ArticleNucleic acids research2017
ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
18 citing papers in PubMed.
- 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
- Chimeric RNAs as Novel Neoantigens for Extracellular Vesicles-Based Vaccines Against Cancer.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.Briefings in bioinformatics · 2024Article
- Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer.Frontiers in immunology · 2023Article
- Novornabreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data.Journal of bioinformatics and systems biology : Open access · 2023Article
- Fusion gene recurrence in non-small cell lung cancers and its association with cigarette smoke exposure.Translational lung cancer research · 2022Article
- Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing.RNA biology · 2021Article
- Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy.Cancer letters · 2021Review
- Computational Oncology in the Multi-Omics Era: State of the Art.Frontiers in oncology · 2020Review
- Alignment-free filtering for cfNA fusion fragments.Bioinformatics (Oxford, England) · 2019Article
- Bridging the gap between reference and real transcriptomes.Genome biology · 2019Article
- Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy.Cellular and molecular life sciences : CMLS · 2018Review
- Review
- NFIX Circular RNA Promotes Glioma Progression by Regulating miR-34a-5p via Notch Signaling Pathway.Frontiers in molecular neuroscience · 2018Article
- CRISPRMatch: An Automatic Calculation and Visualization Tool for High-throughput CRISPR Genome-editing Data Analysis.International journal of biological sciences · 2018Article
- Alignment-free sequence comparison: benefits, applications, and tools.Genome biology · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms. The alignment of sequencing reads from fusion transcript loci in cancer genomes can be highly challenging due to the incorrect mapping induced by genomic alterations, thereby limiting the performance of alignment-based fusion transcript detection methods. Here, we developed a novel alignment-free method, ChimeRScope that accurately predicts fusion transcripts based on the gene fingerprint (as k-mers) profiles of the RNA-Seq paired-end reads. Results on published datasets and in-house cancer cell line datasets followed by experimental validations demonstrate that ChimeRScope consistently outperforms other popular methods irrespective of the read lengths and sequencing depth. More importantly, results on our in-house datasets show that ChimeRScope is a better tool that is capable of identifying novel fusion transcripts with potential oncogenic functions. ChimeRScope is accessible as a standalone software at (https://github.com/ChimeRScope/ChimeRScope/wiki) or via the Galaxy web-interface at (https://galaxy.unmc.edu/).
Indexed as
Identifiers
What OpenQuestion holds
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.