statistical data interpretation

Summary

Summary: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.

Top Publications

  1. ncbi 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
  2. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
  3. ncbi Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's CT difference" formula
    Jan H Schefe
    Center for Cardiovascular Research CCR Institute of Pharmacology and Toxicology, Charite Universitatsmedizin Berlin, Hessische Strasse 3 4, 10115, Berlin, Germany
    J Mol Med (Berl) 84:901-10. 2006
  4. ncbi Patterns of intra-cluster correlation from primary care research to inform study design and analysis
    Geoffrey Adams
    Department of Public Health Sciences, King s College London, Capital House, 42 Weston Street, London SE1 3QD, UK
    J Clin Epidemiol 57:785-94. 2004
  5. ncbi Validating the independent components of neuroimaging time series via clustering and visualization
    Johan Himberg
    Neural Networks Research Centre, Helsinki University of Technology, Helsinki, Finland
    Neuroimage 22:1214-22. 2004
  6. ncbi ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
  7. ncbi 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
  8. ncbi Statistics in medicine--reporting of subgroup analyses in clinical trials
    Rui Wang
    N Engl J Med 357:2189-94. 2007
  9. pmc Metagenes and molecular pattern discovery using matrix factorization
    Jean Philippe Brunet
    The Eli and Edythe L Broad Institute, Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 101:4164-9. 2004
  10. pmc GoMiner: a resource for biological interpretation of genomic and proteomic data
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 4:R28. 2003

Detail Information

Publications299 found, 100 shown here

  1. ncbi 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...
  2. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
    ..We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities...
  3. ncbi Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's CT difference" formula
    Jan H Schefe
    Center for Cardiovascular Research CCR Institute of Pharmacology and Toxicology, Charite Universitatsmedizin Berlin, Hessische Strasse 3 4, 10115, Berlin, Germany
    J Mol Med (Berl) 84:901-10. 2006
    ..Additionally, this article offers some technical considerations and information on statistical analysis of real-time PCR data...
  4. ncbi Patterns of intra-cluster correlation from primary care research to inform study design and analysis
    Geoffrey Adams
    Department of Public Health Sciences, King s College London, Capital House, 42 Weston Street, London SE1 3QD, UK
    J Clin Epidemiol 57:785-94. 2004
    ..To provide information concerning the magnitude of the intraclass correlation coefficient (ICC) for cluster-based studies set in primary care...
  5. ncbi Validating the independent components of neuroimaging time series via clustering and visualization
    Johan Himberg
    Neural Networks Research Centre, Helsinki University of Technology, Helsinki, Finland
    Neuroimage 22:1214-22. 2004
    ..The method is implemented in a software package called Icasso...
  6. ncbi ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
    ..Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage...
  7. ncbi 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...
  8. ncbi Statistics in medicine--reporting of subgroup analyses in clinical trials
    Rui Wang
    N Engl J Med 357:2189-94. 2007
  9. pmc Metagenes and molecular pattern discovery using matrix factorization
    Jean Philippe Brunet
    The Eli and Edythe L Broad Institute, Massachusetts Institute of Technology and Harvard University, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 101:4164-9. 2004
    ..This ability, similar to semantic polysemy in text, provides a general method for robust molecular pattern discovery...
  10. pmc GoMiner: a resource for biological interpretation of genomic and proteomic data
    Barry R Zeeberg
    Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Biol 4:R28. 2003
    ..The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources...
  11. ncbi Subgroup analyses in randomised controlled trials: quantifying the risks of false-positives and false-negatives
    S T Brookes
    Department of Social Medicine, University of Bristol, UK
    Health Technol Assess 5:1-56. 2001
    ....
  12. pmc Detection of functional DNA motifs via statistical over-representation
    Martin C Frith
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:1372-81. 2004
    ..It also demonstrates superior performance over two contingency table based over-representation methods. In conclusion, Clover has the potential to greatly accelerate characterization of signals that regulate transcription...
  13. pmc WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Bing Zhang
    Graduate School in Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nucleic Acids Res 33:W741-8. 2005
    ..Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php...
  14. pmc Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    Matthew Stephens
    Department of Statistics, University of Washington, Seattle, WA 98195 4322, USA
    Am J Hum Genet 76:449-62. 2005
    ..Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site...
