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Collection of Biostatistics Research Archive

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    Content Posted in 2006

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    A Comparative Analysis of the Chronic Effects of Fine Particulate Matter, Sorina E. Eftim, Holly Janes, Aidan McDermott, Jonathan M. Samet, and Francesca Dominici

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    A Comparison of Methods for Estimating the Causal Effect of a Treatment in Randomized Clinical Trials Subject to Noncompliance, Rod Little, Qi Long, and Xihong Lin

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    A Computationally Tractable Multivariate Random Effects Model for Clustered Binary Data, Brent A. Coull, E. Andres Houseman, and Rebecca A. Betensky

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    A Diagnostic Test for the Mixing Distribution in a Generalised Linear Mixed Model, Eric J. Tchetgen and Brent A. Coull

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    Adjusting for Covariate Effects on Classification Accuracy Using the Covariate-Adjusted ROC Curve, Holly Janes and Margaret S. Pepe

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    A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data, E S. Venkatraman and Adam Olshen

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    A FLEXIBLE GENERAL CLASS OF MARGINAL AND CONDITIONAL RANDOM INTERCEPT MODELS FOR BINARY OUTCOMES USING MIXTURES OF NORMALS, Brian Caffo, Ming-Wen An, and Charles A. Rohde

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    A Flexible Statistical Method for Detecting Genomic Copy-Number Changes Using Hidden Markov Models with Reversible Jump MCMC , Oscar M. Rueda and Ramon Diaz-Uriarte

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    A General Framework for Statistical Performance Comparison of Evolutionary Computation Algorithms, David Shilane, Jarno Martikainen, Sandrine Dudoit, and Seppo Ovaska

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    A Likelihood Based Method for Real Time Estimation of the Serial Interval and Reproductive Number of an Epidemic, Laura Forsberg White and Marcello Pagano

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    A Marginalized Diffusion Model for Estimating Age at First Endoscopy Examination from Current Status Data, Diana Miglioretti and Elizabeth Brown

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    A Matrix Pooling Algorithm for Disease Detection, Bethany L. Hedt and Marcello Pagano

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    Analysis of Case-Control Age-at-Onset Data Using a Modified Case-Cohort Method, Bin Nan and Xihong Lin

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    An Informative Bayesian Structural Equation Model to Assess Source-Specific Health Effects of Air Pollution, Margaret C. Nikolov, Brent A. Coull, Paul J. Catalano, and John J. Godleski

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    A note on bias due to fitting prospective multivariate generalized linear models to categorical outcomes ignoring retrospective sampling schemes, Bhramar Mukherjee and Ivy Liu

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    A Semiparametric Approach for the Nonparametric Transformation Survival Model With Multiple Covariates, Xiao Song, Shuangge Ma, Jian Huang, and Xiao-Hua Zhou

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    Assessing the Adequacy of Variance Function in Heteroscedastic Regression Models, Lan Wang and Xiao-Hua Andrew Zhou

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    A Theory of Sufficient Cause Interactions, Tyler J. VanderWeele and James M. Robins

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    A unifying approach for haplotype analysis of quantitative traits in family-based association studies: Testing and estimating gene-environment interactions with complex exposure variables, Stijn Vansteelandt and Christoph Lange

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    Bayesian Smoothing of Irregularly-spaced Data Using Fourier Basis Functions, Christopher J. Paciorek

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    Biologic Interaction and Their Identification, Tyler J. VanderWeele and James Robins

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    BIVARIATE BINOMIAL SPATIAL MODELLING LOA loa PREVALENCE IN TROPICAL AFRICA, Ciprian M. Crainiceanu, Peter J. Diggle, and Barry Rowlingson

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    Case-cohort Methods for Survival Data on Families from Routine Registers, Tron Anders Moger, Yudi Pawitan, and Ørnulf Borgan

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    Causal Comparisons in Randomized Trials of Two Active Treatments: The Effect of Supervised Exercise to Promote Smoking Cessation, Jason Roy and Joseph W. Hogan

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    Causal Effect Models for Intention to Treat and Realistic Individualized Treatment Rules, Mark J. van der Laan

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    Causal Inference in Hybrid Intervention Trials Involving Treatment Choice, Qi Long, Rod Little, and Xihong Lin

