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 …
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …
Computational analysis of cancer genome sequencing data
Distilling biologically meaningful information from cancer genome sequencing data requires
comprehensive identification of somatic alterations using rigorous computational methods …
comprehensive identification of somatic alterations using rigorous computational methods …
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 …
these changes arise is largely unknown. Here we combined nascent RNA sequencing and …
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 …
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …
Grey wolf genomic history reveals a dual ancestry of dogs
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 …
they remained widespread throughout the last Ice Age when many other large mammal …
cfDNA methylome profiling for detection and subtyping of small cell lung cancers
Small cell lung cancer (SCLC) is characterized by morphologic, epigenetic and
transcriptomic heterogeneity. Subtypes based upon predominant transcription factor …
transcriptomic heterogeneity. Subtypes based upon predominant transcription factor …
Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2
The COVID-19 outbreak has become a global health risk, and understanding the response
of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host …
of the host to the SARS-CoV-2 virus will help to combat the disease. RNA editing by host …
Population genomics of the critically endangered kākāpō
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago,
only 201 individuals remain today, most of them descending from an isolated island …
only 201 individuals remain today, most of them descending from an isolated island …
Spatial mapping of the total transcriptome by in situ polyadenylation
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 …
are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that …
A developmental landscape of 3D-cultured human pre-gastrulation embryos
L Xiang, Y Yin, Y Zheng, Y Ma, Y Li, Z Zhao, J Guo, Z Ai… - Nature, 2020 - nature.com
Our understanding of how human embryos develop before gastrulation, including spatial
self-organization and cell type ontogeny, remains limited by available two-dimensional …
self-organization and cell type ontogeny, remains limited by available two-dimensional …