  15. ncbi Clustering by passing messages between data points
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Science 315:972-6. 2007
    ..Affinity propagation found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time...
  16. ncbi External validity of randomised controlled trials: "to whom do the results of this trial apply?"
    Peter M Rothwell
    Stroke Prevention Research Unit, University Department of Clinical Neurology, Radcliffe Infirmary, Oxford OX2 6HE, UK
    Lancet 365:82-93. 2005
    ..This review discusses those determinants, presents a checklist for clinicians, and makes recommendations for greater consideration of external validity in the design and reporting of RCTs...
  17. ncbi Time-series studies of particulate matter
    Michelle L Bell
    Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Annu Rev Public Health 25:247-80. 2004
    ....
  18. ncbi Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    Wolfgang Huber
    Department of Molecular Genome Analysis, German Cancer Research Center, INF 280, Heidelberg, 69120, Germany
    Bioinformatics 18:S96-104. 2002
    ..We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays...
  19. doi Inferring and validating horizontal gene transfer events using bipartition dissimilarity
    Alix Boc
    Departement d informatique, Universite du Quebec a Montreal, C P 8888, Succ Centre Ville, Montreal, Quebec, Canada
    Syst Biol 59:195-211. 2010
    ..Finally, a statistical framework for assessing the reliability of obtained HGTs by bootstrap analysis is also presented...
  20. doi Some methods of propensity-score matching had superior performance to others: results of an empirical investigation and Monte Carlo simulations
    Peter C Austin
    Institute for Clinical Evaluative Sciences, Toronto, ON, Canada
    Biom J 51:171-84. 2009
    ..2 of the standard deviation of the logit of the propensity score and the use of calipers of width 0.02 and 0.03 tended to have superior performance for estimating treatment effects...
  21. ncbi Enrichment or depletion of a GO category within a class of genes: which test?
    Isabelle Rivals
    Equipe de Statistique Appliquée, 10 rue Vauquelin, 75005 Paris, France
    Bioinformatics 23:401-7. 2007
    ..Whereas a correct formulation of the problem leads to a single exact null distribution, these GO tools use a large variety of statistical tests whose denominations often do not clarify the underlying P-value computations...
  22. ncbi Limitations of the odds ratio in gauging the performance of a diagnostic, prognostic, or screening marker
    Margaret Sullivan Pepe
    Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
    Am J Epidemiol 159:882-90. 2004
    ..In addition, the serious pitfalls of using more traditional methods based on parameters in logistic regression models are illustrated...
  23. ncbi Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach
    Miguel Perez-Enciso
    Station d Amélioration Génétique des Animaux, Institut National de la Recherche Agronomique, BP 27, 31326 Castanet Tolosan, France
    Hum Genet 112:581-92. 2003
    ..We conclude that PLS-DA is a powerful yet simple tool for analysing microarray data...
  24. ncbi Multiple imputation: a primer
    J L Schafer
    Department of Statistics, Pennsylvania State University, University Park 16802 6202, USA
    Stat Methods Med Res 8:3-15. 1999
    ..Essential features of multiple imputation are reviewed, with answers to frequently asked questions about using the method in practice...
  25. ncbi Localization of the event-related potential novelty response as defined by principal components analysis
    Joseph Dien
    Department of Psychology, University of Illinois, Urbana Champaign, IL, USA
    Brain Res Cogn Brain Res 17:637-50. 2003
    ..Source modeling on 129-channel data with BESA and BrainVoyager suggests the P300 has sources in the temporal-parietal junction whereas the Novelty P3 has sources in the anterior cingulate...
  26. ncbi A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes
    P Baldi
    Department of Information and Computer Science, University of California at Irvine, Irvine, CA 92697 3425, USA
    Bioinformatics 17:509-19. 2001
    ..Current methods are unsatisfactory due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data...
  27. ncbi The bootstrap: a technique for data-driven statistics. Using computer-intensive analyses to explore experimental data
    A Ralph Henderson
    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada N6A 5C1
    Clin Chim Acta 359:1-26. 2005
    ..Most of the published literature is concerned with the mathematical aspects of the bootstrap but increasingly this technique is being utilized in medical and other fields...
