Microbial production of advanced biofuels
Concerns over climate change have necessitated a rethinking of our transportation
infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced …
infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced …
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Reconstructed microbial metabolic networks facilitate a mechanistic description of the
genotype–phenotype relationship through the deployment of constraint-based …
genotype–phenotype relationship through the deployment of constraint-based …
A protocol for generating a high-quality genome-scale metabolic reconstruction
I Thiele, BØ Palsson - Nature protocols, 2010 - nature.com
Network reconstructions are a common denominator in systems biology. Bottom–up
metabolic network reconstructions have been developed over the last 10 years. These …
metabolic network reconstructions have been developed over the last 10 years. These …
A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications
MR Antoniewicz - Metabolic engineering, 2021 - Elsevier
The field of metabolic engineering is primarily concerned with improving the biological
production of value-added chemicals, fuels and pharmaceuticals through the design …
production of value-added chemicals, fuels and pharmaceuticals through the design …
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models …
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models …
Multidimensional optimality of microbial metabolism
Although the network topology of metabolism is well known, understanding the principles
that govern the distribution of fluxes through metabolism lags behind. Experimentally, these …
that govern the distribution of fluxes through metabolism lags behind. Experimentally, these …
Reconstruction of biochemical networks in microorganisms
Abstract Systems analysis of metabolic and growth functions in microbial organisms is
rapidly developing and maturing. Such studies are enabled by reconstruction, at the …
rapidly developing and maturing. Such studies are enabled by reconstruction, at the …
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
D McCloskey, BØ Palsson, AM Feist - Molecular systems biology, 2013 - embopress.org
The genome‐scale model (GEM) of metabolism in the bacterium Escherichia coli K‐12 has
been in development for over a decade and is now in wide use. GEM‐enabled studies of E …
been in development for over a decade and is now in wide use. GEM‐enabled studies of E …
[HTML][HTML] Synthetic and systems biology for microbial production of commodity chemicals
The combination of synthetic and systems biology is a powerful framework to study
fundamental questions in biology and produce chemicals of immediate practical application …
fundamental questions in biology and produce chemicals of immediate practical application …
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
To which extent can optimality principles describe the operation of metabolic networks? By
explicitly considering experimental errors and in silico alternate optima in flux balance …
explicitly considering experimental errors and in silico alternate optima in flux balance …