Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

AM Piper, J Batovska, NOI Cogan, J Weiss… - …, 2019 - academic.oup.com
Trap-based surveillance strategies are widely used for monitoring of invasive insect species,
aiming to detect newly arrived exotic taxa as well as track the population levels of …

Bioinformatics resources for SARS-CoV-2 discovery and surveillance

T Hu, J Li, H Zhou, C Li, EC Holmes… - Briefings in …, 2021 - academic.oup.com
In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia
outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and …

[HTML][HTML] Trafficked Malayan pangolins contain viral pathogens of humans

W Shi, M Shi, TC Que, XM Cui, RZ Ye, LY Xia… - Nature …, 2022 - nature.com
Pangolins are the most trafficked wild animal in the world according to the World Wildlife
Fund. The discovery of SARS-CoV-2-related coronaviruses in Malayan pangolins has …

[HTML][HTML] Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

M Xiao, X Liu, J Ji, M Li, J Li, L Yang, W Sun, P Ren… - Genome medicine, 2020 - Springer
Abstract Background COVID-19 (coronavirus disease 2019) has caused a major epidemic
worldwide; however, much is yet to be known about the epidemiology and evolution of the …

[HTML][HTML] Genomic answers for children: Dynamic analyses of> 1000 pediatric rare disease genomes

ASA Cohen, EG Farrow, AT Abdelmoity, JT Alaimo… - Genetics in …, 2022 - Elsevier
Purpose This study aimed to provide comprehensive diagnostic and candidate analyses in a
pediatric rare disease cohort through the Genomic Answers for Kids program. Methods …

Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives

Y Zhao, F Huang, W Wang, R Gao, L Fan… - Science of the Total …, 2023 - Elsevier
The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi,
and protozoa, in urban water systems poses a significant risk to public health. The …

[HTML][HTML] Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies

Y Jia, S Zhao, W Guo, L Peng, F Zhao, L Wang… - Environmental …, 2022 - Springer
Background Increasing studies have demonstrated potential disproportionate functional and
ecological contributions of rare taxa in a microbial community. However, the study of the …

[HTML][HTML] The application of metagenomics to study microbial communities and develop desirable traits in fermented foods

M Srinivas, O O'Sullivan, PD Cotter, D Sinderen… - Foods, 2022 - mdpi.com
The microbial communities present within fermented foods are diverse and dynamic,
producing a variety of metabolites responsible for the fermentation processes, imparting …

[HTML][HTML] Impact of sequencing depth and technology on de novo RNA-Seq assembly

J Patterson, EJ Carpenter, Z Zhu, D An, X Liang… - BMC genomics, 2019 - Springer
Background RNA-Seq data is inherently nonuniform for different transcripts because of
differences in gene expression. This makes it challenging to decide how much data should …

[HTML][HTML] Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

S Anslan, V Mikryukov, K Armolaitis, J Ankuda… - PeerJ, 2021 - peerj.com
With the developments in DNA nanoball sequencing technologies and the emergence of
new platforms, there is an increasing interest in their performance in comparison with the …