Xintao Qiu

Lymphatic ERG Governs Junctional Plasticity and Fluid Clearance via an EDNRB Signaling Axis in Pulmonary Fibrosis

This study identifies ERG-EDNRB signaling in lymphatic endothelial cells as critical for junctional plasticity and fluid clearance in pulmonary fibrosis, showing that its disruption protects against fibrosis.

A tumor-cell MHC-II program is associated with checkpoint-blockade outcomes across stages of bladder cancer

This study identifies a tumor-cell MHC-II program linked to immunotherapy outcomes in bladder cancer across different stages and treatment settings.

ACKR1-expressing venous endothelial cells establish a pro-fibrotic niche in pulmonary fibrosis

The paper identifies ACKR1-expressing venous endothelial cells as key drivers of fibrosis in IPF and shows ACKR1 inhibition reduces fibrosis in vivo.

Epigenetic Subtypes of High-Grade T1 Bladder Cancer Reveal Intra-Tumor Heterogeneity and Distinct Interactions with Tumor Microenvironment.

This study identifies epigenetic subtypes of high-grade T1 bladder cancer using integrated chromatin and transcriptomic data, revealing intra-tumor heterogeneity and distinct tumor microenvironment interactions.

Lack of synergy between AR targeted therapies and PARP inhibitors in homologous recombination-proficient prostate cancer

This study shows that AR inhibition does not enhance PARP inhibitor efficacy in HR-proficient prostate cancer and instead impairs response in castration-sensitive cells.

scATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data

scATAnno automatically annotates scATAC-seq data using reference atlases, outperforming existing methods across multiple datasets.

EZH2-TTP-mTORC1 Axis Drives Phenotypic Plasticity and Therapeutic Vulnerability in Lethal Prostate Cancer

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.

EED Maintains the Small Cell Lung Cancer Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation

This study shows EED inactivation impairs SCLC tumorigenesis and drives LUAD-to-SCLC transformation, highlighting its role in maintaining SCLC neuroendocrine identity.

Targeting the BAG-1 family of co-chaperones in lethal prostate cancer.

This study investigates Thio-2's mechanism of action in inhibiting AR signaling in CRPC, showing it acts independently of BAG-1 isoforms and with potential AR NTD binding.

MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

This study shows MYC overexpression disrupts AR transcriptional pause release, promoting aggressive prostate cancer progression.

CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis

CoBRA provides a reproducible pipeline for ChIP/ATAC-seq analysis, including peak calling, clustering, and pathway analysis, with code available at the given URL.

CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data

CHIPS is a Snakemake pipeline for processing chromatin profiling data, providing quality control metrics and reproducible analysis workflows for ChIP-seq, ATAC-seq, and DNase-seq experiments.