Office Address	Phone	Fax	E-mail
Executive Plaza North Room 8148 National Cancer Institute Bethesda, MD 20892	(301) 496-2876	(301) 402-0560	zhaoy@helix.nih.gov

Research Interests

Data analysis of cDNA microarray and combinatorial peptide library, T-cell epitope prediction, informatics on protein function and structure relationship, bioinformatics tool development

Publications
As of Nov. 19, 2002

Rubio-Godoy, V., Dutoit, V., Zhao, Y., Simon, R., Guillaume, P., Houghten, R. A., Romero, P, Cerottini, J. C., Pinilla, C., and Valmori, D. Positional scanning-synthetic peptide library-based analysis of self- and pathogen-derived peptide cross-reactivity with tumor-reactive Melan-A-specific CTL. J. Immunol., 169:5696-5707, 2002.

Assersohn, L., Gangi, L., Zhao, Y., Dowsett, M., Simon, R., Powles, T., & Liu, E. T. The feasibility of using fine needle aspiration from primary breast cancers for cDNA microarray analysis. Clinical Cancer Research 8:794-801, 2002.

Sung, M., Zhao, Y., Martin, R., and Simon, R. T-cell epitope prediction with combinatorial peptide libraries. J. of Computational Biology 9: 527-539, 2002.

Huai, Q., Kim, H., Liu, Y., Zhao, Y., Mondragon, A., Liu, J. O., and Ke, H. Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes. Proc. Natl. Acad. Sci. USA 99:12037-12042, 2002.

Wang, E., Miller, L. D., Ohnmacht, G. A, Mocellin, S., Perez-Diez, A., Petersen, D., Zhao, Y. , Simon, R., Powell, J. I., Asaki, E., Alexander, H. R., Duray, P. H., Herlyn, M., Restifo, P., Liu, E. T., Rosenberg, S. A., & Marincola, F. M. Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness Cancer Research 62: 3581-3586, 2002.

Rubio-Godoy, V., Pinilla, C., Dutoit, V., Borras, E., Simon, R., Zhao, Y., Cerottini, J., Romero, P, Houghten, R. A., and Valmori, D. Towards PS-SCL based identification of CD8+ tumor reactive T cell ligands: a comparative analysis of PS-SCLs recognition by a single tumor-reactive CD8+CL clone1. Cancer Research 62:2058-2063, 2002.

Rubio-Godoy, V., Ayyoub, M., Dutoit, V., Servis, C., Schink, A., Rimoldi, D., Romero, P., Cerottini, J. C., Simon, R., Zhao, Y., Houghten, R. A., Pinilla, C., and Valmori, D. Combinatorial peptide library based identification of peptide ligands for tumor-reactive cytolytic T lymphocytes of unknown specificity. Eur. J. Immunol. 32:2292-2299, 2002.

Borras, E., Martin, R., Judkowski, V., Shukaliak, J, Zhao, Y., Rubio-Godoy, V., Valmori, D., Wilson, D., Simon, R., Houghten, R. A., and Pinilla, C. Findings on T cell specificity revealed by synthetic combinatorial libraries. J. Immunol. Methods, 267:79-97,2002.

Zhao, Y., Gran, B., Pinilla, C., Markovic-Plese, S., Hemmer, B., Tzou, A., Whitney, L. W., Biddison, W. E., Martin, R., & Simon, R. Combinatorial peptide libraries and biometric score matrices permit the quantitative analysis of specific and degenerate interactions between clonotypic T-cell receptors and MHC-peptide ligands. J. Immunol., 167:2130-3141, 2001.

Zhao, Y., Grovel, L., and Simon, R. TEST: a web-based T-cell Epitope Search Tool. Proceedings of the 14th IEEE symposium on computer-based medical systems, p.493- 497, 2001.

Pinilla, C., Rubio-Godoy, V., Dutoit, V., Guillaume, P., Simon, R., Zhao, Y., Houghten, R. A., Cerottini, J., Romero, P, and Valmori, D. Combinatorial peptide libraries as an alternative approach to the identification of ligands for tumor reactive cytolytic T lymphocytes. Cancer Research 61:5153-5160, 2001.

Martin, R., Gran, B., Zhao, Y., Markovic-Plese, S., Bielekova, B., Marques, A., Sung, M., Hemmer, B., Simon, R., MaFarlan, H. F., & Pinilla, C. Molecular mimicry and antigen-specific T-cell response in multiple sclerosis and chronic CNS lyme disease. J. Autoimmunity, 16:187-192, 2001.

Assersohn, L. C., Gangi, L., Powles, T. J., Simon, R., Zhao, Y., Powell, J., Dowsett, M., Staudt, L., & Liu, E. T. Gene expression profiles from fine needle aspirations (FNAs) of breast cancers complementary DNA (cDNA) microarrays. Annals of Oncology, 11 Suppl.4:11, 2000.

Huai, Q., Colandene, J., Chen, Y., Luo, F., Zhao, Y., Topal, M. & Ke, H. Crystal structure of NaeI:an evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J. 19: 3110-3118,2000.

Xu, R., Hassell, A., Vanderwall, D., Lambert, M., Holmes, W., Luther, M., Rocque, W., Milburn, M., Zhao, Y., Ke, H. & Nolte, R. Atomic Structure of PDE4: Insights into Phosphodiesterase Mechanism and Specificity. Science 288:1822-1825, 2000.

Hemmer, B., Gran, B., Zhao, Y., Marques, A., Pascal, J., Tzou, A., Kondo, T., Cortese, I., Bielekova, B., Straus, S., McFarland, H.F., Houghten, R., Simon, R., Pinilla, C. & Martin, R. Identifiction of candidate T cell epitopes and molecular mimics in chronic Lyme disease. Nature Medicine 5:1375-82, 1999.

Zhao, Y., Chen,Y., Schutkowski, M., Fischer, G. & Ke, H. Crystal structure of cyclophilin A complexed with a fragment of HIV-1 capsid protein: insight into the HIV-1 activity. Structure 5: 139-146, 1997.

Gu, Y., Zheng, C., Zhao, Y., Ke, H., & Fan, H. A new procedure of combining direct methods with solvent flattening: dealing with the phase ambiguity in protein crystallography. Acta Crystallographica D53: 792-794, 1997.

Zhao, Y. & Ke, H. Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization. Biochemistry 35: 7356-7361, 1996.

Zhao, Y. & Ke, H. Mechanistic implication of crystal structures of cyclophilin A-dipeptides complexes. Biochemistry 35:7362-7368, 1996.

Ke, H., Zhao, Y., Luo, F., Weissman, I., & Friedman, J. Crystal structure of murine cyclophilin C complexed with immunosuppressive drug cyclosporin A. Proc. Natl. Acad. Sci. USA 90: 11850-11854, 1993.

Please send comments and suggestions to brb@linus-dev.nci.nih.gov