ArticleGenome biology2018
SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 455 papers.
What it found
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Who cites it
455 citing papers in PubMed.
- CB1 receptor inhibition restores synaptoneurosomal alternative splicing landscape in fragile X syndrome mice.iScience · 2026Article
- Alternative splicing dynamics in pig tissues under soybean oil supplementation.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- RBMS1 Contributes to Early Arteriovenous Fistula Neointimal Remodeling Through Modulation of VSMC Phenotypic Responses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Developmental divergence in gene regulation underlies trophic innovation in Lake Victoria cichlids.Proceedings. Biological sciences · 2026Article
- TCASIA: an integrative atlas linking alternative splicing landscapes for cancer immunotherapy.Journal for immunotherapy of cancer · 2026Article
- Review
- Conserved and Tissue-Specific RNA and Protein Cargos of Small Extracellular Vesicles From 120 Tissue Sites Across 34 Organs in a Single Pig.Journal of extracellular vesicles · 2026Article
- LncRNA-driven alternative splicing landscapes associate with survival outcomes in ovarian cancer.Non-coding RNA research · 2026Article
- Article
- NCBP1 stress signaling drives alternative S6K1 splicing inhibiting translation.Nature chemical biology · 2026Article
- Article
- A Real-Data-Driven Framework for Evaluating Differential Transcript Usage Methods Across Long-Read Bulk, Single-Cell, and Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Specificity Analysis of Alternative Splicing DuringMicroorganisms · 2026Article
- Alternative Splicing Constitutes a Transcription-independent Regulatory Layer in Replicative Senescence of Human Umbilical Cord Mesenchymal Stem Cells.Stem cell reviews and reports · 2026Article
- Isoform Remodeling and Promoter Switching Identify Altered Transcriptional Regulation in Alzheimer's Disease Frontal Cortex.Research square · 2026Article
- Full-Length Transcriptome Comparison of Male and Female Gonads inBiomolecules · 2026Article
- Changes in Alternative Splicing are Associated with Insecticide Response and Resistance.Genome biology and evolution · 2026Article
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- Long-read sequencing reveals widespread novel splicing and neojunction-derived neoantigens in nasopharyngeal carcinoma.Genome research · 2026Article
- Mutation accumulation in a hybrid parthenogenetic vertebrate.Molecular biology and evolution · 2026Article
395 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, and enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental and simulated data, we show that SUPPA2 achieves higher accuracy compared to other methods, especially at low sequencing depth and short read length. We use SUPPA2 to identify novel Transformer2-regulated exons, novel microexons induced during differentiation of bipolar neurons, and novel intron retention events during erythroblast differentiation.
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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.