Genomes and Genes
statistical data interpretation
Summary: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
Publications332 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...
- Subgroup analysis, covariate adjustment and baseline comparisons in clinical trial reporting: current practice and problemsStuart J Pocock
Medical Statistics Unit, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
Stat Med 21:2917-30. 2002....
- 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...
- 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...
- 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....
- 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...
- Statistics in medicine--reporting of subgroup analyses in clinical trialsRui Wang
N Engl J Med 357:2189-94. 2007
- 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...
- 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...
- Missing value estimation methods for DNA microarraysO Troyanskaya
Stanford Medical Informatics Stanford University School of Medicine, Stanford, CA, USA
Bioinformatics 17:520-5. 2001..We report results of the comparative experiments and provide recommendations and tools for accurate estimation of missing microarray data under a variety of conditions...
- Statistical methods for identifying differentially expressed genes in DNA microarraysJohn D Storey
Department of Statistics, Stanford University, Palo Alto, CA, USA
Methods Mol Biol 224:149-57. 2003
- 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...
- 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...
- 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...
- Evaluating different methods of microarray data normalizationAndre Fujita
Institute of Mathematics and Statistics, University of Sao Paulo, Rua do Matao, 1010 São Paulo, 05508 090 SP, Brazil
BMC Bioinformatics 7:469. 2006..Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration...
- 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....
- 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...
- 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...
- Caution regarding the use of pilot studies to guide power calculations for study proposalsHelena Chmura Kraemer
Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, Calif 94305, USA
Arch Gen Psychiatry 63:484-9. 2006..The argument herein is not meant to discourage clinical researchers from performing pilot studies (or review committees from requiring them) but simply to caution against their use for the objective of guiding power calculations...
- Meta-analysis, Simpson's paradox, and the number needed to treatDouglas G Altman
Centre for Statistics in Medicine, Institute of Health Sciences, Old Road, Headington, Oxford, UK
BMC Med Res Methodol 2:3. 2002..There is debate concerning methods for calculating numbers needed to treat (NNT) from results of systematic reviews...
- Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency of gene selection criterionWen Fury
Regeneron Pharmaceutical Inc, Tarrytown, NY 10591, USA
Conf Proc IEEE Eng Med Biol Soc 1:5531-4. 2006..It is concluded that overlapping probability is indeed a function of the gene list length, and its statistical significance should be quoted in the context of gene selection criterion...
- Systematic analysis of bicistronic reporter assay dataJonathan L Jacobs
Department of Cell Biology and Molecular Genetics, 2135 Microbiology Building, University of Maryland, College Park, MD 20742, USA
Nucleic Acids Res 32:e160. 2004..umd.edu/statistics). These spreadsheets could be easily adapted to any bicistronic reporter assay system...
- 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....
- 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....
- 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)...
- Design and analysis of clinical trials with clustering effects due to treatmentChris Roberts
Biostatistics Group, Division of Epidemiology and Health Sciences, University of Manchester, UK
Clin Trials 2:152-62. 2005..It is argued that the design and analysis of this type of trial should take account of possible heterogeneity in cluster size and intracluster correlation...
- Dynamic brain sources of visual evoked responsesS Makeig
Computational Neurobiology Laboratory and, The Howard Hughes Medical Institute, The Salk Institute, 10010 North Torrey Pines Road, San Diego, CA 92037, USA
Science 295:690-4. 2002..Scalp topographies of these components were consistent with their generation in compact cortical domains...
- Factors affecting statistical power in the detection of genetic associationDerek Gordon
Laboratory of Statistical Genetics, Rockefeller University, New York, New York 10021, USA
J Clin Invest 115:1408-18. 2005..We define the factors that determine statistical power and show how study design and analysis should be designed to maximize the probability of localizing disease genes...
- g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experimentsJüri Reimand
Institute of Computer Science, University of Tartu, Liivi 2, 50409 Tartu, Estonia
Nucleic Acids Res 35:W193-200. 2007..g:Profiler supports 31 different species, and underlying data is updated regularly from sources like the Ensembl database. Bioinformatics communities wishing to integrate with g:Profiler can use alternative simple textual outputs...
- 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...
- Intraclass correlation coefficient and outcome prevalence are associated in clustered binary dataM C Gulliford
Department of Public Health Sciences, King s College London, Capital House, 42 Weston St, London SE1 3QD, UK
J Clin Epidemiol 58:246-51. 2005..To describe the association between values for a proportion and the intraclass correlation coefficient (ICC)...
