RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Challenges in unsupervised clustering of single-cell RNA-seq data

VY Kiselev, TS Andrews, M Hemberg - Nature Reviews Genetics, 2019 - nature.com
Single-cell RNA sequencing (scRNA-seq) allows researchers to collect large catalogues
detailing the transcriptomes of individual cells. Unsupervised clustering is of central …

Aging is associated with a systemic length-associated transcriptome imbalance

T Stoeger, RA Grant, AC McQuattie-Pimentel… - Nature Aging, 2022 - nature.com
Aging is among the most important risk factors for morbidity and mortality. To contribute
toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data …

Genetic insights into the neurodevelopmental origins of schizophrenia

R Birnbaum, DR Weinberger - Nature Reviews Neuroscience, 2017 - nature.com
Schizophrenia is a severe neuropsychiatric disorder with a longstanding history of
neurobiological investigation. Although the underlying causal mechanisms remain …

Schrödinger's microbes: tools for distinguishing the living from the dead in microbial ecosystems

JB Emerson, RI Adams, CMB Román, B Brooks… - Microbiome, 2017 - Springer
While often obvious for macroscopic organisms, determining whether a microbe is dead or
alive is fraught with complications. Fields such as microbial ecology, environmental health …

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

E Madissoon, A Wilbrey-Clark, RJ Miragaia… - Genome biology, 2020 - Springer
Abstract Background The Human Cell Atlas is a large international collaborative effort to
map all cell types of the human body. Single-cell RNA sequencing can generate high-quality …

A novel approach to high-quality postmortem tissue procurement: the GTEx project

LJ Carithers, K Ardlie, M Barcus… - Biopreservation and …, 2015 - liebertpub.com
The Genotype-Tissue Expression (GTEx) project, sponsored by the NIH Common Fund, was
established to study the correlation between human genetic variation and tissue-specific …

variancePartition: interpreting drivers of variation in complex gene expression studies

GE Hoffman, EE Schadt - BMC bioinformatics, 2016 - Springer
Background As large-scale studies of gene expression with multiple sources of biological
and technical variation become widely adopted, characterizing these drivers of variation …

Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer

NL Burdett, MO Willis, K Alsop, AL Hunt, A Pandey… - Nature …, 2023 - nature.com
High-grade serous ovarian cancer (HGSC) is frequently characterized by homologous
recombination (HR) DNA repair deficiency and, while most such tumors are sensitive to …

Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq–based resource for pain and sensory neuroscience research

P Ray, A Torck, L Quigley, A Wangzhou, M Neiman… - Pain, 2018 - journals.lww.com
2. Methods We performed RNA-seq for hDRG and integratively analyzed the transcriptome
by comparing it with publicly available human and mouse RNA-seq data sets (sources …