ArticleNature communications2024
Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Interpretable machine learning enables de novo mapping of cell type-specific RNA splicing regulation from scRNA-seq data.Nature communications · 2026Article
- scASprofiler: profiling single-cell RNA splicing with a deep convolutional generative network.Briefings in bioinformatics · 2026Article
- Harnessing Tumor-Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma.MedComm · 2026Article
- T Cell Heterogeneity Shaped by Alternative Splicing Predicts Prognosis in Hepatocellular Carcinoma.Cancer science · 2026Article
- Transcriptome Reprogramming in Heart Failure: The Hidden Splicing Code.Current cardiology reports · 2026Review
- Stepwise Protocol for Alternative Splicing Analysis in Single-Cell SMART-Seq2 RNA-Seq Data.Bio-protocol · 2026Article
- Comprehensive assessment of alternative splicing analysis methods for single-cell RNA-seq.iScience · 2026Article
- Reference-free discovery with barcoded single-cell sequencing.Nature biotechnology · 2026Article
- Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.Nucleic acids research · 2025Article
- Deciphering splicing heterogeneity at single-cell resolution by SCSES.Nature communications · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads.Nature communications · 2025Article
- AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level.GigaScience · 2025Article
- Advancing automated cell type annotation with large language models and single-cell isoform sequencing.Computational and structural biotechnology journal · 2025Review
- Beyond the Heartbeat: Single-Cell Omics Redefining Cardiovascular Research.Current cardiology reports · 2024Review
- Mechanisms of RNA alternative splicing dysregulation in triple-negative breast cancer.Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2024Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
RNA splicing shapes the gene regulatory programs that underlie various physiological and disease processes. Here, we present the SCASL (single-cell clustering based on alternative splicing landscapes) method for interrogating the heterogeneity of RNA splicing with single-cell RNA-seq data. SCASL resolves the issue of biased and sparse data coverage on single-cell RNA splicing and provides a new scheme for classifications of cell identities. With previously published datasets as examples, SCASL identifies new cell clusters indicating potentially precancerous and early-tumor stages in triple-negative breast cancer, illustrates cell lineages of embryonic liver development, and provides fine clusters of highly heterogeneous tumor-associated CD4 and CD8 T cells with functional and physiological relevance. Most of these findings are not readily available via conventional cell clustering based on single-cell gene expression data. Our study shows the potential of SCASL in revealing the intrinsic RNA splicing heterogeneity and generating biological insights into the dynamic and functional cell landscapes in complex tissues.
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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 Socratic graph.