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 …

Multi-omics approaches to disease

Y Hasin, M Seldin, A Lusis - Genome biology, 2017 - Springer
High-throughput technologies have revolutionized medical research. The advent of
genoty** arrays enabled large-scale genome-wide association studies and methods for …

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

A Zhu, JG Ibrahim, MI Love - Bioinformatics, 2019 - academic.oup.com
Motivation In RNA-seq differential expression analysis, investigators aim to detect those
genes with changes in expression level across conditions, despite technical and biological …

[HTML][HTML] From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Y Chen, ATL Lun, GK Smyth - F1000Research, 2016 - ncbi.nlm.nih.gov
In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for
profiling gene expression. One of the most common aims of RNA-seq profiling is to identify …

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Y Li, X Ge, F Peng, W Li, JJ Li - Genome biology, 2022 - Springer
When identifying differentially expressed genes between two conditions using human
population RNA-seq samples, we found a phenomenon by permutation analysis: two …

RNA-Seq differential expression analysis: An extended review and a software tool

J Costa-Silva, D Domingues, FM Lopes - PloS one, 2017 - journals.plos.org
The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

MT Parker, K Knop, AV Sherwood, NJ Schurch… - Elife, 2020 - elifesciences.org
Understanding genome organization and gene regulation requires insight into RNA
transcription, processing and modification. We adapted nanopore direct RNA sequencing to …

Applications of multi‐omics analysis in human diseases

C Chen, J Wang, D Pan, X Wang, Y Xu, J Yan… - MedComm, 2023 - Wiley Online Library
Multi‐omics usually refers to the crossover application of multiple high‐throughput screening
technologies represented by genomics, transcriptomics, single‐cell transcriptomics …

Systematic investigation of cytokine signaling activity at the tissue and single-cell levels

P Jiang, Y Zhang, B Ru, Y Yang, T Vu, R Paul… - Nature …, 2021 - nature.com
Cytokines are critical for intercellular communication in human health and disease, but the
investigation of cytokine signaling activity has remained challenging due to the short half …

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

AD Tang, CM Soulette, MJ van Baren, K Hart… - Nature …, 2020 - nature.com
While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-
length isoform changes may better elucidate the functional consequences of these …