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Biometric Research Program (BRP)

Dr. Yingdong Zhao

Chief, Computational and Systems Biology Branch

Research Interests

biomarker discovery, mechanism of drug resistance in cancer chemotherapy, survival prognostic and predictive models, machine learning, T-cell epitope prediction, bioinformatics tool development.

Selected Publications:

Zhao Y, Sung MH, Simon R. Artificial intelligence methods for predicting T-cell epitopes. Immunoinformatics: predicting Immunogenicity in silico. Methods in Molecular Biology. Flower D.R. (eds) Humana Press, Totawa NJ, 2007.

Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y. Analysis of gene expression data using BRB-array tools. Cancer Informatics, vol. 3, pp. 11.17, 2007.

Zhao Y and Simon R. BRB ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource. Cancer Informatics 6:9-15, 2008.

Zhao Y and Simon R. Deconvolution of positional scanning synthetic combinatorial libraries: mathematical models and bioinformatics approaches. "Computational Biology: New Research", Nova Publishers, 2009.

Landi MT, Zhao Y, et al. MicroRNA expression differentiates histology and predicts survival of lung cancer. Clinical Cancer Research 16:430-441, 2010.

Zhao Y, Simon R. Development and validation of predictive indices for a continuous outcome using gene expression profiles. Cancer Informatics 9:105-114, 2010.

Zhao Y, Simon R. Gene expression deconvolution in clinical samples. Genome Medicine, 2(12) 2010.

Zhao Y, Wang E, Liu H, Rotunno M, Koshiol J, Landi MT, McShane LM. Evaluation of normalization methods for two-channel microRNA microarray. Journal of Translational Medicine, 8:69, 2010.

Wang E, Zhao Y, Monaco A, Uccellini L, Kirkwood JM, Spyropoulou-Vlachou M, Panelli MC, Marincola FM, Gogas H. A multi-factorial genetic model for prognostic assessment of high risk melanoma patients receiving adjuvant interferon. PLoS ONE, vol. 7, no. 7, 2012.

Zhao Y, Simon R. T cell epitope, prediction with peptide libraries. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (editors) Encyclopedia of System Biology, Springer New York, 2013.

Zhao Y, Polley E, Li MC, Lih CJ, Palmisano A, Sims D, Rubinstein L, Conley B, Chen A, Williams PM, Kummar S, Doroshow JH, Simon RM. GeneMed: an informatics hub for the coordination of next-generation sequencing studies that support precision oncology clinical trials, Cancer Informatics, 14 (Suppl. 2), 45-55, 2015.

Kummar S, Williams PM, Lih CJ, Polley EC, Chen AP, Rubinstein LV, Zhao Y, Simon RM, Conley BA, Doroshow JH. Application of Molecular Profiling in Clinical Trials for Advanced Metastatic Cancers. JNCI J Natl Cancer Inst 107 (4), djv003, 2015.

Palmisano A, Zhao Y, Li MC, Polley EC, Simon R. OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trialsr. Briefings in Bioinformatics doi: 10.1093/bib/bbw059, 2016.

Krushkal J, Zhao Y, Hose C, Monks A, Doroshow JH, Simon R. Concerted changes in transcriptional regulation of genes involved in DNA methylation, demethylation, and folate-mediated one-carbon metabolism pathways in the NCI-60 cancer cell line panel in response to cancer drug treatment. Clinical Epigenetics 8(1):73, 2016.

Krushkal J, Zhao Y, Hose C, Monks A, Doroshow JH, Simon R. Longitudinal Transcriptional Response of Glycosylation-Related Genes, Regulators, and Targets in Cancer Cell Lines Treated With 11 Antitumor Agents. Cancer informatics 16, 2017.

Palmisano A, Zhao Y, Simon RM. D3Oncoprint: Stand-Alone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files. JCO Clinical Cancer Informatics 2, 1-9, 2018.

Jing P, Chen W, Ren J, Chen S, Wood L, Zhao Y, et al. Adenoviral Vector Transduction of Dendritic Cells is Inhibited by Plasma from Cancer Patients, Cytotherapy 20 (5), 728-739, 2018.

Monks A, Zhao Y, Hose C, Hamed H, Krushkal J, Fang J, Sonkin D, Palmisano A, Polley E, Fogli L, Konaté M, Miller S, Simpson M, Voth A, Li M, Harris E, Wu X, Connelly J, Rapisarda A, Teicher B, Simon R, and Doroshow J. The NCI Transcriptional Pharmacodynamics Workbench: a tool to examine dynamic expression profiling of therapeutic response in the NCI-60 cell line panel. Cancer Research, 78 (24), 6807-6817, 2018.

Liu S, Stroncek DF, Zhao Y, et al. Single cell sequencing reveals gene expression signatures associated with bone marrow stromal cell subpopulations and time in culture. Journal of translational medicine 17 (1), 23, 2019.

Min DJ, Zhao Y, Monks A, Palmisano A, Hose C, Teicher B, Doroshow J, Simon R. Identification of Pharmacodynamic Biomarkers and Common Molecular Mechanisms of Response to Genotoxic Agents in Cancer Cell Lines. Cancer Chemotherapy Pharmacology, 2019.

Palmisano A, Krushkal J, Li MC, Fang J, Sonkin D, Wright G, Yee L, Zhao Y, McShane L. Bioinformatics Tools and Resources for Cancer Immunotherapy Study. Biomarkers for Immunotherapy of Cancer, 649-678, 2019.

Dr. Yingdong Zhao

Office Address:
Room 5W104
9609 Medical Center Dr
Rockville, MD 20850

Contact Information:
Tel: (240) 276-6025
Fax: (240) 276-7888