Richard M Simon

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Evaluating the efficiency of targeted designs for randomized clinical trials
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, Maryland 20892 7634, USA
    Clin Cancer Res 10:6759-63. 2004
  2. ncbi request reprint New challenges for 21st century clinical trials
    Richard Simon
    Biometic Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Clin Trials 4:167-9; discussion 173-7. 2007
  3. ncbi request reprint Biomarker-adaptive threshold design: a procedure for evaluating treatment with possible biomarker-defined subset effect
    Wenyu Jiang
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, EPN 8122, National Cancer Institute, Bethesda, MD 20892, USA
    J Natl Cancer Inst 99:1036-43. 2007
  4. pmc Moving from correlative science to predictive oncology
    Richard Simon
    National Cancer Institute, 9000 Rockville Pike, Bethesda, MD, 20892 7434 USA
    EPMA J 1:377-87. 2010
  5. doi request reprint Designs and adaptive analysis plans for pivotal clinical trials of therapeutics and companion diagnostics
    Richard Simon
    Chief National Cancer Institute, Biometric Research Branch, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA 1 301 496 0975 1 301 402 0560
    Expert Opin Med Diagn 2:721-9. 2008
  6. doi request reprint Clinical trials for predictive medicine
    Richard Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC7434, Bethesda, MD 20892 7434, U S A
    Stat Med 31:3031-40. 2012
  7. doi request reprint How to develop treatments for biologically heterogeneous "diseases"
    Richard M Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
    Clin Cancer Res 18:4001-3. 2012
  8. pmc Gene expression deconvolution in clinical samples
    Yingdong Zhao
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Genome Med 2:93. 2010
  9. pmc Evaluation of normalization methods for microarray data
    Taesung Park
    Department of Statistics, Seoul National University, Seoul, Korea
    BMC Bioinformatics 4:33. 2003
  10. ncbi request reprint Clinical trial designs for therapeutic cancer vaccines
    Richard Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892 7434, USA
    Cancer Treat Res 123:339-50. 2005

Detail Information

Publications82

  1. ncbi request reprint Evaluating the efficiency of targeted designs for randomized clinical trials
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, Maryland 20892 7634, USA
    Clin Cancer Res 10:6759-63. 2004
    ..This creates the opportunity to conduct targeted clinical trials with eligibility restricted to patients predicted to be responsive to the drug...
  2. ncbi request reprint New challenges for 21st century clinical trials
    Richard Simon
    Biometic Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Clin Trials 4:167-9; discussion 173-7. 2007
  3. ncbi request reprint Biomarker-adaptive threshold design: a procedure for evaluating treatment with possible biomarker-defined subset effect
    Wenyu Jiang
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, EPN 8122, National Cancer Institute, Bethesda, MD 20892, USA
    J Natl Cancer Inst 99:1036-43. 2007
    ..We propose a statistically rigorous biomarker-adaptive threshold phase III design for settings in which a putative biomarker to identify patients who are sensitive to the new agent is measured on a continuous or graded scale...
  4. pmc Moving from correlative science to predictive oncology
    Richard Simon
    National Cancer Institute, 9000 Rockville Pike, Bethesda, MD, 20892 7434 USA
    EPMA J 1:377-87. 2010
    ..In this paper we attempt to address some of these issues and to comment specifically on the design of clinical studies for evaluating the clinical utility and robustness of prognostic and predictive biomarkers...
  5. doi request reprint Designs and adaptive analysis plans for pivotal clinical trials of therapeutics and companion diagnostics
    Richard Simon
    Chief National Cancer Institute, Biometric Research Branch, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA 1 301 496 0975 1 301 402 0560
    Expert Opin Med Diagn 2:721-9. 2008
    ....
  6. doi request reprint Clinical trials for predictive medicine
    Richard Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC7434, Bethesda, MD 20892 7434, U S A
    Stat Med 31:3031-40. 2012
    ....
