Housheng Hansen He

This paper identifies the EZH2-TTP-mTORC1 axis as a driver of phenotypic plasticity and therapeutic vulnerability in prostate cancer, showing that combined inhibition of EZH2 and PI3K/mTORC1 improves anti-tumor activity.

This paper introduces a framework to interpret attention mechanisms in genomic transformer models by correlating attention scores with biological annotations, showing how biological features are learned through pre-training and fine-tuning.

iSHARC is a pipeline for analyzing scMultiome data, enabling quality control, integration, clustering, annotation, and regulatory analysis in cancer studies.

The paper identifies essential circRNAs in human cancer cells and introduces FunCirc, a database of functional circRNAs across cancer cell lines and tissues.

The paper identifies circNSD1 as a tumor suppressor in breast cancer that inhibits autophagy and oxidative stress tolerance.

This study identifies huntingtin as an RNA-binding protein that interacts with G-rich RNA sequences, including those in the NEAT1 paraspeckle lncRNA.

The paper introduces memo-eQTL, a method to identify DNA methylation-modulated eQTLs, and finds 1,731 novel memo-eQTLs in prostate samples that alter SNP-gene expression interactions through CTCF-based chromatin structure changes.

MEDIPIPE provides an automated pipeline for cfMeDIP-seq data quality control, methylation quantification, and sample aggregation, offering ease of use and scalability for large-scale analysis.

The paper assesses the inter-lab consistency of circular RNA expression in cancer cell lines and identifies factors affecting reproducibility.

This study identifies HNRNPM as a splicing factor critical for prostate cancer cell growth by regulating splicing fidelity and circRNA biogenesis, suggesting it as a therapeutic target.

The paper identifies rs1997243 as a risk variant for hypercholesterolemia that increases GPR146 expression, showing its role in regulating blood cholesterol in human and mouse models.

sgTiler designs tiling sgRNAs for CRISPR/Cas9 screening efficiently and with minimal off-target effects.

Variant Set Enrichment identifies disease-associated functional genomic regions by analyzing the enrichment of variants in annotated regions.