Multi-omics integration in the age of million single-cell data

Z Miao, BD Humphreys, AP McMahon… - Nature Reviews …, 2021 - nature.com
An explosion in single-cell technologies has revealed a previously underappreciated
heterogeneity of cell types and novel cell-state associations with sex, disease, development …

Statistics or biology: the zero-inflation controversy about scRNA-seq data

R Jiang, T Sun, D Song, JJ Li - Genome biology, 2022 - Springer
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as
biological signals representing no or low gene expression, while others regard zeros as …

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

J Ding, X Adiconis, SK Simmons, MS Kowalczyk… - Nature …, 2020 - nature.com
The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly
in recent years, enabling major discoveries and large-scale cell mapping efforts. However …

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

A Byrne, AE Beaudin, HE Olsen, M Jain, C Cole… - Nature …, 2017 - nature.com
Understanding gene regulation and function requires a genome-wide method capable of
capturing both gene expression levels and isoform diversity at the single-cell level. Short …

Unravelling biology and shifting paradigms in cancer with single-cell sequencing

T Baslan, J Hicks - Nature Reviews Cancer, 2017 - nature.com
The fundamental operative unit of a cancer is the genetically and epigenetically innovative
single cell. Whether proliferating or quiescent, in the primary tumour mass or disseminated …

Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq

CR Cadwell, F Scala, S Li, G Livrizzi, S Shen… - Nature protocols, 2017 - nature.com
Neurons exhibit a rich diversity of morphological phenotypes, electrophysiological
properties, and gene-expression patterns. Understanding how these different characteristics …

Systematic comparative analysis of single cell RNA-sequencing methods

J Ding, X Adiconis, SK Simmons, MS Kowalczyk… - BioRxiv, 2019 - biorxiv.org
ABSTRACT A multitude of single-cell RNA sequencing methods have been developed in
recent years, with dramatic advances in scale and power, and enabling major discoveries …

Gene expression in the primate orbitofrontal cortex related to anxious temperament

MM Kenwood, T Souaiaia, R Kovner… - Proceedings of the …, 2023 - National Acad Sciences
Anxiety disorders are among the most prevalent psychiatric disorders, causing significant
suffering and disability. Relative to other psychiatric disorders, anxiety disorders tend to …

Rare cell detection by single-cell RNA sequencing as guided by single-molecule RNA FISH

E Torre, H Dueck, S Shaffer, J Gospocic, R Gupte… - Cell systems, 2018 - cell.com
Although single-cell RNA sequencing can reliably detect large-scale transcriptional
programs, it is unclear whether it accurately captures the behavior of individual genes …

Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions

JA Morrison, R McLennan, LA Wolfe, MM Gogol… - Elife, 2017 - elifesciences.org
Neural crest cells migrate throughout the embryo, but how cells move in a directed and
collective manner has remained unclear. Here, we perform the first single-cell transcriptome …