ArticleNature communications2025
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- Review
- RNA splicing and cardiovascular disease: a guide for cardiologists.European heart journal · 2026Review
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Review
- Tools and tactics for studying alternative splicing.Nature reviews. Genetics · 2026Review
- The splice of life: an isoform-centric view of disease, technology, and therapeutics.The Journal of clinical investigation · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing.Nature communications · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries.bioRxiv : the preprint server for biology · 2026Article
- Pan-Transcriptome Analyses of Multiple Tissues and Growth Stages Create Expression Atlases for the SilkwormAnimals : an open access journal from MDPI · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Review
- Review
- Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM.Nature biotechnology · 2026Article
- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- Enhancing targeted strategies for cancer immunotherapy by elucidating mRNA processing mechanisms.Frontiers in immunology · 2026Review
- Alternative Splicing: Molecular Mechanisms, Biological Functions, Diseases, and Potential Therapeutic Targets.MedComm · 2025Review
- Research Progress Regarding the Use of Single-Cell Sequencing Technology in Analyzing Tumor Endothelial Cell Pathophysiology.International journal of molecular sciences · 2025Review
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Long-read sequencing boosts alternative splicing analysis but faces technical and computational barriers in single-cell and spatial settings. High Nanopore error rates compromise cell barcode and UMI recovery, while read truncation and misalignment undermine isoform quantification. Downstream, a statistical framework to assess splicing variation within and between cells or spatial spots is lacking. We introduce Longcell, a statistical and computational pipeline for isoform quantification from single-cell and spatially barcoded Nanopore long reads. Longcell efficiently recovers cell barcodes and UMIs, corrects sequencing errors, and models splicing diversity within and between cells or spots. Applied across multiple datasets, Longcell allows accurate identification of spatial isoform switching. Longcell also reveals widespread high intra-cell isoform heterogeneity for highly expressed genes. Finally, on a perturbation experiment for 9 splicing factors, Longcell identifies regulatory targets that are validated by targeted sequencing.
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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.