Lei Li

MAAS integrates multimodal scATAC-seq data to identify clinically relevant tumor subpopulations and improve prognostic prediction.

This paper introduces REDMAPCre, a red-light-activated Cre recombinase system that enables rapid and efficient DNA recombination in mammalian cells and mice.

SCALPEL quantifies single-cell transcript isoforms with higher sensitivity than existing tools, revealing novel cell populations and isoform regulation in mouse spermatogenesis and iPSC differentiation.

The paper identifies a nuclear RNA degradation code (NRDC) that recognizes transcripts with both a 5' splice site and a poly(A) junction, leading to their degradation and contributing to disease.

eRNA-IDO identifies enhancer RNAs, discovers their interactomes, and annotates their functions using a computational platform.

This study identifies eRNA-QTLs and susceptibility eRNAs across 23 cancer types, revealing new cancer susceptibility genes through eRNA-based transcriptome-wide association.

This study identifies 413 APA-linked cancer susceptibility genes by integrating GWAS data with APA quantification, showing genetic variants associated with APA explain a large portion of cancer heritability.

xQTLbiolinks is a tool for integrative analysis of molecular QTLs, enabling retrieval, preprocessing, and colocalization with GWAS data to identify disease-risk genes.

The paper benchmarks PCA against hidden variable inference methods for QTL mapping, finding PCA to be faster, better-performing, and more interpretable.

scDaPars analyzes alternative polyadenylation in scRNA-seq data to identify cell subpopulations missed by gene expression analysis.

The paper identifies an atlas of 3QTLs associated with alternative polyadenylation across 46 tissues, showing they explain 16.1% of trait-associated variants and contribute to disease independently of gene expression.

The paper reports the first whole genome sequence of Mekong tiger perch, resolving phylogenetic relationships and providing insights into its demographic history and conservation.