Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment
LJ Marcos-Zambrano… - Frontiers in …, 2021 - frontiersin.org
The number of microbiome-related studies has notably increased the availability of data on
human microbiome composition and function. These studies provide the essential material …
human microbiome composition and function. These studies provide the essential material …
Microbial genome analysis: the COG approach
MY Galperin, DM Kristensen… - Briefings in …, 2019 - academic.oup.com
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a
popular tool for microbial genome annotation and comparative genomics. Initially created for …
popular tool for microbial genome annotation and comparative genomics. Initially created for …
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Advances in sequencing technologies and bioinformatics tools have dramatically increased
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
Abstract eggNOG is a public database of orthology relationships, gene evolutionary histories
and functional annotations. Here, we present version 5.0, featuring a major update of the …
and functional annotations. Here, we present version 5.0, featuring a major update of the …
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
M Steinegger, J Söding - Nature biotechnology, 2017 - nature.com
To the Editor: The throughput of DNA sequencing has increased much faster than
computational speed in the past decade, and sensitive-sequence searching has become the …
computational speed in the past decade, and sensitive-sequence searching has become the …
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database
is a bioinformatics resource providing orthology data and comprehensive functional …
is a bioinformatics resource providing orthology data and comprehensive functional …
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
Abstract eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at
different taxonomic levels, each with integrated and summarized functional annotations …
different taxonomic levels, each with integrated and summarized functional annotations …
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
Identifying homology relationships between sequences is fundamental to biological
research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that …
research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that …
Richness of human gut microbiome correlates with metabolic markers
We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we
report the human gut microbial composition in a population sample of 123 non-obese and …
report the human gut microbial composition in a population sample of 123 non-obese and …
MG-RAST, a metagenomics service for analysis of microbial community structure and function
Approaches in molecular biology, particularly those that deal with high-throughput
sequencing of entire microbial communities (the field of metagenomics), are rapidly …
sequencing of entire microbial communities (the field of metagenomics), are rapidly …