ArticleGenome biology2021
BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments.
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 31 papers.
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Who cites it
31 citing papers in PubMed.
- scASprofiler: profiling single-cell RNA splicing with a deep convolutional generative network.Briefings in bioinformatics · 2026Article
- Stepwise Protocol for Alternative Splicing Analysis in Single-Cell SMART-Seq2 RNA-Seq Data.Bio-protocol · 2026Article
- Comprehensive assessment of alternative splicing analysis methods for single-cell RNA-seq.iScience · 2026Article
- Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.Nucleic acids research · 2025Article
- Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs.PLoS computational biology · 2025Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Deciphering splicing heterogeneity at single-cell resolution by SCSES.Nature communications · 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
- DOLPHIN advances single-cell transcriptomics beyond gene level by leveraging exon and junction reads.Nature communications · 2025Article
- Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms.Nucleic acids research · 2025Article
- ELLIPSIS: robust quantification of splicing in scRNA-seq.Bioinformatics (Oxford, England) · 2025Article
- Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms.bioRxiv : the preprint server for biology · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.Biostatistics (Oxford, England) · 2024Article
- Mining alternative splicing patterns in scRNA-seq data using scASfind.Genome biology · 2024Article
- DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.bioRxiv : the preprint server for biology · 2024Article
- Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.Brain : a journal of neurology · 2024Article
- CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.Nature communications · 2023Article
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Authors and funding
2 authors.
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Abstract
RNA splicing is an important driver of heterogeneity in single cells through the expression of alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic coverage limitations of scRNA-seq technologies make it challenging to associate specific splicing events to cell-level phenotypes. BRIE2 is a scalable computational method that resolves these issues by regressing single-cell transcriptomic data against cell-level features. We show that BRIE2 effectively identifies differential disease-associated alternative splicing events and allows a principled selection of genes that capture heterogeneity in transcriptional kinetics and improve RNA velocity analyses, enabling the identification of splicing phenotypes associated with biological changes.
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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.