  28. ncbi A review and comparison of classification algorithms for medical decision making
    Paul R Harper
    School of Mathematics, University of Southampton, SO17 1BJ, Southampton, UK
    Health Policy 71:315-31. 2005
    ....
  29. ncbi Molecular taxonomy of major neuronal classes in the adult mouse forebrain
    Ken Sugino
    Department of Biology and National Center for Behavioral Genomics, Brandeis University, MS 008, 415 South Street, Waltham, Massachusetts 02454 9110, USA
    Nat Neurosci 9:99-107. 2006
    ..This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements...
  30. ncbi Diagnosis and exploration of massively univariate neuroimaging models
    Wen lin Luo
    Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
    Neuroimage 19:1014-32. 2003
    ..We apply our methods to a fMRI data set, demonstrating their ability to localize subtle artifacts and to discover systematic experimental variation not captured by the model...
  31. pmc Metrics for external model evaluation with an application to the population pharmacokinetics of gliclazide
    Karl Brendel
    INSERM U738, Paris, France
    Pharm Res 23:2036-49. 2006
    ..The aim of this study is to define and illustrate metrics for the external evaluation of a population model...
  32. ncbi Statistical issues in cDNA microarray data analysis
    Gordon K Smyth
    Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
    Methods Mol Biol 224:111-36. 2003
  33. pmc Incongruence between test statistics and P values in medical papers
    Emili García-Berthou
    Department of Environmental Sciences, University of Girona, E 17071 Girona, Spain
    BMC Med Res Methodol 4:13. 2004
    ..Given an observed test statistic and its degrees of freedom, one may compute the observed P value with most statistical packages. It is unknown to what extent test statistics and P values are congruent in published medical papers...
  34. pmc Theoretical uncertainty of measurements using quantitative polymerase chain reaction
    J Peccoud
    TIMC IMAG, Institut Albert Bonniot, Faculte de Medecine de Grenoble, La Tronche
    Biophys J 71:101-8. 1996
    ..The confidence interval amplitude is the theoretical uncertainty of measurements using quantitative PCR. We expect these results to be applicable to the data produced by the next generation of thermocyclers for quantitative applications...
  35. pmc Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome
    Mark Bieda
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Genome Res 16:595-605. 2006
    ....
  36. pmc Bias in random forest variable importance measures: illustrations, sources and a solution
    Carolin Strobl
    Institut für Statistik, Ludwig Maximilians Universitat Munchen, Ludwigstr, 33, 80539 Munchen, Germany
    BMC Bioinformatics 8:25. 2007
    ....
  37. pmc A statistical approach for array CGH data analysis
    Franck Picard
    Institut National Agronomique Paris Grignon, UMR INAPG ENGREF INRA MIA 518, Paris, France
    BMC Bioinformatics 6:27. 2005
    ..Two major problems arise: to determine which parameters are affected by the abrupt changes (the mean and the variance, or the mean only), and the selection of the number of segments in the profile...
  38. ncbi Rosetta error model for gene expression analysis
    Lee Weng
    Rosetta Inpharmatics LLC 401 Terry Avenue North, Seattle, WA 98109, USA
    Bioinformatics 22:1111-21. 2006
    ..The unreliable variance estimation is further complicated by the fact that the technology-specific variance is intrinsically intensity-dependent...
  39. ncbi What's the relative risk? A method of correcting the odds ratio in cohort studies of common outcomes
    J Zhang
    Division of Epidemiology, Statistics and Prevention Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892 7510, USA
    JAMA 280:1690-1. 1998
    ..We propose a simple method to approximate a risk ratio from the adjusted odds ratio and derive an estimate of an association or treatment effect that better represents the true relative risk...
  40. pmc Tilescope: online analysis pipeline for high-density tiling microarray data
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 8:R81. 2007
    ..The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis...
  41. pmc DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
    Mu Gao
    Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
    Nucleic Acids Res 36:3978-92. 2008
    ..DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/...
  42. ncbi Ipsilateral motor cortex activation on functional magnetic resonance imaging during unilateral hand movements is related to interhemispheric interactions
    Masahito Kobayashi
    Laboratory for Magnetic Brain Stimulation, Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
    Neuroimage 20:2259-70. 2003
    ..Instead, IpsiLM1 may reveal an enhanced interhemispheric inhibition from the right hemisphere upon the left to suppress superfluous, excessive activation...
