Genomes and Genes
statistical data interpretation
Summary: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
Publications299 found, 100 shown here
- Prediction error estimation: a comparison of resampling methodsAnnette 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...
- Exploration, normalization, and summaries of high density oligonucleotide array probe level dataRafael 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...
- Quantitative real-time RT-PCR data analysis: current concepts and the novel "gene expression's CT difference" formulaJan 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...
- Patterns of intra-cluster correlation from primary care research to inform study design and analysisGeoffrey 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...
- Validating the independent components of neuroimaging time series via clustering and visualizationJohan 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...
- ROCR: visualizing classifier performance in RTobias 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...
- Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reportingAlain 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...
- Statistics in medicine--reporting of subgroup analyses in clinical trialsRui Wang
N Engl J Med 357:2189-94. 2007
- Metagenes and molecular pattern discovery using matrix factorizationJean 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...
- GoMiner: a resource for biological interpretation of genomic and proteomic dataBarry 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...
- Subgroup analyses in randomised controlled trials: quantifying the risks of false-positives and false-negativesS T Brookes
Department of Social Medicine, University of Bristol, UK
Health Technol Assess 5:1-56. 2001....
- Detection of functional DNA motifs via statistical over-representationMartin 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...
- WebGestalt: an integrated system for exploring gene sets in various biological contextsBing 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...
- Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputationMatthew 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...
- Clustering by passing messages between data pointsBrendan 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...
- 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...
- Time-series studies of particulate matterMichelle L Bell
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
Annu Rev Public Health 25:247-80. 2004....
- Variance stabilization applied to microarray data calibration and to the quantification of differential expressionWolfgang 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...
- Inferring and validating horizontal gene transfer events using bipartition dissimilarityAlix 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...
- Some methods of propensity-score matching had superior performance to others: results of an empirical investigation and Monte Carlo simulationsPeter 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...
- 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...
- Limitations of the odds ratio in gauging the performance of a diagnostic, prognostic, or screening markerMargaret 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...
- Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approachMiguel 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...
- Multiple imputation: a primerJ 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...
- Localization of the event-related potential novelty response as defined by principal components analysisJoseph 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...
- A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changesP 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...
- The bootstrap: a technique for data-driven statistics. Using computer-intensive analyses to explore experimental dataA 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...
- A review and comparison of classification algorithms for medical decision makingPaul R Harper
School of Mathematics, University of Southampton, SO17 1BJ, Southampton, UK
Health Policy 71:315-31. 2005....
- Molecular taxonomy of major neuronal classes in the adult mouse forebrainKen 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...
- Diagnosis and exploration of massively univariate neuroimaging modelsWen 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...
- Metrics for external model evaluation with an application to the population pharmacokinetics of gliclazideKarl 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...
- Statistical issues in cDNA microarray data analysisGordon K Smyth
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Methods Mol Biol 224:111-36. 2003
- Incongruence between test statistics and P values in medical papersEmili 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...
- Theoretical uncertainty of measurements using quantitative polymerase chain reactionJ 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...
- Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genomeMark Bieda
Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
Genome Res 16:595-605. 2006....
- Bias in random forest variable importance measures: illustrations, sources and a solutionCarolin Strobl
Institut für Statistik, Ludwig Maximilians Universitat Munchen, Ludwigstr, 33, 80539 Munchen, Germany
BMC Bioinformatics 8:25. 2007....
- A statistical approach for array CGH data analysisFranck 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...
- Rosetta error model for gene expression analysisLee 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...
- What's the relative risk? A method of correcting the odds ratio in cohort studies of common outcomesJ 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...
- Tilescope: online analysis pipeline for high-density tiling microarray dataZhengdong 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...
- DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactionsMu 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/...
- Ipsilateral motor cortex activation on functional magnetic resonance imaging during unilateral hand movements is related to interhemispheric interactionsMasahito 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...
- DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene listsDa 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...
- Feed forward neural networks for the analysis of censored survival data: a partial logistic regression approachE 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....
- Statistics in medical journals: some recent trendsD 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...
- The application of statistical physics to evolutionary biologyGuy 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...
- Association between unreported outcomes and effect size estimates in Cochrane meta-analysesToshi A Furukawa
JAMA 297:468-70. 2007
- Microarray data normalization and transformationJohn Quackenbush
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
Nat Genet 32:496-501. 2002....
