Computational identification of splicing phenotypes from single cell transcriptomic experiments

Y Huang, G Sanguinetti - biorxiv, 2020 - biorxiv.org
RNA splicing is an important driver of heterogeneity in single cells, both through the
expression of alternative transcripts and as a major determinant of transcriptional kinetics …

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 …

Mining alternative splicing patterns in scRNA-seq data using scASfind

Y Song, G Parada, JTH Lee, M Hemberg - bioRxiv, 2023 - biorxiv.org
Single-cell RNA-seq is widely used for transcriptome profiling, but most analyses have
focused on gene-level events, with much less attention devoted to alternative splicing. Here …

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 …

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads

D He, Y Gao, SS Chan, N Quintana-Parrilla, R Patro - bioRxiv, 2024 - biorxiv.org
Motivation: Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study
cellular heterogeneity, cellular fate, and transcriptional dynamics. Modeling splicing …

Investigating RNA splicing as a source of cellular diversity using a binomial mixture model

K Isaev, DA Knowles - Machine Learning in Computational …, 2024 - proceedings.mlr.press
Alternative splicing (AS) contributes significantly to RNA and protein variability yet its role in
defining cellular diversity is not fully understood. While Smart-seq2 offers enhanced …

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 …

Genomic sequences and RNA-binding proteins predict RNA splicing efficiency in various single-cell contexts

R Hou, Y Huang - Bioinformatics, 2022 - academic.oup.com
Motivation The RNA splicing efficiency is of high interest for both understanding the
regulatory machinery of gene expression and estimating the RNA velocity in single cells …

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 …

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 …