  43. pmc DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, SAIC Frederick, Inc, National Cancer Institute at Frederick, MD 21702, USA
    Nucleic Acids Res 35:W169-75. 2007
    ..With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists...
  44. ncbi Feed forward neural networks for the analysis of censored survival data: a partial logistic regression approach
    E Biganzoli
    Divsione di Statistica Medica e Biometria, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milano, Italy
    Stat Med 17:1169-86. 1998
    ....
  45. ncbi Statistics in medical journals: some recent trends
    D G Altman
    ICRF Medical Statistics Group, Centre for Statistics in Medicine, Institute of Health Sciences, Old Road, Oxford OX3 7LF, UK
    Stat Med 19:3275-89. 2000
    ..I also consider developments in the reporting of research in medical journals...
  46. pmc The application of statistical physics to evolutionary biology
    Guy Sella
    Center for the Study of Rationality, Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
    Proc Natl Acad Sci U S A 102:9541-6. 2005
    ..Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift...
  47. ncbi Association between unreported outcomes and effect size estimates in Cochrane meta-analyses
    Toshi A Furukawa
    JAMA 297:468-70. 2007
  48. ncbi Microarray data normalization and transformation
    John Quackenbush
    The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
    Nat Genet 32:496-501. 2002
    ....
  49. ncbi Adjustments and measures of differential expression for microarray data
    A Tsodikov
    Huntsman Cancer Institute and Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112 5550, USA
    Bioinformatics 18:251-60. 2002
    ..Given a considerable diversity of data adjustment procedures, the question of their performance, comparison and ranking for various microarray experiments was of interest...
  50. pmc Identifying null meta-analyses that are ripe for updating
    Nicholas J Barrowman
    Chalmers Research Group, Children s Hospital of Eastern Ontario Research Institute, Ottawa, Canada
    BMC Med Res Methodol 3:13. 2003
    ..As an increasingly large number of meta-analyses are published, quantitative methods are needed to help clinicians and systematic review teams determine when meta-analyses are not up to date...
  51. ncbi A review of ordinal regression models applied on health-related quality of life assessments
    R Lall
    Institute of General Practice and Primary Care, University of Sheffield, Community Sciences Centre, Northern General Hospital, Herries Road, Sheffield S5 7AU, UK
    Stat Methods Med Res 11:49-67. 2002
    ..Different methods of generating scores yield data with different properties. It is now possible to fit a variety of ordinal regression models and so select the appropriate one that correctly models the data...
  52. pmc Why most published research findings are false
    John P A Ioannidis
    Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
    PLoS Med 2:e124. 2005
    ..In this essay, I discuss the implications of these problems for the conduct and interpretation of research...
  53. ncbi Research guidelines for the Delphi survey technique
    F Hasson
    Centre for Nursing Research, University of Ulster, Newtownabbey, Northern Ireland
    J Adv Nurs 32:1008-15. 2000
    ..The paper does not claim to be definitive; it purports to act as a guide for those researchers who wish to exploit the Delphi methodology...
  54. ncbi Codelink: an R package for analysis of GE healthcare gene expression bioarrays
    Diego Diez
    Instituto de Investigaciones Biomedicas Alberto Sols, Consejo Superior de Investigaciones Cientificas Universidad Autonoma de Madrid, Madrid, Spain
    Bioinformatics 23:1168-9. 2007
    ..Here, we report the availability of a package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays within the R environment...
  55. ncbi Analysis of data with excess zeros
    Peter A Lachenbruch
    FDA Center for Biologics Research and Review, Office of Biostatistics and Epidemiology, Rockville, MD, USA
    Stat Methods Med Res 11:297-302. 2002
    ..The second part of the paper summarizes results of a study of the size and power of two-part models. It proposes that two-part models are a useful alternative to the t-test and the Wilcoxon test...
  56. ncbi Biological profiling of gene groups utilizing Gene Ontology
    Nils Blüthgen
    Institute for Theoretical Biology, Humboldt University Berlin, Germany
    Genome Inform 16:106-15. 2005
    ..The software package GOSSIP implements our method and is made freely available at http://gossip.gene-groups.net/...
