John Canniff

APEX infers cancer gene expression from plasma cfChIP-seq data, outperforming existing methods and enabling subtype classification and biomarker identification.

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

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.