Dr. Richard Simon
Chief, Biometric Research Branch

Office Address:
Room 8134
6130 Executive Plaza
Rockville, MD 20852

Contact Information:
Tel: (301) 496-0975
Fax: (301) 402-0560
Email:rsimon@mail.nih.gov

       

Research Interests
Current research interests include Bayesian methods in clinical trial design and analysis, and the development of methods for the analysis of genome sequence and expression data to identify cancer related genes, elucidate their functions, determine the steps of tumor development, identify molecular targets and develop genome based approaches to the prevention, detection, diagnosis and treatment of cancer.

Resume (updated Jan, 2009)

Selected Publications (since 2000)

Simon R, Korn E, McShane L, Radmacher M, Wright G, Zhao Y. Design and Analysis of DNA Microarray Investigations, Springer-Verlag, New York, 2003.

Simon RM, Steinberg SM, Hamilton M, Hildesheim A, Khleif S, Kwak LW, Mackall CL, Schlom J, Topalian SL, Berzofsky JA. Clinical Trial Designs for the Early Clinical Development of Therapeutic Cancer Vaccines. Journal of Clinical Oncology 19:1848-54, 2001.

Simon R. Clinical trial designs for therapeutic vaccine studies. In Handbook of Cancer Vaccines, pp 519-526, Morse MA, Lyerly HK and Clay TM (eds), Humana Press, Totawa NJ, ((2004).

Simon R. Clinical trial designs for therapeutic cancer vaccines. In Tumor Immunology and Cancer Vaccines,pp 339-350, Khleif S (ed), Kluwer Academic Publishers, Norwell MA, (2005).

Simon R. Are Placebo-controlled clinical trials ethical or needed when alternative treatment exists? Editorial, Annals of Internal Medicine 133:474-5, 2000.

Thall PF, Simon RM and Shen Y. Approximate Bayesian evaluation of multiple treatment effects. Biometrics 56:213-219, 2000.

Simon R. Commentary on "Clinical and sample size considerations: Another perspective" by Lee and Zelen, Statistical Science 15:95-110, 2000.

Simon R. Bayesian subset analysis: Application to studying treatment by gender interactions. Statistics in Medicine 21:2909-2916, 2002.

Simon R, Desper R, Papadimitriou C, Peng A, Alberts DS, Taetle R, Trent JM, Schaffer AA. Chromosome abnormalities in ovarian adenocarcinoma III: Using breakpoint data to infer and test mathematical models of oncogenesis. Genes, Chromosomes and Cancer 28:106-120, 2000.

Radmacher MD and Simon R. A measure of the efficacy of tamoxifen for preventing the initiation and growth of breast tumors. Journal of the National Cancer Institute 92:48-53, 2000.

Radmacher MD, Simon R, Desper R, Taetle R, Schaffer AA and Nelson MA. Graph models of oncogenesis with an application to melanoma. Journal of Theoretical Biology 212:535-548, 2001.

Radmacher MD, McShane LM and Simon R. A paradigm for class prediction using gene expression profiles. Journal of Computational Biology 9:505-511, 2002.

Simon R, Radmacher MD, Dobbin K. Design of studies with DNA microarrays. Genetic Epidemiology 23:21-36, 2002.

McShane LM, Radmacher MD, Freidlin B, Yu R, Li MC, Simon R. Methods of assessing reproducibility of clustering patterns observed in analyses of microarray data. Bioinformatics 18:1462-1469, 2002.

Dobbin K, Simon R. Comparison of microarray designs for class comparison and class discovery. Bioinformatics 18:1462-69, 2002.

Dobbin K, Shih J, Simon R. Statistical design of reverse dye microarrays. Bioinformatics 19:803-810, 2003.

Dobbin K, Shih J and Simon R. Questions and answers on design of dual-label microarrays for identifying differentially expressed genes. Journal of the National Cancer Institute 95:1362-69, 2003.

