...
متن کاملRobust generation of elementary flux modes
Elementary flux modes (EFMs) are vectors defined from a metabolic reaction network, giving the connections between substrates and products. EFMs-based metabolic flux analysis (MFA) estimates the flux over each EFM from external flux measurements through least-squares data fitting. In previous work we presented an optimization method of column generation type that facilitates EFMs-based MFA when...
متن کاملOn dynamically generating relevant elementary flux modes in a metabolic network using optimization.
Elementary flux modes (EFMs) are pathways through a metabolic reaction network that connect external substrates to products. Using EFMs, a metabolic network can be transformed into its macroscopic counterpart, in which the internal metabolites have been eliminated and only external metabolites remain. In EFMs-based metabolic flux analysis (MFA) experimentally determined external fluxes are used...
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ژورنال
عنوان ژورنال: Bulletin of Mathematical Biology
سال: 2019
ISSN: 0092-8240,1522-9602
DOI: 10.1007/s11538-019-00579-z