  7. doi request reprint How to develop treatments for biologically heterogeneous "diseases"
    Richard M Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
    Clin Cancer Res 18:4001-3. 2012
    ..Here, we comment on alternative clinical trial designs and propose a prospective discovery/evaluation framework for using tumor genomics in the design of phase III trials...
  8. pmc Gene expression deconvolution in clinical samples
    Yingdong Zhao
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Genome Med 2:93. 2010
    ..Consequently, the deconvolution approach can be useful in the analysis of mixtures of cell populations in clinical samples...
  9. pmc Evaluation of normalization methods for microarray data
    Taesung Park
    Department of Statistics, Seoul National University, Seoul, Korea
    BMC Bioinformatics 4:33. 2003
    ..Normalization plays an important role in the earlier stage of microarray data analysis. The subsequent analysis results are highly dependent on normalization...
  10. ncbi request reprint Clinical trial designs for therapeutic cancer vaccines
    Richard Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892 7434, USA
    Cancer Treat Res 123:339-50. 2005
    ..Interim monitoring plans may effectively limit the size of the trials by terminating accrual early when results are not consistent with the targeted improvement...
  11. ncbi request reprint Roadmap for developing and validating therapeutically relevant genomic classifiers
    Richard Simon
    National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892, USA
    J Clin Oncol 23:7332-41. 2005
    ....
  12. ncbi request reprint An agenda for clinical trials: clinical trials in the genomic era
    Richard M Simon
    National Cancer Institute, Bethesda, MD 20892 7434, USA
    Clin Trials 1:468-70. 2004
  13. ncbi request reprint Use of genomic signatures in therapeutics development in oncology and other diseases
    R Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Pharmacogenomics J 6:166-73. 2006
    ..Some of the same considerations apply, however, to development of efficacy and safety classifiers in nononcologic diseases based on single-nucleotide germline polymorphisms...
  14. ncbi request reprint A checklist for evaluating reports of expression profiling for treatment selection
    Richard Simon
    Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Clin Adv Hematol Oncol 4:219-24. 2006
    ..A checklist is presented to help oncologists evaluate publications on expression profiling of human tumors to determine whether the results are ready for use with their patients...
  15. pmc Microarray-based expression profiling and informatics
    Richard Simon
    National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892, United States
    Curr Opin Biotechnol 19:26-9. 2008
    ..We review here the current state-of-the-art for design and analysis of microarray-based investigations...
  16. ncbi request reprint When is a genomic classifier ready for prime time?
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892, USA
    Nat Clin Pract Oncol 1:4-5. 2004
  17. ncbi request reprint On the dynamics of breast tumor development in women carrying germline BRCA1 and BRCA2 mutations
    Richard Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Int J Cancer 122:1916-7. 2008
    ..A second event increasing proliferation of the partially malignant intermediate clone may lead inexorably to production and selection of cells with additional mutations in genes that facilitate tumor progression...
  18. pmc Using cross-validation to evaluate predictive accuracy of survival risk classifiers based on high-dimensional data
    Richard M Simon
    Biometric Research Branch, US National Cancer Institute, Bethesda, MD 20892 7434, USA
    Brief Bioinform 12:203-14. 2011
    ..We have also discussed evaluation of the statistical significance of a survival risk model and evaluation of whether high-dimensional genomic data adds predictive accuracy to a model based on standard covariates alone...
  19. doi request reprint Translational research in oncology: key bottlenecks and new paradigms
    Richard Simon
    National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Expert Rev Mol Med 12:e32. 2010
    ..I review here some prospective Phase III designs that have been developed for transition from the era of correlative science to one of reliable predictive and personalised oncology...
  20. doi request reprint Clinical trials for predictive medicine: new challenges and paradigms
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Clin Trials 7:516-24. 2010
    ..Heterogeneity of human diseases and new technology for characterizing them presents new opportunities and challenges for the design and analysis of clinical trials...
  21. pmc Use of archived specimens in evaluation of prognostic and predictive biomarkers
    Richard M Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    J Natl Cancer Inst 101:1446-52. 2009
    ....