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    Censored Data Regression in High-Dimension and Low-Sample Size Settings For Genomic Applications, Hongzhe Li

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    Combining Information from Two Surveys to Estimate County-Level Prevalence Rates of Cancer Risk Factors and Screening, Trivellore E. Raghuanthan, Dawei Xie, Nathaniel Schenker, Van Parsons, William W. Davis, Kevin W. Dodd, and Eric J. Feuer

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    Comparing the Predictive Values of Diagnostic Tests: Sample Size and Analysis for Paired Study Designs, Chaya S. Moskowitz and Margaret S. Pepe

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    Comparison of Haplotype-based and Tree-based SNP Imputation in Association Studies, James Y. Dai, Ingo Ruczinski, Michael LeBlanc, and Charles Kooperberg

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    Conditional Likelihood Methods for Haplotype-based Association Analysis Using Matched Case-Control Data, Jinbo Chen and Carmen Rodriguez

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    COVARIATE SPECIFIC ROC CURVE WITH SURVIVAL OUTCOME, Xiao Song and Xiao-Hua Zhou

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    COX MODELS WITH NONLINEAR EFFECT OF COVARIATES MEASURED WITH ERROR: A CASE STUDY OF CHRONIC KIDNEY DISEASE INCIDENCE, Ciprian M. Crainiceanu, David Ruppert, and Josef Coresh

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    Crude Cumulative Incidence in the form of a Horvitz-Thompson like and Kaplan-Meier like Estimator, Laura Antolini, Elia Mario Biganzoli, and Patrizia Boracchi

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    Detecting Pulsatile Hormone Secretion Events: A Bayesian Approach, Tim Johnson

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    Diagnosing Bias in the Inverse Probability of Treatment Weighted Estimator Resulting from Violation of Experimental Treatment Assignment, Yue Wang, Maya L. Petersen, David Bangsberg, and Mark J. van der Laan

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    Different Public Health Interventions have Varying Effects, Paula Diehr, Anne B. Newman, Liming Cai, and Ann Derleth

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    Disease Mapping and Spatial Regression with Count Data, Jon Wakefield

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    Doubly Penalized Buckley-James Method for Survival Data with High-Dimensional Covariates, Sijian Wang, Bin Nan, Ji Zhu, and David G. Beer

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    Doubly Robust Censoring Unbiased Transformations, Daniel Rubin and Mark J. van der Laan

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    Empirical Bayes Approach to Controlling Familywise Error: An Application to HIV Resistance Data, Rhoderick N. Machekano and Alan E. Hubbard

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    ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS, Wenyi Wang , Benilton Caravalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, and Rafael A. Irizarry

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    Estimating the Integrated Likelihood via Posterior Simulation Using the Harmonic Mean Identity, Adrian E. Raftery, Michael A. Newton, Jaya M. Satagopan, and Pavel N. Krivitsky

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    Estimation in Semiparametric Transition Measurement Error Models for Longitudinal Data, Wenqin Pan, Donglin Zeng, and Xihong Lin

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    Evaluating Causal Effect Predictiveness of Candidate Surrogate Endpoints, Peter B. Gilbert and Michael Hudgens

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    Evaluating Prediction Rules for t-Year Survivors With Censored Regression Models, Hajime Uno, Tianxi Cai, Lu Tian, and L.J. Wei

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    Evaluating the Predictiveness of a Continuous Marker, Ying Huang, Margaret S. Pepe, and Ziding Feng

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    Exploiting Gene-Environment Independence for Analysis of Case-Control Studies: An Empirical Bayes Approach to Trade Off between Bias and Efficiency , Bhramar Mukherjee

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    Exploiting Gene-Environment Independence for Analysis of Case-Control Studies: An Empirical Bayes Approach to Trade Off between Bias and Efficiency, Bhramar Mukherjee and Nilanjan Chatterjee

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    EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA, Benilton Carvalho, Terence P. Speed, and Rafael A. Irizarry

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    Exploration of distributional models for a novel intensity-dependent normalization , Nicola Lama, Patrizia Boracchi, and Elia Mario Biganzoli

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    Extending Marginal Structural Models through Local, Penalized, and Additive Learning, Daniel Rubin and Mark J. van der Laan

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    FAST ADAPTIVE PENALIZED SPLINES, Tatyana Krivobokova, Ciprian M. Crainiceanu, and Goran Kauermann

