Shotgun metagenomics, from sampling to analysis
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …
have crucial roles in the environment and in human health. However, microbes are …
DIAMOND+ MEGAN: fast and easy taxonomic and functional analysis of short and long microbiome sequences
One main approach to computational analysis of microbiome sequences is to first align
against a reference database of annotated protein sequences (NCBI‐nr) and then perform …
against a reference database of annotated protein sequences (NCBI‐nr) and then perform …
Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces
Abstract Background The International Space Station (ISS) is an ideal test bed for studying
the effects of microbial persistence and succession on a closed system during long space …
the effects of microbial persistence and succession on a closed system during long space …
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae
ME Schön, VV Zlatogursky, RP Singh, C Poirier… - Nature …, 2021 - nature.com
The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic
capabilities and launched the diversification of countless forms of algae. These primary …
capabilities and launched the diversification of countless forms of algae. These primary …
Translational informatics for human microbiota: data resources, models and applications
With the rapid development of human intestinal microbiology and diverse microbiome-
related studies and investigations, a large amount of data have been generated and …
related studies and investigations, a large amount of data have been generated and …
ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes
YW Wu - BMC genomics, 2018 - Springer
Background Inferring phylogenetic trees for newly recovered genomes from metagenomic
samples is very useful in determining the identities of uncultivated microorganisms. Even …
samples is very useful in determining the identities of uncultivated microorganisms. Even …
Introduction to the analysis of environmental sequences: metagenomics with MEGAN
Metagenomics has become a part of the standard toolkit for scientists interested in studying
microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse …
microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse …
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling
A Ugarte, R Vicedomini, J Bernardes, A Carbone - Microbiome, 2018 - Springer
Background Biochemical and regulatory pathways have until recently been thought and
modelled within one cell type, one organism and one species. This vision is being …
modelled within one cell type, one organism and one species. This vision is being …
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used
technique for investigating a range of questions, particularly related to health and …
technique for investigating a range of questions, particularly related to health and …
Performance of multiple metagenomics pipelines in understanding microbial diversity of a low-biomass spacecraft assembly facility
NASA planetary protection (PP) requires an assessment of the biological contamination of
the potential microbial burden on spacecraft destined to explore planetary bodies that may …
the potential microbial burden on spacecraft destined to explore planetary bodies that may …