TECHNICAL REPORT

1. A paradigm for class prediction using gene expression profiles Michael D. Radmacher, Lisa M. Mcshane, and Richard Simon Journal of Computational Biology 9:505-511, 2002.

2. Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data Lisa M. McShane, Michael D. Radmacher, Boris Freidlin, Ren Yu, Ming-Chung Li, and Richard Simon Bioinformatics 18:1462-1469, 2002.

3. Controlling the number of false discoveries:Application to high-dimensional genomic data Edward L. Korn, James F. Troendle, Lisa M. McShane, and Richard Simon Journal of Statistical Planning and Inference 124:379-398, 2004.

4. Design of studies using DNA microarrays Richard Simon, Michael D. Radmacher, and Kevin Dobbin Genetic Epidemiology 23:21-36, 2002.

5. Bioinformatics and Whole Genome Technologies Richard Simon

6. Comparison of Microarray Design Kevin Dobbin and Richard Simon Supplement

7. BRB Array-Tools Users Guide (version 3.2) Richard Simon and Amy Peng Lam

8. Statistical design of reverse dye microarrays Kevin Dobbin, Joanna Shih, and Richard Simon Bioinformatics 19: 803-10, 2003. Supplement

9. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification Richard Simon, Michael D. Radmacher, Kevin Dobbin, and Lisa M. McShane Journal of the National Cancer Institute 95:14-18, 2003. Supplement

10. Experimental Design of DNA Microarray Experiments Richard Simon and Kevin Dobbin Biotechniques 34: 1-5, 2002.

11. Phase I Clinical Trial Design L. V. Rubinstein and R. M. Simon

12. Clinical Trial Designs for Therapeutic Vaccine Studies Richard Simon

13. A random variance model for differential gene detection in small sample microarray experiments George Wright and Richard Simon Bioinformatics 19: 2448-55, 2003. Supplement and Tables & Figures

14. Using DNA Microarrays For Diagnostic and Prognostic Prediction Richard Simon Expert Review of Molecular Diagnostics 3(5) 587-595, 2003.

15. Statistical issues in the design and analysis of gene expression microarray studies of animal models Lisa Mcshane, Joanna Shih, and Aleksandra Michalowska Journal of Mammary Gland Biology and Neoplasia 8, 359-374, 2003.

16. Questions and Answers on Design of Dual Label Microarrays Kevin Dobbin, Joanna Shih, and Richard Simon Journal of the National Cancer Institute 95, 1362-1369, 2003.

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

18. Supervised analysis when the number of candidate features (p) greatly exceeds the number of cases (n) Richard Simon Association of Computing Machinery, SIGKDD Explorations 5(2) 31-36, 2003.

19. Sample Size Determination in Microarray Experiments for Class Comparison and Prognostic Classification Kevin Dobbin and Richard Simon Biostatistics, 6, 27-38, 2005. Supplement

20. On the efficiency of targeted clinical trials Aboubakar Maitournam and Richard Simon Statistics in Medicine 24:329-339, 2005.

21. Evaluating the efficiency of targeted designs for randomized clinical trials Richard Simon and Aboubakar Maitournam Clinical Cancer Research 10:6759-6763, 2005. Supplement

22. Experimental Design Kevin Dobbin and Richard Simon Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley and Sons, New York.

23. Guidelines for the Design of Clinical Studies for Development and Validation of Therapeutically Relevant Biomarkers and Biomarker Based Classification Systems Richard Simon to appear in Biomarkers in Breast Cancer, DF Hayes & G Gasparini (eds)

24. When is a Genomic Classifier Ready for Prime Time Richard Simon Nature Clinical Practice Oncology 1:4-5, 2004.

25. An agenda for Clinical Trials: clinical trials in genomic era Richard Simon Clinical Trials 1:468-470, 2004.

26. Characterizing dye bias in microarray experiments Dobbin,K.K., Kawasaki, E.S., Petersen, D.W., and Simon, R.M. Bioinformatics, 21, 2430-2437, 2005. Supplement1, Supplement2

27. Estimating the number of rate limiting genomic changes for human breast cancer Xinan Zhang and Richard Simon Breast Cancer Research and Treatment 2005;91:121-124 Supplement

28. Bioinformatics in Cancer Therapeutics - Hype or Hope? Richard Simon Nature Clinical Practice Oncology 2:223, 2005.

29. BRB Array-Tools Users Guide (version 3.3) Richard Simon and Amy Peng Lam

30. Prediction Error Estimation: A Comparison of Resampling Methods Molinaro AM, Simon R, Pfeiffer RM.

31. Development and Validation of Therapeutically Relevant Multi-Gene Biomarker Classifiers Richard Simon Journal of the National Cancer Institute, Vol 97, No. 12, 866-867, 2005.

32. Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data Lusa L, McShane LM, Radmacher MD, Shih, JH, Wright, GW and Simon R. submitted to Statistics in Medicine

33. Road map for developing and validating therapeutically relevant genomic classifiers Richard Simon Journal of Clinical Oncology Vol 23, No.29, 2005.

34. Designing prospective clinical pharmacogenomic(PG) trials: meeting report on drug development strategies to enhance therapeutic decision making WL Trepicchio, D Essayan, ST Hall, G Schechter, Z Tezak, SJ Wang, D Weinreich and R Simon. The Pharmacogenomics Journal, 2006, in press.

35. Development and validation of biomarker classifiers for treatment selection Richard Simon To appear in Journal of Statistical Planning & Inference, Special Issue on Design of Medical Experiments.

36. Validation of pharmacogenomic biomarker classifiers for treatment selection Richard Simon To appear in Disease Markers 21 1-8, 2005.

37. An evaluation of randomized discontinuation design Boris Freidlin & Richard Simon Journal of Clinical Oncology 23, 5094-5098.

38. Adaptive signature design: An adaptive clinical trial design for generating and prospectively testing a gene expression signature for sensitive patients Boris Freidlin & Richard Simon Clinical Cancer Research 11:7872-7878.

39. Bias in error estimation when using cross-validation for model selection Sudhir Varma & Richard Simon BMC Bioinformatics 7:91, 2006.

40. On estimating diagnostic accuracy with multiple raters and partial gold standard evaluation Paul S. Albert and Lori E. Dodd under review at the Journal of the American Statistical Association.

41. Imputation approaches for estimating diagnostic accuracy for multiple tests from partially verified designs Paul S. Albert under review at Biometrics

42. Sample size planning for developing classifiers using high dimensional data Kevin Dobbin and Richard Simon Biostatistics (In Press).

43. Sample size determination in microarray experiments for class comparison and prognostic classification Kevin Dobbin and Richard Simon Biostatistics 6:27-38, January 2005.

44. Use of genomic signatures in therapeutics development in oncology and other diseases Richard Simon and S-J Wang The Pharmacogenomics Journal 6:166-173, 2006.

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

46. BRB Array-Tools Users Guide (version 3.4) Richard Simon and Amy Peng Lam

 

TALKS

1. Myths and Statistical Principles in DNA Microarray Research. Richard Simon

2. Statistical Analysis of Microarray Data. Richard Simon, Lisa M. McShane, & Michael D. Radmacher

3. The State of the Art of Microarray Informatics. Richard Simon

4. Molecular Biometry in the Genomic Era DNA Microarrays. Richard Simon

5. Statistical Issues in the Analysis of Gene Expression Microarray Data. Lisa M. McShane

6. Microarray Myths and Microarray Truths. Richard Simon

7. CIT Training Class: Statistical Analysis of Gene Expression Microarray Data. Lisa M. McShane, Joanna H. Shih & Richard Simon

8. Design Issues in DNA Microarray Based Studies. Richard Simon

9. CIT Training Class: Statistical Analysis of Gene Expression Microarray Data. Lisa M. McShane, Joanna H. Shih, and Kevin K. Dobbin Oct. 26, 2005

10. Myths & Truths About Microarray Expression Profiling. Richard Simon

11. Statistical design, analysis and interpretation of gene expression microarray data. Lisa M. McShane

12. Design and Analysis of DNA Microarray Studies for Translational Medicine. Richard Simon Presented at the NIH Research Festival (October 15, 2003)

13. "Methods and Myths in Prognostic Prediction with Microarray and Proteomic Data" Richard Simon Presented at the Harvard Medical School International Conference on Analysis of Genomic Data (May 10-11, 2004)

14. Key Aspects in the Design and Analysis of DNA Microarray Studies for Diagnostic & Prognostic Prediction Richard Simon Presented at the Statistical Society of Canada in Montreal (June 1, 2004).

15. Genomics of Breast Cancer: Is it Ready for Prime Time? Richard Simon Presented at the American Society of Clinical Oncology, New Orleans, La (June, 2004). Audio & Slides

16. Development and Validation of Gene Expression Based Diagnostic Classification Richard Simon Presented in a session titled "Integrating Microarrays Into Clinical Trials" at the American Society of Clinical Oncology, New Orleans, La (June, 2004).

