ArticleMolecular systems biology2022
CellRegMap: a statistical framework for mapping context-specific regulatory variants using scRNA-seq.
Article in Molecular systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Scalable context-dependent single-cell eQTL mapping reveals disease-relevant regulatory variation beyond static models.medRxiv : the preprint server for health sciences · 2026Article
- FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data.Cell genomics · 2026Article
- Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics.Immune network · 2026Review
- Identifying Single-Cell Expression Quantitative Trait Loci Using a Bootstrap Penalized Hurdle Model.Genes · 2026Article
- eQTL analysis: A bridge from genome to mechanism.Genes & diseases · 2026Review
- Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells.medRxiv : the preprint server for health sciences · 2026Article
- Multi-omics Data Integration.Advances in experimental medicine and biology · 2026Review
- Airqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping.Nature communications · 2025Article
- Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs.Nature genetics · 2025Article
- A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information.Genome biology · 2025Article
- Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids.Genome research · 2025Article
- Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping.medRxiv : the preprint server for health sciences · 2025Article
- A unified framework for cell-type-specific eQTL prioritization by integrating bulk and scRNA-seq data.American journal of human genetics · 2025Article
- Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution.Nature methods · 2025Article
- Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.bioRxiv : the preprint server for biology · 2024Article
- Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures.Cell genomics · 2024Article
- A brief guide to analyzing expression quantitative trait loci.Molecules and cells · 2024Review
- Genetic association mapping leveraging Gaussian processes.Journal of human genetics · 2024Review
- Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids.bioRxiv : the preprint server for biology · 2024Article
- Building and analyzing metacells in single-cell genomics data.Molecular systems biology · 2024Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing (scRNA-seq) enables characterizing the cellular heterogeneity in human tissues. Recent technological advances have enabled the first population-scale scRNA-seq studies in hundreds of individuals, allowing to assay genetic effects with single-cell resolution. However, existing strategies to analyze these data remain based on principles established for the genetic analysis of bulk RNA-seq. In particular, current methods depend on a priori definitions of discrete cell types, and hence cannot assess allelic effects across subtle cell types and cell states. To address this, we propose the Cell Regulatory Map (CellRegMap), a statistical framework to test for and quantify genetic effects on gene expression in individual cells. CellRegMap provides a principled approach to identify and characterize genotype-context interactions of known eQTL variants using scRNA-seq data. This model-based approach resolves allelic effects across cellular contexts of different granularity, including genetic effects specific to cell subtypes and continuous cell transitions. We validate CellRegMap using simulated data and apply it to previously identified eQTL from two recent studies of differentiating iPSCs, where we uncover hundreds of eQTL displaying heterogeneity of genetic effects across cellular contexts. Finally, we identify fine-grained genetic regulation in neuronal subtypes for eQTL that are colocalized with human disease variants.
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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.