ArticleNature communications2024
Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with Isosceles.
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 24 papers.
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Who cites it
24 citing papers in PubMed.
- Review
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Role of alternative splicing in cancer progression.Irish journal of medical science · 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
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
- BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing.bioRxiv : the preprint server for biology · 2026Article
- Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution.bioRxiv : the preprint server for biology · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Review
- Molecular arms races at the virus-host splicing interface and their pathogenic implications.Frontiers in microbiology · 2026Review
- TNRSim - a simulator of truncated oxford nanopore direct RNA long reads for isoform analysis.Frontiers in bioinformatics · 2026Article
- Beyond counting: how single-cell long-read sequencing turns transcriptome complexity into precision targets.Frontiers in oncology · 2026Review
- Long-read sequencing transcriptome quantification with lr-kallisto.PLoS computational biology · 2025Article
- Integrated single-cell multi-omics profiling reveals a senescence-associated hematopoietic landscape and regulatory network in aging bone marrow.Biogerontology · 2025Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- ScIsoX: a multidimensional framework for measuring isoform-level transcriptomic complexity in single cells.Genome biology · 2025Article
- Single cell and spatial alternative splicing analysis with Nanopore long read sequencing.Nature communications · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate detection and quantification of mRNA isoforms from nanopore long-read sequencing remains challenged by technical noise, particularly in single cells. To address this, we introduce Isosceles, a computational toolkit that outperforms other methods in isoform detection sensitivity and quantification accuracy across single-cell, pseudo-bulk and bulk resolution levels, as demonstrated using synthetic and biologically-derived datasets. Here we show Isosceles improves the fidelity of single-cell transcriptome quantification at the isoform-level, and enables flexible downstream analysis. As a case study, we apply Isosceles, uncovering coordinated splicing within and between neuronal differentiation lineages. Isosceles is suitable to be applied in diverse biological systems, facilitating studies of cellular heterogeneity across biomedical research applications.
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