Best practices for variant calling in clinical sequencing

DC Koboldt - Genome medicine, 2020 - Springer
Next-generation sequencing technologies have enabled a dramatic expansion of clinical
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …

Design and computational analysis of single-cell RNA-sequencing experiments

R Bacher, C Kendziorski - Genome biology, 2016 - Springer
Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows
us to address scientific questions that eluded examination just a few years ago. With the …

Genome-wide RNA polymerase stalling shapes the transcriptome during aging

A Gyenis, J Chang, JJPG Demmers, ST Bruens… - Nature …, 2023 - nature.com
Gene expression profiling has identified numerous processes altered in aging, but how
these changes arise is largely unknown. Here we combined nascent RNA sequencing and …

Grey wolf genomic history reveals a dual ancestry of dogs

A Bergström, DWG Stanton, UH Taron, L Frantz… - Nature, 2022 - nature.com
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and
they remained widespread throughout the last Ice Age when many other large mammal …

Bile salt hydrolase catalyses formation of amine-conjugated bile acids

B Rimal, SL Collins, CE Tanes, ER Rocha, MA Granda… - Nature, 2024 - nature.com
Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect
host-mediated metabolic processes,,,,–; however, the bacterial gene (s) responsible for their …

An antibiotic from an uncultured bacterium binds to an immutable target

R Shukla, AJ Peoples, KC Ludwig, S Maity, MGN Derks… - Cell, 2023 - cell.com
Antimicrobial resistance is a leading mortality factor worldwide. Here, we report the
discovery of clovibactin, an antibiotic isolated from uncultured soil bacteria. Clovibactin …

Hybrid speciation driven by multilocus introgression of ecological traits

N Rosser, F Seixas, LM Queste, B Cama, R Mori-Pezo… - Nature, 2024 - nature.com
Hybridization allows adaptations to be shared among lineages and may trigger the evolution
of new species,. However, convincing examples of homoploid hybrid speciation remain rare …

A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

Y Deng, S Liu, Y Zhang, J Tan, X Li, X Chu, B Xu… - Molecular plant, 2022 - cell.com
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …

Radiogenomic-based multiomic analysis reveals imaging intratumor heterogeneity phenotypes and therapeutic targets

GH Su, Y ** of the total transcriptome by in situ polyadenylation
DW McKellar, M Mantri, MM Hinchman… - Nature …, 2023 - nature.com
Spatial transcriptomics reveals the spatial context of gene expression, but current methods
are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that …