Reconstructing organisms in silico: genome-scale models and their emerging applications
X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020 - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …
of published studies detailing its genes, its genome and the biochemical functions of its …
Using genome-scale models to predict biological capabilities
Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …
been under development since the first whole-genome sequences appeared in the mid …
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
Genome‐scale metabolic models (GEM s) are widely used to calculate metabolic
phenotypes. They rely on defining a set of constraints, the most common of which is that the …
phenotypes. They rely on defining a set of constraints, the most common of which is that the …
Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
Escher is a web application for visualizing data on biological pathways. Three key features
make Escher a uniquely effective tool for pathway visualization. First, users can rapidly …
make Escher a uniquely effective tool for pathway visualization. First, users can rapidly …
A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications
MR Antoniewicz - Metabolic engineering, 2021 - Elsevier
The field of metabolic engineering is primarily concerned with improving the biological
production of value-added chemicals, fuels and pharmaceuticals through the design …
production of value-added chemicals, fuels and pharmaceuticals through the design …
Genome-scale metabolic modeling enables in-depth understanding of big data
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …
metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a …
Recent advances in systems metabolic engineering tools and strategies
Highlights•Microbial cell factories are becoming important in sustainable chemical
production.•Systems metabolic engineering allows efficient microbial cell factory …
production.•Systems metabolic engineering allows efficient microbial cell factory …
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful
systems biology approach, with applications ranging from basic understanding of genotype …
systems biology approach, with applications ranging from basic understanding of genotype …
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …
Next-generation genome-scale models for metabolic engineering
Highlights•COBRA methods have become widely used tools in metabolic engineering.•
Predictions of COBRA methods have led to experimental strain improvements.•Next …
Predictions of COBRA methods have led to experimental strain improvements.•Next …