ArticleGenome biology2022
scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- 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
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- STRIVE: interpretable multimodal subtype discovery in Women's cancers using an attention-weighted joint variational autoencoder.Frontiers in bioinformatics · 2026Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.PLoS computational biology · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- Computational methods for allele-specific expression in single cells.Trends in genetics : TIG · 2024Review
- The dynamic genetic determinants of increased transcriptional divergence in spermatids.Nature communications · 2024Article
- STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer.Genome biology · 2023Article
- Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects.Nature communications · 2023Article
- Methods and Insights from Single-Cell Expression Quantitative Trait Loci.Annual review of genomics and human genetics · 2023Review
- ALKBH5 promotes hypopharyngeal squamous cell carcinoma apoptosis by targeting TLR2 in a YTHDF1/IGF2BP2-mediated manner.Cell death discovery · 2023Article
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Article
- Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets.Bioinformatics (Oxford, England) · 2022Article
- scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation.Genome biology · 2022Article
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6 authors.
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Abstract
While it is established that the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies using bulk sequencing either ignore this heterogeneity or use sorted cell populations, reducing discovery and explanatory power. Here, we develop scDALI, a versatile computational framework that integrates information on cellular states with allelic quantifications of single-cell sequencing data to characterize cell-state-specific genetic effects. We apply scDALI to scATAC-seq profiles from developing F1 Drosophila embryos and scRNA-seq from differentiating human iPSCs, uncovering heterogeneous genetic effects in specific lineages, developmental stages, or cell types.
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