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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:

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.

Simon R, Zhao Y. Constructing Software for Cancer Research in Support of Molecular PPM. Personalized and Precision Medicine Informatics, 133-150, 2020.

Polley E, Zhao Y. Precision Trials Informatics. Personalized and Precision Medicine Informatics, 215-222, 2020.

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, Konaté 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.

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 (1), 1-9, 2022.

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, 2022.

Konaté MM, Li MC, McShane LM, Zhao Y. Discovery of pathway-independent protein signatures associated with clinical outcome in human cancer cohorts. Sci Rep 12 (11), 1-10, 2022.

Sankaran H, Negi S, McShane LM, Zhao Y, Krushkal J. Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products. BMC cancer 22 (1), 1-22, 2022.

Shao L, Shi R, Zhao Y, et al. Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products Journal of translational medicine 20 (1), 1-15, 2022.

Krushkal J, Vural S, Jensen TJ, Wright G, Zhao Y. Increased copy number of imprinted genes in the chromosomal region 20q11-q13.32 is associated with resistance to antitumor agents in cancer cell lines Clinical Epigenetics 14 (1), 1-26, 2022.

Naghavian R, Faigle W, Oldrati P, Wang J, Toussaint NC, Qiu Y, Medici G, Wacker M, Freudenmann LK, Bonté PE, Weller M, Regli L, Amigorena S, Rammensee HG, Walz JS, Brugger SD, Mohme M, Zhao Y, Sospedra M, Neidert MC, Martin R. Microbial peptides activate tumour-infiltrating lymphocytes in glioblastoma. Nature 617(7962):807-817, 2023.

Krauze AV, Zhao Y, Li MC, Shih J, Jiang W, Tasci E, Cooley Zgela T, Sproull M, Mackey M, Shankavaram U, Tofilon P, Camphausen K. Revisiting Concurrent Radiation Therapy, Temozolomide, and the Histone Deacetylase Inhibitor Valproic Acid for Patients with Glioblastoma-Proteomic Alteration and Comparison Analysis with the Standard-of-Care Chemoirradiation. Biomolecules13(10):1499, 2023.