ArticleGenome biology2019
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 383 papers, 1 of them a synthesis that pooled it.
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Who cites it
383 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic study of molecular diagnosis, treatment, and prognosis in infant-type hemispheric glioma: An individual patient data meta-analysis of 164 patients.Neuro-oncology · 2026Pooled it
- Comprehensive genomic profiling of mucosal melanoma reveals novel fusion transcripts and dysregulation of cell-cycle, MAPK, and PI3K pathways.The Journal of pathology · 2026Article
- Computational design and translational development of TCR-mimic scFv antibodies for peptide-HLA neoantigen targeting.npj drug discovery · 2026Review
- Abundant CD8British journal of cancer · 2026Article
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- Comparative genomic analysis reveals spine formation and coral prostaglandin tolerance in crown-of-thorns starfish.Fundamental research · 2026Article
- Anchored random reverse primer sequencing for quantitative detection of novel gene fusions.Nature biomedical engineering · 2026Article
- Fusion gene heterogeneity and kinase enrichment in high-grade serous carcinomas.Neoplasia (New York, N.Y.) · 2026Article
- Cancer-associated fusion transcripts: mechanisms, functional roles, and clinical implications.Clinical and experimental medicine · 2026Review
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- 5' Rapid Amplification of cDNA Ends (5' RACE)-Based Targeted RNA Sequencing Assay for the Analysis of Clinically Relevant Alterations in Lung Cancer Patients.International journal of molecular sciences · 2026Article
- Mitochondrial DNA mutations drive tumor heterogeneity in papillary thyroid carcinoma.iScience · 2026Article
- Single-cell multi-omic analyses resolve the cellular diversity of ALK/ROS1/MET/NTRK-fused gliomas in infants and older children.bioRxiv : the preprint server for biology · 2026Article
- pVACtools v6: A comprehensive suite for neoantigen prediction, visualization, and therapy design.ArXiv · 2026Article
- MiT fusions, TSC1-TSC2 divergence, and stem-like programs reveal distinct origins and vulnerabilities in PEComa.Nature communications · 2026Article
- PFGPred: a stack ensemble classifier for the identification of fusion genes in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- T2Pdecoder enables protein-centric analyses from transcriptomic data.Nature communications · 2026Article
- Article
- Transcriptional network analysis of PTEN-protein-deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication.Molecular oncology · 2026Article
323 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundAccurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq, based on either read mapping or de novo fusion transcript assembly.
resultsWe benchmark 23 different methods including applications we develop, STAR-Fusion and TrinityFusion, leveraging both simulated and real RNA-seq. Overall, STAR-Fusion, Arriba, and STAR-SEQR are the most accurate and fastest for fusion detection on cancer transcriptomes.
conclusionThe lower accuracy of de novo assembly-based methods notwithstanding, they are useful for reconstructing fusion isoforms and tumor viruses, both of which are important in cancer research.
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