- Adjustments and measures of differential expression for microarray dataA 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...
- Identifying null meta-analyses that are ripe for updatingNicholas 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...
- A review of ordinal regression models applied on health-related quality of life assessmentsR 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...
- Why most published research findings are falseJohn 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...
- Research guidelines for the Delphi survey techniqueF 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...
- Codelink: an R package for analysis of GE healthcare gene expression bioarraysDiego 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...
- Analysis of data with excess zerosPeter 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...
- Biological profiling of gene groups utilizing Gene OntologyNils 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/...
- Computational cluster validation in post-genomic data analysisJulia 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...
- Exploring the demographic history of DNA sequences using the generalized skyline plotK 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...
- SVDMAN--singular value decomposition analysis of microarray dataM E Wall
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Bioinformatics 17:566-8. 2001....
- Protein function in the post-genomic eraD 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....
- Statistical evaluation of learning curve effects in surgical trialsJonathan 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...
- Funnel plots for institutional comparisonD Spiegelhalter
Qual Saf Health Care 11:390-1. 2002
- Boolean networks using the chi-square test for inferring large-scale gene regulatory networksHaseong 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...
- Analyzing gene expression data in terms of gene sets: methodological issuesJelle 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...
- Advances in flux balance analysisKenneth 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...
- EXPANDER--an integrative program suite for microarray data analysisRon 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...
- Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic supportThomas 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...
- Modelling covariance structure in the analysis of repeated measures dataR 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...
- The investigation of functional brain lateralization by transcranial Doppler sonographyMichael Deppe
Department of Neurology, University of Munster, D 48129 Munster, Germany
Neuroimage 21:1124-46. 2004....
- 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...
- Meta-DiSc: a software for meta-analysis of test accuracy dataJavier 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...
- Issues in using progression-free survival when evaluating oncology productsThomas R Fleming
Department of Biostatistics, University of Washington, Box 357232, Seattle, WA 98195 7232, USA
J Clin Oncol 27:2874-80. 2009....
- Structural asymmetries in the human brain: a voxel-based statistical analysis of 142 MRI scansK 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...
- The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene listsDa 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...
- Informativeness of genetic markers for inference of ancestryNoah 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...
- Transforming self-rated health and the SF-36 scales to include death and improve interpretabilityP 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...
- A comparison of methods for estimating the causal effect of a treatment in randomized clinical trials subject to noncomplianceRoderick 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...
- Outlier sums for differential gene expression analysisRobert 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)...
- Missing data in Likert ratings: A comparison of replacement methodsR 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...
- Post-randomisation exclusions: the intention to treat principle and excluding patients from analysisDean Fergusson
Ottawa Health Research Institute, 501 Smyth Road, Box 201, Ottawa, ON, Canada K1H 8L6
BMJ 325:652-4. 2002
- Regression to the mean: what it is and how to deal with itAdrian 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...
- Imputation of missing data when measuring physical activity by accelerometryDiane 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...
- A general approach to single-nucleotide polymorphism discoveryG 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...
- Comparisons of two-part models with competitorsP 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...
- People are variables too: multilevel structural equations modelingParas 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...
- Bivariate analysis of sensitivity and specificity produces informative summary measures in diagnostic reviewsJohannes 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...
- Missing data, incomplete taxa, and phylogenetic accuracyJohn 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....
- Motor learning transiently changes cortical somatotopyKatiuska 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...
- Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approachesAdam 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...
- Allowing for imprecision of the intracluster correlation coefficient in the design of cluster randomized trialsRebecca 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...
- Bioinformatics applications for pathway analysis of microarray dataThomas 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...
- A substantial and confusing variation exists in handling of baseline covariates in randomized controlled trials: a review of trials published in leading medical journalsPeter 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...
- Imputation strategies for missing data in a school-based multi-centre study: the Pathways studyS 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...
- 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...
- Statistical analysis of real-time PCR dataJoshua 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...
- Trend tests for case-control studies of genetic markers: power, sample size and robustnessB 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...
- RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screensNora 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...
- Bias in error estimation when using cross-validation for model selectionSudhir 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...
