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 analysis of genomic data, development of predictive biomarkers, development of clinical trial designs for the co-development of therapeutics and molecular diagnostics, systems and computational biology for elucidating the nature of oncogenesis, and development of software for genomic analysis.

Resume (updated Jan, 2009)

Selected Recent Publications

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. 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.

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.

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. 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.

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

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.

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.

Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. Journal of Clinical Oncology 23:7332-41, 2005.

Freidlin B and Simon R. Adaptive signature design: An adaptive clinical trial design for generating and prospectively testing a gene expression signature for sensitive patients. Clinical Cancer Research 11:7872-8, 2005.

Simon R. Validation of pharmacogenomic biomarker classifiers for treatment selection. Cancer Biomarkers 2:89-96, 2006.

Simon R, Wang SJ. Use of genomic signatures in therapeutics development. The Pharmacogenomics Journal 6:166-173, 2006.

Simon R. A checklist for evaluating reports of expression profiling for treatment selection. Clinical Advances in Hematology and Oncology 4:219-224, 2006.

Sospedra M, Muraro P, Stefanova I, Zhao Y, Chung K, Li Y, Giulianotti M, Simon R, Mariuzza R, Pinilla C, Martin R. Redundancy in antigen presenting function of the HLA-DR and -DQ molecules in the multiple sclerosis associated HLA-DR2 haplotype1, Journal of Immunology 176:1951-1961, 2006.

Simon R, Norton L. The Norton-Simon hypothesis for designing more effective and less toxic chemotherapeutic regimens. Nature Clinical Practice-Oncology 3:406, 2006.

Simon R. Development and validation of biomarker classifiers for treatment selection. Journal of Statistical Planning and Inference 138(2):308-320, 2008.

Simon R. Development and validation of therapeutically relevant predictive classifiers using gene expression profiling. Journal of the National Cancer Institute 98:1169-71, 2006.

Varma S, Simon R. Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics 7:91, 2006.

Dobbin K and Simon R. Sample size planning for developing classifiers using high dimensional DNA microarray data. Biostatistics 8:101-117, 2007.

Simon R. New challenges for 21stcentury clinical trials, Clinical Trials 4:167-169, 2007.

Dupuy A and Simon RM, Critical review of published Microarray studies for cancer outcome and guidelines on statistical analysis and reporting, Journal of the National Cancer Institute 99:147-157, 2007.

Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y. Analysis of gene expression data using BRB-Array Tools,Cancer Informatics 2:11-17, 2007.

Jiang W and Simon R. A comparison of bootstrap methods and an adjusted bootstrap approach for estimating prediction error in microarray classification. Statistics in Medicine 26:5320-5334.

Jiang W, Freidlin B, and Simon R. Biomarker adaptive threshold design: A procedure for evaluating treatment with possible biomarker-defined subset effect. Journal of the National Cancer Institute 99:1036-43, 2007.

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

Simon R, Zhang X. On the dynamics of breast tumor development in women carrying germline BRCA1 and BRCA2 mutations. International Journal of Cancer 122:1916-17, 2008.

Simon R. Microarray based expression profiling and informatics. Current Opinion in Biotechnology 19:26-29, 2008.

Simon R. Interpretation of genomic data: Questions and answers. Seminars in Hematology (in press).

Simon R. Using genomics in clinical trial design. Clinical Cancer Research (in press).

Simon, R. Designs and adaptive analysis plans for pivotal clinical trials of therapeutics and companion diagnostics. Expert Opinion in Medical Diagnostics (in press).

Simon R. Lost in translation: Problems and pitfalls in translating laboratory observations to clinical utility. European Journal of Cancer (in press).

Jiang W, Varma S, Simon R. Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling, Statistical Applications in Genetics and Molecular Biology :7(1) article 8, 2008.

 

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

last updated: Jan. 8, 2009