[HTML][HTML] Hybrid metabolic flux analysis: combining stoichiometric and statistical constraints to model the formation of complex recombinant products
Background Stoichiometric models constitute the basic framework for fluxome quantification
in the realm of metabolic engineering. A recurrent bottleneck, however, is the establishment …
in the realm of metabolic engineering. A recurrent bottleneck, however, is the establishment …
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] Advances in flux balance analysis by integrating machine learning and mechanism-based models
The availability of multi-omics data sets and genome-scale metabolic models for various
organisms provide a platform for modeling and analyzing genotype-to-phenotype …
organisms provide a platform for modeling and analyzing genotype-to-phenotype …
From annotated genomes to metabolic flux models and kinetic parameter fitting
Significant advances in system-level modeling of cellular behavior can be achieved based
on constraints derived from genomic information and on optimality hypotheses. For steady …
on constraints derived from genomic information and on optimality hypotheses. For steady …
Improving the accuracy of flux balance analysis through the implementation of carbon availability constraints for intracellular reactions
M Lularevic, AJ Racher, C Jaques… - Biotechnology and …, 2019 - Wiley Online Library
Constraint‐based modeling methods, such as Flux Balance Analysis (FBA), have been
extensively used to decipher complex, information rich‐omics datasets to elicit system‐wide …
extensively used to decipher complex, information rich‐omics datasets to elicit system‐wide …
Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants
One of the well-established approaches for the quantitative characterization of large-scale
underdetermined metabolic network is constraint-based flux analysis, which quantifies …
underdetermined metabolic network is constraint-based flux analysis, which quantifies …
[HTML][HTML] E-Flux2 and SPOT: validated methods for inferring intracellular metabolic flux distributions from transcriptomic data
Background Several methods have been developed to predict system-wide and condition-
specific intracellular metabolic fluxes by integrating transcriptomic data with genome-scale …
specific intracellular metabolic fluxes by integrating transcriptomic data with genome-scale …
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 …
iSCHRUNK–in silico approach to characterization and reduction of uncertainty in the kinetic models of genome-scale metabolic networks
S Andreozzi, L Miskovic, V Hatzimanikatis - Metabolic engineering, 2016 - Elsevier
Accurate determination of physiological states of cellular metabolism requires detailed
information about metabolic fluxes, metabolite concentrations and distribution of enzyme …
information about metabolic fluxes, metabolite concentrations and distribution of enzyme …
[HTML][HTML] Opportunities at the interface of network science and metabolic modeling
Metabolism plays a central role in cell physiology because it provides the molecular
machinery for growth. At the genome-scale, metabolism is made up of thousands of …
machinery for growth. At the genome-scale, metabolism is made up of thousands of …