  22. pmc Analysis of DNA microarray expression data
    Richard Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Best Pract Res Clin Haematol 22:271-82. 2009
    ..This manuscript attempts to provide a non-technical summary of the key principles of statistical design and analysis for studies that utilize microarray expression profiling...
  23. pmc Analysis of gene expression data using BRB-ArrayTools
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Cancer Inform 3:11-7. 2007
    ....
  24. pmc Lost in translation: problems and pitfalls in translating laboratory observations to clinical utility
    Richard Simon
    National Cancer Institute, Division of Cancer Treatment and Diagnosis, Bethesda, MD 20892, USA
    Eur J Cancer 44:2707-13. 2008
    ..Some of these issues are addressed here, specifically in the context of developing molecular diagnostics in a manner that moves retrospective correlative science to prospective predictive medicine...
  25. pmc Interpretation of genomic data: questions and answers
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Semin Hematol 45:196-204. 2008
    ..Achieving these goals involves challenges in rethinking many paradigms for the conduct of basic and clinical cancer research and for the organization of interdisciplinary collaboration...
  26. pmc Diagnostic and prognostic prediction using gene expression profiles in high-dimensional microarray data
    R Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892, USA
    Br J Cancer 89:1599-604. 2003
    ....
  27. ncbi request reprint Using DNA microarrays for diagnostic and prognostic prediction
    Richard Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892, USA
    Expert Rev Mol Diagn 3:587-95. 2003
    ..It also attempts to outline some of the steps needed to develop initial microarray research findings into classification systems suitable for broad clinical application...
  28. doi request reprint The use of genomics in clinical trial design
    Richard Simon
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
    Clin Cancer Res 14:5984-93. 2008
    ..This article reviews some designs for phase III clinical trials that may facilitate movement to a more predictive oncology...
  29. ncbi request reprint Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification
    Richard Simon
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    J Natl Cancer Inst 95:14-8. 2003
  30. ncbi request reprint Design of studies using DNA microarrays
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, Maryland 20892 7434, USA
    Genet Epidemiol 23:21-36. 2002
    ....
  31. ncbi request reprint Molecular differentiation of high- and moderate-grade human prostate cancer by cDNA microarray analysis
    Carolyn J M Best
    Pathogenetics Unit, Laboratory of Pathology and Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Diagn Mol Pathol 12:63-70. 2003
    ..We suggest that these data provide insight into the molecular nature of clinically aggressive prostate cancer...
  32. doi request reprint Challenges of microarray data and the evaluation of gene expression profile signatures
    Richard Simon
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, USA
    Cancer Invest 26:327-32. 2008
  33. ncbi request reprint Molecular diagnosis of Burkitt's lymphoma
    Sandeep S Dave
    National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
    N Engl J Med 354:2431-42. 2006
    ..We examined whether gene-expression profiling could reliably distinguish Burkitt's lymphoma from diffuse large-B-cell lymphoma...
  34. ncbi request reprint A comparison of bootstrap methods and an adjusted bootstrap approach for estimating the prediction error in microarray classification
    Wenyu Jiang
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 6130 Executive Boulevard, Rockville, MD 20852, USA
    Stat Med 26:5320-34. 2007
    ..Even with small samples, it does not suffer from large upward bias as the leave-one-out bootstrap and the 0.632+ bootstrap, and it does not suffer from large variability as the leave-one-out cross-validation in microarray applications...
  35. ncbi request reprint Sample size planning for developing classifiers using high-dimensional DNA microarray data
    Kevin K Dobbin
    Biometric Research Branch, National Cancer Institute, 6130 Executive Boulevard, Rockville, MD 20852, USA
    Biostatistics 8:101-17. 2007
    ..We find that many prediction problems do not require a large training set of arrays for classifier development...
  36. doi request reprint How large a training set is needed to develop a classifier for microarray data?
    Kevin K Dobbin
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Rockville, Maryland 20852, USA
    Clin Cancer Res 14:108-14. 2008
    ..The question of how many samples are needed in the training set to produce a good classifier from high-dimensional microarray data is challenging...
