Detection of SARS-CoV-2 and its mutated variants via CRISPR-Cas13-based transcription amplification

Y Wang, Y Zhang, J Chen, M Wang, T Zhang… - Analytical …, 2021 - ACS Publications
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a
global health emergency, and its gene mutation and evolution further posed uncertainty of …

Plasma-derived HIV-1 virions contain considerable levels of defective genomes

K Fisher, XQ Wang, A Lee, V Morcilla… - Journal of …, 2022 - Am Soc Microbiol
Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact
genomes and for comparing these RNA genomes to proviral DNA. We have developed a …

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

K Sahlin, M Tomaszkiewicz, KD Makova… - Nature …, 2018 - nature.com
A significant portion of genes in vertebrate genomes belongs to multigene families, with
each family containing several gene copies whose presence/absence, as well as isoform …

Discrete measurements of RNA polymerase and reverse transcriptase fidelity reveal evolutionary tuning

V Potapov, S Krudup, S Maguire, I Unlu, S Guan… - RNA, 2024 - rnajournal.cshlp.org
Direct methods for determining the fidelity of DNA polymerases are robust, with relatively
little sample manipulation before sequencing. In contrast, methods for measuring RNA …

Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing

A Chappleboim, D Joseph-Strauss, A Rahat… - Science Translational …, 2021 - science.org
Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests have
relied on RNA extraction followed by reverse transcription quantitative polymerase chain …

Rare taxa exhibit disproportionate cell-level metabolic activity in enriched anaerobic digestion microbial communities

Y Jia, MHY Leung, X Tong, D Wilkins, PKH Lee - Msystems, 2019 - Am Soc Microbiol
Microbial communities are composed of populations with vastly different abundances and
levels of metabolic and replicative activity, ranging from actively metabolizing and dividing to …

Ampliconic genes on the great ape Y chromosomes: rapid evolution of copy number but conservation of expression levels

R Vegesna, M Tomaszkiewicz, OA Ryder… - Genome biology and …, 2020 - academic.oup.com
Multicopy ampliconic gene families on the Y chromosome play an important role in
spermatogenesis. Thus, studying their genetic variation in endangered great ape species is …

Cryo‐X‐Ray Phase Contrast Imaging Enables Combined 3D Structural Quantification and Nucleic Acid Analysis of Myocardial Biopsies

KYC Li, P Syrris, A Bonnin, TA Treibel… - Advanced …, 2024 - Wiley Online Library
Snap‐frozen biopsies serve as a valuable clinical resource of archival material for disease
research, as they enable a comprehensive array of downstream analyses to be performed …

Re-analysis of mobile mRNA datasets highlights challenges in the detection of mobile transcripts from short-read RNA-Seq data

P Paajanen, M Tomkins, F Hoerbst, R Veevers… - bioRxiv, 2024 - biorxiv.org
Short-read RNA-Seq analyses of grafted plants have led to the proposal that large numbers
of mRNAs move over long distances between plant tissues, acting as potential signals. The …

Relatively semi-conservative replication and a folded slippage model for short tandem repeats

H Zhang, D Li, X Zhao, S Pan, X Wu, S Peng, H Huang… - BMC genomics, 2020 - Springer
Background The ubiquitous presence of short tandem repeats (STRs) in virtually all
genomes implicates their functional relevance, while a widely-accepted definition of STR is …