Content Posted in 2004
2^k Factorials in Blocks of Size 2, with Application to Two-Color Microarray Experiments, Kathleen F. Kerr
A Bayesian Hierarchical Approach to Multirater Correlated ROC Analysis, Tim Johnson and Valen Johnson
A Bayesian method for finding interactions in genomic studies, Wei Chen, Debashis Ghosh, Trivellore E. Raghuanthan, and Sharon Kardia
A Bayesian Mixture Model Relating Dose to Critical Organs and Functional Complication in 3D Conformal Radiation Therapy, Tim Johnson, Jeremy Taylor, Randall K. Ten Haken, and Avraham Eisbruch
Accuracy of MSI Testing in Predicting Germline Mutations of MSH2 and MLH1: A Case Study in Bayesian Meta-Analysis of Diagnostic Tests Without a Gold Standard, Sining Chen, Patrice Watson, and Giovanni Parmigiani
A Cox Model for Biostatistics of the Future, Scott L. Zeger, Peter J. Diggle, and Kung-Yee Liang
A Functional-Based Distribution Diagnostic for a Linear Model with Correlated Outcomes: Technical Report, E. Andres Houseman, Brent Coull, and Louise Ryan
A graph theoretic approach to testing associations between disparate sources of functional genomic data, Raji Balasubramanian, Thomas LaFramboise, Denise Scholtens, and Robert Gentleman
A Hierarchical Multivariate Two-Part Model for Profiling Providers' Effects on Healthcare Charges, John W. Robinson, Scott L. Zeger, and Christopher B. Forrest
A Hypothesis Test for the End of a Common Source Outbreak, Ron Brookmeyer and Xiaojun You
A Marginal Model Approach for Analysis of Multi-reader Multi-test Receiver Operating Characteristic (ROC) Data, Xiao Song and Xiao-Hua Zhou
A Nonstationary Negative Binomial Time Series with Time-Dependent Covariates: Enterococcus Counts in Boston Harbor, E. Andres Houseman, Brent Coull, and James P. Shine
A Note on Empirical Likelihood Inference of Residual Life Regression, Ying Qing Chen and Yichuan Zhao
A Robust Regression Model for a First-Order Autoregressive Time Series with Unequal Spacing: Technical Report, E. Andres Houseman
A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data , Biao Xing and Mark J. van der Laan
Asymptotic Results for Simultaneous Group Sequential Analysis of Rank-Based and Weighted Kaplan-Meier Tests with Paired Survival Data in the Presence of Censoring. Technical report, Adin-Cristian Andrei and Susan Murray
Bayes Factors Based on Test Statistics, Valen Johnson
Bayesian Analysis for Penalized Spline Regression Using Win BUGS, Ciprian M. Crainiceanu, David Ruppert, and M.P. Wand
Bayesian Geostatistical Design, Peter J. Diggle and Soren Lophaven
Bayesian Hierarchical Distributed Lag Models for Summer Ozone Exposure and Cardio-Respiratory Mortality, Yi Huang, Francesca Dominici, and Michelle L. Bell
BayesMendel: An R Environment for Mendelian Risk Prediction, Sining Chen, Wenyi Wang, Karl Broman, Hormuzd A. Katki, and Giovanni Parmigiani
Binary isotonic regression procedures, with application to cancer biomarkers, Debashis Ghosh, Moulinath Banerjee, and Pinaki Biswas
Bioconductor: Open software development for computational biology and bioinformatics, Robert C. Gentleman, Vincent J. Carey, Douglas J. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J. Rossini, Guenther Sawitzki, Colin Smith, Gordon K. Smyth, Luke Tierney, Yee Hwa Yang, and Jianhua Zhang
Calibrating Observed Differential Gene Expression for the Multiplicity of Genes on the Array, Yingye Zheng and Margaret S. Pepe
Causal Inference in Hybrid Intervention Trials Involving Treatment Choice, Qi Long, Rod Little, and Xihong Lin
Censored Linear Regression for Case-Cohort Studies, Bin Nan, Menggang Yu, and Jack Kalbfleisch
Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data, Nicholas P. Jewell, Mark J. van der Laan, and Stephen Shiboski
Cholesky Residuals for Assessing Normal Errors in a Linear Model with Correlated Outcomes: Technical Report, E. Andres Houseman, Louise Ryan, and Brent Coull
Choosing Smoothness Parameters for Smoothing Splines by Minimizing and Estimate of Risk, Rafael A. Irizarry
Classification and selection of biomarkers in genomic data using LASSO, Debashis Ghosh and Arul Chinnaiyan
