Sylvan C. Baca

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylomes

The paper introduces decemedip, a Bayesian hierarchical model for cell type deconvolution of MeDIP-seq data, showing its accuracy and utility in identifying methylation signatures.

Transcription Factor Subtype Governs Response and Resistance to DLL3-Directed T-Cell Engagement in Small Cell Lung Cancer

This study investigates how transcription factor subtypes in small cell lung cancer influence response and resistance to DLL3-targeted therapy, revealing subtype-specific mechanisms of resistance.

Detection and monitoring of translocation renal cell carcinoma via plasma cell-free epigenomic profiling

This paper detects and monitors translocation renal cell carcinoma (tRCC) using plasma cell-free epigenomic profiling, achieving high accuracy in distinguishing tRCC from other cancers and healthy controls.

SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin

SNAP improves classification performance for cell-free chromatin data while maintaining data retention through optimized quality filters and modular design.

Circulating chromatin reveals the effects of disease-associated variants on gene regulation

The paper identifies cell-free chromatin QTLs (cfcQTLs) from cancer patients' blood to uncover regulatory effects of genetic variants across diverse tissues and diseases.

A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements

The paper infers enhancer activity from cfDNA fragmentation patterns and proposes a chromatin fiber model to explain these signatures.

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.

Epigenomic signatures as circulating and predictive biomarkers in sarcomatoid renal cell carcinoma

The paper identifies epigenomic signatures in sarcomatoid renal cell carcinoma (sRCC) that predict response to immune checkpoint inhibitors and are detectable in plasma, enabling non-invasive diagnosis.

Utilizing Electronic Health Records (EHR) and Tumor Panel Sequencing to Demystify Prognosis of Cancer of Unknown Primary (CUP) patients

This paper develops OncoNPC, a machine learning classifier for CUP patients using tumor sequencing data, showing improved survival outcomes with treatment aligned to predicted cancer types.

Optimized high-throughput screening of non-coding variants identified from genome-wide association studies

This study develops snpSTARRseq, a high-throughput method to test non-coding variants from GWAS, showing 37% of prostate cancer risk loci alter enhancer activity.

Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation

The paper introduces CWAS, a method linking genetic variation to chromatin states, identifying novel prostate cancer risk loci and regulatory mechanisms not detectable by eQTLs.

A genome-scale CRISPR screen reveals PRMT1 as a critical regulator of androgen receptor signaling in prostate cancer

This study identifies PRMT1 as a critical regulator of AR signaling in prostate cancer through genome-scale CRISPR screening and shows its potential as a therapeutic target.

H3k27ac-HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility

The paper uses HiChIP to link prostate cancer GWAS risk variants to target genes, finding new associations not detected by eQTL methods and validating them with CRISPRi.