The focus of Dr. Elemento’s group is on the systems biology of cancer; they focus on prostate cancer and hematological malignancies.
In these cancers, Dr. Elemento and his team are elucidating the patterns of aberrant pathway activities, rewiring of regulatory networks and cancer mutations that have occurred in cancer cells.
They are also trying to understand how tumors evolve at the genomic and epigenomic level. They 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.
Dr. Elemento’s 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).
Dr. Elemento’s 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). They use drug repositioning to identify small molecules that can target mutated signaling pathways and classically undruggable proteins such as transcription factors. They model complex signaling pathways to identify drug combinations that can most efficiently shutdown aberrantly active pathways in cancer.
In addition, Dr. Elemento is the Director of the Englander Institute for Precision Medicine, which increasingly involve using cloud analytics and storage.
Furthermore, Dr. Elemento is also the Associate Director of the Institute for Computational Biomedicine, Co-Assistant Dean for Scientific Computing and Co-leader of the Cancer Center Program on Genetics and Epigenetics.