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 …
Systems metabolic engineering strategies: integrating systems and synthetic biology with metabolic engineering
Metabolic engineering allows development of microbial strains efficiently producing
chemicals and materials, but it requires much time, effort, and cost to make the strains …
chemicals and materials, but it requires much time, effort, and cost to make the strains …
An atlas of human metabolism
Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and
provide a scaffold for the integrative analysis of omics data. Researchers have developed …
provide a scaffold for the integrative analysis of omics data. Researchers have developed …
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
Knowing the catalytic turnover numbers of enzymes is essential for understanding the
growth rate, proteome composition, and physiology of organisms, but experimental data on …
growth rate, proteome composition, and physiology of organisms, but experimental data on …
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex
evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available …
evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available …
Multiscale models quantifying yeast physiology: towards a whole-cell model
The yeast Saccharomyces cerevisiae is widely used as a cell factory and as an important
eukaryal model organism for studying cellular physiology related to human health and …
eukaryal model organism for studying cellular physiology related to human health and …
Path to improving the life cycle and quality of genome-scale models of metabolism
Y Seif, BØ Palsson - Cell systems, 2021 - cell.com
Genome-scale models of metabolism (GEMs) are key computational tools for the systems-
level study of metabolic networks. Here, we describe the" GEM life cycle," which we …
level study of metabolic networks. Here, we describe the" GEM life cycle," which we …
The role of artificial intelligence in the battle against antimicrobial-resistant bacteria
Antimicrobial resistance (AMR) in bacteria is a global health crisis due to the rapid
emergence of multidrug-resistant bacteria and the lengthy development of new …
emergence of multidrug-resistant bacteria and the lengthy development of new …
Constraint-based reconstruction and analyses of metabolic models: open-source python tools and applications to cancer
The influence of metabolism on signaling, epigenetic markers, and transcription is highly
complex yet important for understanding cancer physiology. Despite the development of …
complex yet important for understanding cancer physiology. Despite the development of …
[HTML][HTML] Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods
Highlights•Hybrid methods of three kinds combine normal mode analysis and MD
simulations•Normal mode (NM)-driven simulations use NMs to enhance energy landscape …
simulations•Normal mode (NM)-driven simulations use NMs to enhance energy landscape …