- A computational platform for MALDI-TOF mass spectrometry data: application to serum and plasma samplesDante 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...
- Classification of microarrays to nearest centroidsAlan 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...
- Commentary: Heterogeneity in meta-analysis should be expected and appropriately quantifiedJulian P T Higgins
MRC Biostatistics Unit, Institute of Public Health, Robinson Way, Cambridge CB2 0SR, UK
Int J Epidemiol 37:1158-60. 2008
- Core--Informatics, Biostatistics and data managementJeffrey 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...
- The Effect of Exercise on Progression of Knee OAANDREW CONCOFF; Fiscal Year: 2003..Eventually, optimal exercise regimens will be sought for both primary and secondary prevention of OA at various joints and stages. ..
- The Effect of Exercise on Progression of Knee OAANDREW CONCOFF; Fiscal Year: 2002..Eventually, optimal exercise regimens will be sought for both primary and secondary prevention of OA at various joints and stages. ..
- The Effect of Exercise on Progression of Knee OAANDREW CONCOFF; Fiscal Year: 2001..Eventually, optimal exercise regimens will be sought for both primary and secondary prevention of OA at various joints and stages. ..
- Regulation of Apical-Basal Cell polarity during Intestinal Epithelial MorphogenesNan Gao; Fiscal Year: 2010..The award will protect my time for generating new genetic models including the intestine-specific Cdc42 knockout mice. ..
- Clinical Research Consortium for Spinocerebellar AtaxiasTetsuo Ashizawa; Fiscal Year: 2010..We will establish a clinical research consortium for SCA (CRC-SCA), which will provide multidisciplinary infrastructure to bring these novel treatment ideas to bedside. ..
- Clinical Research Consortium for Spinocerebellar AtaxiasTetsuo Ashizawa; Fiscal Year: 2009..We will establish a clinical research consortium for SCA (CRC-SCA), which will provide multidisciplinary infrastructure to bring these novel treatment ideas to bedside. ..
- Pro-Inflammatory HDL as a Novel Target for the Indentification of AtherosclerosisMaureen McMahon; Fiscal Year: 2009..Targeting PiHDL with interventions that restore protective function to HDL might be considered for prevention of ATH in both lupus and non lupus patients. ..
- Pro-Inflammatory HDL as a Novel Target for the Indentification of AtherosclerosisMaureen 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. ..
- Pro-Inflammatory HDL as a Novel Target for the Indentification of AtherosclerosisMAUREEN A MCMAHON; Fiscal Year: 2010..Targeting PiHDL with interventions that restore protective function to HDL might be considered for prevention of ATH in both lupus and non lupus patients. ..
- Serum-based assays for pancreatic cancer detectionROSAURA VALLE; Fiscal Year: 2009..The development of a simple immunodiagnostic assay based on patient serum to detect pancreatic cancer would have a profound impact on patient survival and reduce mortality from this disease. ..
- Bayesian Variable Selection in Generalized Linear Models with Missing VariblesXiaowei Yang; Fiscal Year: 2012..Development of these procedures and contribution of the software to statisticians and researchers in medical research would significantly improve the quality of evaluation of important and clinically relevant data. ..
- EFFECT OF ELEVATED FREE FATTY ACIDS ON INSULIN SECRETIONMelissa Cavaghan; Fiscal Year: 1999..abstract_text> ..
- EFFECT OF ELEVATED FREE FATTY ACIDS ON INSULIN SECRETIONMelissa Cavaghan; Fiscal Year: 2000..abstract_text> ..
- Data Management/GIS/Biostatistics CoreMirko Zimic; Fiscal Year: 2007..Datasets and their documentation will be available at the web page of the program, password protected and using a secure site, providing limited access to involved personnel. ..
- Longitudinal Effects of Family Violence on the Dev of Delinquency & AggressionMIGUEL VILLODAS; Fiscal Year: 2009..In addition, the applicant will contribute to the academic community through publication in professional journals and presentations at international and national conferences. ..
- Core--Biostatistics and information managementKenneth Hess; Fiscal Year: 2003..7. To collaborate and assist all project investigators in the publication of scientific results. 8. To assist in the design, evaluation, and analysis of new research arising from the individual projects. ..
- Longitudinal Effects of Family Violence on the Dev of Delinquency & AggressionMIGUEL T VILLODAS; Fiscal Year: 2010..In addition, the applicant will contribute to the academic community through publication in professional journals and presentations at international and national conferences. ..
- CORE--DATA MANAGEMENT AND STATISTICSVahram Haroutunian; Fiscal Year: 2002..abstract_text> ..
- BIOSTATISTICS AND DATA MANAGEMENT COREJack Lee; Fiscal Year: 2004..8. To generate statistical reports for all projects and to collaborate and assist all project investigators in the publication of scientific results. ..
- LONG QT SYNDROME--POPULATION, GENETIC & CARDIAC STUDIESArthur Moss; Fiscal Year: 1999..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. ..
- LONG QT SYNDROME--POPULATION, GENETIC & CARDIAC STUDIESArthur Moss; Fiscal Year: 2001..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. ..
- LONG QT SYNDROME--POPULATION, GENETIC & CARDIAC STUDIESArthur 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. ..
- LONG QT SYNDROME--POPULATION, GENETIC & CARDIAC STUDIESArthur Moss; Fiscal Year: 2000
- DATA MANAGEMENT AND STATISTICS COREVahram Haroutunian; Fiscal Year: 2004..abstract_text> ..
- HIV PROTEASE INHIBITORS AND ATHEROSCLEROSISJames Stein; Fiscal Year: 2001..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. ..
- CORE--BIOSTATISTICSWilliam Shannon; Fiscal Year: 2003..Shannon and where the work of the Core will be done, and they will be coordinated with the CALGB Statistical Center for consistency of approach. ..
- Mild Cognitive Impairment: Cerebrovascular Dysfunction and Exercise TrainingRONG contact ZHANG; Fiscal Year: 2010..The new knowledge will have significant impact on prevention or treatment of AD. ..
- Mild Cognitive Impairment: Cerebrovascular Dysfunction and Exercise TrainingRong Zhang; Fiscal Year: 2009..The new knowledge will have significant impact on prevention or treatment of AD. ..
- VIBRATIONAL OPTICAL ACTIVITY--BIOCHEMISTRY APPLICATIONSTIMOTHY KEIDERLING; Fiscal Year: 1993..7. Determination of specific characteristic spectral forms for uniquely folded nucleic acid structures...
- Mentored Patient-Oriented Research Career Development AwJames Stein; Fiscal Year: 2003..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. ..
- Mentored Patient-Oriented Research Career Development AwJames Stein; Fiscal Year: 2002..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. ..
- Mentored Patient-Oriented Research Career Development AwJames Stein; Fiscal Year: 2004
- Mentored Patient-Oriented Research Career Development AwJames Stein; Fiscal Year: 2005
- CORE--BIOSTATISTICS AND DATA MANAGEMENTJack Lee; Fiscal Year: 2002..7) To collaborate and assist all project investigators in the publication of scientific results. ..
- Core--Data & statistical analysisWILLIAM CUMBERLAND; Fiscal Year: 2000..The Core will also interact with other cores within the Program Project to resolve any statistical issues they may have or to consult with them about questions in their expertise. ..
- NEUROPHARMACOLOGY--ANESTHESIA AND THE NERVOUS SYSTEMLUKE KITAHATA; Fiscal Year: 1980..To simulate surgical stimuli, a thermal stimulus will be used, which is controllable, reproducible, conveniently applied and causes minimal tissue damage...
- Core--Data managementVahram Haroutunian; Fiscal Year: 2005..abstract_text> ..
- HEALTH RESEARCH TRAINING PROGRAMGenevieve Ames; Fiscal Year: 2000....
- HEALTH RESEARCH TRAINING PROGRAMGenevieve Ames; Fiscal Year: 2001....
- HEALTH RESEARCH TRAINING PROGRAMGenevieve Ames; Fiscal Year: 2002....
- DATA MANAGEMENT AND BIOSTATISTICS COREAlfred Bartolucci; Fiscal Year: 2004..It is our purpose to participate fully in Center activities including data presentations, Center Training activities including seminars, curriculum advise to fellows, and mentoring. ..
- Quality Threshold Analysis of Prostate CancersCarlos Moreno; Fiscal Year: 2003..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. ..
