Using BRIE to detect and analyze splicing isoforms in scRNA-Seq data
Y Huang, G Sanguinetti - Computational Methods for Single-Cell Data …, 2019 - 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 …
in transcription, but the limitations of the technology have prevented its application to dissect …
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 …
in transcription, but the limitations of the technology have prevented its application to dissect …
Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
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 …
measure gene expression variations at cellular level. This breakthrough enables the …
Probabilistic estimation of short sequence expression using RNA-Seq data and the “positional bootstrap”
When estimating expression of a transcript or part of a transcript using RNA-seq data, it is
commonly assumed that reads are generated uniformly from positions within the transcript …
commonly assumed that reads are generated uniformly from positions within the transcript …
SparseIso: a novel Bayesian approach to identify alternatively spliced isoforms from RNA-seq data
Motivation Recent advances in high-throughput RNA sequencing (RNA-seq) technologies
have made it possible to reconstruct the full transcriptome of various types of cells. It is …
have made it possible to reconstruct the full transcriptome of various types of cells. It is …
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 …
alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic …
Obstacles to detecting isoforms using full-length scRNA-seq data
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 …
to see more than one isoform being produced from a gene in a single cell, even when …
Statistical modeling of isoform splicing dynamics from RNA-seq time series data
Y Huang, G Sanguinetti - Bioinformatics, 2016 - academic.oup.com
Motivation: Isoform quantification is an important goal of RNA-seq experiments, yet it
remains problematic for genes with low expression or several isoforms. These difficulties …
remains problematic for genes with low expression or several isoforms. These difficulties …
Mining alternative splicing patterns in scRNA-seq data using scASfind
Single-cell RNA-seq (scRNA-seq) is widely used for transcriptome profiling, but most
analyses focus on gene-level events, with less attention devoted to alternative splicing …
analyses focus on gene-level events, with less attention devoted to alternative splicing …
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
I Alqassem, Y Sonthalia, E Klitzke-Feser, H Shim… - …, 2021 - academic.oup.com
Motivation Alternative splicing removes intronic sequences from pre-mRNAs in alternative
ways to produce different forms (isoforms) of mature mRNA. The composition of expressed …
ways to produce different forms (isoforms) of mature mRNA. The composition of expressed …