ArticleGenome biology2021
IRFinder-S: a comprehensive suite to discover and explore intron retention.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Review
- Intron retention in health and amyotrophic lateral sclerosis.Brain : a journal of neurology · 2026Review
- The minor spliceosome component U4atac regulates JAK/STAT signaling to modulate hematopoiesis and immune responses in Drosophila melanogaster.Nature communications · 2026Article
- Pre-mRNA splicing regulates cellular dedifferentiation via lipid metabolism in a cytokinin-dependent manner in Arabidopsis.Plant physiology · 2026Article
- Biallelic variants in the noncoding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes.Nature genetics · 2026Article
- Live-cell single-molecule dynamics of eukaryotic RNA polymerase machineries.Science (New York, N.Y.) · 2026Article
- Changes in both gene expression and intron retention tune themicroPublication biology · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- MYC-mediated transcriptional control of splicing factors promotes RNA splicing in activated B lymphocytes.Scientific reports · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA.Nucleic acids research · 2025Article
- Studying relative RNA localization from nucleus to the cytosol.NAR genomics and bioinformatics · 2025Article
- Small nucleolar RNAs promote the restoration of muscle differentiation defects in cells from myotonic dystrophy type 1.Nucleic acids research · 2025Article
- U4 snRNP inhibits premature cleavage and polyadenylation of pre-mRNAs.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome.Nucleic acids research · 2024Article
- hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates.The Journal of cell biology · 2024Article
- Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates.Bioinformatics advances · 2024Article
- Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons.Cell reports · 2023Article
- SpliceWiz: interactive analysis and visualization of alternative splicing in R.Briefings in bioinformatics · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention.
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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.