ReviewComputational and structural biotechnology journal2020
Challenges in detecting and quantifying intron retention from next generation sequencing data.
Review in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 49 citations in OpenAlex.
- HiFi long-read RNA sequencing enhances clinical diagnostics in rare disorders.European journal of human genetics : EJHG · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Origins and implications of intron retention quantitative trait loci in human tissues.American journal of human genetics · 2025Article
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- Charting the regulatory landscape of TP53 on transposable elements in cancer.Genome research · 2025Article
- Alternative splicing fine-tunes prey shift of Coccinellini lady beetles to non-target insect.BMC genomics · 2025Article
- Differential quantification of alternative splicing events on spliced pangenome graphs.PLoS computational biology · 2024Article
- Intronic RNA secondary structural information captured for the humanNAR genomics and bioinformatics · 2024Article
- Serine/arginine-rich splicing factor 7 promotes the type I interferon response by activating Irf7 transcription.Cell reports · 2024Article
- Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates.Bioinformatics advances · 2024Article
- Pan-Cancer Profiling of Intron Retention and Its Clinical Significance in Diagnosis and Prognosis.Cancers · 2023Article
- Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.Briefings in bioinformatics · 2023Review
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
- MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data.Nucleic acids research · 2023Article
- mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing.International journal of molecular sciences · 2022Article
- Practical Considerations for Single-Cell Genomics.Current protocols · 2022Review
- Differential fates of introns in gene expression due to global alternative splicing.Human genetics · 2022Review
- IRFinder-S: a comprehensive suite to discover and explore intron retention.Genome biology · 2021Article
- Implications of Antigen Selection on T Cell-Based Immunotherapy.Pharmaceuticals (Basel, Switzerland) · 2021Review
- A second hit somatic (p.R905W) and a novel germline intron-mutation of TSC2 gene is found in intestinal lymphangioleiomyomatosis: a case report with literature review.Diagnostic pathology · 2021Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computational assumptions that may lead to dramatically different results. We describe the various approaches for mitigating errors in detecting intron retention and for discovering IR signatures between different conditions.
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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.