Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0
Genome-scale metabolic models (GEMs) are computational representations that enable
mathematical exploration of metabolic behaviors within cellular and environmental …
mathematical exploration of metabolic behaviors within cellular and environmental …
Genome-scale modeling of yeast metabolism: retrospectives and perspectives
Yeasts have been widely used for production of bread, beer and wine, as well as for
production of bioethanol, but they have also been designed as cell factories to produce …
production of bioethanol, but they have also been designed as cell factories to produce …
A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth
Metabolic modeling and machine learning are key components in the emerging next
generation of systems and synthetic biology tools, targeting the genotype–phenotype …
generation of systems and synthetic biology tools, targeting the genotype–phenotype …
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
The molecular basis of how temperature affects cell metabolism has been a long-standing
question in biology, where the main obstacles are the lack of high-quality data and methods …
question in biology, where the main obstacles are the lack of high-quality data and methods …
Yeast optimizes metal utilization based on metabolic network and enzyme kinetics
Metal ions are vital to metabolism, as they can act as cofactors on enzymes and thus
modulate individual enzymatic reactions. Although many enzymes have been reported to …
modulate individual enzymatic reactions. Although many enzymes have been reported to …
Information theory in computational biology: where we stand today
P Chanda, E Costa, J Hu, S Sukumar, J Van Hemert… - Entropy, 2020 - mdpi.com
“A Mathematical Theory of Communication” was published in 1948 by Claude Shannon to
address the problems in the field of data compression and communication over (noisy) …
address the problems in the field of data compression and communication over (noisy) …
Genome‐scale modeling for Bacillus coagulans to understand the metabolic characteristics
Y Chen, Y Sun, Z Liu, F Dong, Y Li… - Biotechnology and …, 2020 - Wiley Online Library
Lactic acid is widely used in many industries, especially in the production of poly‐lactic acid.
Bacillus coagulans is a promising lactic acid producer in industrial fermentation due to its …
Bacillus coagulans is a promising lactic acid producer in industrial fermentation due to its …
Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells
SM Schinn, C Morrison, W Wei, L Zhang… - Metabolic Engineering, 2021 - Elsevier
Genome-scale metabolic models describe cellular metabolism with mechanistic detail.
Given their high complexity, such models need to be parameterized correctly to yield …
Given their high complexity, such models need to be parameterized correctly to yield …
standard-GEM: standardization of open-source genome-scale metabolic models
The field of metabolic modelling at the genomescale continues to grow with more models
being created and curated. This comes with an increasing demand for adopting common …
being created and curated. This comes with an increasing demand for adopting common …
Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species
Metabolic network reconstructions have become an important tool for probing cellular
metabolism in the field of systems biology. They are used as tools for quantitative prediction …
metabolism in the field of systems biology. They are used as tools for quantitative prediction …