- Computing average shaped tissue probability templatesJohn Ashburner
Wellcome Trust Centre for Neuroimaging, 12 Queen Square, London, WC1N 3BG, UK
Neuroimage 45:333-41. 2009..g. grey and white matter) are registered simultaneously with the current template estimate. In order to generalise the resulting template to a broader range of subjects, a template blurriness prior is included within the model...
- 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...
- 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...
- 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....
- Global functional profiling of gene expressionSorin Draghici
Department of Computer Science, Wayne State University, 5143 Cass Avenue, Detroit, MI 48202, USA
Genomics 81:98-104. 2003..OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms...
- Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common diseaseKirk E Lohmueller
Whitehead Massachuetts Institute of Technology Center for Genome Research, Cambridge, Massachusetts 02139, USA
Nat Genet 33:177-82. 2003..We conclude that there are probably many common variants in the human genome with modest but real effects on common disease risk, and that studies using large samples will convincingly identify such variants...
- 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...
- Evaluating cutpoints for the MHI-5 and MCS using the GHQ-12: a comparison of five different methodsMark J Kelly
Dept of Primary Care and Public Health, Centre for Health Sciences Research, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4YS, UK
BMC Psychiatry 8:10. 2008..This paper aims to produce cutpoints for the MHI-5 and MCS by comparison with the General Health Questionnaire (GHQ-12)...
- 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...
- 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...
- Randomized controlled trials with time-to-event outcomes: how much does prespecified covariate adjustment increase power?Adrian V Hernandez
Center for Clinical Decision Sciences, Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands
Ann Epidemiol 16:41-8. 2006..We evaluated the effects of various strategies of covariate adjustment on type I error, power, and potential reduction in sample size in randomized controlled trials (RCTs) with time-to-event outcomes...
- 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...
- 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....
- 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....
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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
- 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...
- Neural substrates of faulty decision-making in abstinent marijuana usersKaren I Bolla
Department of Neurology, Johns Hopkins University School of Medicine, Bayview Medical Center, Baltimore, MD 21224, USA
Neuroimage 26:480-92. 2005..Finally, it is unclear if these neurologic findings will become progressively worse with continued heavy MJ use or if they will resolve with abstinence from MJ use...
- 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...
- Seven items were identified for inclusion when reporting a Bayesian analysis of a clinical studyLillian Sung
Division of Hematology Oncology, Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada
J Clin Epidemiol 58:261-8. 2005....
- Highly parallel SNP genotypingJ B Fan
llumina, Inc, San Diego, California 92121, USA
Cold Spring Harb Symp Quant Biol 68:69-78. 2003
- 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 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...
- 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...
- 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...
- 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...
- End points for colon cancer adjuvant trials: observations and recommendations based on individual patient data from 20,898 patients enrolled onto 18 randomized trials from the ACCENT GroupDaniel J Sargent
Department of Health Sciences Research, North Central Cancer Treatment Group, Mayo Clinic, Rochester, MN 55905, USA
J Clin Oncol 25:4569-74. 2007..We previously validated disease-free survival (DFS) after 3-year follow-up as an excellent predictor of 5-year OS results. Here we explore shorter term DFS and OS end points, as well as stage dependency...
- Clinical reasoning: the relative contribution of identification, interpretation and hypothesis errors to misdiagnosisMichele Groves
Faculty of Biological and Chemical Sciences, University of Queensland, St Lucia 4072, Australia
Med Teach 25:621-5. 2003....
- Interpreting the results of patient reported outcome measures in clinical trials: the clinician's perspectiveHolger J Schunemann
Division of Clinical Research Development and INFORMAtion Translation, Department of Epidemiology, Istituto Regina Elena Italian National Cancer Institute Rome, Rome, Italy
Health Qual Life Outcomes 4:62. 2006..Thus, there are several steps investigators can take to facilitate this process to help bringing HRQL information closer to the bedside...
- 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/...
- 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...
- A guide to modern statistical analysis of immunological dataBernd Genser
BMC Immunol 8:27. 2007..Such approaches are used in many other scientific disciplines, but immunological studies on the whole still use simple statistical techniques for data analysis...
- An accessible analytical approach for investigating what happens between the rounds of a Delphi studyJ Greatorex
University of Cambridge Local Examinations Syndicate, England
J Adv Nurs 32:1016-24. 2000..An example Delphi study from a healthcare setting is used to illustrate the methodology...
- Estimation and prediction in a multi-state model for breast cancerHein Putter
Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, The Netherlands
Biom J 48:366-80. 2006..The estimated transition rates between the states in the model are used to obtain predictions for patients with a given history. Formulas are developed and illustrated for these prediction probabilities for the clock reset approach...