  37. ncbi request reprint Gene expression patterns and profile changes pre- and post-erlotinib treatment in patients with metastatic breast cancer
    Sherry X Yang
    Cancer Therapeutics Branch in Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20889, USA
    Clin Cancer Res 11:6226-32. 2005
    ....
  38. ncbi request reprint A random variance model for detection of differential gene expression in small microarray experiments
    George W Wright
    National Cancer Institute Biometric Research Branch, National Institutes of Health, 6130 Executive Blvd, MSC 7434, Bethesda, MD 20892 7434, USA
    Bioinformatics 19:2448-55. 2003
    ..This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true...
  39. ncbi request reprint Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays
    Kevin K Dobbin
    Cancer Diagnosis Program, National Cancer Institute NIH, Bethesda, MD 20894, USA
    Clin Cancer Res 11:565-72. 2005
    ..The findings indicate that under properly controlled conditions it is feasible to perform complete tumor microarray analysis, from tissue processing to hybridization and scanning, at multiple independent laboratories for a single study...
  40. ncbi request reprint Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
    Alain Dupuy
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
    J Natl Cancer Inst 99:147-57. 2007
    ..There is a need for critical review of the statistical analysis and reporting in published microarray studies that focus on cancer-related clinical outcomes...
  41. pmc Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma
    Andreas Rosenwald
    Metabolism Branch, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
    J Exp Med 198:851-62. 2003
    ..The molecular diagnosis of PMBL should significantly aid in the development of therapies tailored to this clinically and pathogenetically distinctive subgroup of DLBCL...
  42. ncbi request reprint Experimental design of DNA microarray experiments
    Richard M Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, MD, USA
    Biotechniques . 2003
  43. ncbi request reprint The Norton-Simon hypothesis: designing more effective and less toxic chemotherapeutic regimens
    Richard Simon
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892, USA
    Nat Clin Pract Oncol 3:406-7. 2006
  44. ncbi request reprint A paradigm for class prediction using gene expression profiles
    Michael D Radmacher
    Biometric Research Branch, National Cancer Institute, 6130 Executive Boulevard, Bethesda, MD 20892 7434, USA
    J Comput Biol 9:505-11. 2002
    ..The prediction paradigm will serve as a good framework for comparing different prediction methods and may accelerate the development of molecular classifiers that are clinically useful...
  45. ncbi request reprint The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma
    Andreas Rosenwald
    Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    N Engl J Med 346:1937-47. 2002
    ..The survival of patients with diffuse large-B-cell lymphoma after chemotherapy is influenced by molecular features of the tumors. We used the gene-expression profiles of these lymphomas to develop a molecular predictor of survival...
  46. pmc Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness
    Ena Wang
    Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, Maryland 20892, USA
    Cancer Res 62:3581-6. 2002
    ..001). Analysis of their annotations denoted that approximately half of them were related to T-cell regulation, suggesting that immune responsiveness might be predetermined by a tumor microenvironment conducive to immune recognition...
  47. ncbi request reprint Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data
    Lisa M McShane
    National Cancer Institute, Biometric Research Branch, DCTD, NIH, Bethesda, MD 20892 7434, USA
    Bioinformatics 18:1462-9. 2002
    ..However, clustering algorithms always detect clusters, even on random data, and it is easy to misinterpret the results without some objective measure of the reproducibility of the clusters...
  48. pmc B cell gene signature with massive intrahepatic production of antibodies to hepatitis B core antigen in hepatitis B virus-associated acute liver failure
    Patrizia Farci
    Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 107:8766-71. 2010
    ..These data suggest that humoral immunity may exert a primary role in the pathogenesis of HBV-associated ALF...
  49. doi request reprint The cross-validated adaptive signature design
    Boris Freidlin
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland 20892, USA
    Clin Cancer Res 16:691-8. 2010
    ..However, due to the high-dimensional nature of the genomic data, developing a reliable classifier by the time the definitive phase III trail is designed may not be feasible...
