ArticleRNA (New York, N.Y.)2015
IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed, 68 citations in OpenAlex.
- Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation.Genome research · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- TDP-43 loss induces cryptic polyadenylation in ALS/FTD.Nature neuroscience · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Neuropeptides specify and reprogram division of labor in the leafcutter ant Atta cephalotes.Cell · 2025Article
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- Neuropeptides specify and reprogram division of labor in the leafcutter antbioRxiv : the preprint server for biology · 2024Article
- Article
- Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.RNA (New York, N.Y.) · 2023Review
- Full-length transcript alterations in human bronchial epithelial cells withLife science alliance · 2023Article
- Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants.Cell · 2023Article
- Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts.PLoS genetics · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum.Human mutation · 2022Review
- ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq.Genome biology · 2022Article
- Diverse cell-specific patterns of alternative polyadenylation in Drosophila.Nature communications · 2022Article
- Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins.Frontiers in genetics · 2022Review
- Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain.BMC biology · 2021Article
- Article
- The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer.Briefings in bioinformatics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Major applications of RNA-seq data include studies of how the transcriptome is modulated at the levels of gene expression and RNA processing, and how these events are related to cellular identity, environmental condition, and/or disease status. While many excellent tools have been developed to analyze RNA-seq data, these generally have limited efficacy for annotating 3' UTRs. Existing assembly strategies often fragment long 3' UTRs, and importantly, none of the algorithms in popular use can apportion data into tandem 3' UTR isoforms, which are frequently generated by alternative cleavage and polyadenylation (APA). Consequently, it is often not possible to identify patterns of differential APA using existing assembly tools. To address these limitations, we present a new method for transcript assembly, Isoform Structural Change Model (IsoSCM) that incorporates change-point analysis to improve the 3' UTR annotation process. Through evaluation on simulated and genuine data sets, we demonstrate that IsoSCM annotates 3' termini with higher sensitivity and specificity than can be achieved with existing methods. We highlight the utility of IsoSCM by demonstrating its ability to recover known patterns of tissue-regulated APA. IsoSCM will facilitate future efforts for 3' UTR annotation and genome-wide studies of the breadth, regulation, and roles of APA leveraging RNA-seq data. The IsoSCM software and source code are available from our website https://github.com/shenkers/isoscm.
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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.