Classification Using Generalized Partial Least Squares, Beiying Ding and Robert Gentleman
Clustering and Classification Methods for Gene Expression Data Analysis, Elizabeth Garrett-Mayer and Giovanni Parmigiani
Covariate adjustment in the analysis of microarray data from clinical studies, Debashis Ghosh and Arul Chinnaiyan
Cross-study Validation and Combined Analysis of Gene Expression Microarray Data, Elizabeth Garrett-Mayer, Giovanni Parmigiani, Xiaogang Zhong, Leslie Cope, and Edward Gabrielson
Data Adaptive Estimation of the Treatment Specific Mean, Yue Wang, Oliver Bembom, and Mark J. van der Laan
Deletion/Substitution/Addition Algorithm for Partitioning the Covariate Space in Prediction, Annette Molinaro and Mark J. van der Laan
Differential Expression with the Bioconductor Project, Anja von Heydebreck, Wolfgang Huber, and Robert Gentleman
Does Weighting for Nonresponse Increase the Variance of Survey Means?, Rod Little and Sonya L. Vartivarian
Effect of Misreported Family History on Mendelian Mutation Prediction Models, Hormuzd A. Katki
Empirical and Kernel Estimation of Covariate Distribution Conditional on Survival Time, Xiaochun Li and Ronghui Xu
Error models for microarray intensities, Wolfgang Huber, Anja von Heydebreck, and Martin Vingron
Estimating a Survival Distribution with Current Status Data and High-Dimensional Covariates, Mark J. van der Laan and Aad van der Vaart
Estimating Percentile-Specific Causal Effects: A Case Study of Micronutrient Supplementation, Birth Weight, and Infant Mortality, Francesca Dominici, Scott L. Zeger, Giovanni Parmigiani, Joanne Katz, and Parul Christian
Estimation of Direct and Indirect Causal Effects in Longitudinal Studies, Mark J. van der Laan and Maya L. Petersen
Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome , Mark J. van der Laan, Alan E. Hubbard, and Nicholas P. Jewell
Finding cancer subtypes in microarray data using random projections, Debashis Ghosh
GLLAMM Manual, Sophia Rabe-Hesketh, Anders Skrondal, and Andrew Pickles
History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimes, Mark J. van der Laan and Maya L. Petersen
Incorporating Death into Health-Related Variables in Longitudinal Studies, Paula Diehr, Laura Lee Johnson, Donald L. Patrick, and Bruce Psaty
Individualized predictions of disease progression following radiation therapy for prostate cancer., Jeremy Taylor, Menggang Yu, and Howard M. Sandler
Individual Prediction in Prostate Cancer Studies Using a Joint Longitudinal-Survival-Cure Model, Menggang Yu, Jeremy Taylor, and Howard M. Sandler
Inequity Measures for Evaluations of Environmental Justice: A Case Study of Close Proximity to Highways in NYC, Jerry O. Jacobson, Nicolas W. Hengartner, and Thomas A. Louis
LIKELIHOOD ESTIMATION OF CONJUGACY RELATIONSHIPS IN LINEAR MODELS WITH APPLICATIONS TO HIGH-THROUGHPUT GENOMICS, Brian S. Caffo, Liu Dongmei, Robert Scharpf, and Giovanni Parmigiani
Linear Life Expectancy Regression with Censored Data, Ying Qing Chen and Su-Chun Cheng
Loss-Based Cross-Validated Deletion/Substitution/Addition Algorithms in Estimation, Sandra E. Sinisi and Mark J. van der Laan
Mean Response Models of Repeated Measurements in Presence of Varying Effectiveness Onset, Ying Qing Chen and Su-Chun Cheng
MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data, Leslie Cope, Xiaogang Zhong, Elizabeth S. Garrett-Mayer, and Giovanni Parmigiani
Mixture models for assessing differential expression in complex tissues using microarray data, Debashis Ghosh
Model checking techniques for regression models in cancer screening, Debashis Ghosh
Model Choice in Time Series Studies of Air Pollution and Mortality, Roger D. Peng, Francesca Dominici, and Thomas A. Louis
Monotone Constrained Tensor-product B-spline with application to screening studies, Yue Wang and Jeremy Taylor
Multiple Imputation For Interval Censored Data With Auxiliary Variables, Chiu-Hsieh Hsu, Jeremy Taylor, and Susan Murray
Multiple Lab Comparison of Microarray Platforms, Rafael A. Irizarry et al.
Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data, Merrill D. Birkner, Sandra E. Sinisi, and Mark J. van der Laan
Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data, Sunduz Keles, Mark J. van der Laan, Sandrine Dudoit, and Simon E. Cawley
Multiple Testing. Part III. Procedures for Control of the Generalized Family-Wise Error Rate and Proportion of False Positives, Mark J. van der Laan, Sandrine Dudoit, and Katherine S. Pollard
Multiple Testing Procedures for Controlling Tail Probability Error Rates, Sandrine Dudoit, Mark J. van der Laan, and Merrill D. Birkner
Multiple Testing Procedures: R multtest Package and Applications to Genomics, Katherine S. Pollard, Sandrine Dudoit, and Mark J. van der Laan
Nonparametric and semiparametric inference for models of tumor size and metastasis, Debashis Ghosh
Nonparametric Confidence Intervals for the One- and Two-Sample Problems, Xiao-Hua Zhou and Phillip Dinh
Non-Parametric Estimation of ROC Curves in the Absence of a Gold Standard, Xiao-Hua Zhou, Pete Castelluccio, and Chuan Zhou
Nonparametric methods for analyzing replication origins in genomewide data, Debashis Ghosh
On Corrected Score Approach for Proportional Hazards Model with Covariate Measurement Error, Xiao Song and Yijian Huang
One- and Two-Sample Nonparametric Inference Procedures in the Presence of Dependent Censoring, Yuhyun Park, Lu Tian, and L. J. Wei
On the Accelerated Failure Time Model for Current Status and Interval Censored Data, Lu Tian and Tianxi Cai
On Time Series Analysis of Public Health and Biomedical Data, Scott L. Zeger, Rafael A. Irizarry, and Roger D. Peng
Optimal Sample Size for Multiple Testing: the Case of Gene Expression Microarrays, Peter Muller, Giovanni Parmigiani, Christian Robert, and Judith Rousseau
Optimal Sampling Times in Bioequivalence Studies Using a Simulated Annealing Algorithm , Leena Choi, Brian Caffo, and Charles Rohde
Ozone and Mortality: A Meta-Analysis of Time-Series Studies and Comparison to a Multi-City Study (The National Morbidity, Mortality, and Air Pollution Study), Michelle L. Bell, Jonathan M. Samet, and Francesca Dominici
Piecewise Constant Cross-Ratio Estimation for Association in Bivariate Survival Data with Application to Studying Markers of Menopausal Transition, Bin Nan, Xihong Lin, Lynda D. Lisabet, and Sioban Harlow
Point Process Methodology for On-line Spatio-temporal Disease Surveillance, Peter J. Diggle, Barry Rowlingson, and Ting-li Su
Power and Robustness of Linkage Tests for Quantitative Traits in General Pedigrees, Weimin Chen, Karl Broman, and Kung-Yee Liang
Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks, Yan Wang and Sandrine Dudoit
Quantifying and Comparing the Accuracy of Binary Biomarkers When Predicting a Failure Time Outcome, Chaya S. Moskowitz and Margaret S. Pepe
Quantitative Methods for Tracking Cognitive Change 3 Years After Coronary Artery Bypass Surgery, Sarah Barry; Scott L. Zeger; Ola A. Selnes; Maura A. Grega; Louis M. Borowicz, Jr.; and Guy M. McKhann
Ranking USRDS Provider-Specific SMRs from 1998-2001, Rongheng Lin, Thomas A. Louis, Susan M. Paddock, and Greg Ridgeway
Regulatory Motif Finding by Logic Regression, Sunduz Keles, Mark J. van der Laan, and Chris Vulpe
Reproducible Research: A Bioinformatics Case Study, Robert Gentleman
Resampling methods for estimating functions with U-statistic structure, Wenyu Jiang and Jack Kalbfleisch
Screening for Differentially Expressed Genes: Are Multilevel Models Helpful?, Dongmei Liu, Giovanni Parmigiani, and Brian Caffo