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    FDR and Bayesian Multiple Comparisons Rules, Peter Muller, Giovanni Parmigiani, and Kenneth Rice

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    FEATURE-LEVEL EXPLORATION OF THE CHOE ET AL. AFFYMETRIX GENECHIP CONTROL DATASET, Rafael A. Irizarry, Leslie Cope, and Zhijin Wu

     

    Functional ANOVA Normalization of Two-Channel Microarrays, Alan Dabney and John D. Storey

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    GAMMA SHAPE MIXTURES FOR HEAVY-TAILED DISTRIBUTIONS, Sergio Venturini, Francesca Dominici, and Giovanni Parmigiani

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    Generalized confidence intervals for the ratio or difference of two means for lognormal populations with zeros, Yea-Hung Chen and Xiao-Hua Zhou

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    Generalized Monotonic Functional Mixed Models with Application to Modeling Normal Tissue Complications , Matthew Schipper, Jeremy Taylor, and Xihong Lin

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    Genome Scanning Methods for Comparing Sequences Between Groups, with Application to HIV Vaccine Trials, Peter B. Gilbert, Chunyuan Wu, and David V. Jobes

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    Group Additive Regression Models for Genomic Data Analysis, Yihui Luan and Hongzhe Li

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    Hierarchical Lévy Frailty Models and a Frailty Analysis of Data on Infant Mortality in Norwegian Siblings, Tron Anders Moger and Odd O. Aalen

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    Hierarchical Models for Combining Ecological and Case-control Data, Sebastien Haneuse and Jon Wakefield

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    Improved generalized estimating equation analysis via xtqls for implementation of quasi-least squares in Stata, Justine Shults, Sarah J. Ratcliffe, and Mary Leonard

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    Individualized Treatment Rules: Generating Candidate Clinical Trials, Maya L. Petersen, Steven G. Deeks, and Mark J. van der Laan

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    Integrating the Predictiveness of a Marker with its Performance as a Classifier, Margaret S. Pepe, Ziding Feng, Ying Huang, Gary M. Longton, Ross Prentice, Ian M. Thompson, and Yingye Zheng

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    INTERACTING WITH DATA USING THE FILEHASH PACKAGE FOR R, Roger Peng

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    INTERACTING WITH LOCAL AND REMOTE DATA RESPOSITORIES USING THE stashR PACKAGE, Sandrah P. Eckel and Roger Peng

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    INVESTIGATING MEDIATION WHEN COUNTERFACTUALS ARE NOT METAPHYSICAL: DOES SUNLIGHT UVB EXPOSURE MEDIATE THE EFFECT OF EYEGLASSES ON CATARACTS?, Brian Egleston, Daniel O. Scharfstein, Beatriz Munoz, and Sheila West

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    Large Cluster Asymptotics for GEE: Working Correlation Models, Hyoju Chung and Thomas Lumley

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    Lehmann Family of ROC Curves, Mithat Gonen and glenn heller

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    Longitudinal Nested Compliance Class Model in the Presence of Time-Varying Noncompliance, Julia Y. Lin, Thomas R. TenHave, and Michael R. Elliott

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    Matrix Pooling: An Accurate and Cost Effective Testing Algorithm for Detection of Acute HIV Infection, Bethany L. Hedt and Marcello Pagano

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    Mixed Multiplicative Factor Analysis Model for Air Pollution Exposure Assessment, Margaret C. Nikolov, Brent A. Coull, Paul J. Catalano, and John J. Godleski

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    MULTIPLE DISEASES IN CARRIER PROBABILITY ESTIMATION: ACCOUNTING FOR SURVIVING ALL CANCERS OTHER THAN BREAST AND OVARY IN BRCAPRO, Hormuzd A. Katki, Amanda Blackford, Sining Chen, and Giovanni Parmigiani

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    Multiple imputation for the comparison of two screening tests in two-phase Alzheimer studies, Ofer Harel and Xiao-Hua Zhou

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    Multiple Imputation in the Presence of Outliers, Michael Elliott

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    Multiple imputation - Review of theory, implementation and software, Ofer Harel and Xiao-Hua Zhou

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    Multiple Testing With an Empirical Alternative Hypothesis, James E. Signorovitch

