Biology & Genetics

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Finding quantitative trait loci genes with collaborative targeted maximum likelihood learning (with Hui Wang and Sherri Rose), Statistics & Probability Letters (2010)
 

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Targeted Maximum Likelihood Method for Repeated Measures Semiparametric Regression: Discovery for Transcription Factor Activity (with Catherine Tuglus), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 
An Application of Collaborative Targeted Maximum Likelihood Estimation in Causal Inference and Genomics (with Susan Gruber), The International Journal of Biostatistics (2010)
 
Modified FDR Controlling Procedure for Multi-Stage Analyses (with Catherine Tuglus), Statistical Applications in Genetics and Molecular Biology (2009)
 
Supervised Distance Matrices (with Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2008)
 

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Supervised detection of conserved motifs in DNA sequences with cosmo (with Oliver Bembom and Sunduz Keles), Statistical Applications in Genetics and Molecular Biology (2007)
 
A Comparison of Methods to Control Type I Errors in Microarray Studies (with Jinsong Chen, Martyn T. Smith, and Alan E. Hubbard), Statistical Applications in Genetics and Molecular Biology (2007)
 
Super Learning: An Application to the Prediction of HIV-1 Drug Resistance (with Sandra E. Sinisi, Eric C. Polley, Maya L. Petersen, and Soo-Yon Rhee), Statistical Applications in Genetics and Molecular Biology (2007)
 
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (with Oliver Bembom and Sunduz Keles), Statistical Applications in Genetics and Molecular Biology (2007)
 
Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data (with Merrill D. Birkner, Alan E. Hubbard, Christine F. Skibola, Christine M. Hegedus, and Martyn T. Smith), Statistical Applications in Genetics and Molecular Biology (2006)
 
Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics (with Sandra E. Sinisi), Statistical Applications in Genetics and Molecular Biology (2006)
 
Supervised Detection of Regulatory Motifs in DNA Sequences (with Sunduz Keles, Sandrine Dudoit, Biao Xing, and Michael B. Eisen), Statistical Applications in Genetics and Molecular Biology (2006)
 

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Supervised Detection of Conserved Motifs in DNA Sequences with cosmo (with Oliver Bembom and Sunduz Keles), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Multiple Testing Methods For ChIP–Chip High Density Oligonucleotide Array Data (with Sündüz Keleş, Sandrine Dudoit, and Simon E. Cawley), Journal of Computational Biology (2006)
 

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Multiple Tests of Association with Biological Annotation Metadata (with Sandrine Dudoit and Sunduz Keles), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Application of a Variable Importance Measure Method to HIV-1 Sequence Data (with Merrill D. Birkner), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Colon cancer prognosis prediction by gene expression profiling (with Alain Barrier, Antoinette Lemoine, Pierre-Yves Boelle, Chantal Tse, Didier Brault, Franck Chiappini, Julia Breittschneider, François Lacaine, Sidney Houry, Michel Huguier, Terry Speed, Brigitte Debuire, Antoine Flahault, and Sandrine Dudoit), Oncogene (2005)
 

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Colon Cancer Prognosis Prediction by Gene Expression Profiling (with Alain Barrier and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Colon Cancer Prognosis Prediction by Gene Expression Profiling (with Alain Barrier and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling (with Alain Barrier and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling (with Alain Barrier and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Multiple Testing Procedures: R multtest Package and Applications to Genomics (with Katherine S. Pollard and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (with Sunduz Keles, Sandrine Dudoit, and Simon E. Cawley), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Regulatory Motif Finding by Logic Regression (with Sunduz Keles and Chris Vulpe), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data (with Biao Xing), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Supervised Detection of Regulatory Motifs in DNA Sequences (with Sunduz Keles, Sandrine Dudoit, Biao Xing, and Michael B. Eisen), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Comparative Genomic Hybridization Array Analysis (with Annette M. Molinaro and Dan H. Moore), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Identification of Regulatory Elements Using A Feature Selection Method (with Sunduz Keles and Michael B. Eisen), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 

Causal Inference

A Targeted Maximum Likelihood Estimator for Two-Stage Designs (with Sherri Rose), The International Journal of Biostatistics (2011)
 

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Asymptotic Theory for Cross-validated Targeted Maximum Likelihood Estimation (with Wenjing Zheng), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Diagnosing and Responding to Violations in the Positivity Assumption (with Maya L. Petersen, Kristin Porter, Susan Gruber, and Yue Wang), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Estimation of Causal Effects of Community Based Interventions, U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Collaborative Targeted Maximum Likelihood For Time To Event Data (with Ori M. Stitelman), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Targeted Maximum Likelihood Based Causal Inference, U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 
An Application of Collaborative Targeted Maximum Likelihood Estimation in Causal Inference and Genomics (with Susan Gruber), The International Journal of Biostatistics (2010)
 
A Targeted Maximum Likelihood Estimator of a Causal Effect on a Bounded Continuous Outcome (with Susan Gruber), The International Journal of Biostatistics (2010)
 