  50. pmc Gene expression-based prognostic signatures in lung cancer: ready for clinical use?
    Jyothi Subramanian
    Biometric Research Branch, Department of Cancer Treatment and Diagnosis, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    J Natl Cancer Inst 102:464-74. 2010
    ....
  51. pmc Development and validation of predictive indices for a continuous outcome using gene expression profiles
    Yingdong Zhao
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA Email
    Cancer Inform 9:105-14. 2010
    ..We have developed a plug-in for BRB-ArrayTools that implements the LAR and the LASSO algorithms with complete cross-validation...
  52. pmc A comparison of phase II study strategies
    Sally Hunsberger
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland 20892, USA
    Clin Cancer Res 15:5950-5. 2009
    ..In this article, we compare different phase II study strategies to determine the most efficient drug development path in terms of number of patients and length of time to conclusion of drug efficacy on overall survival...
  53. ncbi request reprint Evaluation of randomized discontinuation design
    Boris Freidlin
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    J Clin Oncol 23:5094-8. 2005
    ..Single-arm phase II trials may not be appropriate for testing cytostatic agents. We evaluate two kinds of randomized designs for the early development of target-based cytostatic agents...
  54. ncbi request reprint Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells
    Sandeep S Dave
    National Cancer Institute, NIH, Bethesda, MD 20892, USA
    N Engl J Med 351:2159-69. 2004
    ..We used gene-expression profiles of tumor-biopsy specimens obtained at diagnosis to develop a molecular predictor of the length of survival...
  55. pmc Iterative class discovery and feature selection using Minimal Spanning Trees
    Sudhir Varma
    Biometric Research Branch, National Cancer Institute, Rockville, USA
    BMC Bioinformatics 5:126. 2004
    ..This has the effect of obscuring clustering in samples that may be evident only when looking at a subset of genes, because noise from irrelevant genes dominates the signal from the relevant genes in the distance calculation...
  56. ncbi request reprint Adaptive signature design: an adaptive clinical trial design for generating and prospectively testing a gene expression signature for sensitive patients
    Boris Freidlin
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
    Clin Cancer Res 11:7872-8. 2005
    ..Thus, there is a need for development of novel statistical methodology for rapid evaluation of these agents...
  57. ncbi request reprint Sample size determination in microarray experiments for class comparison and prognostic classification
    Kevin Dobbin
    Biometric Research Branch, National Cancer Institute, 6130 Executive Blvd, Bethesda, MD, 20892 7434, USA
    Biostatistics 6:27-38. 2005
    ..We discuss procedures for controlling the false discovery rate. Our calculations are based on relatively simple yet realistic statistical models for the data, and provide straightforward sample size calculation formulae...
  58. ncbi request reprint Application of support vector machines for T-cell epitopes prediction
    Yingdong Zhao
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Bioinformatics 19:1978-84. 2003
    ..Recent data also indicate that it is highly flexible, and one receptor may recognize thousands of different peptides. Deciphering the patterns of peptides that elicit a MHC restricted T-cell response is critical for vaccine development...
  59. pmc Bias in error estimation when using cross-validation for model selection
    Sudhir Varma
    Biometric Research Branch, National Cancer Institute, Bethesda, MD, USA
    BMC Bioinformatics 7:91. 2006
    ..We have evaluated the validity of using the CV error estimate of the optimized classifier as an estimate of the true error expected on independent data...
  60. ncbi request reprint Candidate epitope identification using peptide property models: application to cancer immunotherapy
    Myong Hee Sung
    Molecular Statistics and Bioinformatics Section, Biometric Research Branch, National Cancer Institute, National Institutes of Health, 6130 Executive Blvd EPN 8146, MSC 7434, Bethesda, MD 20892, USA
    Methods 34:460-7. 2004
    ..The candidate epitopes identified by such a computational approach must be evaluated experimentally but the approach can provide an efficient and focused strategy for anti-cancer immunotherapy development...
