Comprehensive Analysis and Multi-Omics Data Integration for Cancer-Related Studies

Project Summary/Abstract I am a principal data scientist and bioinformatics manager of The Experimental and Computational Genomics Core in the Sidney Kimmel Comprehensive Cancer Center (ECGC) at Johns Hopkins University. This Core offers comprehensive bioinformatics support to members of both the Cancer Center, the Bloomberg~Kimmel Institute for Cancer Immunotherapy (BKI), and the Convergence Institute at Johns Hopkins including both standard informatics and innovative analysis pipeline development. To this work, I bring expertise in multi-omics data analysis methods through my role leading the DNA methylation analysis in several tumor types for The Cancer Genome Atlas (TCGA). In my role as bioinformatics manager of ECGC, I oversee day-to-day bioinformatics services and supports the bioinformatics needs of investigators in areas of data integration, annotation, high-throughput and spatial data analysis. In this capacity, I develop bioinformatics software tools to support many cancer research activities. I collaborate with a number of investigators across different research programs in the cancer center. I highlight the key collaborations in this application as illustrative of my research portfolio. For example, I played a key role in development of the comprehensive analysis of T-cell receptor sequencing data for the FEST (Functional Expansion of Specific T cells) assay. I also perform multi-omic analyses of changes in the tumor microenvironment due to immunotherapy and correlate those changes with clinical outcomes. With the support of this R50 award, I will extend my current pipeline development to state of the art single cell spatial technologies and data integration techniques and train future bioinformatics analysts to benefit various cancer-related studies throughout the cancer center.