ArticleGenome biology2021
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
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Who cites it
157 citing papers in PubMed, 215 citations in OpenAlex.
- Review
- Long-read sequencing-based atlas of tissue-specific expression of DNM1L transcript variants.The FEBS journal · 2026Article
- A Real-Data-Driven Framework for Evaluating Differential Transcript Usage Methods Across Long-Read Bulk, Single-Cell, and Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence.bioRxiv : the preprint server for biology · 2026Article
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Full-length single-cell spatial transcriptomics reveals spatial and cell-type-specific transcript isoforms in the primate brain.Nature methods · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Integrating short-read and long-read single-cell transcriptomics of pig pituitary reveals mechanisms of high-altitude hypoxia adaptation.PLoS genetics · 2026Article
- Single-cell long-read genotyping of transcripts reveals discrete mechanisms of clonal evolution in post-MPN AML.Blood advances · 2026Article
- Single-cell long- and short-read transcriptomics sheds light on high-altitude adaptation in the porcine cerebral cortex.Translational psychiatry · 2026Article
- The splice of life: an isoform-centric view of disease, technology, and therapeutics.The Journal of clinical investigation · 2026Review
- Mast cells and endothelial cells mediate interleukin-33 and ST2 responses in distal chronic obstructive pulmonary disease lungs.American journal of respiratory and critical care medicine · 2026Article
- T Cell Heterogeneity Shaped by Alternative Splicing Predicts Prognosis in Hepatocellular Carcinoma.Cancer science · 2026Article
- LOTR-Seq: A protocol for large-scale simultaneous single-cell long-read genotyping of transcripts.STAR protocols · 2026Article
- Augmenting transcriptome annotations through the lens of splicing evolution.Genome research · 2026Article
- MASQ: A multiplex qPCR platform for quantitative alternative splicing analysis in clinical specimens.Molecular therapy. Nucleic acids · 2026Article
- RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis.bioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing.Nature communications · 2026Article
97 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
31 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.
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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.