Yeqiao Zhou

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

The paper shows lineage-determining transcription factors position enhancers and promoters to enable multi-enhancer regulation of oncogenes in lymphoma and T-cell leukemia.

OLIVE Provides Rapid Visualization and Analysis of Chromatin Tracing Experiments

OLIVE provides a web-based tool for visualizing and analyzing chromatin tracing data, enabling interactive exploration and quantitative analysis of three-dimensional chromatin structures.

Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells

The paper uses single-allele chromatin tracing to show that genomic clustering of paralogous transcription factors enables developmental robustness in T cells by allowing compensatory interactions when regulatory elements are lost.

Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance

This study identifies enhancer-promoter hubs in cancer types and shows their role in oncogenesis and drug resistance through topological and transcriptional changes.

Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

This study identifies heightened TNF pathway activity and chromatin remodeling in pancreatic lymph node CD4+ T cells from T1D patients, supporting the use of TNF inhibitors in clinical trials.

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics data, showing improved performance over existing methods in diabetic tissue analysis.

TooManyCells identifies and visualizes relationships of single-cell clades

TooManyCells identifies and visualizes cell clades using graph-based tools, outperforming existing methods in detecting rare populations in single-cell RNA-seq data.

Differential Integration of Transcriptome and Proteome Identifies Pan-cancer Prognostic Biomarkers

This paper introduces inteGREAT, a method for integrating transcriptome and proteome data to identify prognostic biomarkers across cancers, showing high performance in synthetic and real data analyses.