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 …
A white-box machine learning approach for revealing antibiotic mechanisms of action
Current machine learning techniques enable robust association of biological signals with
measured phenotypes, but these approaches are incapable of identifying causal …
measured phenotypes, but these approaches are incapable of identifying causal …
Metabolic models of human gut microbiota: Advances and challenges
The human gut is a complex ecosystem consisting of hundreds of microbial species
interacting with each other and with the human host. Mathematical models of the gut …
interacting with each other and with the human host. Mathematical models of the gut …
Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces
W Wang, S Li, Z Li, J Zhang, K Fan, G Tan, G Ai… - Nature …, 2020 - nature.com
Pharmaceutically important polyketides such as avermectin are mainly produced as
secondary metabolites during the stationary phase of growth of Streptomyces species in …
secondary metabolites during the stationary phase of growth of Streptomyces species in …
Stable diverse food webs become more common when interactions are more biologically constrained
Ecologists have long sought to understand how diversity and structure mediate the stability
of whole ecosystems. For high-diversity food webs, the interactions between species are …
of whole ecosystems. For high-diversity food webs, the interactions between species are …
SteadyCom: predicting microbial abundances while ensuring community stability
SHJ Chan, MN Simons… - PLoS computational …, 2017 - journals.plos.org
Genome-scale metabolic modeling has become widespread for analyzing microbial
metabolism. Extending this established paradigm to more complex microbial communities is …
metabolism. Extending this established paradigm to more complex microbial communities is …
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Abstract Systems biology has long been interested in models capturing both metabolism
and expression in a cell. We propose here an implementation of the metabolism and …
and expression in a cell. We propose here an implementation of the metabolism and …
Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei
Among CO2-fixing metabolic pathways in nature, the linear Wood–Ljungdahl pathway
(WLP) in phylogenetically diverse acetate-forming acetogens comprises the most …
(WLP) in phylogenetically diverse acetate-forming acetogens comprises the most …
Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth
Microbial communities comprised of phototrophs and heterotrophs hold great promise for
sustainable biotechnology. Successful application of these communities relies on the …
sustainable biotechnology. Successful application of these communities relies on the …
Flux sampling is a powerful tool to study metabolism under changing environmental conditions
HA Herrmann, BC Dyson, L Vass… - NPJ systems biology …, 2019 - nature.com
The development of high-throughput 'omic techniques has sparked a rising interest in
genome-scale metabolic models, with applications ranging from disease diagnostics to crop …
genome-scale metabolic models, with applications ranging from disease diagnostics to crop …