ArticleNature communications2023
Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 22 citations in OpenAlex.
- Allele-specific expression in the brain links genetic risk and cortical thinning in psychiatric disorders.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- Analysis of Allele-Specific Expression Highlights Novel Participants of Empagliflozin-Driven Effects on T2DM-Associated Regulatory Pathways.International journal of molecular sciences · 2026Article
- FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data.Cell genomics · 2026Article
- Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.Genome biology · 2026Article
- DAESC + : high-performance, integrated software for single-cell allele-specific expression data.BMC bioinformatics · 2026Article
- Application of RNA markers in forensic body fluid analysis: from specificity and stability to polymorphism.International journal of legal medicine · 2026Review
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 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
- Challenges and emerging strategies for genome-wide evaluation of loss of imprinting in cancer.British journal of biomedical science · 2026Review
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.PLoS computational biology · 2025Article
- Gain of Alternative Allele Expression of LINC02449 at rs149707223 in Schizophrenia and Bipolar Disorder: Inducing Synaptic Transmission and Behavioral Deficits in Mice.Nature communications · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- Single-cell analyses reveal increased gene expression variability in human neurodevelopmental conditions.American journal of human genetics · 2025Article
- Reprogramming of iPSCs to NPCEC-like cells by biomimetic scaffolds for zonular fiber reconstruction.Bioactive materials · 2025Article
- Application and Progression of Single-Cell RNA Sequencing in Diabetes Mellitus and Diabetes Complications.Journal of diabetes research · 2025Review
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- The role of imprinting genes' loss of imprints in cancers and their clinical implications.Frontiers in oncology · 2024Review
- Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects.Nature communications · 2023Article
- Single-cell genomics meets human genetics.Nature reviews. Genetics · 2023Review
- Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Differential allele-specific expression (ASE) is a powerful tool to study context-specific cis-regulation of gene expression. Such effects can reflect the interaction between genetic or epigenetic factors and a measured context or condition. Single-cell RNA sequencing (scRNA-seq) allows the measurement of ASE at individual-cell resolution, but there is a lack of statistical methods to analyze such data. We present Differential Allelic Expression using Single-Cell data (DAESC), a powerful method for differential ASE analysis using scRNA-seq from multiple individuals, with statistical behavior confirmed through simulation. DAESC accounts for non-independence between cells from the same individual and incorporates implicit haplotype phasing. Application to data from 105 induced pluripotent stem cell (iPSC) lines identifies 657 genes dynamically regulated during endoderm differentiation, with enrichment for changes in chromatin state. Application to a type-2 diabetes dataset identifies several differentially regulated genes between patients and controls in pancreatic endocrine cells. DAESC is a powerful method for single-cell ASE analysis and can uncover novel insights on gene regulation.
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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.