Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data

C Cheng, J Easton, C Rosencrance, Y Li… - Nucleic Acids …, 2019 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for characterizing the cell-to-cell
variation and cellular dynamics in populations which appear homogeneous otherwise in …

Uncovering the complexity of transcriptomes with RNASeq

V Costa, C Angelini, I De Feis… - BioMed Research …, 2010 - Wiley Online Library
… force accounting for diversity and biological complexity of living organisms. … of RNA
transcripts from repeated sequences, offering a limited dynamic range, unable to detect very subtle

The power and promise of RNAseq in ecology and evolution

EV Todd, MA Black, NJ Gemmell - Molecular ecology, 2016 - Wiley Online Library
… The true sensitivity of RNA-seq for detecting subtle expression differences has been … and
taxonomic diversity, so will the depth of biological insight possible through RNA-seq analysis in …

Comparison of alternative approaches for analysing multi-level RNA-seq data

I Mohorianu, A Bretman, DT Smith, EK Fowler… - PLoS …, 2017 - journals.plos.org
… , RNA-seq generates a diverse set of reads and facilitates analyses of expression level variation
for known and unknown RNA … which we analysed the subtle effects on gene expression …

Toward Best Practice in Identifying Subtle Differential Expression with RNA-seq: A Real-World Multi-Center Benchmarking Study Using Quartet and MAQC Reference …

D Wang, Y Liu, Y Zhang, Q Chen, Y Han, W Hou, C Liu… - bioRxiv, 2023 - biorxiv.org
… 85 processing, experimental protocols, sequencing platforms, and analysis pipelines across
… 87 reproducibility of RNA-seq 14, 15, 22. In the context of such diverse experimental and 88 …

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

GH Perry, P Melsted, JC Marioni, Y Wang… - Genome …, 2012 - genome.cshlp.org
diversity data on a large panel of species, we used RNA-seq combined with a de novo gene
assembly strategy. We prepared RNA-seqsequence due to true SNPs could have subtle

Abundant and diverse RNA viruses in insects revealed by RNA-Seq analysis: ecological and evolutionary implications

H Wu, R Pang, T Cheng, L Xue, H Zeng, T Lei… - Msystems, 2020 - Am Soc Microbiol
… ecological habitats and recovered more than 1,213 RNA viruses that were recapitulated in
40 … ecologically diverse viral populations in insects greatly expand our understanding of RNA

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

J Majewski, T Pastinen - Trends in Genetics, 2011 - cell.com
… by RNA-seq and summarize current progress towards understanding the role of eQTLs in
determining human phenotypic diversity. … acting in trans have more subtle effects, appear more …

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

BB Lake, R Ai, GE Kaeser, NS Salathia, YC Yung… - Science, 2016 - science.org
… Therefore, our data highlight subtle yet region-defining gene expression signatures
among specific neuronal subtypes that could not be detected from bulk analyses (fig. S14B). …

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

S Shen, JW Park, Z Lu, L Lin… - Proceedings of the …, 2014 - National Acad Sciences
… of RNA-Seq continues to grow, we expect rMATS will be useful for studies of alternative
splicing in diverse RNA-Seq … This suggests the paired rMATS model can reveal more subtle but …