Dr. Chen is the Principle Investigator of multiple National Cancer Institute (NCI) grants. The project of Integrative prediction models for metastasis risk in colon cancer collects data on mRNA expression, somatic mutations, and clinical information to develop clinical-genomic risk prediction models and subtypes for colon cancer patients. Dr. Chen is also a major contributor for identifying six triple-negative breast cancer (TNBC) subtypes and corresponding gene signatures. He is the developer of the web-based software 'TNBCtype', which has been widely used by breast cancer research community. Recently Dr. Chen also participated in the Proteogenomic Data Analysis Centers for Clinical Proteomic Tumor Analysis Consortium (CPTAC), which is the parallel project of The Cancer Genome Atlas (TCGA) by NCI, as a site Principal Investigator. As part of the multidisciplinary Proteogenomic Data Analysis Center (PGDAC), Dr. Chen and his group will participate in providing data analysis as well as biological and clinical interpretation of CPTAC data. The team will develop computational tools for data analysis, data integration, and visualization and apply these tools to CPTAC data.