Korn EL, McShane LM, Troendle JF, Rosenwald A and Simon R. Identifying pre-post chemotherapy differences in gene expression in breast tumors: a statistical method appropriate for this aim. British Journal of Cancer 86:1093-1096, 2002.

Sung MH, Zhao Y, Martin R and Simon R. T-cell Epitope Prediction with Combinatorial Peptide Libraries, Journal of Computational Biology 9:527-39, 2002.

Sung MH, Simon R. Candidate epitope identification using peptide property models: Application to cancer immunotherapy. Methods (In Press).

Sung MH, Simon R. Genome-wide conserved epitope profiles of HIV-1 predicted by quantitative properties of MHC binding peptides. Journal of Computational Biology 11:125-145, 2004.

Zhao Y, Gran B, Pinilla C, Markovic-Plese S, Hemmer B, Tzou A, Whitney L, 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. Journal of Immunology 167:2130-41, 2001.

Zhao Y, Pinilla C, Valmori D, Martin R, Simon R. Application of support vector machines in T-cell epitope prediction. Bioinformatics 19:1978-84, 2003.

Simon R, Dobbin K. Experimental design of DNA microarray experiments, Biotechniques, 34:1-5, 2002.

Simon R, Radmacher M, Dobbin K, McShane, LM. Pitfalls in the Use of DNA Microarray Data for Diagnostic and Prognostic Classification, Journal of the National Cancer Institute 95:14-18, 2003.

Simon R. Using DNA microarrays for diagnostic and prognostic prediction. Expert Reviews of Molecular Diagnostics 3(5), 587-95, 2003.

Simon R. Diagnostic and prognostic prediction using gene expression profiles in high dimensional microarray data. British Journal of Cancer 89: 1599-1604, 2003.

Korn EL, Troenndle JF, McShane LM, Simon R. Controlling the number of false discoveries: Application to high-dimensional genomic data. Journal of Statistical Planning and Inference 124: 2448-55, 2003.

Wright GW, Simon R. A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19:2448-55, 2003.

Simon R. Supervised analysis when the number of candidate features greatly exceeds the number of cases. Association for Computing Machinery SIGKDD Explorations 5:2:31-36, 2003.

Sung MH, Simon R. In Silico simulation of inhibitor drug effects on NF-kB pathway dynamics. Molecular Pharmacology 66:70-75, 2004.

Dobbin K, Simon R. Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics 6:27-38, 2005.

Simon R, Maitnourim A. Evaluating the efficiency of targeted designs for randomized clinical trials. Clinical Cancer Research 10:6759-63, 2004.

Maitnourim A, Simon R. On the efficiency of targeted clinical trials. Statistics in Medicine 24:329-339, 2005.

Freidlin B, Simon R. An evaluation of the randomized discontinuation design. Journal of Clinical Oncology 23:1-5, 2005.

Varma S, Simon R. Iterative class discovery and feature selection using minimal spanning trees. BMC Bioinformatics 5:126, 2004.

Simon R. When is a genomic classifier ready for prime time? Nature Clinical Practice Oncology 1:4-5, 2004.

Simon R. An agenda for clinical trials: clinical trials in the genomic era. Clinical Trials 1:468-70, 2004.

Zhang X, Simon R. Estimating the number of rate-limiting genomic changes for human breast cancer. Breast Cancer Research and Treatment 91:121-24, 2005.

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

Dobbin KK, Kawasaki ES, Peterson DW, Simon RM. Characterizing dye bias in microarray experiments. Bioinformatics 21:2430-37, 2005.

Simon R. Development and validation of therapeutically relevant multi-gene biomarker classifiers, Journal of the National Cancer Institute 97:866-7, 2005.

Molinaro A, Simon R, Pfeiffer R. Prediction error estimation: A comparison of resampling methods. Bioinformatics 21:3301-7, 2005.

Simon R. Bioinformatics in cancer therapeutics hype or hope? Nature Clinical Practice Oncology 2:223, 2005.

 

 

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

last updated: Jan. 8, 2009