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    Multiple Tests of Association with Biological Annotation Metadata, Sandrine Dudoit, Sunduz Keles, and Mark J. van der Laan

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    MULTIVARIATE ANALYSIS AND VISUALIZATION OF SPLICING CORRELATIONS IN SINGLE-GENE TRANSCRIPTOMES, Mark C. Emerick, Giovanni Parmigiani, and William S. Agnew

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    Nested Markov Compliance Class Model in the Presence of Time-Varying Noncompliance, Julia Y. Lin, Thomas R. TenHave, and Michael R. Elliott

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    New Spiked-In Probe Sets for the Affymetrix HGU-133A Latin Square Experiment, Monnie McGee and Zhongxue Chen

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    Nonparametric Pathway-Based Regression Models for Analysis of Genomic Data, Zhi Wei and Hongzhe Li

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    Nonparametric Regression Using Local Kernel Estimating Equations for Correlated Failure Time Data, Zhangsheng Yu and Xihong Lin

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    ON MARGINALIZED MULTILEVEL MODELS AND THEIR COMPUTATION, Michael E. Griswold and Scott L. Zeger

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    ON THE EQUIVALENCE OF CASE-CROSSOVER AND TIME SERIES METHODS IN ENVIRONMENTAL EPIDEMIOLOGY, Yun Lu and Scott L. Zeger

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    ON THE POTENTIAL FOR ILL-LOGIC WITH LOGICALLY DEFINED OUTCOMES, Xianbin Li, Brian S. Caffo, and Daniel O. Scharfstein

     

    On the Structure of Multiple Testing Procedures, Jeffrey Leek and John D. Storey

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    On The Violation Of Bounds For The Correlation In Generalized Estimating Equation Analyses Of Binary Data From Longitudinal Trials, Justine Shults, Wenguang Sun, Xin Tu, and Jay Amsterdam

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    PENALIZED LIKELIHOOD AND BAYESIAN METHODS FOR SPARSE CONTINGENCY TABLES: AN ANALYSIS OF ALTERNATIVE SPLICING IN FULL-LENGTH cDNA LIBRARIES, Corinne Dahinden, Giovanni Parmigiani, Mark C. Emerick, and Peter Buhlmann

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    Permutation Methods in Relative Risk Regression Models, Wenyu Jiang and Jack Kalbfleisch

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    PLASQ: A Generalized Linear Model-Based Procedure to Determine Allelic Dosage ini Cancer Cells from SNP Array Data, Thomas LaFramboise, David P. Harrington, and Barbara A. Weir

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    POOR PERFORMANCE OF BOOTSTRAP CONFIDENCE INTERVALS FOR THE LOCATION OF A QUANTITATIVE TRAIT LOUCS, Ani Manichaikul, Josee Dupuis, Saunak Sen, and Karl W. Broman

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    Posterior Simulation in the Generalized Linear Model with Semiparmetric Random Effects, Subharup Guha

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    Predicting Future Responses Based on Possibly Misspecified Working Models, Tianxi Cai, Lu Tian, Scott D. Solomon, and L.J. Wei

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    PRINCIPAL STRATIFICATION DESIGNS TO ESTIMATE INPUT DATA MISSING DUE TO DEATH, Constantine E. Frangakis, Donald B. Rubin, Ming-Wen An, and Ellen MacKenzie

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    Properties of Monotonic Effects, Tyler J. VanderWeele and James M. Robins

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    RECURRENT EVENT MODELS IN THE PRESENCE OF A TERMINAL EVENT: COMPARISON, INFERENCE AND DATA ANALYSIS, Xianghua Luo and Mei-Cheng Wang

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    Regression Analysis for the Partial Area Under the ROC Curve, Tianxi Cai and Lori E. Dodd

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    Regression Models for Bivariate Binary Responses, Juni Palmgren

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    Relative Risk Regression in Medical Research: Models, Contrasts, Estimators, and Algorithms, Thomas Lumley, Richard Kronmal, and Shuangge Ma

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    Reliability, Effect Size, and Responsiveness and Intraclass Correlation of Health Status Measures Used in Randomized and Cluster-Randomized Trials, Paula Diehr, Lu Chen, Donald L. Patrick, Ziding Feng, and Yutaka Yasui