Seasonal Analyses of Air Pollution and Mortality in 100 U.S. Cities, Roger D. Peng, Francesca Dominici, Roberto Pastor-Barriuso, Scott L. Zeger, and Jonathan M. Samet
Self-Reported Memory Symptoms with Coronary Artery Disease: A Prospective of CABG Patients and Nonsurgical Controls, Ola A. Selnes; Maura A. Grega; Louis M. Borowicz, Jr.; Sarah Barry; Scott L. Zeger; and Guy M. McKhann
Semiparametic models and estimation procedures for binormal ROC curves with multiple biomarkers, Debashis Ghosh
Semiparametric binary regression under monotonicity constraints, Moulinath Banerjee, Pinaki Biswas, and Debashis Ghosh
Semiparametric methods for identification of tumor progression genes from microarray data, Debashis Ghosh and Arul Chinnaiyan
Semiparametric Methods for Semi-competing Risks Problem with Censoring and Truncation, Hongyu Jiang, Jason Fine, and Richard J. Chappell
Semiparametric methods for the binormal model with multiple biomarkers, Debashis Ghosh
Semiparametric Quantitative-Trait-Locus Mapping: II. on Censored Age-at-Onset, Ying Qing Chen, Chengcheng Hu, and Rongling Wu
Semiparametric Quantitative-Trait-Locus Mapping: I. on Functional Growth Curves, Ying Qing Chen and Rongling Wu
Semiparametric Regression Analysis of Mean Residual Life with Censored Survival Data, Ying Qing Chen and Su-Chun Cheng
Semiparametric Regression in Capture-Recapture Modelling, O. Gimenez, C. Barbraud, Ciprian M. Crainiceanu, S. Jenouvrier, and B.T. Morgan
Semi-parametric Single-index Two-Part Regression Models, Xiao-Hua Zhou and Hua Liang
Significance Analysis of Time Course Microarray Experiments, John D. Storey, Wenzhong Xiao, Jeffrey T. Leek, Ronald G. Tompkins, and Ron W. Davis
Spatially Adaptive Bayesian P-Splines with Heteroscedastic Errors, Ciprian M. Crainiceanu, David Ruppert, and Raymond J. Carroll
Squared Extrapolation Methods (SQUAREM): A New Class of Simple and Efficient Numerical Schemes for Accelerating the Convergence of the EM Algorithm, Ravi Varadhan and Ch. Roland
Statistical Analyses and Reproducible Research, Robert Gentleman and Duncan Temple Lang
Studying Effects of Primary Care Physicians and Patients on the Trade-Off Between Charges for Primary Care and Specialty Care Using a Hierarchical Multivariate Two-Part Model, John W. Robinson, Scott L. Zeger, and Christopher B. Forrest
Survival Analysis Using Auxiliary Variables Via Nonparametric Multiple Imputation, Chiu-Hsieh Hsu, Jeremy Taylor, Susan Murray, and Daniel Commenges
Survival Point Estimate Prediction in Matched and Non-Matched Case-Control Subsample Designed Studies, Annette M. Molinaro, Mark J. van der Laan, Dan H. Moore, and Karla Kerlikowske
The Cross-Validated Adaptive Epsilon-Net Estimator, Mark J. van der Laan, Sandrine Dudoit, and Aad W. van der Vaart
The false discovery rate: a variable selection perspective, Debashis Ghosh, Wei Chen, and Trivellore E. Raghuanthan
The Genomes of Recombinant Inbred Lines: The Gory Details, Karl W. Broman
The National Morbidity, Mortality, and Air Pollution Study Database in R, Roger D. Peng, Leah J. Welty, and Aidan McDermott
The Optimal Confidence Region for a Random Parameter, Hajime Uno, Lu Tian, and L.J. Wei
The Proportional Odds Model for Assessing Rater Agreement with Multiple Modalities, Elizabeth Garrett-Mayer, Steven N. Goodman, and Ralph H. Hruban
When Should One Substract Background Fluorescence in Two Color Microarrays?, Robert B. Scharpf, Christine A. Iacobuzio-Donahue, Julie B. Sneddon, and Giovanni Parmigiani