  57. ncbi Computational cluster validation in post-genomic data analysis
    Julia Handl
    School of Chemistry, University of Manchester, Faraday Building, Sackville Street, PO Box 88, Manchester M60 1QD, UK
    Bioinformatics 21:3201-12. 2005
    ..Suitable computational cluster validation techniques are available in the general data-mining literature, but have been given only a fraction of the same attention in bioinformatics...
  58. ncbi Exploring the demographic history of DNA sequences using the generalized skyline plot
    K Strimmer
    Department of Zoology, University of Oxford
    Mol Biol Evol 18:2298-305. 2001
    ..We investigate the performance of our approach using simulation and subsequently apply it to HIV-1 sequences from central Africa and mtDNA sequences from red pandas...
  59. ncbi SVDMAN--singular value decomposition analysis of microarray data
    M E Wall
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Bioinformatics 17:566-8. 2001
    ....
  60. ncbi Protein function in the post-genomic era
    D Eisenberg
    Molecular Biology Institute and UCLA DOE Laboratory of Structural Biology and Molecular Medicine, University of California at Los Angeles, 90095 1570, USA
    Nature 405:823-6. 2000
    ....
  61. ncbi Statistical evaluation of learning curve effects in surgical trials
    Jonathan A Cook
    Health Services Research Unit, University of Aberdeen, Foresterhill, UK
    Clin Trials 1:421-7. 2004
    ..Bayesian hierarchical models are proposed to adjust the trial results for the existence of a learning curve effect. The implications for trial evaluation and data collection are considered...
  62. pmc Funnel plots for institutional comparison
    D Spiegelhalter
    Qual Saf Health Care 11:390-1. 2002
  63. pmc Boolean networks using the chi-square test for inferring large-scale gene regulatory networks
    Haseong Kim
    Interdisciplinary Program in Bioinformatics, Seoul National University, South Korea
    BMC Bioinformatics 8:37. 2007
    ..We propose a variable selection method that are not only reduces BN computation times significantly but also obtains optimal network constructions by using chi-square statistics for testing the independence in contingency tables...
  64. ncbi Analyzing gene expression data in terms of gene sets: methodological issues
    Jelle J Goeman
    Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Bioinformatics 23:980-7. 2007
    ..This article aims to clarify the assumptions behind different approaches and to indicate a preferential methodology of gene set testing...
  65. ncbi Advances in flux balance analysis
    Kenneth J Kauffman
    University of Delaware, Department of Chemical Engineering, Newark, DE 19716, USA
    Curr Opin Biotechnol 14:491-6. 2003
    ..Recent advances have been made in the area of flux balance analysis, a mathematical modeling approach often utilized by metabolic engineers to quantitatively simulate microbial metabolism...
  66. pmc EXPANDER--an integrative program suite for microarray data analysis
    Ron Shamir
    School of Computer Science, Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Bioinformatics 6:232. 2005
    ..Of special need are integrative packages that provide biologist users with advanced but yet easy to use, set of algorithms, together covering the whole range of steps in microarray data analysis...
  67. ncbi Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
    Thomas P Wilcox
    Section of Integrative Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
    Mol Phylogenet Evol 25:361-71. 2002
    ..Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study...
  68. ncbi Modelling covariance structure in the analysis of repeated measures data
    R C Littell
    Department of Statistics, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA
    Stat Med 19:1793-819. 2000
    ..In many situations, estimates of linear combinations are invariant with respect to covariance structure, yet standard errors of the estimates may still depend on the covariance structure...
  69. ncbi The investigation of functional brain lateralization by transcranial Doppler sonography
    Michael Deppe
    Department of Neurology, University of Munster, D 48129 Munster, Germany
    Neuroimage 21:1124-46. 2004
    ....
  70. ncbi Assessing heterogeneity in meta-analysis: Q statistic or I2 index?
    Tania B Huedo-Medina
    Department of Basic Psychology and Methodology, University of Murcia, Murcia, Spain
    Psychol Methods 11:193-206. 2006
    ..The results show the utility of the I(2) index as a complement to the Q test, although it has the same problems of power with a small number of studies...
  71. pmc Meta-DiSc: a software for meta-analysis of test accuracy data
    Javier Zamora
    Clinical Biostatistics Unit, Ramon y Cajal Hospital, Spain
    BMC Med Res Methodol 6:31. 2006
    ..In this article, we present Meta-DiSc, a Windows-based, user-friendly, freely available (for academic use) software that we have developed, piloted, and validated to perform diagnostic meta-analysis...
