Current status and applications of genome-scale metabolic models
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …
associations for entire metabolic genes in an organism, and can be simulated to predict …
Regulation of glycolytic flux and overflow metabolism depending on the source of energy generation for energy demand
K Shimizu, Y Matsuoka - Biotechnology advances, 2019 - Elsevier
Overflow metabolism is a common phenomenon observed at higher glycolytic flux in many
bacteria, yeast (known as Crabtree effect), and mammalian cells including cancer cells …
bacteria, yeast (known as Crabtree effect), and mammalian cells including cancer cells …
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid …
Background Genome-scale metabolic models (GEMs) allow predicting metabolic
phenotypes from limited data on uptake and secretion fluxes by defining the space of all the …
phenotypes from limited data on uptake and secretion fluxes by defining the space of all the …
Automated generation of bacterial resource allocation models
A Bulović, S Fischer, M Dinh, F Golib… - Metabolic …, 2019 - Elsevier
Abstract Resource Balance Analysis (RBA) is a computational method based on resource
allocation, which performs accurate quantitative predictions of whole-cell states (ie growth …
allocation, which performs accurate quantitative predictions of whole-cell states (ie growth …
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
Background Genome-scale models of metabolism and macromolecular expression (ME
models) enable systems-level computation of proteome allocation coupled to metabolic …
models) enable systems-level computation of proteome allocation coupled to metabolic …
The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates
DH De Groot, C Van Boxtel, R Planqué… - PLOS Computational …, 2019 - journals.plos.org
Growth rate is a near-universal selective pressure across microbial species. High growth
rates require hundreds of metabolic enzymes, each with different nonlinear kinetics, to be …
rates require hundreds of metabolic enzymes, each with different nonlinear kinetics, to be …
Modelling microbial communities using biochemical resource allocation analysis
To understand the functioning and dynamics of microbial communities is a fundamental
challenge in current biology. To tackle this challenge, the construction of computational …
challenge in current biology. To tackle this challenge, the construction of computational …
Quantification of proteomic and metabolic burdens predicts growth retardation and overflow metabolism in recombinant Escherichia coli
Escherichia coli has been the host organism most frequently investigated for efficient
recombinant protein production. However, the production of a foreign protein in recombinant …
recombinant protein production. However, the production of a foreign protein in recombinant …
Differential expression of a prophage-encoded glycocin and its immunity protein suggests a mutualistic strategy of a phage and its host
EL Denham, S Piersma, M Rinket, E Reilman… - Scientific Reports, 2019 - nature.com
Sublancin 168 is a highly potent and stable antimicrobial peptide secreted by the Gram-
positive bacterium Bacillus subtilis. Production of sublancin gives B. subtilis a major …
positive bacterium Bacillus subtilis. Production of sublancin gives B. subtilis a major …
RBA for eukaryotic cells: foundations and theoretical developments
A Goelzer, V Fromion - bioRxiv, 2019 - biorxiv.org
Resource allocation models were recently identified as new ways to investigate cell design
principles. In particular, the Resource Balance Analysis (RBA) framework is the first …
principles. In particular, the Resource Balance Analysis (RBA) framework is the first …