Shahabeddin Sotudian

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

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

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

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

The paper introduces ITNR, a transformer-based model for predicting cancer drug responses using genomic data, showing improved performance over existing methods.