Flux-balance modelling of plant metabolism
Frontiers in Plant Science, 2011 Flux-balance modelling of plant metabolic networks provides an important complement to 13C-based metabolic flux analysis. Flux-balance modelling is a constraints-based approach in which steady-state fluxes in a metabolic network are predicted by using ...
Lee James Sweetlove +1 more
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Hybrid physics-informed metabolic cybergenetics: process rates augmented with machine-learning surrogates informed by flux balance analysis [PDF]
Industrial & Engineering Chemistry ResearchMetabolic cybergenetics is a promising concept that interfaces gene expression and cellular metabolism with computers for real-time dynamic metabolic control.
Sebastián Espinel-Ríos +1 more
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mSystems, 2022 The human intestinal microbiota starts to form immediately after birth and is important for the health of the host. During the first days, facultatively anaerobic bacterial species generally dominate, such as Enterobacteriaceae.
David M. Versluis +7 more
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Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways. [PDF]
BMC Syst Biol, 2019 BackgroundThe formation of acetate by fast-growing Escherichia coli (E. coli) is a commonly observed phenomenon, often referred to as overflow metabolism. Among various studies that have been carried over decades, a recent work (Basan, M.
Zeng H, Yang A.
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The Plant Journal, 2020 Cell expansion is a significant contributor to organ growth and is driven by the accumulation of osmolytes to increase cell turgor pressure. Metabolic modelling has the potential to provide insights into the processes that underpin osmolyte synthesis and
Sanu Shameer +4 more
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Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions. [PDF]
PLoS Comput Biol, 2019 We present a novel surrogate modeling method that can be used to accelerate the solution of uncertainty quantification (UQ) problems arising in nonlinear and non-smooth models of biological systems.
Paulson JA, Martin-Casas M, Mesbah A.
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Stoichiometry Based Steady-State Hepatic Flux Analysis: Computational and Experimental Aspects
Metabolites, 2012 The liver has many complex physiological functions, including lipid, protein and carbohydrate metabolism, as well as bile and urea production. It detoxifies toxic substances and medicinal products. It also plays a key role in the onset and maintenance of
Mehmet A. Orman +4 more
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Cell Reports, 2017 White adipocytes are specialized for energy storage, whereas brown adipocytes are specialized for energy expenditure. Explicating this difference can help identify therapeutic targets for obesity.
Alfred K. Ramirez +7 more
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Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks [PDF]
, 2008 Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass production rate.
Samal, Areejit
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Escher-FBA: a web application for interactive flux balance analysis. [PDF]
BMC Syst Biol, 2018 BackgroundFlux balance analysis (FBA) is a widely-used method for analyzing metabolic networks. However, most existing tools that implement FBA require downloading software and writing code.
Rowe E, Palsson BO, King ZA.
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