- 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...
- 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...
- Fast detection of arbitrarily shaped disease clustersR Assunção
Departamento de Estatistica, Universidade Federal de Minas Gerais, 31270 901, Belo Horizonte, MG Brazil
Stat Med 25:723-42. 2006..This calls for a new approach different from the maximum likelihood method for this important public health problem...
- Intracluster correlation coefficients in cluster randomized trials: empirical insights into how should they be reportedMarion K Campbell
Health Services Research Unit, University of Aberdeen, Aberdeen, UK
BMC Med Res Methodol 4:9. 2004..Similarly, the need for appropriate standards of reporting of cluster trials is more widely acknowledged...
- New gene selection method for classification of cancer subtypes considering within-class variationJi Hoon Cho
Department of Chemical Engineering, Pohang University of Science and Technology, San 31 Hyoja Dong, 790 784 Pohang, South Korea
FEBS Lett 551:3-7. 2003..The proposed method provides a very small number of genes compared with the previous methods without loss of discriminating power and thus it can effectively facilitate further biological and clinical researches...
- Hidden likelihood support in genomic data: can forty-five wrongs make a right?John Gatesy
Department of Biology, University of California Riverside, Riverside, CA 92521, USA
Syst Biol 54:483-92. 2005..Consensus and supertree procedures that ignore hidden phylogenetic signals are, at best, incomplete...
- 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...
- 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...
- 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...
- 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...
- Association between unreported outcomes and effect size estimates in Cochrane meta-analysesToshi A Furukawa
JAMA 297:468-70. 2007
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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/...
- A general best-fit method for concentration-response curves and the estimation of low-effect concentrationsM Scholze
Department of Biology and Chemistry, University of Bremen, Germany
Environ Toxicol Chem 20:448-57. 2001..In comparison with common methods of concentration-response analysis, a clear improvement is achieved...
- Combining multiple microarray studies and modeling interstudy variationJung Kyoon Choi
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 371 1 Guseong dong Yuseong gu, Daejeon 305 701, Korea
Bioinformatics 19:i84-90. 2003..We also developed an alternative modeling procedure based on a Bayesian approach, which would offer flexibility and robustness compared to the classical procedure...
- Determination of activation areas in the human auditory cortex by means of synthetic aperture magnetometryAnthony T Herdman
Rotman Research Institute, Baycrest Centre for Geriatric Care, University of Toronto, Toronto, Canada M6A 2E1
Neuroimage 20:995-1005. 2003..Source waveforms from SAM and ECD analyses show comparable temporal information. Results from this study suggest that SAM is a useful technique for imaging cortical structures involved in processing perceptual information...
- 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....
- Regulation of Apical-Basal Cell polarity during Intestinal Epithelial MorphogenesNan Gao; Fiscal Year: 2013..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. ..
- Mild Cognitive Impairment: Cerebrovascular Dysfunction and Exercise TrainingRong Zhang; Fiscal Year: 2012..The new knowledge will have significant impact on prevention or treatment of AD. ..
- Statistical Models for Genome Sequencing and AssociationNancy R Zhang; Fiscal Year: 2013..Public, open source software will be made available for all of the developed methods. ..
- Statistical Methods for Incomplete Data with Measurement ErrorsEdward C Chao; Fiscal Year: 2012..There is no commercial software to deal with complicated case as Laso. PUBLIC HEALTH RELEVANCE: This project aims to develop statistical methods and tools for analyzing incomplete data with missing data and measurement errors. ..
- Bayesian Variable Selection in Generalized Linear Models with Missing VariblesXiaowei Yang; Fiscal Year: 2013..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. ..
- 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. ..
- 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. ..
- 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. ..
- EFFECT OF ELEVATED FREE FATTY ACIDS ON INSULIN SECRETIONMelissa Cavaghan; Fiscal Year: 2000..abstract_text> ..
- Mentored Patient-Oriented Research Career Development AwJames 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. ..
- HEALTH RESEARCH TRAINING PROGRAMGenevieve Ames; Fiscal Year: 2002....
- 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. ..
- 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. ..
- BIODEMOGRAPHIC ANALYSIS OF AGING TRAJECTORIESShiro Horiuchi; Fiscal Year: 2002....
- Statistical Methods for the Analysis of Functional Genomic DataDebashis Ghosh; Fiscal Year: 2008..unreadable] 5. Dissemination of these results in user-friendly statistical software. ..
- Semiparametric Regression Analysis of Censored DataDanyu Lin; Fiscal Year: 2004..Applications to real medical studies will be provided. The research results will be disseminated to practicing statisticians and medical investigators via publications, lectures and software distributions. ..
- STATISTICAL ISSUES IN AIDS RESEARCHThomas Fleming; Fiscal Year: 2008..Research into optimal designs of Phase HE "Intermediate Trials" of candidate HIV vaccines will also be continued. ..
- Effects of Aging on Executive ProcessesTimothy Salthouse; Fiscal Year: 2006..e., specific to individual variables or common to many variables) at which age-related influences operate on executive process variables. ..
- Three-Class ROC Analysis for Task-Based Medical Image Quality AssessmentXin He; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- HIV PREVENTION TRIALS NETWORK LEADERSHIP GROUPThomas Fleming; Fiscal Year: 2005..abstract_text> ..
- American Indian MS to PHD Nursing Science Bridge-Phase 2SUSAN HENLY; Fiscal Year: 2006..The project evaluation plan is a refinement of the Phase 1 plan designed to efficiently obtain maximum information about the structure, process, and outcomes of the project. ..
- Fetal & Adolescent Nicotine Effects on CNS 5HT SystemsTheodore Slotkin; Fiscal Year: 2003..abstract_text> ..
- PERCEPTUAL MODEL FOR WORKSTATION DISPLAY OPTIMIZATIONDev Chakraborty; Fiscal Year: 2002..Also to be generated are iso-contour plots of the effects of common workstation variables on image quality in both tasks. This will allow digital mammography workstations to be more intelligently used. ..
- MECHANISMS OF CHLORPYRIFOS DEVELOPMENTAL NEUROTOXICITYTheodore Slotkin; Fiscal Year: 2004..Molecular mechanisms of developmental neurotoxicity can be determined and linked to eventual alterations in behavioral performance. ..
- PERCEPTUAL MODEL FOR WORKSTATION DISPLAY OPTIMIZATIONDev Chakraborty; Fiscal Year: 2003..Also to be generated are iso-contour plots of the effects of common workstation variables on image quality in both tasks. This will allow digital mammography workstations to be more intelligently used. ..
- DRUGS AND DEVELOPMENT OF THE ADRENERGIC NERVOUS SYSTEMTheodore Slotkin; Fiscal Year: 2003....
- Mechanisms Linking Hostility and SmokingChristopher Kahler; Fiscal Year: 2007..unreadable] [unreadable]..
- STRUCTURAL ORGANIZATION AND PROTEOMICS OF TBThomas Terwilliger; Fiscal Year: 2005..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
- Clinic-based Intervention to Improve Medication Adherence to Reduce CVD RisksJames Christian; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Cholestasis Reversal (Phase ll): Efficacy of lV Fish Oil Mark Puder; Fiscal Year: 2010..Although the proposed study is not a randomized trial, it is thought that sufficient evidence could be generated that would result in FDA approval of an lFE such as Omegaven. ..
- In silico genome scan with high-throughput addiction related phenotypes in miceEdwin van den Oord; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- College Facilitation for Alcohol ProblemsWilliam Zywiak; Fiscal Year: 2009..The proposed study will be one of the first to examine the efficacy of this many contacts spread out over this long a period in a college sample. ..
- Protective Influence of Residential Learning CommunitiesSEAN MCCABE; Fiscal Year: 2006..At each measurement point, participants will complete a set of measures that assess substance use behaviors and constructs addressed by RLCs. ..
- Nonmedical Prescription Drug Use among College StudentsSEAN MCCABE; Fiscal Year: 2005..Findings from this research will have important implications for the understanding of the epidemiology, prevention and treatment of prescription drug abuse. ..
- MULTIMEDIA SMOKING CESSATION FOR ALCOHOLIC CLIENTSStephen Butler; Fiscal Year: 2002..If a computerized, affordable smoking cessation program can be shown, in field trials, to have demonstrable efficacy, the commercial potential can be extraordinary. ..
- Bayesian methods for analyzing genetic diversityKENT HOLSINGER; Fiscal Year: 2006..Moreover, we develop refinements to existing user-friendly software implementing the methods we develop and make the software and the associated source code freely available under the GNU General Public license. ..
- Decoupling of Principal Renal Autoregulatory MechanismsKi Chon; Fiscal Year: 2005..By exercising this model, as described under Specific Aim (5), we plan to begin understanding the underlying reasons for the changes observed in autoregulation under pathological conditions. ..
- Fetal and Infant Neurobehavior in Opiate Dependent WomenLauren Jansson; Fiscal Year: 2009..Information gained from this proposal has the potential to significantly impact the way in which we treat the difficult and high-risk population of opiate dependent pregnant women. ..