  72. pmc Issues in using progression-free survival when evaluating oncology products
    Thomas R Fleming
    Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195 7232, USA
    J Clin Oncol 27:2874-80. 2009
    ....
  73. ncbi Structural asymmetries in the human brain: a voxel-based statistical analysis of 142 MRI scans
    K E Watkins
    Cognitive Neuroscience Unit, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
    Cereb Cortex 11:868-77. 2001
    ..The above asymmetries were observed in men and women. Our results thus provide confirmation of the known structural asymmetries in the human brain as well as new findings that may stimulate further research of hemispheric specialization...
  74. pmc The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
    Da Wei Huang
    Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    Genome Biol 8:R183. 2007
    ..It is a powerful method to group functionally related genes and terms into a manageable number of biological modules for efficient interpretation of gene lists in a network context...
  75. pmc Informativeness of genetic markers for inference of ancestry
    Noah A Rosenberg
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
    Am J Hum Genet 73:1402-22. 2003
    ..Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry...
  76. ncbi Transforming self-rated health and the SF-36 scales to include death and improve interpretability
    P Diehr
    Department of Biostatistics, University of Washington, Seattle, Washington 98195-7232, USA
    Med Care 39:670-80. 2001
    ..Using the transformed variables for longitudinal analyses of health when deaths occur, either for secondary or primary analysis, is recommended. This approach can be applied to other measures of health...
  77. doi A comparison of methods for estimating the causal effect of a treatment in randomized clinical trials subject to noncompliance
    Roderick J Little
    Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Biometrics 65:640-9. 2009
    ..Methods are illustrated on data from the Women Take Pride study, an assessment of behavioral treatments for women with heart disease...
  78. ncbi Outlier sums for differential gene expression analysis
    Robert Tibshirani
    Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA
    Biostatistics 8:2-8. 2007
    ..We also compare our approach to the recent cancer profile outlier analysis proposal of Tomlins and others (2005)...
  79. ncbi Missing data in Likert ratings: A comparison of replacement methods
    R G Downey
    Institutional Research andAnalysis, 226 Anderson Hall, Kansas State University, Manhattan66506
    J Gen Psychol 125:175-91. 1998
    ..The item mean substitution reduced the reliability estimates of the scale. These results suggest caution in the use of the person mean substitution method as the numbers of missing items and respondents increase...
  80. pmc Post-randomisation exclusions: the intention to treat principle and excluding patients from analysis
    Dean Fergusson
    Ottawa Health Research Institute, 501 Smyth Road, Box 201, Ottawa, ON, Canada K1H 8L6
    BMJ 325:652-4. 2002
  81. ncbi Regression to the mean: what it is and how to deal with it
    Adrian G Barnett
    School of Population Health, The University of Queensland, Herston, Brisbane, QLD 4006, Australia
    Int J Epidemiol 34:215-20. 2005
    ..It happens when unusually large or small measurements tend to be followed by measurements that are closer to the mean...
  82. pmc Imputation of missing data when measuring physical activity by accelerometry
    Diane J Catellier
    Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27514 4145, USA
    Med Sci Sports Exerc 37:S555-62. 2005
    ..The fact that counts are not being recorded during periods in which the monitor is not worn means that many common estimators of daily physical activity are biased downward...
  83. ncbi A general approach to single-nucleotide polymorphism discovery
    G T Marth
    Washington University Department of Genetics and Genome Sequencing Center, St Louis, Missouri, USA
    Nat Genet 23:452-6. 1999
    ..We demonstrate this approach by accurate SNP predictions in human ESTs aligned to finished and working-draft quality genomic sequences, a data set representative of the typical challenges of sequence-based SNP discovery...
  84. ncbi Comparisons of two-part models with competitors
    P A Lachenbruch
    FDA CBER Division of Biostatistics and Epidemiology, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852 1448, USA
    Stat Med 20:1215-34. 2001
    ..In those cases, the two-part models are not far behind, although statistically significantly poorer with respect to power. Published in 2001 by John Wiley & Sons, Ltd...
