Richard Simon

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. doi request reprint Using single cell sequencing data to model the evolutionary history of a tumor
    Kyung In Kim
    Biometric Research Branch, National Cancer Institute, 9609 Medical Center Dr, MSC 9735 Bethesda, MD 20892, USA
    BMC Bioinformatics 15:27. 2014
  7. doi request reprint Using passenger mutations to estimate the timing of driver mutations and identify mutator alterations
    Ahrim Youn
    Biometric Research Branch, National Cancer Institute, Bethesda, Maryland, USA
    BMC Bioinformatics 14:363. 2013
  8. pmc Optimally splitting cases for training and testing high dimensional classifiers
    Kevin K Dobbin
    Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA
    BMC Med Genomics 4:31. 2011
  9. 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
  10. 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

Detail Information

Publications97

  1. 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...
  2. 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
    ....
  3. 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...
  4. 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...
  5. 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...
  6. doi request reprint Using single cell sequencing data to model the evolutionary history of a tumor
    Kyung In Kim
    Biometric Research Branch, National Cancer Institute, 9609 Medical Center Dr, MSC 9735 Bethesda, MD 20892, USA
    BMC Bioinformatics 15:27. 2014
    ..This may facilitate understanding how key mutations accumulate and evolve in lineages to form a heterogeneous tumor...
  7. doi request reprint Using passenger mutations to estimate the timing of driver mutations and identify mutator alterations
    Ahrim Youn
    Biometric Research Branch, National Cancer Institute, Bethesda, Maryland, USA
    BMC Bioinformatics 14:363. 2013
    ..Although most research efforts are focused on analyzing driver alterations, the passenger alterations also provide valuable information about the history of tumor development...
  8. pmc Optimally splitting cases for training and testing high dimensional classifiers
    Kevin K Dobbin
    Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA
    BMC Med Genomics 4:31. 2011
    ..In this paper we address the question of what proportion of the samples should be devoted to the training set. How does this proportion impact the mean squared error (MSE) of the prediction accuracy estimate?..
  9. 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...
  10. 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
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. ncbi request reprint Prediction error estimation: a comparison of resampling methods
    Annette M Molinaro
    Biostatistics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, MD 20852, USA
    Bioinformatics 21:3301-7. 2005
    ..With a focus on prediction assessment, we compare several methods for estimating the 'true' prediction error of a prediction model in the presence of feature selection...
  21. 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
    ....
  22. 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
  23. pmc Estimating the order of mutations during tumorigenesis from tumor genome sequencing data
    Ahrim Youn
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892 7434, USA
    Bioinformatics 28:1555-61. 2012
    ..This method does not assume that the sequence of driver alterations is the same for each tumor, but enables the degree of similarity or difference in the sequence to be evaluated...
  24. doi request reprint A two-stage Bayesian design for co-development of new drugs and companion diagnostics
    Stella Wanjugu Karuri
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Stat Med 31:901-14. 2012
    ....
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  31. doi request reprint An evaluation of resampling methods for assessment of survival risk prediction in high-dimensional settings
    Jyothi Subramanian
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892 7434, USA
    Stat Med 30:642-53. 2011
    ..A k-fold cross-validation with k = 5 or 10 was seen to provide a good balance between bias and variability for a wide range of data settings and should be more widely adopted in practice...
  32. 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
  33. 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...
  34. pmc Probabilistic classifiers with high-dimensional data
    Kyung In Kim
    Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892 7434, USA
    Biostatistics 12:399-412. 2011
    ..We also present a cross-validation method for evaluating the calibration and refinement of any probabilistic classifier on any data set...
  35. pmc Run-in phase III trial design with pharmacodynamics predictive biomarkers
    Fangxin Hong
    Affiliations of authors Departments of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA FH Biometric Research Branch, National Cancer Institute, Bethesda, MD RS
    J Natl Cancer Inst 105:1628-33. 2013
    ..In many cases, it has been very difficult to identify such biomarkers. Promising candidate biomarkers can sometimes be effectively measured after a short run-in period on the new treatment...
