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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.


Recent Publications:

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.

Yuan J, Hegde PS, Clynes R, Foukas PG, Harari A, Kleen TO, Kvistborg P, Maccalli C, Maecker HT, Page DB, Robins H, Song W, Stack EC, Wang E, Whiteside TL, Zhao Y, Zwierzina H, Butterfield LH, Fox BA. Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer. 2016.

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. https://doi.org/10.1007/s00280-019-03898-z

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, 2020.

Krushkal J, Negi S, Yee LM, Evans JR, Grkovic T, Palmisano A, Fang J, Sankaran H, McShane LM, Zhao Y, O'Keefe BR. Molecular genomic features associated with in vitro response of the NCI60 cancer cell line panel to natural products. Mol Oncol. 2020.

Wang J, Jelcic I, Mühlenbruch L, Haunerdinger V, Toussaint NC, Zhao Y, Cruciani C, Faigle W, Naghavian R, Foege M, Binder TMC, Eiermann T, Opitz L, Fuentes-Font L, Reynolds R, Kwok WW, Nguyen JT, Lee JH, Lutterotti A, Münz C, Rammensee HG, Hauri-Hohl M, Sospedra M, Stevanovic S, Martin R. HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis. Cell 183(5):1264-1281. 2020.

Hu-Lieskovan S, Bhaumik S, Dhodapkar K, Grivel J, Gupta S, Hanks BA, Janetzki S, Kleen TO, Koguchi Y, Lung AW, Maccalli C, Mahnke YD, Novosiadly RD, Selvan SR, Sims T, Zhao Y, Maecker HT. SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. Journal for ImmunoTherapy of Cancer 2020;8:e000705.

Chen AP, Kummar S, Moore N, Rubinstein LV, Zhao Y, Williams PM, Palmisano A, Sims D, Coyne GO, Rosenberger CL, Simpson M, Raghav K, Meric-Bernstam F, Leong S, Waqar S, Foster JC, Konaté M, Das B, Karlovich C, Lih CJ, Polley E, Simon RM, Li MC, Piekarz R, Doroshow JH. Molecular Profiling-Based Assignment of Cancer Therapy (NCI-MPACT): A Randomized Multicenter Phase 2 Trial. JCO Precision Oncology, 2021.

Palmisano A, Vural S, Zhao Y, Sonkin D. MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing. Human Mutation 42(4):342-345, 2021.

Krushkal J, Negi S, Yee LM, Evans JR, Grkovic T, Palmisano A, Fang J, Sankaran H, McShane LM, Zhao Y, O'Keefe BR. Molecular genomic features associated with in vitro response of the NCI‐60 cancer cell line panel to natural products. Mol Oncol. 15 (2):381-406, 2021.

Zhao Y, Li M, Konate MM, Chen L, Das B, Karlovich C, Williams PM, Evrard YA, Doroshow JH, McShane LM. TPM, FPKM, or Normalized Count? A Case Study on Comparison of Quantitative Units for RNA-seq Data from the Patient Derived Xenograft Models in NCI PDMR Database. Journal of Translational Medicine 19(1):269, 2021.

Zhang P, Palmisano A, Kumar R, Li MC, Doroshow J, Zhao Y. TPWshiny: an R/Bioconductor package and interactive Shiny app to explore the therapeutic response of NCI-60 cell lines. Bioinformatics, 38 (2):570-572, 2021.

Vega DM, Yee LM, McShane LM, et al. Aligning Tumor Mutational Burden (TMB) quantification across diagnostic platforms: Phase 2 of the Friends of Cancer Research TMB Harmonization Project. Annals of Oncology 32(12):1626-1636, 2021.

Coghill AE, Fang J, Liu Z, Chen CJ, Jarrett RF, Hjalgrim H, Proietti C, Mulvenna J, Yu KJ, Hsu WL, Lou PJ, Wang CP, Zhao Y, Doolan DL, Hildesheim A. Identifying Epstein-Barr virus peptide sequences associated with differential IgG antibody response. International Journal of Infectious Diseases, 2021.

Shao L., Iyer A., Zhao Y. et al. Identification of genomic signatures in bone marrow associated with clinical response of CD19 CAR T-cell therapy. Sci Rep 12, 2830 (2022).

Dr. Yingdong Zhao

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

Contact Information:
Tel: (240) 276-6025
Fax: (240) 276-7888
Email:zhaoy@mail.nih.gov