Analysis of optimality in natural and perturbed metabolic networks
An important goal of whole-cell computational modeling is to integrate detailed biochemical
information with biological intuition to produce testable predictions. Based on the premise …
information with biological intuition to produce testable predictions. Based on the premise …
The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum
WR Harcombe, NF Delaney, N Leiby… - PLoS computational …, 2013 - journals.plos.org
The most powerful genome-scale framework to model metabolism, flux balance analysis
(FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed …
(FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed …
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 …
The activity reaction core and plasticity of metabolic networks
Understanding the system-level adaptive changes taking place in an organism in response
to variations in the environment is a key issue of contemporary biology. Current modeling …
to variations in the environment is a key issue of contemporary biology. Current modeling …
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 …
Identification of genome-scale metabolic network models using experimentally measured flux profiles
Genome-scale metabolic network models can be reconstructed for well-characterized
organisms using genomic annotation and literature information. However, there are many …
organisms using genomic annotation and literature information. However, there are many …
Metabolic flux analysis and metabolic engineering of microorganisms
Recent advances in metabolic flux analysis including genome-scale constraints-based flux
analysis and its applications in metabolic engineering are reviewed. Various computational …
analysis and its applications in metabolic engineering are reviewed. Various computational …
Constrained allocation flux balance analysis
New experimental results on bacterial growth inspire a novel top-down approach to study
cell metabolism, combining mass balance and proteomic constraints to extend and …
cell metabolism, combining mass balance and proteomic constraints to extend and …
Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population
P Labhsetwar, JA Cole, E Roberts… - Proceedings of the …, 2013 - National Acad Sciences
Stochastic gene expression can lead to phenotypic differences among cells even in isogenic
populations growing under macroscopically identical conditions. Here, we apply flux …
populations growing under macroscopically identical conditions. Here, we apply flux …
A genome‐scale computational study of the interplay between transcriptional regulation and metabolism
This paper presents a new method, steady‐state regulatory flux balance analysis (SR‐FBA),
for predicting gene expression and metabolic fluxes in a large‐scale integrated metabolic …
for predicting gene expression and metabolic fluxes in a large‐scale integrated metabolic …