Selected Publications 
As of January 9, 2008

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.

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.

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

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

Pinilla C, Borras E, Martin R, Zhao Y, Simon R. The Integration of positional scanning libaries with bioinformatics and proteomics. Peptides: The Wave of the Future. Proceedings of the 2nd International/17th American Peptide Symposium, Michal Lebl and Richard A. Houghten (Ed.), American Peptide Society, 2001.

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.

Rubio-Godoy V, Ayyoub M, Dutoit V, Servis C, Schink A, Rimoldi D, Romero P, Cerottini JC, Simon R, Zhao Y, Houghten RA, Pinilla C, 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 RA, Pinilla C. Findings on T cell specificity revealed by synthetic combinatorial libraries. J. Immunol. Methods 267: 79-97, 2002.

Wang E, Miller LD, Ohnmacht GA, Mocellin S, Perez-Diez A, Petersen D, Zhao Y, Simon R, Powell JI, Asaki E, Alexander HR, Duray PH, Herlyn M, Restifo P, Liu ET, Rosenberg SA, Marincola FM. Evolving molecular portraits of metastatic melanoma. Cancer Research 62: 3581-3586, 2002.

Rubio-Godoy V, Pinilla C, Dutoit V, Borras E, Simon R, Zhao Y, Cerottini J, Romero P, Houghten RA, 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+CTL clone1. Cancer Research 62:2058-2063, 2002.

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.

Huai Q, Kim H, Liu Y, Zhao Y, Mondragon A, Liu JO, 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.

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.

Best C, Leiva IM, Chuaqui RF, Gillespie JW, Duray PH, Murgai M, Zhao Y, Simon R, Kang J, Green JE, Bostwick D, Linehan WM, Emmert-Buck MR. Comparative Gene Expression Profiling of Different Grades of Human Prostate Cancer and Prostate Cancer Cell Lines. Diagnostic Molecular Pathology 12:67-70, 2003.

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.

Nambiar A, Duquesnoy R, Adams S, Zhao Y, Oblitas J, Leitman S, Stroncek D, Marincola FM. HLAMatchmaker-driven analysis of responses to HLA-typed platelet transfusions in alloimmunized thrombocytopenic patients. Blood 107(4):1680-7, 2006.

Li X, Wang E, Zhao Y, Ren J, Jin P, Yao K, Marincola FM. Chromosomal imbalances in nasopharyngeal carcinoma: a meta-analysis of comparative genomic hybridization results. J. Translational Medicine 4(1):4, 2006.

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.

Sospedra M, Muraro P, Stefanova I, Zhao Y, Chung K, Li Y, Hamashin C, Simon R, Mariuzza R, Clemencia P, Martin R. Redundancy in Antigen-Presenting Function of the HLA-DR and -DQ Molecules in the Multiple Sclerosis-Associated HLA-DR2 Haplotype J. Immunology 176(3):1951-61, 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.

Panelli MC, Stashower ME, Slade HB, Smith K, Norwood C, Abati A, Fetsch P, Filie A, Walters SA, Astry C, Arico E, Zhao Y, Selleri S, Wang E, Marincola FM. Sequential gene profiling of basal cell carcinomas treated with imiquimod in a placebo-controlled study defines the requirements for tissue rejection. Genome Biology 8(1), 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.

Meade KG, Gormley E, Farrelly C, Costello E, Keane J, Zhao Y, MacHugh D. Innate immune suppression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease. In press at BMC Genomics.

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. In press at Cancer Research.

Xu X, Zhao Y, Simon R. Gene set expression comparison kit for BRB-ArrayTools. In press at Bioinformatics.

Zhao Y, Simon R. BRB ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource. In press at Cancer Informatics.