Recent advances in the reconstruction of metabolic models and integration of omics data
Highlights•Metabolic models of different types (eg single cell/tissue specific/whole-
organism).•Ever-increasing applications of metabolic models.•Model reconstruction process …
organism).•Ever-increasing applications of metabolic models.•Model reconstruction process …
Constructing kinetic models of metabolism at genome‐scales: a review
S Srinivasan, WR Cluett, R Mahadevan - Biotechnology journal, 2015 - Wiley Online Library
Constraint‐based modeling of biological networks (metabolism, transcription and signal
transduction), although used successfully in many applications, suffer from specific …
transduction), although used successfully in many applications, suffer from specific …
A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data
In contrast to stoichiometric-based models, the development of large-scale kinetic models of
metabolism has been hindered by the challenge of identifying kinetic parameter values and …
metabolism has been hindered by the challenge of identifying kinetic parameter values and …
k-OptForce: integrating kinetics with flux balance analysis for strain design
A Chowdhury, AR Zomorrodi… - PLoS computational …, 2014 - journals.plos.org
Computational strain design protocols aim at the system-wide identification of intervention
strategies for the enhanced production of biochemicals in microorganisms. Existing …
strategies for the enhanced production of biochemicals in microorganisms. Existing …
Genome scale engineering techniques for metabolic engineering
Metabolic engineering has expanded from a focus on designs requiring a small number of
genetic modifications to increasingly complex designs driven by advances in genome-scale …
genetic modifications to increasingly complex designs driven by advances in genome-scale …
Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain
Highlights•Constraint-based models are useful but do not always sufficiently answer a
question.•Kinetic models provide deeper insight into behavior of complex metabolic …
question.•Kinetic models provide deeper insight into behavior of complex metabolic …
K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data
Kinetic models predict the metabolic flows by directly linking metabolite concentrations and
enzyme levels to reaction fluxes. Robust parameterization of organism-level kinetic models …
enzyme levels to reaction fluxes. Robust parameterization of organism-level kinetic models …
Bayesian inference of metabolic kinetics from genome-scale multiomics data
Modern biological tools generate a wealth of data on metabolite and protein concentrations
that can be used to help inform new strain designs. However, learning from these data to …
that can be used to help inform new strain designs. However, learning from these data to …
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
CJ Foster, S Gopalakrishnan… - PLoS computational …, 2019 - journals.plos.org
Kinetic models of metabolic networks offer the promise of quantitative phenotype prediction.
The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect …
The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect …
Kinetic modeling of metabolism: Present and future
Kinetic models of metabolism are predictors of temporal metabolic behavior of living
organisms that integrate multi-omics data sets with reaction network models to interpret …
organisms that integrate multi-omics data sets with reaction network models to interpret …