- Development automated assay-regulators insulin synthesisPatrick McDonough; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- METHADONE, BUPRENORPHINE AND FETAL DEVELOPMENTLauren Jansson; Fiscal Year: 2004..Upon completing the 5-year funding period, Dr. Jansson plans to have written an RO1 grant application to pursue research ideas identified during KO8 funding. ..
- IRSG STUDIES OF ALVEOLAR RHABDOMYOSARCOMA GENE FUSIONSFREDERIC BARR; Fiscal Year: 2005..These studies will provide a definitive analysis of the occurrence and clinical significance of these genetic alterations in ARMS, and will ultimately impact on the future design of clinical protocols for the treatment of ARMS patients. ..
- Neurobiologic Study of Psychological Distress & DementiaRobert S Wilson; Fiscal Year: 2010....
- Treatment Utilization for Alcohol-Related ProblemsLi Tzy Wu; Fiscal Year: 2002....
- DIETARY FAT, PLASMA LIPIDS AND OTHER CHD RISK FACTORS.Alice Lichtenstein; Fiscal Year: 2003..The investigators state that data derived from the proposed studies could contribute to the database on which to formulate more specific public health recommendations regarding the variables described. ..
- NEUROIMAGING OF HIV AND COMORBID DISORDERSLance Bauer; Fiscal Year: 2003..An analysis of change scores across groups will permit a formal test of the effects of antiviral treatment on neurophysiological status. ..
- PARAMEDIC FIELD INITIATION OF MAGNESIUM NEUROPROTECTIVEJeffrey Saver; Fiscal Year: 2003..abstract_text> ..
- SOY PROTEIN +/- ISOFLAVONOIDS AND PLASMA LIPIDSAlice Lichtenstein; Fiscal Year: 2002..The results of these studies, whether positive or negative, should contribute to the data base on which to formulate more specific public health recommendations with respect to decreasing risk of developing CHD. ..
- A PROSPECTIVE STUDY OF RISK OF MORTALITY AFTER SCIJames Krause; Fiscal Year: 2002..Risk profiles will be generated to identify individuals at greatest risk for early mortality. Separate analyses and risk profiles will be generated based on injury severity, gender and race/ethnicity. ..
- Meta-Analysis of Interventions to Increase Exercise/Physical AcivityVicki Conn; Fiscal Year: 2009..The compelling importance and broad scope of this work make funding necessary to achieve these important aims. ..
- A High Throughput Imaging Assay for Hepatic Lipid Droplet FormationPatrick McDonough; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- Early-Stage Breast Cancer Treatment Decisions by Women with Physical DisabilitiesLisa Iezzoni; Fiscal Year: 2007..Our findings will help begin educating patients and physicians and could perhaps improve breast cancer care for women with physical disabilities. [unreadable] [unreadable] [unreadable]..
- Effects of Depression on Short-Term Recovery from MIKenneth Freedland; Fiscal Year: 2007..The results will clarify the early course of post-MI depression and the mechanisms linking depression to cardiac events, and they will inform efforts to develop more efficacious treatments. ..
- Epidemiology of Recurrent Aphthous StomatitisLorena Baccaglini; Fiscal Year: 2007..Understanding the cause of canker sores can lead to better treatments for patients affected by this condition. [unreadable] [unreadable] [unreadable]..
- High Throughput Imaging Assay for Beta-CateninPatrick McDonough; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- DYNAMIC GROWTH & CHANGE IN ADULT INTELLECTUAL ABILITIESJohn McArdle; Fiscal Year: 2004..abstract_text> ..
- MRI of Brain Function and Receptors in Cocaine AddictionCraig Ferris; Fiscal Year: 2005..With this repeated 'in vivo autoradiography,' it is possible to correlate changes in cocaine associated brain activity with discrete changes in NT binding in the mesocorticolimbic system. ..
- A Randomized Trial of Home Self-Efficacy EnhancementAnthony Jerant; Fiscal Year: 2007..The findings will help policymakers, payers, and providers identify which interventions to implement. ..
- Project CARE(Cocaine Abuse in the Rural Environment)FONDA EYLER; Fiscal Year: 2007..abstract_text> ..
- CCBAR Workshop 2006-2007STACY LINDAU; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Biometrical Modeling of Fertility Using the NLSYJOSEPH RODGERS; Fiscal Year: 2006..Potential moderators/mediators include education, family structure, and quality of the family environment. ..
- 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. ..
- 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. ..