  61. pmc An adaptive method for cDNA microarray normalization
    Yingdong Zhao
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
    BMC Bioinformatics 6:28. 2005
    ..These assumptions can be inappropriate for custom arrays or arrays in which the reference RNA is very different from the experimental samples...
  62. ncbi request reprint Questions and answers on design of dual-label microarrays for identifying differentially expressed genes
    Kevin Dobbin
    Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892 7434, USA
    J Natl Cancer Inst 95:1362-9. 2003
  63. ncbi request reprint Combined breast ductal lavage and ductal endoscopy for the evaluation of the high-risk breast: a feasibility study
    David N Danforth
    Surgery Branch, The Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Surg Oncol 94:555-64. 2006
    ....
  64. ncbi request reprint In silico simulation of inhibitor drug effects on nuclear factor-kappaB pathway dynamics
    Myong Hee Sung
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, 6130 Executive Blvd EPN 8146, MSC 7434, Bethesda, MD 20892, USA
    Mol Pharmacol 66:70-5. 2004
    ..Such kinetic analyses of the "drugged" molecular system will facilitate optimal drug target selection and the development of treatment protocols for a molecularly targeted therapy...
  65. ncbi request reprint Validation of pharmacogenomic biomarker classifiers for treatment selection
    Richard Simon
    Biometric Research Branch, National Cancer Institute, NIH, Bethesda, MD 20892 7434, USA
    Cancer Biomark 2:89-96. 2006
    ..In this paper we attempt to clarify these issues and to provide guidance on the design of clinical trials for evaluating the clinical utility and robustness of pharmacogenomic classifiers...
  66. ncbi request reprint Genomewide conserved epitope profiles of HIV-1 predicted by biophysical properties of MHC binding peptides
    Myong Hee Sung
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, 6130 Executive Boulevard EPN 8146, MSC 7434, Bethesda, MD 20892, USA
    J Comput Biol 11:125-45. 2004
    ..As an essential step in designing vaccines, the revealed patterns may provide valuable information in identifying the immunologically important regions...
  67. ncbi request reprint An investigation of two multivariate permutation methods for controlling the false discovery proportion
    Edward L Korn
    Biometric Research Branch, National Cancer Institute, EPN 8129, Bethesda, MD 20892 7434, USA
    Stat Med 26:4428-40. 2007
    ..We find that the top-down MPT-based method probabilistically controls the FDP, whereas our implementation of the top-down SAM-based method does not. Bottom-up MPT-based or SAM-based methods can result in poor control of the FDP...
  68. ncbi request reprint Estimating the number of rate limiting genomic changes for human breast cancer
    Xinan Zhang
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Breast Cancer Res Treat 91:121-4. 2005
    ....
  69. ncbi request reprint Effectiveness of gene expression profiling for response prediction of rectal adenocarcinomas to preoperative chemoradiotherapy
    B Michael Ghadimi
    Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bldg 50, Rm 1408, 50 South Dr, Bethesda, MD 20892 8010, USA
    J Clin Oncol 23:1826-38. 2005
    ..This study aimed to investigate whether parallel gene expression profiling of the primary tumor can contribute to stratification of patients into groups of responders or nonresponders...
  70. pmc Initiating oncogenic event determines gene-expression patterns of human breast cancer models
    Kartiki V Desai
    Laboratory of Cell Regulation and Carcinogenesis, National Cancer Institute, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 99:6967-72. 2002
    ..Moreover, similarities in gene expression between human breast cancers and the mouse models have been identified, thus providing an important component for the validation of transgenic mammary cancer models...
  71. ncbi request reprint The proliferation gene expression signature is a quantitative integrator of oncogenic events that predicts survival in mantle cell lymphoma
    Andreas Rosenwald
    The Lymphoma Leukemia Molecular Profiling Project, National Cancer Institute NIH, Bethesda, MD, USA
    Cancer Cell 3:185-97. 2003
    ..We propose a quantitative model of the aberrant cell cycle regulation in MCL that provides a rationale for the design of cell cycle inhibitor therapy in this malignancy...