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    Selecting 'Significant' Differentially Expressed Genes from the Combined Perspective of the Null and the Alternative, Beatrijs Moerkerke and Els Goetghebeur

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    Semiparametric Analysis for Correlated Recurrent and Terminal Events, Yining Ye, Jack Kalbfleisch, and Doug E. Schaubel

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    Semiparametric Bayesian Modeling of Multivariate Average Bioequivalence, Pulak Ghosh Dr. and Mithat Gonen

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    Semiparametric Latent Variable Regression Models for Spatio-temporal Modeling of Mobile Source Particles in the Greater Boston Area, Alexandros Gryparis, Brent A. Coull, Joel Schwartz, and Helen H. Suh

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    Semiparametric Regression of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines and Linear Mixed Models, Dawei Liu, Xihong Lin, and Debashis Ghosh

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    Semiparametric Regression of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines and Linear Mixed Models, Dawei Liu, Xihong Lin, and Debashis Ghosh

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    Sequential Quantitative Trait Locus Mapping in Experimental Crosses, Jaya M. Satagopan, Saunak Sen, and Gary A. Churchill

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    Simple Records Matching Method for diagnostic and clinical datasets of patient’s records, Salvo Reina, Vito M. Reina, and Eugenio A. Debbia

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    Simultaneously Optimizing Dose and Schedule of a New Cytotoxic Agent, Thomas M. Braun, Peter F. Thall, Hoang Nguyen, and Marcos de Lima

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    Smoothed Rank Regression with Censored Data, glenn heller

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    Spatial Cluster Detection for Censored Outcome Data, Andrea J. Cook, Diane Gold, and Yi Li

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    Spatio-Temporal Analysis of Areal Data and Discovery of Neighborhood Relationships in Conditionally Autoregressive Models, Subharup Guha and Louise Ryan

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    Statistical Analysis of Air Pollution Panel Studies: An Illustration, Holly Janes, Lianne Sheppard, and Kristen Shepherd

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    Statistical Learning of Origin-Specific Statically Optimal Individualized Treatment Rules, Mark J. van der Laan and Maya L. Petersen

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    STATISTICAL METHODS FOR THE ANALYSIS OF CANCER GENOME SEQUENCING DATA, Giovanni Parmigiani, J. Lin, Simina Boca, T. Sjoblom, K.W. Kinzler, V.E. Velculescu, and B. Vogelstein

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    Structural Inference in Transition Measurement Error Models for Longitudinal Data, Wenqin Pan, Xihong Lin, and Donglin Zeng

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    Super Learning: An Application to Prediction of HIV-1 Drug Susceptibility, Sandra E. Sinisi, Maya L. Petersen, and Mark J. van der Laan

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    Supervised Detection of Conserved Motifs in DNA Sequences with cosmo, Oliver Bembom, Sunduz Keles, and Mark J. van der Laan

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    Survival Analysis Methods in Genetic Epidemiology, Hongzhe Li

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    Survival Analysis of Longitudinal Microarrays, Natasa Rajicic, Dianne M. Finkelstein, and David A. Schoenfeld

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    Survival Analysis with Change Point Hazard Functions, Melody S. Goodman, Yi Li, and Ram C. Tiwari

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    Targeted Maximum Likelihood Learning, Mark J. van der Laan and Daniel Rubin

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    The Combination of Ecological and Case-Control Data, Sebastien Haneuse and Jon Wakefield

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    The Two-sample Problem for Failure Rates Depending on a Continuous Mark: An Application to Vaccine Efficacy, Peter B. Gilbert, Ian W. McKeague, and Yanqing Sun

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    TRENDS IN PARTICULATE MATTER AND MORTALITY: AN APPROACH TO THE ASSESSMENT OF UNMEASURED CONFOUNDING, Holly Janes, Francesca Dominici, and Scott Zeger

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    USE OF HIDDEN MARKOV MODELS FOR QTL MAPPING, Karl W. Broman

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    Using Profile Likelihood for Semiparametric Model Selection with Application to Proportional Hazards Mixed Models, Ronghui Xu, Anthony Gamst, Michael Donohue, Florin Vaida, and David P. Harrington

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    Visualizing Genomic Data, Robert Gentleman, Florian Hahne, and Wolfgang Huber

 
 
 

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