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Computing the shortest elementary flux modes in genome-scale metabolic networks [PDF]
, 2009 This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective ...
Acuña +54 more
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OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis
Microbial Cell Factories, 2009 Background The quantitative analysis of metabolic fluxes, i.e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach
Nielsen Lars K +3 more
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Bioengineering, 2023 Omics data was acquired, and the development and research of metabolic simulation and analysis methods using them were also actively carried out. However, it was a laborious task to acquire such data each time the medium composition, culture conditions ...
Yuki Kuriya +4 more
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Analyzing and Resolving Infeasibility in Flux Balance Analysis of Metabolic Networks
Metabolites, 2022 Flux balance analysis (FBA) is a key method for the constraint-based analysis of metabolic networks. A technical problem may occur in FBA when known (e.g., measured) fluxes of certain reactions are integrated into an FBA scenario rendering the underlying
Steffen Klamt, Axel von Kamp
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Elementary vectors and conformal sums in polyhedral geometry and their relevance for metabolic pathway analysis [PDF]
, 2016 A fundamental result in metabolic pathway analysis states that every flux mode can be decomposed into a sum of elementary modes. However, only a decomposition without cancelations is biochemically meaningful, since a reversible reaction cannot have ...
Müller, Stefan, Regensburger, Georg
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Transcript abundance on its own cannot be used to infer fluxes in central metabolism
Frontiers in Plant Science, 2014 An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus)
Jörg eSchwender +13 more
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The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases
Metabolites, 2021 Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental ...
Julia Koblitz +5 more
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Genome-scale architecture of small molecule regulatory networks and the fundamental trade-off between regulation and enzymatic activity [PDF]
, 2017 Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of ...
Briars, Emma +6 more
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13C-based metabolic flux analysis
Nature Protocols, 2009 Stable isotope, and in particular (13)C-based flux analysis, is the exclusive approach to experimentally quantify the integrated responses of metabolic networks. Here we describe a protocol that is based on growing microbes on (13)C-labeled glucose and subsequent gas chromatography mass spectrometric detection of (13)C-patterns in protein-bound amino ...
Zamboni, Nicola +3 more
openaire +4 more sources
Mapping the landscape of metabolic goals of a cell [PDF]
, 2016 Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function.
Paschalidis, Ioannis Ch. +4 more
core +3 more sources