Dr. Yingdong Zhao

Office Address:
Room 8148
6130 Executive Plaza
Rockville, MD 20852

Contact Information:
Tel: (301) 496-2876
Fax: (301) 402-0560
Email:zhaoy@mail.nih.gov

Research Interests  

  • Development of statistical methods and bioinformatics approaches for using transcript expression profiling, SNP, aCGH, and microRNA data to identify cancer-specific markers that can be used broadly to increase the sensitivity and accuracy of cancer diagnosis and treatment.

  • Development of statistical methods and immunoinformatic approaches for using genomic data and immunologic assays to elucidate the molecular events in T-cell immune response to pathogens in autoimmune processes and to identify molecular targets for therapeutic vaccines.

    • Selected Publications 
    As of Jan. 15, 2009

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

    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.

    Zhao Y, Grovel L, 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.

    Zhao Y, Gran B, Pinilla C, Markovic-Plese S, Hemmer B, Tzou A, Whitney LW, Biddison WE, 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.

    Assersohn L, Gangi L, Zhao Y, Dowsett M, Simon R, Powles T, Liu ET. 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, Simon R. T-cell epitope prediction with Combinatorial Peptide Libraries. J. of Computational Biology 9: 527-539, 2002.

    Rubio-Godoy V, Dutoit V, Zhao Y, Simon R, Guillaume P, Houghten RA, Romero P, Cerottini JC, Pinilla C, 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.

    Wang E, Adams S, Zhao Y, Panelli M, Simon R, Klein H, Marincola FM. A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides. J. of Translational Medicine 1:4, 2003.

    Zhao Y, Pinilla C, Valmori D, Martin R, Simon R. Application of support vector machine in T-cell epitope prediction. Bioinformatics 19:1978-1984, 2003.

    Jin P, Zhao Y, Ngalame Y, Panelli MC, Nagorsen D, Monsurró Smith K, Hu N, Su H, Taylor PR, Marincola FM, Wang E. Selection and validation of endogenous reference genes using a high throughput approach. BMC Genomics 5(1):55, 2004.

    Simon R, Korn EL, McShane LM, Radmacher MD, Wright G, Zhao Y. Design and Analysis of DNA Microarray Investigations, Springer Verlag, 2004.

    Zhao Y, Li MC, Simon R. An adaptive method for cDNA microarray normalization. BMC Bioinformatics 6:28, 2005.

    Markovic-Plese S, Hemmer B, Zhao Y, Simon R, Pinilla C, Martin R. High level of cross-reactivity in influenza virus hemagglutinin-specific CD4+ T-cell response: Implications for the initiation of autoimmune response in multiple sclerosis. J Neuroimmunol 169(1-2):31-8, 2005.

    Sospedra M, Zhao Y, Hausen H, Muraro PA, Villiers EM, Pinilla C, Martin R. Recognition of Conserved Amino Acid Motifs of Common Viruses and Its Role in Autoimmunity. PLoS Pathogens 1(4):e41, 2005.

    Venturini S, Allicotti G, Zhao Y, Simon R, Burton DR, Pinilla C, Poignard P. Identification of peptides from human pathogens able to cross-activate an HIV-1-gag specific CD4+ T cell clone. Eur. J. Immunol. 36(1):27-36, 2006.

    Basil CF, Zhao Y, Zavaglia K, Jin P, Panelli MC, Voiculescu S, Mandruzzato S, Lee HM, Seliger B, Freedman RS, Taylor PR, Hu N, Zanovello P, Marincola FM, Wang E. Common Cancer Biomarkers. Cancer Research 66(6):2953-61, 2006.

    Simon R, Lam AP, Li MC, Ngan M, Menenzes S, Zhao Y. Analysis of Gene Expression Data Using BRB-ArrayTools. Cancer Informatics 2:1-7, 2007.

    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.

    Dobbin K, Zhao Y, Simon R. How large a training set is needed to develop a classifier for microarray data? Clinical Cancer Research 14(1):108-114, 2008.

    Sabatino M, Zhao Y, Voiculescu S, Nickoloff BJ, Karai L, Monaco A, Marincola FM, Wang E. Conservation of a core of genetic alterations over a decade of recurrent melanoma supports the melanoma stem cell hypothesis. Cancer Research 68:122-131, 2008.

    Xu X, Zhao Y, Simon R. Gene set expression comparison kit for BRB-ArrayTools. Bioinformatics 24:137-139, 2008.

    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..

    Qi Q, Zhao Y, Li MC, Simon R. Nonnegative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. In press at Bioinformatics.

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

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

    Last updated: Jan. 15, 2009