ArticleGenome biology2018
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.
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 133 papers.
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Who cites it
133 citing papers in PubMed, 202 citations in OpenAlex.
- The Role of Germline Transposable Element Insertions in Pediatric Cancer Predisposition.Cancer research communications · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.Nature communications · 2026Article
- Trdn-as directs m6A-dependent transcriptional termination for accurate triadin isoform switching, preventing aberrant dyads and cardiomyopathy.Nature communications · 2026Article
- Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation.Genome research · 2026Article
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- scDeepAPA: a deep learning framework for single-cell alternative polyadenylation identification.Briefings in bioinformatics · 2026Article
- 3'UTR variants of ALS-linked RNAs modify subcellular and cellular phenotypes.The FEBS journal · 2026Article
- The RNA-binding protein SRSF3 controls epicardial formation by regulating splicing and proliferation.Development (Cambridge, England) · 2026Article
- CRISPR/Cas9 screening with destabilized bicistronic fluorescent protein reporter revealed PABPN1 as a hub of regulators for alternative polyadenylation.Nucleic acids research · 2026Article
- Article
- Acute testicular hyperthermia leads to rapid loss of global piRNA and a concurrent increase in LINE1 activity within heat sensitive male germ cells.Mobile DNA · 2026Article
- KnockRBP: an integrated multi-omics database of functional perturbation profiles for RNA-binding proteins.Nucleic acids research · 2026Article
- PolyA-GLM: A comprehensive framework forComputational and structural biotechnology journal · 2026Article
- Article
- A Human-specific Protein Regulated by Alternative Polyadenylation Shapes Uniqueness of Human Brain Development.Genomics, proteomics & bioinformatics · 2025Article
- Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes.Nature neuroscience · 2025Article
- IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data.PLoS computational biology · 2025Article
73 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Alternative polyadenylation (APA) affects most mammalian genes. The genome-wide investigation of APA has been hampered by an inability to reliably profile it using conventional RNA-seq. We describe 'Quantification of APA' (QAPA), a method that infers APA from conventional RNA-seq data. QAPA is faster and more sensitive than other methods. Application of QAPA reveals discrete, temporally coordinated APA programs during neurogenesis and that there is little overlap between genes regulated by alternative splicing and those by APA. Modeling of these data uncovers an APA sequence code. QAPA thus enables the discovery and characterization of programs of regulated APA using conventional RNA-seq.
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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.