- STATISTICAL SOFTWARE FOR SCALE SPACE SMOOTHINGMAXIMILLIAN KARLOVITZ; Fiscal Year: 2000..The commercial potential is strengthened by making the software widely and easily available via the Internet. ..
- Quality Threshold Analysis of Prostate CancersCarlos Moreno; Fiscal Year: 2002..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. ..
- Quality Threshold Analysis of Prostate CancersCarlos 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. ..
- Biostatistics/Data Management CoreMEI CHENG WANG; Fiscal Year: 2009..abstract_text> ..
- BIODEMOGRAPHIC ANALYSIS OF AGING TRAJECTORIESShiro Horiuchi; Fiscal Year: 1999....
- CORE--BIOSTATISTICS AND DATA MANAGEMENTBercedis Peterson; Fiscal Year: 2003..Computer and data systems are operational for fulfilling the missions described above. The team is composed of a Project Leader, Biostatistician, Systems Programmer, Analyst Programmer, and two Data Technicians. ..
- The Neurobiological Basis of Prodromal States and Psychosis in AdolescenceMelita L Daley; Fiscal Year: 2010....
- BIODEMOGRAPHIC ANALYSIS OF AGING TRAJECTORIESShiro Horiuchi; Fiscal Year: 2000....
- The Neurobiological Basis of Prodromal States and Psychosis in AdolescenceMelita Daley; Fiscal Year: 2009....
- The Neurobiological Basis of Prodromal States and Psychosis in AdolescenceMelita Daley; Fiscal Year: 2007....
- CORE--BIOSTATISTICS AND DATA MANAGEMENTDonna Niedzwiecki; Fiscal Year: 2002..Computer and data systems are operational for fulfilling the missions described above. The team is composed of a Project Leader, Statistician, Programmer Analyst, Database Administrator and a Data Technician. ..
- CORE--BIOSTATISTICS AND DATA MANAGEMENTJack Lee; Fiscal Year: 2001..To collaborate and assist all project investigators in the publication of scientific results. ..
- BIODEMOGRAPHIC ANALYSIS OF AGING TRAJECTORIESShiro Horiuchi; Fiscal Year: 2001....
- BIODEMOGRAPHIC ANALYSIS OF AGING TRAJECTORIESShiro Horiuchi; Fiscal Year: 2002....
- Heart Failure Clinical Research Network - DCCKerry Lee; Fiscal Year: 2009..End of Abstract) ..
- Heart Failure Clinical Research Network - DCCKerry Lee; Fiscal Year: 2007..End of Abstract) ..
- Heart Failure Clinical Research Network - DCCKerry Lee; Fiscal Year: 2006..End of Abstract) ..
- CORE--BIOSTATISTICSMichael Province; Fiscal Year: 1999....
- CORE--BIOSTATISTICSMichael Province; Fiscal Year: 1999....
- BIOSTATISTICSChengjie Xiong; Fiscal Year: 2009..6. Develop, apply, and implement appropriate statistical data analysis techniques for combining the cross-sectional and longitudinal data that have been gathered. ..
- Racial Disparity in Access High Quality Cardiac SurgeonsDana Mukamel; Fiscal Year: 2003..The knowledge gained in this project is essential for development of targeted programs that could successfully address the disparity in access to high quality cardiac care among elderly racial minorities. ..
- Nursing Homes Response to Quality Indictors PublicationDana Mukamel; Fiscal Year: 2004..Statistical regression techniques will be used to analyze the data and test specific hypotheses. ..
- STRUCTURE, PROCESS AND OUTCOMES IN THE PACE PROGRAMDana 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. ..
- Placental injury and adaptationYoel Sadovsky; Fiscal Year: 2005..Conclusions from our studies are likely to shed light on the mechanisms of villous injury, and may provide new tools to identify and manage IUGR and its sequelae. ..
- Biometrical Modeling of Fertility Using the NLSYJOSEPH RODGERS; Fiscal Year: 2006..Potential moderators/mediators include education, family structure, and quality of the family environment. ..
- Pittsburgh Mind-Body Center-IIKaren Matthews; Fiscal Year: 2008..Support-in-kind from the host institutions will enable us to leverage the funds provided by the RFA to expand Center activities that would not otherwise be possible. ..