Jacob E. Berchuck

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.

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.

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.

Moving Beyond Binary Biomarkers: Machine Learning Model Resolves Concurrent and Molecularly Heterogeneous Mismatch Repair and Homologous Recombination Deficiencies in Prostate Cancer

This paper develops a machine learning model to identify molecularly distinct DDR subgroups in prostate cancer, revealing concurrent repair deficiencies and improving therapeutic stratification.

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.

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.