  36. doi request reprint Implementing personalized cancer genomics in clinical trials
    Richard Simon
    Biometric Research Branch, US National Cancer Institute, Bethesda, Maryland 20892 7434, USA
    Nat Rev Drug Discov 12:358-69. 2013
    ....
  37. 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...
  38. pmc Microarray-based cancer prediction using single genes
    Xiaosheng Wang
    Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, MD 20852, USA
    BMC Bioinformatics 12:391. 2011
    ..We first identified the genes with the most powerful univariate class discrimination ability and then constructed simple classification rules for class prediction using the single genes...
  39. 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...
  40. 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...
  41. 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
    ..Using this module of BRB-ArrayTools, researchers can efficiently analyze pre-defined sets of gene whose expression is correlated with a categorical quantitative phenotype or patient survival...
  42. 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...
  43. 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...
  44. pmc Identifying cancer driver genes in tumor genome sequencing studies
    Ahrim Youn
    Biometric Research Branch, National Cancer Institute, Bethesda, MD 20892 7434, USA
    Bioinformatics 27:175-81. 2011
    ..Several methods have been used for estimating the background mutation rate...
  45. 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...
  46. 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
    ....
  47. 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...
  48. 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...
  49. 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...
  50. pmc Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
    Jeff Skinner
    Bioinformatics and Computational Biosciences Branch BCBB, Office of Cyber Infrastructure and Computational Biology OCICB, National Institute of Allergy and Infectious Disease NIAID, National Institutes if Health NIH, Bethesda, Maryland, USA
    BMC Bioinformatics 12:286. 2011
    ..DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes...
  51. 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...
  52. 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
    ....
  53. 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...
  54. 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...
  55. 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...
  56. 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...
  57. pmc Redundancy in antigen-presenting function of the HLA-DR and -DQ molecules in the multiple sclerosis-associated HLA-DR2 haplotype
    Mireia Sospedra
    Cellular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
    J Immunol 176:1951-61. 2006
    ..A T cell signaling machinery tuned for efficient responses to weak ligands together with structural features of the TCR-HLA/peptide complex result in this promiscuous HLA class II restriction...
  58. 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...
  59. 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...
  60. 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...
  61. 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...
  62. 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...
  63. 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...
  64. 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
    ....
  65. 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...
  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. 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...
  68. 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
    ....
  69. pmc Cediranib for metastatic alveolar soft part sarcoma
    Shivaani Kummar
    National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    J Clin Oncol 31:2296-302. 2013
    ..Cediranib is a potent, oral small-molecule inhibitor of all three vascular endothelial growth factor receptors (VEGFRs)...
  70. pmc IRF5 gene polymorphisms in melanoma
    Lorenzo Uccellini
    Infectious Disease and Immunogenetics Section, Department of Transfusion Medicine, Clinical Center and trans NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
    J Transl Med 10:170. 2012
    ....
  71. 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
  72. 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
    ....
  73. 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
    ....
  74. 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...
  75. doi request reprint Stable disease is not preferentially observed with targeted therapies and as currently defined has limited value in drug development
    Tatiana Vidaurre
    Medical Oncology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Cancer J 15:366-73. 2009
    ..Studies that use SD as an end point require an adequate control to distinguish antitumor activity from normal variability in time to progression...
  76. 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...
  77. 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
  78. 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
    ....
  79. 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
  80. 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...
  81. 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...
  82. ncbi request reprint PSA velocity and prostate cancer
    Lori E Dodd
    N Engl J Med 351:1800-2; author reply 1800-2. 2004
  83. ncbi request reprint Positional scanning-synthetic peptide library-based analysis of self- and pathogen-derived peptide cross-reactivity with tumor-reactive Melan-A-specific CTL
    Verena Rubio-Godoy
    Division of Clinical Onco Immunology, Ludwig Institute for Cancer Research, Lausanne Branch, University Hospital, Lausanne, Switzerland
    J Immunol 169:5696-707. 2002
    ..Together, these results underline the high predictive value of PS-SCL for the identification of sequences cross-recognized by Ag-specific T cells...
