ArticleScientific reports2021
Improved methods for RNAseq-based alternative splicing analysis.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 43 citations in OpenAlex.
- Review
- Pipettes and Pipelines: The Weapons of Omics Sciences for a New Age of Clinical Studies.Current issues in molecular biology · 2026Review
- Characterization of aberrant alternative splicing landscape in patients with metastatic renal cell carcinoma.Journal for immunotherapy of cancer · 2026Article
- Investigational New Drug-enabling studies in a human vessel-chip: Are we there yet?Bioengineering & translational medicine · 2026Review
- Review
- Comprehensive tumor-immune profiling reveals mediators of paradoxical immune sensitivity in sarcomatoid renal cell carcinoma.Cancer cell · 2025Article
- Human Coronavirus-229E Hijacks Key Host-Cell RNA-Processing Complexes for Replication.Journal of proteome research · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Loss of SMARCA4 Leads to Intron Retention and Generation of Tumor-Associated Antigens in Small Cell Carcinoma of the Ovary, Hypercalcemic Type.Cancer research · 2025Article
- DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads.Nature communications · 2025Article
- Long noncoding RNAs in acute myeloid leukemia: biomarkers, prognostic indicators, and treatment potential.Cancer cell international · 2025Review
- Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.F1000Research · 2025Review
- Transcriptome Analysis Reveals Norathyriol Prolongs the Lifespan via Regulating Metabolism inMetabolites · 2024Article
- Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis.Experimental hematology · 2024Review
- Global transcriptome modulation by xenobiotics: the role of alternative splicing in adaptive responses to chemical exposures.Human genomics · 2024Article
- Short-Read RNA-Seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Method to Quantitatively Examine Heat Stress-Induced Alternative Splicing in Plants by RNA-Seq and RT-PCR.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Prediction of alternative pre-mRNA splicing outcomes.Scientific reports · 2023Article
- Single-cell transcriptomics of the ocular anterior segment: a comprehensive review.Eye (London, England) · 2023Review
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 1 country.
Funding
Abstract
The robust detection of disease-associated splice events from RNAseq data is challenging due to the potential confounding effect of gene expression levels and the often limited number of patients with relevant RNAseq data. Here we present a novel statistical approach to splicing outlier detection and differential splicing analysis. Our approach tests for differences in the percentages of sequence reads representing local splice events. We describe a software package called Bisbee which can predict the protein-level effect of splice alterations, a key feature lacking in many other splicing analysis resources. We leverage Bisbee's prediction of protein level effects as a benchmark of its capabilities using matched sets of RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches and can be used to identify tissue-specific splice variants whose protein-level expression can be confirmed by mass spectrometry. We also applied Bisbee to assess evidence for a pathogenic splicing variant contributing to a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic mutation. Bisbee was able to rediscover previously validated results in both of these cases and also identify common tumor-associated splice isoforms replicated in two independent melanoma datasets.
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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.