ArticleGenome biology2017
SCALE: modeling allele-specific gene expression by single-cell RNA sequencing.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- DAESC + : high-performance, integrated software for single-cell allele-specific expression data.BMC bioinformatics · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- AI/ML-Driven Gene Analysis: New Perspectives on Variant Calling in Normal Human Tissue Using scRNA-seq Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.PLoS computational biology · 2025Article
- distQTL: distribution quantitative trait loci identification by population-scale single-cell data.NAR genomics and bioinformatics · 2025Article
- Scalable inference and identifiability of kinetic parameters for transcriptional bursting from single cell data.Bioinformatics (Oxford, England) · 2025Article
- distQTL: Distribution Quantitative Trait Loci Identification by Population-Scale Single-Cell Data.bioRxiv : the preprint server for biology · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- Single-Cell Multiomic Analysis of Circadian Rhythmicity in Mouse Liver.bioRxiv : the preprint server for biology · 2025Article
- Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data.Nucleic acids research · 2025Article
- Marker genes reveal dynamic features of cell evolving processes.Bioinformatics advances · 2025Article
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- Detection of allele-specific expression in spatial transcriptomics with spASE.Genome biology · 2024Article
- Single-cell genomics and regulatory networks for 388 human brains.Science (New York, N.Y.) · 2024Article
- Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming.Life science alliance · 2024Article
- Single-cell genomics and regulatory networks for 388 human brains.bioRxiv : the preprint server for biology · 2024Article
- Allele-specific DNA methylation and gene expression during shoot organogenesis in tissue culture of hybrid poplar.Horticulture research · 2024Article
- Transcriptional bursting dynamics in gene expression.Frontiers in genetics · 2024Review
- STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer.Genome biology · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SCALE to analyze genome-wide allele-specific bursting, with adjustment of technical variability. SCALE detects genes exhibiting allelic differences in bursting parameters and genes whose alleles burst non-independently. We apply SCALE to mouse blastocyst and human fibroblast cells and find that cis control in gene expression overwhelmingly manifests as differences in burst frequency.
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