Myles A Brown

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

The paper identifies circadian misalignment between cancer and immune cells in breast tumors as a mechanism of immune evasion and therapeutic resistance.

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.

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

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.

The paper uses super-resolution microscopy to show that estrogen receptor activity regulates distinct chromatin structures marked by H3K27ac, revealing dynamic epigenetic states and their implications for transcriptional activity and cancer resistance.

This study investigates transcription factor dynamics during human enteroendocrine cell differentiation, finding that oscillations of ASCL1 and NEUROD1 enable accurate cell type diversification.

MetaTiME identifies data-driven meta-components in tumor immune microenvironment scRNA-seq data to annotate cell states and reveal transcriptional regulators.

This study identifies BRCA1-IRIS as a critical isoform for ICL repair, distinct from BRCA1-p220, by interacting with FANCD2 and promoting its ubiquitylation.

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.

MIRA jointly models gene expression and chromatin accessibility in single cells to infer regulatory circuits and lineage trees during development.

The paper identifies an intermediate-effect variant in UMOD associated with chronic kidney disease risk and shows it has reduced disease severity compared to canonical ADTKD mutations.

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

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 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.

The paper identifies two classes of transcription factors based on their regulatory range and shows that long-range TFs' activity depends on chromatin state.

Lisa predicts transcriptional regulators of gene sets by integrating chromatin accessibility and ChIP-seq data to identify relevant regulators.

The paper introduces MAGeCK-NEST, a method to improve CRISPR screen analysis by integrating PPI data and refining sgRNA design, leading to better hit calling and library design.

MACS calls ChIP-Seq peaks by estimating tag shift from Watson/Crick strand offsets and testing enrichment against a locally adaptive Poisson background, improving specificity and binding-site resolution.