Director of the Englander Institute for Precision Medicine
Professor of Physiology and Biophysics
Professor of Computational Genomics in Computational Biomedicine
The focus of my research group is on the systems biology of cancer; we focus on prostate cancer and hematological malignancies. In these cancers, we are elucidating the patterns of aberrant pathway activities, rewiring of regulatory networks and cancer mutations that have occurred in cancer cells. We are also trying to understand how tumors evolve at the genomic and epigenomic level. We use high-throughput sequencing (ChIP-seq, RNA-seq, bisulfite conversion followed by sequencing – specifically RRBS-, ATAC-seq, exome capture and sequencing, single cell RNAseq using DropSeq) to decipher epigenetic mechanisms and regulatory networks at play in malignant cells and study how they affect gene expression. My lab has developed several computational approaches for analysis of deep sequencing data, e.g. ChIPseeqer (for integrative analysis of ChIP-seq data) and SNVseeqer/INDELseeqer (full pipeline for mutation detection and characterization from deep sequencing data). My lab has developed several additional computational approaches that include a pathway analysis tool (iPAGE) several tools for regulatory element detection (FIRE and FastCompare) and RRBseeqer for ERRBS analysis (including detection of differentially methylated regions). We use drug repositioning to identify small molecules that can target mutated signaling pathways and classically undruggable proteins such as transcription factors. We model complex signaling pathways to identify drug combinations that can most efficiently shutdown aberrantly active pathways in cancer.