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 …
Modelling approaches for studying the microbiome
Advances in metagenome sequencing of the human microbiome have provided a plethora
of new insights and revealed a close association of this complex ecosystem with a range of …
of new insights and revealed a close association of this complex ecosystem with a range of …
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
RAVEN is a commonly used MATLAB toolbox for genome-scale metabolic model (GEM)
reconstruction, curation and constraint-based modelling and simulation. Here we present …
reconstruction, curation and constraint-based modelling and simulation. Here we present …
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
CJ Norsigian, N Pusarla, JL McConn… - Nucleic acids …, 2020 - academic.oup.com
Abstract The BiGG Models knowledge base (http://bigg. ucsd. edu) is a centralized
repository for high-quality genome-scale metabolic models. For the past 12 years, the …
repository for high-quality genome-scale metabolic models. For the past 12 years, the …
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
Comprehensive molecular‐level models of human metabolism have been generated on a
cellular level. However, models of whole‐body metabolism have not been established as …
cellular level. However, models of whole‐body metabolism have not been established as …
A systematic assessment of current genome-scale metabolic reconstruction tools
Background Several genome-scale metabolic reconstruction software platforms have been
developed and are being continuously updated. These tools have been widely applied to …
developed and are being continuously updated. These tools have been widely applied to …
High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
Genome‐scale reconstructions of metabolism are computational species‐specific
knowledge bases able to compute systemic metabolic properties. We present a …
knowledge bases able to compute systemic metabolic properties. We present a …
Biological insights through omics data integration
The number of studies that collect and publish large-scale multiomics data is rapidly
increasing. So far, we have not realized the full potential of the biological insights that can be …
increasing. So far, we have not realized the full potential of the biological insights that can be …
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
Genome-scale models (GEMs) of bacterial strains' metabolism have been formulated and
used over the past 20 years. Recently, with the number of genome sequences exponentially …
used over the past 20 years. Recently, with the number of genome sequences exponentially …
Genomic and metabolic analysis of Komagataeibacter xylinus DSM 2325 producing bacterial cellulose nanofiber
Bacterial cellulose nanofiber (CNF) is a polymer with a wide range of potential industrial
applications. Several Komagataeibacter species, including Komagataeibacter xylinus as a …
applications. Several Komagataeibacter species, including Komagataeibacter xylinus as a …