  84. doi request reprint Calculating confidence intervals for prediction error in microarray classification using resampling
    Wenyu Jiang
    Concordia University, Quebec, Canada
    Stat Appl Genet Mol Biol 7:Article8. 2008
    ..The method provides mildly conservative inference under all circumstances studied and outperforms the other methods in microarray applications with small to moderate sample sizes...
  85. ncbi request reprint Development and evaluation of therapeutically relevant predictive classifiers using gene expression profiling
    Richard Simon
    J Natl Cancer Inst 98:1169-71. 2006
  86. ncbi request reprint Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data
    Lara Lusa
    Department of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milano, Italy
    Stat Med 26:1102-13. 2007
    ..Our results suggest that caution should be exercised in interpreting some of the claims of exceptional prognostic classifier performance that have been reported in prominent biomedical journals in the past few years...
  87. ncbi request reprint Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning
    Qing Hai Ye
    Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China
    Nat Med 9:416-23. 2003
    ..Thus, osteopontin acts as both a diagnostic marker and a potential therapeutic target for metastatic HCC...
  88. ncbi request reprint Aneuploidy-dependent massive deregulation of the cellular transcriptome and apparent divergence of the Wnt/beta-catenin signaling pathway in human rectal carcinomas
    Marian Grade
    Department of General Surgery, University Medical Center, Gottingen, Germany
    Cancer Res 66:267-82. 2006
    ....
  89. ncbi request reprint Bioinformatics in cancer therapeutics--hype or hope?
    Richard Simon
    Nat Clin Pract Oncol 2:223. 2005
  90. pmc Diffuse large B-cell lymphoma subgroups have distinct genetic profiles that influence tumor biology and improve gene-expression-based survival prediction
    Silvia Bea
    Department of Pathology and Hematology Hospital Clinic, University of Barcelona, Spain
    Blood 106:3183-90. 2005
    ..In addition, gains involving the chromosomal region 3p11-p12 provided prognostic information that was statistically independent of the previously defined gene-expression-based survival model, thereby improving its predictive power...
  91. ncbi request reprint The feasibility of using fine needle aspiration from primary breast cancers for cDNA microarray analyses
    Laura Assersohn
    Royal Marsden Hospital, Surrey SM2 5PT, United Kingdom
    Clin Cancer Res 8:794-801. 2002
    ....
  92. 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...
  93. ncbi request reprint Development and validation of therapeutically relevant multi-gene biomarker classifiers
    Richard Simon
    J Natl Cancer Inst 97:866-7. 2005
  94. ncbi request reprint Toward synthetic combinatorial peptide libraries in positional scanning format (PS-SCL)-based identification of CD8+ Tumor-reactive T-Cell Ligands: a comparative analysis of PS-SCL recognition by a single tumor-reactive CD8+ cytolytic T-lymphocyte clone
    Verena Rubio-Godoy
    Division of Clinical Onco Immunology, Ludwig Institute for Cancer Research, University Hospital CHUV, 1011 Lausanne, Switzerland
    Cancer Res 62:2058-63. 2002
    ..Altogether these results provide insight into the potential of PS-SCL for the identification of CTL-defined tumor-derived antigenic sequences and may significantly implement our ability to interpret the results of these analyses...
  95. ncbi request reprint Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas
    Marian Grade
    Department of General Surgery, University Medical Center, Robert Koch Strasse 40, 37075 Gottingen, Germany
    Cancer Res 67:41-56. 2007
    ....
  96. ncbi request reprint Novel trial designs for novel agents. Interview by Helen Saul
    Richard Simon
    Eur J Cancer 44:170-1. 2008
  97. ncbi request reprint Targets for treatment success
    Richard Simon
    Nat Clin Pract Oncol 3:1. 2006