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

项目总结/摘要 我是一个研究助理和生物信息学经理的实验和 Sidney Kimmel综合癌症中心的计算基因组学核心 （ECGC）在约翰霍普金斯大学。该核心提供全面的生物信息学 支持癌症中心和彭博社的成员~Kimmel研究所为 癌症免疫治疗（BKI），包括标准信息学和创新 分析管道开发。在这项工作中，我将基因组学数据分析方面的专业知识 通过我在几种肿瘤类型中领导DNA甲基化分析的角色， 癌症基因组图谱（TCGA）作为ECGC的生物信息学经理， 我监督日常的生物信息学服务，并支持生物信息学的需求， 数据集成、注释和高通量数据分析领域的研究人员。 在这个职位上，我开发了生物信息学软件工具，以支持许多癌症 研究活动。我与一些研究人员合作， 中心和BKI。我在此应用程序中强调了三个关键协作， 我的研究档案例如，（1）我在综合方面发挥了关键作用 分析FEST（Functional Expansion of 特异性T细胞，http：//www.stat-apps.onc.jhmi.edu/FEST/）测定。(2)我表演 多重数据的综合分析，以找到更好的生物标志物来预测对 使用免疫标记物的表达和密度的癌症免疫疗法 以及表达这些标记的细胞的空间相关性。(3)我负责分析 基础肿瘤生物学，以确定染色质结构如何与基因 表达和可变剪接。在这个R50奖的支持下，我将扩大我的 目前的管道发展到最先进的单细胞测量技术 和数据集成技术，并培训未来的生物信息学分析师， 癌症中心和BKI的各种癌症相关研究。

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.