Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses
Flux balance analysis (FBA) of a genome-scale metabolic model allows calculation of
intracellular fluxes by optimizing an objective function, such as maximization of cell growth …
intracellular fluxes by optimizing an objective function, such as maximization of cell growth …
Predicting metabolic fluxes using gene expression differences as constraints
RJP Van Berlo, D De Ridder, JM Daran… - … ACM transactions on …, 2009 - ieeexplore.ieee.org
A standard approach to estimate intracellular fluxes on a genome-wide scale is flux-balance
analysis (FBA), which optimizes an objective function subject to constraints on (relations …
analysis (FBA), which optimizes an objective function subject to constraints on (relations …
[HTML][HTML] Quantifying the propagation of parametric uncertainty on flux balance analysis
Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-
scale metabolic models play a central role in quantifying metabolic flows and constraining …
scale metabolic models play a central role in quantifying metabolic flows and constraining …
[HTML][HTML] An objective function exploiting suboptimal solutions in metabolic networks
EH Wintermute, TD Lieberman, PA Silver - BMC systems biology, 2013 - Springer
Abstract Background Flux Balance Analysis is a theoretically elegant, computationally
efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models …
efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models …
Bayesian metabolic flux analysis reveals intracellular flux couplings
Motivation Metabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic
reaction rates compatible with measurements, steady-state and the metabolic reaction …
reaction rates compatible with measurements, steady-state and the metabolic reaction …
[HTML][HTML] Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis
JRC Ramos, GP Oliveira, P Dumas… - Bioprocess and biosystems …, 2022 - Springer
Flux balance analysis (FBA) is currently the standard method to compute metabolic fluxes in
genome-scale networks. Several FBA extensions employing diverse objective functions …
genome-scale networks. Several FBA extensions employing diverse objective functions …
[HTML][HTML] ΔFBA—Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data
Genome-scale metabolic models (GEMs) provide a powerful framework for simulating the
entire set of biochemical reactions in a cell using a constraint-based modeling strategy …
entire set of biochemical reactions in a cell using a constraint-based modeling strategy …
Flux balance analysis: interrogating genome-scale metabolic networks
Flux balance analysis (FBA) is a computational method to analyze reconstructions of
biochemical networks. FBA requires the formulation of a biochemical network in a precise …
biochemical networks. FBA requires the formulation of a biochemical network in a precise …
The application of flux balance analysis in systems biology
EP Gianchandani, AK Chavali… - … : Systems Biology and …, 2010 - Wiley Online Library
An increasing number of genome‐scale reconstructions of intracellular biochemical
networks are being generated. Coupled with these stoichiometric models, several systems …
networks are being generated. Coupled with these stoichiometric models, several systems …
Construction and completion of flux balance models from pathway databases
M Latendresse, M Krummenacker, M Trupp… - …, 2012 - academic.oup.com
Motivation: Flux balance analysis (FBA) is a well-known technique for genome-scale
modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification …
modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification …