Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation. [PDF]
Sci Rep, 2020 Empirical kinetic models such as the Monod equation have been widely applied to relate the cell growth with substrate availability. The Monod equation shares a similar form with the mechanistically-based Michaelis-Menten kinetics for enzymatic processes,
Zeng H, Yang A.
europepmc +2 more sources
A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria. [PDF]
iScience, 2020 Vijayakumar S, Rahman PKSM, Angione C.
europepmc +2 more sources
Introducing an Optimization- and explicit Runge-Kutta- based Approach to Perform Dynamic Flux Balance Analysis. [PDF]
Sci Rep, 2020 In this work we introduce the generalized Optimization- and explicit Runge-Kutta-based Approach (ORKA) to perform dynamic Flux Balance Analysis (dFBA), which is numerically more accurate and computationally tractable than existing approaches.
Schroeder WL, Saha R.
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Software applications for flux balance analysis [PDF]
Briefings in Bioinformatics, 2012 Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA.
Lakshmanan, M. +3 more
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Steady state flux balance analysis game [PDF]
, 2021 AbstractFlux balance analysis (FBA) for microbial communities often assumes a global objective function that all species cooperatively maximize in addition to maximizing their own growth. Combining community FBA with dynamic FBA to understand the time course and steady states of communities typically entails discretizing time and solving a community ...
Garud Iyengar, Mitch Perry
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Flux balance analysis: A geometric perspective [PDF]
Journal of Theoretical Biology, 2009 Advances in the field of bioinformatics have led to reconstruction of genome-scale networks for a number of key organisms. The application of physicochemical constraints to these stoichiometric networks allows researchers, through methods such as flux balance analysis, to highlight key sets of reactions necessary to achieve particular objectives.
Smallbone, Kieran, Simeonidis, Evangelos
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Quantifying the propagation of parametric uncertainty on flux balance analysis
bioRxiv, 2021 Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes.
Hoang V. Dinh +2 more
semanticscholar +1 more source
Flux balance analysis accounting for metabolite dilution [PDF]
Genome Biology, 2010 AbstractFlux balance analysis is a common method for predicting steady-state flux distributions within metabolic networks, accounting for the growth demand for the synthesis of a predefined set of essential biomass precursors. Ignoring the growth demand for the synthesis of intermediate metabolites required for balancing their dilution leads flux ...
Benyamini, Tomer +3 more
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MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models [PDF]
, 2012 Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput.
A Freitag +59 more
core +6 more sources
Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor [PDF]
, 2010 Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism.
Alam, Mohammad T. +6 more
core +16 more sources