17. Strengths & Weaknesses of Observational Validation Designs for High Dimensional Data Richard Simon Presented at NCI/FDA Workshop on Study Designs & Statistical Approaches to Biomarkers Validation for Cancer Diagnosis and Detection, Bethesda, MD (July 27-28, 2004).

18. Developing and Evaluating Medical Diagnostics Based on Whole Genome Technologies Richard Simon Presented at Joint Statistical Meetings, Toronto (Aug 12, 2004).

19. Design of DNA Microarray Experiments Richard Simon Presented at Microarray Gene Expression Data Conference (MGED 7), Toronto (Sept. 9, 2004).

20. Key Features in the Design and Analysis of DNA Microarray Studies Richard Simon Presented at Fourth Virtual Conference in Genomics & Bioinformatics (Sept. 22, 2004).

21. Validation of therapeutically relevant diagnostic classifiers based on gene expression data Richard Simon Presented at the NCI Director's Challenge Meeting (Nov. 4, 2004).

22. Key Aspects of the Design and Analysis of DNA Microarray Studies Richard Simon Presented at the CAMDA-2004 conference at Duke University(Nov. 10, 2004).

23. Design of Experiments Using DNA Microarrays Richard Simon Presented at the American Association for the Advancement of Science, Feb 21, 2005, Washington D.C.

24. Conducting Definitive Phase III Trials Using Pharmacogenomcs Richard Simon Presented at the Pharmacogenomics in Drug Development & Regulatory Decision Workshop, April 11, 2005.

25. Is Expression Profile Transforming Clinical Oncology? Richard Simon Presented at the American Association for Cancer Research meeting, April 20, 2005.

26. A Roadmap for Development and Utilization of Therapeutically Relevant Genomic Classifiers Richard Simon Presented at the Center for Devices and Radiological Health of the Food and Drug Administration in Gaithersburg, Maryland, June 20, 2005.

27. A New Paradigm for the Utilization of Genomic Classifiers for Patient Selection in the Critical Path of Medical Product Development Richard Simon Presented at the FDA/Industry Statistics Workshop on "Safety and the Critical Path" in Washington D.C., September, 2005.

28. A Roadmap for Developing & Validating Genomic Classifiers for Treatment Selection Richard Simon Presented at the meeting on "Application and Validation of Genomic Biomarkers for Use in Drug Development and Regulatory Submissions" Bethesda, Maryland, October 6-7, 2005.

29. A Roadmap for Developing & Validating Genomic Classifier for Treatment Selection Richard Simon Presented at Intenational Meeting on Translational Genomics in Neuroblastoma, October 2005.

30. Roadmap for the Development of Targeted Therapeutics in the Genomic Era Richard Simon Visiting Professor Invited Presentation to Food & Drug Administration, Feb. 2, 2006. Audio

31. A Roadmap for Co-Development of Therapeutics and Diagnostics in the Genomic Era Richard Simon Presented at the International Conference on Drug Development. February 13-15, 2006 (Austin, Texas).

32. BRB-ArrayTools Richard Simon Presented at the NIH Microarray Special Interest Group , March 1, 2006. Audio

33. Clinical Trial Design and Biomarker-Based Tumor Classification Systems Richard Simon Presented at the Institute of Medicine Workshop on Developing Biomarker-based Tools for Cancer Screening, Diagnosis and Treatment, Washington D.C., March 21, 2006. Audio

34. Re-examination of the design of early clinical development trials for molecularly targeted agents Richard Simon Presented at ASCO at the Education Session, Atlanta, June 5, 2006. Audio

35. Moving from Correlative Studies to Predictive Medicine Richard Simon Presented at ASCO at the Education Session Integrating Evidence from Clinical and Lab Studies, Atlanta, June 4, 2006.

36. Design & Analysis of Microarray Studies for Diagnostic & Prognostic Classification Richard Simon Presented at pre-conference workshop on design and analysis of studies for the development of predictive classifiers" at CAMDA held at Duke University June 7, 2006. Audio Part 1Audio Part 2Audio Part 3

 

NEWS REPORT

1. The Scientist: Classifying Breast Cancer Models

2. Use of Norton-Simon Model Results in 31% Reduction in Breast Cancer Mortality in National Randomized Clinical Trial

 

Updated on June 22, 2006