  85. ncbi People are variables too: multilevel structural equations modeling
    Paras D Mehta
    Department of Psychology, Texas Institute for Measurement Evaluation and Statistics, University of Houston, Houston, TX 77204 5022, USA
    Psychol Methods 10:259-84. 2005
    ..Methodological issues regarding estimation of complex ML-SEMs and the evaluation of model fit are discussed. Further potential applications of ML-SEMs are explored...
  86. ncbi Bivariate analysis of sensitivity and specificity produces informative summary measures in diagnostic reviews
    Johannes B Reitsma
    Department of Clinical Epidemiology and Biostatistics, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam, The Netherlands
    J Clin Epidemiol 58:982-90. 2005
    ..Studies of diagnostic accuracy most often report pairs of sensitivity and specificity. We demonstrate the advantage of using bivariate meta-regression models to analyze such data...
  87. ncbi Missing data, incomplete taxa, and phylogenetic accuracy
    John J Wiens
    Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794 5245, USA
    Syst Biol 52:528-38. 2003
    ....
  88. doi Motor learning transiently changes cortical somatotopy
    Katiuska Molina-Luna
    Department of General Neurology, Hertie Institute for Clinical Brain Research, University of Tubingen, Hoppe Seyler Str 3, 72076 Tubingen, Germany
    Neuroimage 40:1748-54. 2008
    ..The motor memory trace in rats may require changes in motor cortex organization other than those detected by stimulation mapping...
  89. ncbi Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches
    Adam D Leaché
    Department of Biology, San Diego State University, San Diego, California 92182 4614, USA
    Syst Biol 51:44-68. 2002
    ..This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species...
  90. ncbi Allowing for imprecision of the intracluster correlation coefficient in the design of cluster randomized trials
    Rebecca M Turner
    MRC Biostatistics Unit, Institute of Public Health, Robinson Way, Cambridge CB2 2SR, U K
    Stat Med 23:1195-214. 2004
    ..The methods presented in this paper can be used by applied researchers to protect against loss of power, or to choose a design which reduces the impact of uncertainty in the ICC...
  91. doi Bioinformatics applications for pathway analysis of microarray data
    Thomas Werner
    Genomatix Software GmbH, Bayerstr 85A, D 80335 München, Germany
    Curr Opin Biotechnol 19:50-4. 2008
    ..A brief outlook of the application of such approaches to the newest microarray-based technologies (Chromatin-ImmunoPrecipitation, ChIP-on-chip) concludes the review...
  92. doi A substantial and confusing variation exists in handling of baseline covariates in randomized controlled trials: a review of trials published in leading medical journals
    Peter C Austin
    Institute for Clinical Evaluative Sciences, G1 06, 2075 Bayview Avenue, Toronto, Ontario M4N 3M5, Canada
    J Clin Epidemiol 63:142-53. 2010
    ..Furthermore, some have advocated for the use of regression adjustment to estimate the effect of treatment after adjusting for potential imbalances in prognostically important baseline covariates between treatment groups...
  93. ncbi Imputation strategies for missing data in a school-based multi-centre study: the Pathways study
    S Hunsberger
    National Cancer Institute, Executive Plaza North, Rm 739, 6130 Executive Boulevard, Bethesda, MD 20892, USA
    Stat Med 20:305-16. 2001
    ..The results from our simulation study showed that, for missing data patterns that are relevant to the Pathways study, this procedure has high power and maintains the type I error rate. Published in 2001 by John Wiley & Sons, Ltd...
  94. ncbi Adjusting for multiple testing--when and how?
    R Bender
    Institute of Epidemiology and Medical Statistics, School of Public Health, University of Bielefeld, Germany
    J Clin Epidemiol 54:343-9. 2001
    ..In case of multiple significance tests a note on the error rate that will be controlled for is desirable...
  95. pmc Statistical analysis of real-time PCR data
    Joshua S Yuan
    Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
    BMC Bioinformatics 7:85. 2006
    ..Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data...
  96. ncbi Trend tests for case-control studies of genetic markers: power, sample size and robustness
    B Freidlin
    Biometric Research Branch, National Cancer Institute, Rockville, MD 20892, USA
    Hum Hered 53:146-52. 2002
    ..Simulation results of the robustness of these two tests indicate that the more computationally involved MAX test is preferable...
