ArticleGenome biology2020
Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Alternative Polyadenylation Drives Runaway Pro-Inflammatory Macrophages in Periodontitis by Enabling Escape From miRNA Repression.Cell proliferation · 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
- Unannotated noncoding transcripts as a source of intratumor heterogeneity in malignant cell states.Science China. Life sciences · 2026Article
- Article
- Reference-free discovery with barcoded single-cell sequencing.Nature biotechnology · 2026Article
- Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.Genome biology · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM.Nature biotechnology · 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
- RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.Nature communications · 2025Article
- Alternative cleavage and polyadenylation: key regulatory mechanisms in health and disease.RNA biology · 2025Review
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- ScIsoX: a multidimensional framework for measuring isoform-level transcriptomic complexity in single cells.Genome biology · 2025Article
- Spatial dissimilarity analysis in single-cell transcriptomics.Cell reports methods · 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
- Truncated NTRK2 is induced in CAP1 endothelial cells during mouse lung injury-repair.iScience · 2025Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3
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