ArticleNucleic acids research2016
Robust detection of alternative splicing in a population of single cells.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 74 citations in OpenAlex.
- Comprehensive assessment of alternative splicing analysis methods for single-cell RNA-seq.iScience · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq.Genome research · 2025Article
- Mining alternative splicing patterns in scRNA-seq data using scASfind.Genome biology · 2024Article
- Quantifying transcriptome diversity: a review.Briefings in functional genomics · 2024Review
- Self-supervised deep learning of gene-gene interactions for improved gene expression recovery.Briefings in bioinformatics · 2024Article
- scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data.International journal of molecular sciences · 2022Article
- Robust and annotation-free analysis of alternative splicing across diverse cell types in mice.eLife · 2022Article
- Single-Cell Analysis of the Transcriptome and Epigenome.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Review
- Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench.Nucleic acids research · 2021Article
- Computing the Role of Alternative Splicing in Cancer.Trends in cancer · 2021Review
- Article
- Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq.Journal of translational genetics and genomics · 2021Article
- VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution.PLoS computational biology · 2020Article
- Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data.Genome biology · 2020Article
- Article
- Technological advances and computational approaches for alternative splicing analysis in single cells.Computational and structural biotechnology journal · 2020Review
- Alternative mRNA splicing in cancer immunotherapy.Nature reviews. Immunology · 2019Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
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 cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome variation to the gene level. To address these limitations, we developed SingleSplice, which uses a statistical model to detect genes whose isoform usage shows biological variation significantly exceeding technical noise in a population of single cells. Importantly, SingleSplice is tailored to the unique demands of single cell analysis, detecting isoform usage differences without attempting to infer expression levels for full-length transcripts. Using data from spike-in transcripts, we found that our approach detects variation in isoform usage among single cells with high sensitivity and specificity. We also applied SingleSplice to data from mouse embryonic stem cells and discovered a set of genes that show significant biological variation in isoform usage across the set of cells. A subset of these isoform differences are linked to cell cycle stage, suggesting a novel connection between alternative splicing and the cell cycle.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.