From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing

GK Marinov, BA Williams, K McCue… - Genome …, 2014 - genome.cshlp.org
Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering
cell-to-cell variation in gene expression, transcript processing and editing, and regulatory …

BRIE: transcriptome-wide splicing quantification in single cells

Y Huang, G Sanguinetti - Genome biology, 2017 - Springer
Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity
in transcription, but the limitations of the technology have prevented its application to dissect …

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

JK Kim, AA Kolodziejczyk, T Ilicic… - Nature …, 2015 - nature.com
Single-cell RNA-sequencing (scRNA-seq) facilitates identification of new cell types and
gene regulatory networks as well as dissection of the kinetics of gene expression and …

Obstacles to detecting isoforms using full-length scRNA-seq data

J Westoby, P Artemov, M Hemberg, A Ferguson-Smith - Genome Biology, 2020 - Springer
Background Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual
to see more than one isoform being produced from a gene in a single cell, even when …

Universal alternative splicing of noncoding exons

IW Deveson, ME Brunck, J Blackburn, E Tseng, T Hon… - Cell Systems, 2018 - cell.com
The human transcriptome is so large, diverse, and dynamic that, even after a decade of
investigation by RNA sequencing (RNA-seq), we have yet to resolve its true dimensions …

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

H Dueck, M Khaladkar, TK Kim, JM Spaethling… - Genome biology, 2015 - Springer
Background Differentiation of metazoan cells requires execution of different gene
expression programs but recent single-cell transcriptome profiling has revealed …

Effective detection of variation in single-cell transcriptomes using MATQ-seq

K Sheng, W Cao, Y Niu, Q Deng, C Zong - Nature methods, 2017 - nature.com
The quantification of transcriptional variation in single cells, particularly within the same cell
population, is currently limited by the low sensitivity and high technical noise of single-cell …

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

G Finak, A McDavid, M Yajima, J Deng, V Gersuk… - Genome biology, 2015 - Springer
Single-cell transcriptomics reveals gene expression heterogeneity but suffers from
stochastic dropout and characteristic bimodal expression distributions in which expression is …

Single-cell RNAseq for the study of isoforms—how is that possible?

Á Arzalluz-Luque, A Conesa - Genome biology, 2018 - Springer
Single-cell RNAseq and alternative splicing studies have recently become two of the most
prominent applications of RNAseq. However, the combination of both is still challenging …

bigSCale: an analytical framework for big-scale single-cell data

G Iacono, E Mereu, A Guillaumet-Adkins… - Genome …, 2018 - genome.cshlp.org
Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into
complex tissues, with the latest techniques capable of processing tens of thousands of cells …