Hongyu Liu

Differential Expression and Microsystem Physiology Reveal Predominant and Drug Reversible CFTR-Related Defects in Idiopathic Pancreatitis

This study identifies CFTR-related defects in idiopathic pancreatitis and shows that ivacaftor can reverse these defects in patient-derived models.

A wealth of novel cell-specific expressed SNVs from tumor and normal scRNA-seq datasets

The paper identifies novel expressed SNVs in tumor and normal scRNA-seq data, revealing a significant number of shared and potentially clinically relevant variants.

SCExecute: cell barcode-stratified analyses of scRNA-seq data

SCExecute enables cell barcode-stratified analysis of scRNA-seq data by executing user commands on extracted scBAM files to detect cell-specific variants.

Improved SNV discovery in barcode-stratified scRNA-seq alignments

This study shows that analyzing SNVs from individual cell scRNA-seq alignments identifies more SNVs and reveals functional variants compared to pooled analysis.

SCReadCounts: Estimation of cell-level SNVs from scRNA-seq data

SCReadCounts estimates cell-level SNVs from scRNA-seq data, enabling mutation analysis and downstream applications in cancer and other studies.

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

scReQTL correlates SNVs to gene expression in single-cell RNA-seq data by using variant allele fraction instead of population genotypes, enabling analysis of rare variants.

Estimating allele-specific expression of SNVs from 10x Genomics Single-Cell RNA-Sequencing Data

The paper estimates allele-specific expression from 10x Genomics scRNA-seq data and finds that most SNVs are bi-allelic at higher read thresholds, with intronic SNVs showing more monoallelic expression.

RsQTL: correlation of expressed SNVs with splicing using RNA-sequencing data

RsQTL identifies splicing quantitative trait loci by correlating variant allele fractions with splicing patterns in RNA-seq data from human tissues.