A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

Current challenges and best-practice protocols for microbiome analysis

R Bharti, DG Grimm - Briefings in bioinformatics, 2021 - academic.oup.com
Analyzing the microbiome of diverse species and environments using next-generation
sequencing techniques has significantly enhanced our understanding on metabolic …

The source of the Black Death in fourteenth-century central Eurasia

MA Spyrou, L Musralina, GA Gnecchi Ruscone… - Nature, 2022 - nature.com
The origin of the medieval Black Death pandemic (ad 1346–1353) has been a topic of
continuous investigation because of the pandemic's extensive demographic impact and long …

Genomic diversity of severe acute respiratory syndrome–coronavirus 2 in patients with coronavirus disease 2019

Z Shen, Y **ao, L Kang, W Ma, L Shi… - Clinical infectious …, 2020 - academic.oup.com
Background A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)–CoV-2,
has infected> 75 000 individuals and spread to> 20 countries. It is still unclear how fast the …

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

AL Mitchell, TK Attwood, PC Babbitt… - Nucleic acids …, 2019 - academic.oup.com
Abstract The InterPro database (http://www. ebi. ac. uk/interpro/) classifies protein
sequences into families and predicts the presence of functionally important domains and …

Species-level functional profiling of metagenomes and metatranscriptomes

EA Franzosa, LJ McIver, G Rahnavard, LR Thompson… - Nature …, 2018 - nature.com
Functional profiles of microbial communities are typically generated using comprehensive
metagenomic or metatranscriptomic sequence read searches, which are time-consuming …

Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems

Z Dai, G Liu, H Chen, C Chen, J Wang, S Ai… - The ISME …, 2020 - academic.oup.com
Microorganisms play an important role in soil phosphorus (P) cycling and regulation of P
availability in agroecosystems. However, the responses of the functional and ecological …

[HTML][HTML] Airborne environmental DNA for terrestrial vertebrate community monitoring

C Lynggaard, MF Bertelsen, CV Jensen, MS Johnson… - Current Biology, 2022 - cell.com
Biodiversity monitoring at the community scale is a critical element of assessing and
studying species distributions, ecology, diversity, and movements, and it is key to …

InterPro in 2017—beyond protein family and domain annotations

RD Finn, TK Attwood, PC Babbitt… - Nucleic acids …, 2017 - academic.oup.com
Abstract InterPro (http://www. ebi. ac. uk/interpro/) is a freely available database used to
classify protein sequences into families and to predict the presence of important domains …