Kwangbom Choi

Prevalent cross-cell type QTL trans-regulatory genetic effects impacting innate lymphoid cells in the small intestine

The paper identifies genetic variants affecting innate lymphoid cells in the gut using single-cell RNA-seq and validates their regulatory roles across cell types.

Detecting isoform-level allelic imbalance accounting for inferential uncertainty

The paper introduces SEESAW, a method to detect isoform-level allelic imbalance while accounting for inferential uncertainty, and evaluates it on simulated and real RNA-seq data.

Airpart: Interpretable statistical models for analyzing allelic imbalance in single-cell datasets

Airpart identifies cell-type-specific allelic imbalance from single-cell RNA-seq data using statistical models and provides interpretable partitions of genes and cells.

Decoupling alignment strategy from feature quantification using a standard alignment incidence data structure

The paper introduces a data structure and file format for alignment incidence data to enable flexible and optimal pipelines for read alignment, QC, and quantification across sequencing modalities.

Genotype-free individual genome reconstruction of Multiparental Population Models by RNA sequencing data

The paper introduces GBRS, a method to reconstruct diploid genomes and quantify gene expression in multi-parent populations using RNA-Seq data without requiring genotype information.

Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics

This paper uses Bayesian model selection to show zero inflation in scRNA-Seq data is biological, not technical, and recommends a negative binomial GLM as a reference model.

Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer's disease

The paper uses scRNA-seq to show genetic variation in microglia from different mouse strains affects their heterogeneity and response to amyloidosis in Alzheimer's disease models.

scBASE: A Bayesian mixture model for the analysis of allelic expression in single cells

scBASE improves allelic expression analysis in single cells by classifying allelic states and pooling information across cells.

Genetic variation influences pluripotent ground state stability in mouse embryonic stem cells through a hierarchy of molecular phenotypes

The paper identifies genetic variants influencing metastability in mouse embryonic stem cells by analyzing gene expression and chromatin accessibility in 185 genetically diverse cells.

Tissue-specific trans regulation of the mouse epigenome

The paper identifies tissue-specific trans-regulation of H3K4me3 levels in mouse cell types and links it to histone quantitative trait loci (hQTL) associated with zinc finger genes.

Hierarchical Analysis of Multi-mapping RNA-Seq Reads Improves the Accuracy of Allele-specific Expression

EMASE improves ASE estimation by hierarchically allocating multi-mapping RNA-Seq reads, showing better performance than standard methods in simulations and detecting ASE in F1 hybrid mice.

The Effects of Sex and Diet on Physiology and Liver Gene Expression in Diversity Outbred Mice

This study examines how sex and diet influence physiology and liver gene expression in Diversity Outbred mice, identifying genetic and sex-by-diet interactions affecting metabolic traits.