ArticleCell systems2019
mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
The trial behind it
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
19 citing papers in PubMed, 24 citations in OpenAlex.
- Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.Nature communications · 2026Article
- Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans.PLoS biology · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Benchmarking of methods that identify alternative polyadenylation events in single-/multiple-polyadenylation site genes.NAR genomics and bioinformatics · 2025Review
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for biology · 2025Article
- An Integrated Database for Exploring Alternative Promoters in Animals.Scientific data · 2025Article
- Predicting and comparing transcription start sites in single cell populations.PLoS computational biology · 2025Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation.Science advances · 2024Article
- Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.RNA (New York, N.Y.) · 2023Review
- Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases.Genes · 2023Review
- Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation.NAR genomics and bioinformatics · 2023Article
- Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.Genome research · 2023Article
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Widespread occurrence of hybrid internal-terminal exons in human transcriptomes.Science advances · 2022Article
- Understanding small ORF diversity through a comprehensive transcription feature classification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
- The Detection and Bioinformatic Analysis of Alternative 3International journal of molecular sciences · 2021Review
- APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Alternative transcription start (ATS) and alternative polyadenylation (APA) create alternative RNA isoforms and modulate many aspects of RNA expression and protein production. However, ATS and APA remain difficult to detect in RNA sequencing (RNA-seq). Here, we developed mountainClimber, a de novo cumulative-sum-based approach to identify ATS and APA as change points. Unlike many existing methods, mountainClimber runs on a single sample and identifies multiple ATS or APA sites anywhere in the transcript. We analyzed 2,342 GTEx samples (36 tissues, 215 individuals) and found that tissue type is the predominant driver of transcript end variations. 75% and 65% of genes exhibited differential APA and ATS across tissues, respectively. In particular, testis displayed longer 5' untranslated regions (UTRs) and shorter 3' UTRs, often in genes related to testis-specific biology. Overall, we report the largest study of transcript ends across human tissues to our knowledge. mountainClimber is available at github.com/gxiaolab/mountainClimber.
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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.