Identifying biases and their potential solutions in human microbiome studies

JT Nearing, AM Comeau, MGI Langille - Microbiome, 2021 - Springer
Advances in DNA sequencing technology have vastly improved the ability of researchers to
explore the microbial inhabitants of the human body. Unfortunately, while these studies have …

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

T Cordier, L Alonso‐Sáez… - Molecular …, 2021 - Wiley Online Library
A decade after environmental scientists integrated high‐throughput sequencing
technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on …

Deep learning and computer vision will transform entomology

TT Høye, J Ärje, K Bjerge, OLP Hansen… - Proceedings of the …, 2021 - pnas.org
Most animal species on Earth are insects, and recent reports suggest that their abundance is
in drastic decline. Although these reports come from a wide range of insect taxa and regions …

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

BE Deagle, AC Thomas, JC McInnes… - Molecular …, 2019 - Wiley Online Library
Advances in DNA sequencing technology have revolutionized the field of molecular analysis
of trophic interactions, and it is now possible to recover counts of food DNA sequences from …

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

ND Grubaugh, K Gangavarapu, J Quick, NL Matteson… - Genome biology, 2019 - Springer
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this
process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to …

Consistent and correctable bias in metagenomic sequencing experiments

MR McLaren, AD Willis, BJ Callahan - elife, 2019 - elifesciences.org
Marker-gene and metagenomic sequencing have profoundly expanded our ability to
measure biological communities. But the measurements they provide differ from the truth …

Toward quantitative metabarcoding

AO Shelton, ZJ Gold, AJ Jensen, ED′ Agnese… - Ecology, 2023 - Wiley Online Library
Amplicon‐sequence data from environmental DNA (eDNA) and microbiome studies provide
important information for ecology, conservation, management, and health. At present …

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

LM van der Loos, R Nijland - Molecular Ecology, 2021 - Wiley Online Library
With the growing anthropogenic pressure on marine ecosystems, the need for efficient
monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is …

Genome-wide analysis of somatic noncoding mutation patterns in cancer

F Dietlein, AB Wang, C Fagre, A Tang, NJM Besselink… - Science, 2022 - science.org
We established a genome-wide compendium of somatic mutation events in 3949 whole
cancer genomes representing 19 tumor types. Protein-coding events captured well …

Critical insight into recombinase polymerase amplification technology

MA Munawar - Expert Review of Molecular Diagnostics, 2022 - Taylor & Francis
Introduction Recombinase polymerase amplification (RPA) is a promising and emerging
technology for rapidly amplifying target nucleic acid from minimally processed samples and …