ArticleScientific reports2015
Metabolomics integrated elementary flux mode analysis in large metabolic networks.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Atomic elementary flux modes explain the steady state flow of metabolites in large-scale flux networks.Cell reports methods · 2026Article
- Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth.PLoS computational biology · 2022Article
- Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach.Bioinformatics (Oxford, England) · 2020Article
- Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis.Metabolites · 2020Review
- EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models.Metabolites · 2020Article
- Article
- Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data.Microbial cell factories · 2019Article
- Flux tope analysis: studying the coordination of reaction directions in metabolic networks.Bioinformatics (Oxford, England) · 2019Article
- Metabolomics in Plant Priming Research: The Way Forward?International journal of molecular sciences · 2018Review
- Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.PLoS computational biology · 2018Article
- From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.PLoS computational biology · 2017Review
- Article
- Quantification of Microbial Phenotypes.Metabolites · 2016Review
- Which sets of elementary flux modes form thermodynamically feasible flux distributions?The FEBS journal · 2016Article
- Exact quantification of cellular robustness in genome-scale metabolic networks.Bioinformatics (Oxford, England) · 2016Article
- Ginseng alleviates cyclophosphamide-induced hepatotoxicity via reversing disordered homeostasis of glutathione and bile acid.Scientific reports · 2015Article
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5 authors.
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Abstract
Elementary flux modes (EFMs) are non-decomposable steady-state pathways in metabolic networks. They characterize phenotypes, quantify robustness or identify engineering targets. An EFM analysis (EFMA) is currently restricted to medium-scale models, as the number of EFMs explodes with the network's size. However, many topologically feasible EFMs are biologically irrelevant. We present thermodynamic EFMA (tEFMA), which calculates only the small(er) subset of thermodynamically feasible EFMs. We integrate network embedded thermodynamics into EFMA and show that we can use the metabolome to identify and remove thermodynamically infeasible EFMs during an EFMA without losing biologically relevant EFMs. Calculating only the thermodynamically feasible EFMs strongly reduces memory consumption and program runtime, allowing the analysis of larger networks. We apply tEFMA to study the central carbon metabolism of E. coli and find that up to 80% of its EFMs are thermodynamically infeasible. Moreover, we identify glutamate dehydrogenase as a bottleneck, when E. coli is grown on glucose and explain its inactivity as a consequence of network embedded thermodynamics. We implemented tEFMA as a Java package which is available for download at https://github.com/mpgerstl/tEFMA.
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