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 …
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
Enzyme turnover numbers (k cat) are key to understanding cellular metabolism, proteome
allocation and physiological diversity, but experimentally measured k cat data are sparse …
allocation and physiological diversity, but experimentally measured k cat data are sparse …
[HTML][HTML] Fermentation's pivotal role in sha** the future of plant-based foods: An integrative review of fermentation processes and their impact on sensory and health …
N Abbaspour - Applied Food Research, 2024 - Elsevier
Given the environmental, ethical, and food security challenges posed by conventional
agriculture and animal husbandry, the transition towards sustainable food systems is …
agriculture and animal husbandry, the transition towards sustainable food systems is …
The metabolic domestication syndrome of budding yeast
Cellular metabolism evolves through changes in the structure and quantitative states of
metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by …
metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by …
[HTML][HTML] Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints
EJ Kerkhoven - Current Opinion in Microbiology, 2022 - Elsevier
The concept of metabolic models with resource allocation constraints has been around for
over a decade and has clear advantages even when implementation is relatively …
over a decade and has clear advantages even when implementation is relatively …
Structural and biochemical insights of xylose MFS and SWEET transporters in microbial cell factories: challenges to lignocellulosic hydrolysates fermentation
IC Taveira, CB Carraro, KMV Nogueira… - Frontiers in …, 2024 - frontiersin.org
The production of bioethanol from lignocellulosic biomass requires the efficient conversion
of glucose and xylose to ethanol, a process that depends on the ability of microorganisms to …
of glucose and xylose to ethanol, a process that depends on the ability of microorganisms to …
Horizontal gene transfer in yeasts
Horizontal gene transfer (HGT), defined as the exchange of genetic material other than from
parent to progeny, is very common in bacteria and appears to constitute the most important …
parent to progeny, is very common in bacteria and appears to constitute the most important …
HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer
Background Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-
of-function, and metabolic adaptation to environmental niches. Genome-wide identification …
of-function, and metabolic adaptation to environmental niches. Genome-wide identification …
Metabolic Engineering of Yeast
Microbial cell factories have been developed to produce various compounds in a
sustainable and economically viable manner. The yeast Saccharomyces cerevisiae has …
sustainable and economically viable manner. The yeast Saccharomyces cerevisiae has …