Paloma Cejas

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

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

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 DTP cells in EGFR-mutant lung cancer drive immunosuppression through YAP/TEAD activity, and co-targeting YAP/TEAD improves EGFR TKI therapy efficacy.

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

This study shows that EZH2 influences the evolution of aggressive prostate cancer subtypes but is not essential for neuroendocrine prostate cancer development.

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

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

This study identifies thyroid hormone receptor THRB as a key regulator of hepatocyte maturation from human PSCs, showing that T3 treatment enhances gene expression and epigenetic features of mature hepatocytes.

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 introduces UniNicE-seq, a method for high-resolution accessible chromatin profiling in formaldehyde-fixed and FFPE tissues without optimization steps.