ArticleGenome biology2021
SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells.
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.
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 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
- Regulation of gene expression by alternative polyadenylation in health and disease.Nature reviews. Genetics · 2026Review
- Unannotated noncoding transcripts as a source of intratumor heterogeneity in malignant cell states.Science China. Life sciences · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Macrophage efferocytosis mediated by the TP63-RAC2 pathway promotes immunosuppressive remodeling in esophageal cancer.Cell reports. Medicine · 2026Article
- metaAPA: a tool for integration of PolyA site predictions from single-cell and spatial transcriptomics.Bioinformatics advances · 2026Article
- Single-nucleus transcriptome atlas of orbitofrontal cortex in ALS with a deep learning-based decoding of alternative polyadenylation mechanisms.Cell genomics · 2025Article
- scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3' scRNA-seq data.Genome biology · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- Quantification of transcript isoforms at the single-cell level using SCALPEL.Nature communications · 2025Article
- Article
- Predicting and comparing transcription start sites in single cell populations.PLoS computational biology · 2025Article
- Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA.Briefings in bioinformatics · 2024Article
- SpliceTransformer predicts tissue-specific splicing linked to human diseases.Nature communications · 2024Article
- InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data.Nature communications · 2024Article
- CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.Nature communications · 2023Article
- Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.Genome research · 2023Article
- Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS.NAR genomics and bioinformatics · 2023Article
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8 authors.
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Abstract
Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation sites (PASs) from 3' tag-based scRNA-seq. SCAPTURE detects PASs de novo in single cells with high sensitivity and accuracy, enabling detection of previously unannotated PASs. Quantified alternative PAS transcripts refine cell identity analysis beyond gene expression, enriching information extracted from scRNA-seq data. Using SCAPTURE, we show changes of PAS usage in PBMCs from infected versus healthy individuals at single-cell resolution.
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