Stephanie Hao

The paper identifies target genes and pathways of blood trait loci using CRISPR screens and single-cell RNA sequencing, revealing cis and trans regulatory effects of noncoding variants.

This paper introduces NTT-seq, a method to measure multiple chromatin features at single-cell resolution, and demonstrates its application in immune cells.

Weighted-nearest neighbor (WNN) analysis in Seurat v4 learns per-cell modality weights to define cell states, enabling a 228-antibody human PBMC CITE-seq reference for RNA-only query mapping.

This paper examines how Bacteroides fragilis toxin affects chromatin accessibility and gene expression in colon epithelial cells, linking these changes to colorectal cancer development.

The paper introduces cell hashing using barcoded antibodies to enable multiplexing and doublet detection in single-cell genomics, demonstrating its effectiveness with human PBMC samples.

The paper introduces ECCITE-seq, a method that simultaneously captures transcriptomes, immune clonotypes, surface markers, sample identity, and CRISPR perturbations from single cells.

The paper evaluates 16S rRNA marker gene analysis pipelines using a mixture dataset of human stool samples, finding DADA2 better captures specific features than Mothur and QIIME.