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

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Project Summary/Abstract I am a Research Associate 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 and the Bloomberg~Kimmel Institute for Cancer Immunotherapy (BKI), including both standard informatics and innovative analysis pipeline development. To this work, I bring expertise in genomics 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, and high-throughput data analysis. In this capacity, I develop bioinformatics software tools to support many cancer research activities. I collaborate with a number of investigators across both the cancer center and BKI. I highlight three key collaborations in this application as illustrative of my research portfolio. For example, (1) I played a key role in the comprehensive analysis of T-cell receptor sequencing data for the FEST (Functional Expansion of Specific T cells, http://www.stat-apps.onc.jhmi.edu/FEST/) assay. (2) I perform integrative analysis of multiplex data to find better biomarkers to predict response to cancer immunotherapy using both expression of immune markers in addition to density and a spatial correlation of cells expressing those makers. (3) I am lead analyses for basic tumor biology to determine how chromatin structure is associated with gene expression and alternative splicing. With the support of this R50 award, I will extend my current pipeline development to state of the art single cell measurement technologies and data integration techniques and train future bioinformatics analysts to benefit various cancer-related studies throughout the cancer center and BKI.