Coverage-dependent bias creates the appearance of binary splicing in single cells

CF Buen Abad Najar, N Yosef, LF Lareau - Elife, 2020 - elifesciences.org
Single-cell RNA sequencing provides powerful insight into the factors that determine each
cell's unique identity. Previous studies led to the surprising observation that alternative …

Robust detection of alternative splicing in a population of single cells

JD Welch, Y Hu, JF Prins - Nucleic acids research, 2016 - academic.oup.com
Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but
suffer from low coverage, 3′ bias and technical noise. These unique properties of single …

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 …

Identifying cell state–associated alternative splicing events and their coregulation

CFBA Najar, P Burra, N Yosef, LF Lareau - Genome research, 2022 - genome.cshlp.org
Alternative splicing shapes the transcriptome and contributes to each cell's unique identity,
but single-cell RNA sequencing (scRNA-seq) has struggled to capture the impact of …

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 …

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 …

MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data

WX Wen, AJ Mead, S Thongjuea - Nucleic Acids Research, 2023 - academic.oup.com
Alternative splicing is an important source of heterogeneity underlying gene expression
between individual cells but remains an understudied area due to the paucity of …

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers

Y Hu, K Wang, M Li - PLoS computational biology, 2020 - journals.plos.org
The emergence of single-cell RNA-seq (scRNA-seq) technology has made it possible to
measure gene expression variations at cellular level. This breakthrough enables the …

BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

Y Huang, G Sanguinetti - Genome biology, 2021 - Springer
RNA splicing is an important driver of heterogeneity in single cells through the expression of
alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic …

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 …