Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.

doi:10.1186/s13059-026-04062-6

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Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.

Genome biology - 11 Apr 2026

Simmons Sean K, Adiconis Xian, Haywood Nathan, Parker Jacob, Lin Zechuan, Liao Zhixiang, Tuncali Idil, Shin Asa, Jagadeesh Karthik, Gosik Kirk, Gatzen Michael, Smith Jonathan T, El Kodsi Daniel N, Kuras Yuliya, Baecher-Allan Clare, Serrano Geidy E, Beach Thomas G, Garimella Kiran, Al'Khafaji Aziz M, Rozenblatt-Rosen Orit, Regev Aviv, Dong Xianjun, Scherzer Clemens R, Levin Joshua Z

Abstract excerpt

Combining allele-specific expression (ASE) analysis with single-cell RNA-seq can elucidate how genomic variation affects RNA expression at the single-cell level. We explore how experimental and computational choices impact the power of ASE-based methods and develop a suite of single-cell ASE computational tools. With single-nucleus RNA-Seq, we extract more ASE information from reads in intronic than exonic...

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PMID: 41965748
DOI: 10.1186/s13059-026-04062-6
PMCID: PMC13185290

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