NCBI Taxonomy: a comprehensive update on curation, resources and tools

CL Schoch, S Ciufo, M Domrachev, CL Hotton… - Database, 2020 - academic.oup.com
Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes
organism names and classifications for every sequence in the nucleotide and protein …

[HTML][HTML] The human skin microbiome

AL Byrd, Y Belkaid, JA Segre - Nature Reviews Microbiology, 2018 - nature.com
Functioning as the exterior interface of the human body with the environment, skin acts as a
physical barrier to prevent the invasion of foreign pathogens while providing a home to the …

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

RH Nilsson, KH Larsson, AFS Taylor… - Nucleic acids …, 2019 - academic.oup.com
Abstract UNITE (https://unite. ut. ee/) is a web-based database and sequence management
environment for the molecular identification of fungi. It targets the formal fungal barcode—the …

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

NA O'Leary, MW Wright, JR Brister, S Ciufo… - Nucleic acids …, 2016 - academic.oup.com
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains
and curates a publicly available database of annotated genomic, transcript, and protein …

Diet rapidly and reproducibly alters the human gut microbiome

LA David, CF Maurice, RN Carmody, DB Gootenberg… - Nature, 2014 - nature.com
Long-term dietary intake influences the structure and activity of the trillions of
microorganisms residing in the human gut,,,,, but it remains unclear how rapidly and …

RESCRIPt: Reproducible sequence taxonomy reference database management

MS Robeson, DR O'Rourke, BD Kaehler… - PLoS computational …, 2021 - journals.plos.org
Nucleotide sequence and taxonomy reference databases are critical resources for
widespread applications including marker-gene and metagenome sequencing for …

Fungal diversity revisited: 2.2 to 3.8 million species

DL Hawksworth, R Lücking - Microbiology spectrum, 2017 - Am Soc Microbiol
The question of how many species of Fungi there are has occasioned much speculation,
with figures mostly posited from around half a million to 10 million, and in one extreme case …

Towards a unified paradigm for sequence‐based identification of fungi

U Kõljalg, RH Nilsson, K Abarenkov, L Tedersoo… - 2013 - Wiley Online Library
The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode
and in most cases the marker of choice for the exploration of fungal diversity in …

[HTML][HTML] Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity

PF Thomsen, E Willerslev - Biological conservation, 2015 - Elsevier
The continuous decline in Earth's biodiversity represents a major crisis and challenge for the
21st century, and there is international political agreement to slow down or halt this decline …

Global diversity and geography of soil fungi

L Tedersoo, M Bahram, S Põlme, U Kõljalg, NS Yorou… - science, 2014 - science.org
Introduction The kingdom Fungi is one of the most diverse groups of organisms on Earth,
and they are integral ecosystem agents that govern soil carbon cycling, plant nutrition, and …