  97. doi RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens
    Nora Rieber
    Viroquant Research Group Modeling, University of Heidelberg, Bioquant BQ26, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
    Bioinformatics 25:678-9. 2009
    ..The results of the analysis are presented as a set of HTML pages. Additionally, all values and plots are available as either text files or pdf and png files...
  98. 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...
  99. doi A computational platform for MALDI-TOF mass spectrometry data: application to serum and plasma samples
    Dante Mantini
    Istituto Tecnologie Avanzate Biomediche ITAB, Fondazione G D Annunzio, Chieti, Italy
    J Proteomics 73:562-70. 2010
    ..In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data...
  100. ncbi Classification of microarrays to nearest centroids
    Alan R Dabney
    Department of Biostatistics, University of Washington, Seattle, 98195, USA
    Bioinformatics 21:4148-54. 2005
    ..In this spirit, I seek to assess the performance of classifiers simpler than even PAM...
  101. doi Commentary: Heterogeneity in meta-analysis should be expected and appropriately quantified
    Julian P T Higgins
    MRC Biostatistics Unit, Institute of Public Health, Robinson Way, Cambridge CB2 0SR, UK
    Int J Epidemiol 37:1158-60. 2008

Research Grants69

  1. Core--Informatics, Biostatistics and data management
    Jeffrey Trent; Fiscal Year: 2005
    ..In summary, this Core will provide the bioinformatics that will be crucial to the success of Projects 2 and 3, and will provide statistical support in terms of experimental design and data analysis for all Consortium members...
  2. The Effect of Exercise on Progression of Knee OA
    ANDREW CONCOFF; Fiscal Year: 2003
    ..Eventually, optimal exercise regimens will be sought for both primary and secondary prevention of OA at various joints and stages. ..
  3. Pro-Inflammatory HDL as a Novel Target for the Indentification of Atherosclerosis
    Maureen McMahon; Fiscal Year: 2007
    ..Targeting PiHDL with interventions that restore protective function to HDL might be considered for prevention of ATH in both lupus and non lupus patients. ..
  4. LONG QT SYNDROME--POPULATION, GENETIC & CARDIAC STUDIES
    Arthur Moss; Fiscal Year: 2002
    ..This integrated research program is intended to: 1) improve the presymptomatic diagnosis and treatment of LQTS; and 2) provide a fundamental understanding of the molecular basis of repolarization-related cardiac arrhythmias. ..
  5. Mild Cognitive Impairment: Cerebrovascular Dysfunction and Exercise Training
    RONG contact ZHANG; Fiscal Year: 2010
    ..The new knowledge will have significant impact on prevention or treatment of AD. ..
  6. Mentored Patient-Oriented Research Career Development Aw
    James Stein; Fiscal Year: 2005
    ..Finally, Dr. Stein will determine if these medications impair postprandial clearance of triglyceride-containing lipoproteins by assessing lipid and lipoprotein responses to an oral fat load. ..
  7. HEALTH RESEARCH TRAINING PROGRAM
    Genevieve Ames; Fiscal Year: 2002
    ....
  8. Quality Threshold Analysis of Prostate Cancers
    Carlos Moreno; Fiscal Year: 2004
    ..Identification of genetic profiles associated with prostatic neoplasias that are more likely to result in aggressive disease may lead to improved management of prostate cancer patients. ..
  9. The Neurobiological Basis of Prodromal States and Psychosis in Adolescence
    Melita Daley; Fiscal Year: 2007
    ....
  10. BIODEMOGRAPHIC ANALYSIS OF AGING TRAJECTORIES
    Shiro Horiuchi; Fiscal Year: 2002
    ....
  11. Heart Failure Clinical Research Network - DCC
    Kerry Lee; Fiscal Year: 2007
    ..End of Abstract) ..
  12. STRUCTURE, PROCESS AND OUTCOMES IN THE PACE PROGRAM
    Dana Mukamel; Fiscal Year: 2003
    ..The knowledge gained from this study would have direct bearing on efforts to improve care in PACE programs, as well as implications for other programs serving frail, non-institutionalized elderly. ..
  13. Biometrical Modeling of Fertility Using the NLSY
    JOSEPH RODGERS; Fiscal Year: 2006
    ..Potential moderators/mediators include education, family structure, and quality of the family environment. ..