ArticleNature communications2023
RNA splicing analysis using heterogeneous and large RNA-seq datasets.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- TCASIA: an integrative atlas linking alternative splicing landscapes for cancer immunotherapy.Journal for immunotherapy of cancer · 2026Article
- Splicing genes as main targets of differential splicing.G3 (Bethesda, Md.) · 2026Article
- Review
- Complementary vertebrateeLife · 2026Article
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- HnRNPA2B1 tunes antimycobacterial immune responses in macrophages through alternative splicing ofInfection and immunity · 2026Article
- Data-driven RNA phenotyping captures genetically regulated dimensions of the transcriptome.American journal of human genetics · 2026Article
- 'Missing' disease-causing variants in Alport syndrome.Nature reviews. Nephrology · 2026Review
- Stepwise Protocol for Alternative Splicing Analysis in Single-Cell SMART-Seq2 RNA-Seq Data.Bio-protocol · 2026Article
- Global transcriptional changes across multiple isogeniciScience · 2026Article
- The impact of read depth and read length on RNA-seq splicing analysis.RNA (New York, N.Y.) · 2026Article
- Targeted reflex RNA sequencing for enhanced variant classification on exome and genome sequencing improves patient outcomes.NPJ genomic medicine · 2026Article
- Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.Bioinformatics (Oxford, England) · 2026Article
- Role of alternative splicing in cancer progression.Irish journal of medical science · 2026Review
- Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.Nature chemical biology · 2026Article
- Article
- Article
- The retroelement-derived human protein PEG10 is a regulator of mRNA splicing in neurons.bioRxiv : the preprint server for biology · 2026Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of MAJIQ v2 compared to existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer insights into brain subregion-specific splicing regulation.
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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.