  72. doi request reprint Artificial intelligence methods for predicting T-cell epitopes
    Yingdong Zhao
    National Cancer Institute, National Institutes of Health, Rockville, MD, USA
    Methods Mol Biol 409:217-25. 2007
    ..For predicting T-cell epitopes for an MHC class II-restricted TCC, we built a shift model that integrated MHC-binding data and data from T-cell proliferation assay against a combinatorial library of peptide mixtures...
  73. ncbi request reprint Gene Set Expression Comparison kit for BRB-ArrayTools
    Xiaojiang Xu
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Bioinformatics 24:137-9. 2008
    ..AVAILABILITY: Gene Set Expression Comparison kit is freely available as a module of BRB-ArrayTools for non-commercial users. BRB-ArrayTools is available at http://linus.nci.nih.gov/BRB-ArrayTools.html...
  74. doi request reprint AACR-FDA-NCI Cancer Biomarkers Collaborative consensus report: advancing the use of biomarkers in cancer drug development
    Samir N Khleif
    National Cancer Institute, Raritan, New Jersey, USA
    Clin Cancer Res 16:3299-318. 2010
    ....
  75. doi request reprint Combining positional scanning peptide libraries, HLA-DR transfectants and bioinformatics to dissect the epitope spectrum of HLA class II cross-restricted CD4+ T cell clones
    Mireia Sospedra
    Cellular Immunology Section, Neuroimmunology Branch, NINDS, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Immunol Methods 353:93-101. 2010
    ..In contrast, the use of B cell lines expressing single HLA class II molecules as APCs instead of autologous peripheral blood mononuclear cells markedly improves the capacity to identify target peptides for this type of T cells...
  76. ncbi request reprint Distinguishing right from left colon by the pattern of gene expression
    Oleg K Glebov
    Genetics Branch, Center for Cancer Research, National Cancer Institute NCI, Bethesda, Maryland 20892, USA
    Cancer Epidemiol Biomarkers Prev 12:755-62. 2003
    ....
  77. doi request reprint What should physicians look for in evaluating prognostic gene-expression signatures?
    Jyothi Subramanian
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Nat Rev Clin Oncol 7:327-34. 2010
    ....
  78. ncbi request reprint Bayesian subset analysis: application to studying treatment-by-gender interactions
    Richard Simon
    National Cancer Institute, 6130 Executive Boulevard, Room 8134, Bethesda, MD 20892 7434, USA
    Stat Med 21:2909-16. 2002
    ..The methodology is applied to the problem of designing and analysing clinical trials to estimate treatment effects for males and females...
  79. ncbi request reprint Laser capture microdissection and microarray expression analysis of lung adenocarcinoma reveals tobacco smoking- and prognosis-related molecular profiles
    Koh Miura
    Laboratory of Human Carcinogenesis, Biometric Research Branch, Division of Cancer Treatment and Diagnosis National Cancer Institute, NIH, 37 Convent Drive, Bethesda, MD 20892, USA
    Cancer Res 62:3244-50. 2002
    ..g., hBUB3, hZW10, and APC2, contribute to the molecular pathogenesis and tumor progression of tobacco smoke-induced adenocarcinoma of the lung...
  80. ncbi request reprint Expansion and functional relevance of high-avidity myelin-specific CD4+ T cells in multiple sclerosis
    Bibiana Bielekova
    Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
    J Immunol 172:3893-904. 2004
    ..These data have important implications for autoimmunity research and should be considered in the development of Ag-specific therapies in MS...
  81. pmc Predicting survival in patients with metastatic kidney cancer by gene-expression profiling in the primary tumor
    James R Vasselli
    Urologic Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 100:6958-63. 2003
    ..We conclude that survival in patients with metastatic renal cell cancer can be correlated with the expression of various genes based solely on the expression profile in the primary kidney tumor...
  82. ncbi request reprint Comment on 'Evaluation of the gene-specific dye bias in cDNA microarray experiments'
    Kevin K Dobbin
    Bioinformatics 21:2803-4. 2005