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 …
Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon
sources is currently an advancing area in industrial research. The model yeast …
sources is currently an advancing area in industrial research. The model yeast …
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …
framework for integrative analysis of experimental molecular systems biology data and …
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
D Machado, S Andrejev, M Tramontano… - Nucleic acids …, 2018 - academic.oup.com
Genome-scale metabolic models are instrumental in uncovering operating principles of
cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in …
cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in …
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics,
insecticides and other high-value chemicals. Genome mining of gene clusters that encode …
insecticides and other high-value chemicals. Genome mining of gene clusters that encode …
[HTML][HTML] Insights from 20 years of bacterial genome sequencing
Since the first two complete bacterial genome sequences were published in 1995, the
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …
[HTML][HTML] 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 …
[HTML][HTML] 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 …
[HTML][HTML] COBRApy: constraints-based reconstruction and analysis for python
Abstract Background COnstraint-Based Reconstruction and Analysis (COBRA) methods are
widely used for genome-scale modeling of metabolic networks in both prokaryotes and …
widely used for genome-scale modeling of metabolic networks in both prokaryotes and …
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 …