ArticleGenome biology2022
JAFFAL: detecting fusion genes with long-read transcriptome sequencing.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
- Review
- Nanopore long-read transcriptome sequencing reveals miR-22-3p-mediated transcriptomic remodeling and alternative splicing in chicken pectoral muscle.Poultry science · 2026Article
- Article
- Cancer-associated fusion transcripts: mechanisms, functional roles, and clinical implications.Clinical and experimental medicine · 2026Review
- Characteristics of fusion genes in breast cancer.Cancer cell international · 2026Review
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- From fragments to full pictures: how long-read sequencing platforms are revolutionizing oncology research.Molecular biology reports · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia.The Journal of molecular diagnostics : JMD · 2026Article
- Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.Nature communications · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive evaluation of long-read de novo transcriptome assembly.Genome biology · 2026Article
- Article
- Review
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- Fusion gene discovery in single cells from high throughput long read single cell transcriptomes.bioRxiv : the preprint server for biology · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki .
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Registered trials
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