ArticleMolecular cell2017
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.
Article in Molecular cell, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 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
- ASPIRE: Accurate alternative splicing prediction from limited RNA sequencing data and a minimal gene set.PLoS computational biology · 2026Article
- Single cell analysis of developing Merkel cells reveals the emergence of non-coding RNA biotypes as a hallmark of terminal differentiation.Cell death and differentiation · 2026Article
- 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
- Nitric oxide drives proteomic diversity through alternative splicing.Molecular cell · 2026Article
- Coordinated alternative splicing decisions via stepwise exon definition.Nucleic acids research · 2026Article
- CD19 exon 2 skipping is a potential prognostic correlate of anti-CD19 CAR-T therapy relapse.Frontiers in molecular medicine · 2026Article
- RBM25 Regulates p38 MAPK Pathway Activation via Exon 16 Skipping of MAP4K4 in a Rat Model of Post-Infarction Heart Failure.FASEB bioAdvances · 2025Article
- The Role of mRNA Alternative Processing in Mammalian Neurodevelopment.International journal of molecular sciences · 2025Review
- Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.Nucleic acids research · 2025Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Deciphering splicing heterogeneity at single-cell resolution by SCSES.Nature communications · 2025Article
- SpliPath enhances disease gene discovery in case-control analyses of rare splice-altering genetic variants.Cell reports methods · 2025Article
- Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.Cancer metastasis reviews · 2025Review
- Spatial dissimilarity analysis in single-cell transcriptomics.Cell reports methods · 2025Article
- 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
- Single cell and spatial alternative splicing analysis with Nanopore long read sequencing.Nature communications · 2025Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational framework consisting of outrigger, a de novo splice graph transversal algorithm to detect AS; anchor, a Bayesian approach to assign modalities; and bonvoyage, a visualization tool using non-negative matrix factorization to display modality changes. Applying Expedition to single pluripotent stem cells undergoing neuronal differentiation, we discover that up to 20% of AS exons exhibit bimodality. Bimodal exons are flanked by more conserved intronic sequences harboring distinct cis-regulatory motifs, constitute much of cell-type-specific splicing, are highly dynamic during cellular transitions, preserve reading frame, and reveal intricacy of cell states invisible to conventional gene expression analysis. Systematic AS characterization in single cells redefines our understanding of AS complexity in cell biology.
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