Common principles and best practices for engineering microbiomes
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge
gaps hinder their efficient use for addressing urgent societal and environmental challenges …
gaps hinder their efficient use for addressing urgent societal and environmental challenges …
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 …
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
Carbohydrate active enzymes (CAZymes) are made by various organisms for complex
carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis …
carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis …
The IMG/M data management and analysis system v. 7: content updates and new features
IMA Chen, K Chu, K Palaniappan, A Ratner… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img. jgi.
doe. gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to …
doe. gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to …
[HTML][HTML] Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
The human microbiome influences the efficacy and safety of a wide variety of commonly
prescribed drugs. Designing precision medicine approaches that incorporate microbial …
prescribed drugs. Designing precision medicine approaches that incorporate microbial …
[HTML][HTML] iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
[HTML][HTML] A genomic catalog of Earth's microbiomes
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …
enabled insights into the ecology and evolution of environmental and host-associated …
Community-led, integrated, reproducible multi-omics with anvi'o
Big data abound in microbiology, but the workflows designed to enable researchers to
interpret data can constrain the biological questions that can be asked. Five years after …
interpret data can constrain the biological questions that can be asked. Five years after …
The IMG/M data management and analysis system v. 6.0: new tools and advanced capabilities
IMA Chen, K Chu, K Palaniappan, A Ratner… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img. jgi.
doe. gov/m/) contains annotated isolate genome and metagenome datasets sequenced at …
doe. gov/m/) contains annotated isolate genome and metagenome datasets sequenced at …
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective
taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk …
taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk …