From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. [PDF]
PLoS Computational Biology, 2017 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.
Steffen Klamt +7 more
doaj +9 more sources
On the geometry of elementary flux modes. [PDF]
J Math Biol, 2023 Elementary flux modes (EFMs) play a prominent role in the constraint-based analysis of metabolic networks. They correspond to minimal functional units of the metabolic network at steady-state and as such have been studied for almost 30 years.
Wieder F, Henk M, Bockmayr A.
europepmc +9 more sources
How important is thermodynamics for identifying elementary flux modes? [PDF]
PLoS ONE, 2017 We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations.
Sabine Peres +4 more
doaj +8 more sources
Which sets of elementary flux modes form thermodynamically feasible flux distributions? [PDF]
FEBS Journal, 2016 Elementary flux modes (EFMs) are non‐decomposable steady‐state fluxes through metabolic networks. Every possible flux through a network can be described as a superposition of EFMs.
Matthias P Gerstl +2 more
exaly +6 more sources
A principal components method constrained by elementary flux modes: analysis of flux data sets. [PDF]
BMC Bioinformatics, 2016 Non-negative linear combinations of elementary flux modes (EMs) describe all feasible reaction flux distributions for a given metabolic network under the quasi steady state assumption.
von Stosch M +4 more
europepmc +9 more sources
Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs. [PDF]
PLoS ONE, 2015 Despite the significant progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible.
Christian Jungreuthmayer +4 more
doaj +5 more sources
An integrated approach for modeling and identification of perfusion bioreactors via basis flux modes [PDF]
Computers and Chemical Engineering, 2021 This paper discusses the challenges associated with the reliable and optimal operation of perfusion bioreactors and presents methods for modeling and identification of perfusion bioreactors as well as the vision for their integration.
Diogo Rodrigues +2 more
exaly +3 more sources
EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models. [PDF]
Metabolites, 2020 Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge.
Sarathy C +5 more
europepmc +2 more sources
Effect of Initial Water Flux on the Performance of Anaerobic Membrane Bioreactor: Constant Flux Mode versus Varying Flux Mode [PDF]
Membranes, 2021 Anaerobic membrane bioreactors (AnMBRs) have aroused growing interest in wastewater treatment and energy recovery. However, serious membrane fouling remains a critical hindrance to AnMBRs.
Xiawen Yi +3 more
doaj +3 more sources
Isotopic labelling reveals the efficient adaptation of wheat root TCA cycle flux modes to match carbon demand under ammonium nutrition. [PDF]
Sci Rep, 2019 Proper carbon (C) supply is essential for nitrogen (N) assimilation especially when plants are grown under ammonium (NH4+) nutrition. However, how C and N metabolic fluxes adapt to achieve so remains uncertain.
Vega-Mas I +6 more
europepmc +2 more sources