Collaborative Double Robust Targeted Maximum Likelihood Estimation (with Susan Gruber), The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Based Causal Inference: Part I, The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Based Causal Inference: Part II, The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Estimation of the Parameter of a Marginal Structural Model (with Michael Rosenblum), The International Journal of Biostatistics (2010)
 
Why Match? Investigating Matched Case-Control Study Designs with Causal Effect Estimation (with Sherri Rose), The International Journal of Biostatistics (2009)
 

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Estimation Based on Case-Control Designs with Known Incidence Probability, U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 
Estimation Based on Case-Control Designs with Known Prevalence Probability, The International Journal of Biostatistics (2008)
 
Simple Optimal Weighting of Cases and Controls in Case-Control Studies (with Sherri Rose), The International Journal of Biostatistics (2008)
 

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Statistical Methods for Analyzing Sequentially Randomized Trials (with Oliver Bembom), Journal of the National Cancer Institute (2007)
 

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A Note on Targeted Maximum Likelihood and Right Censored Data (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Biomarker discovery using targeted maximum likelihood estimation: Application to the treatment of antiretroviral resistant HIV infection (with Oliver Bembom, Maya L. Petersen, Soo-Yon Rhee, W. Jeffrey Fessel, Sandra E. Sinisi, and Robert W. Shafer), Oliver Bembom (2007)
 

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Data-adaptive estimation of the treatment-specific mean (with Yue Wang and Oliver Bembom), Journal of Statistical Planning and Inference (2007)
 

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Analyzing Sequentially Randomized Trials Based on Causal Effect Models for Realistic Individualized Treatment Rules (with Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Analyzing Sequentially Randomized Trials based on Causal Effect Models for Realistic Individualized Treatment Rules (with Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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The causal effect of recent leisure-time physical activity on all-cause mortality among the elderly (with Oliver Bembom and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 
Causal Effect Models for Realistic Individualized Treatment and Intention to Treat Rules (with Maya L. Petersen), The International Journal of Biostatistics (2007)
 

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Causal Effect Models for Intention to Treat and Realistic Individualized Treatment Rules, U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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A Causal Inference Approach for Constructing Transcriptional Regulatory Networks (with Biao Xing), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

Clinical Epidemiology

Targeted Maximum Likelihood Estimation of Natural Direct Effects (with Wenjing Zheng), The International Journal of Biostatistics (2012)
 
Targeted Maximum Likelihood Estimation of Effect Modification Parameters in Survival Analysis (with Ori M. Stitelman, C. William Wester, and Victor De Gruttola), The International Journal of Biostatistics (2012)
 

Link

Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials (with Michael Rosenblum, Nicholas P. Jewell, Steven Shiboski, Ariane van der Straten, and Nancy Padian), Journal of the Royal Statistical Society, Series A, (Statistics in Society) (2009)
 
Long-term consequences of the delay between virologic failure of highly active antiretroviral therapy and regimen modification (with Maya L. Petersen, Napravnik Sonia, Joseph J. Eron, Richard G. Moore, and Steven G. Deeks), AIDS (2008)
 
History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification (with Maya Petersen, Steven Deeks, and Jefferey Martin), American Journal of Epidemiology (2007)
 

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Pillbox Organizers are Associated with Improved Adherence to HIV Antiretroviral Therapy and Viral Suppression: A Marginal Structural Model Analysis. (with Maya Petersen, Yue Wang, David Guzman, Elise Riley, and David Bangsberg), Clinical Infectious Diseases (2007)
 

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Biomarker Discovery Using Targeted Maximum Likelihood Estimation: Application to the Treatment of Antiretroviral Resistant HIV Infection (with Oliver Bembom, Maya L. Petersen , Soo-Yon Rhee , W. Jeffrey Fessel , Sandra E. Sinisi, and Robert W. Shafer), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Virologic Efficacy of Boosted Double vs. Boosted Single Protease Inhibitor Therapy. (with Maya Petersen, Yue Wang, Soo-Yon Rhee, Robert Shafer, and W. Jefferey Fessel), AIDS (2007)
 
History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimens (with Maya L. Petersen and Marshall M. Joffe), The International Journal of Biostatistics (2006)
 

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Estimation of direct causal effects. (with Maya L. Petersen and Sandra E. Sinisi), Epidemiology (2006)
 

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Super Learning: an Application to Prediction of HIV-1 Drug Susceptibility (with Sandra E. Sinisi and Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

Clinical Trials

Targeted Maximum Likelihood Estimation of Natural Direct Effects (with Wenjing Zheng), The International Journal of Biostatistics (2012)
 
Targeting the Optimal Design in Randomized Clinical Trials with Binary Outcomes and No Covariate: Simulation Study (with Antoine Chambaz), The International Journal of Biostatistics (2011)
 
Targeting the Optimal Design in Randomized Clinical Trials with Binary Outcomes and No Covariate: Theoretical Study (with Antoine Chambaz), The International Journal of Biostatistics (2011)
 

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Targeting The Optimal Design In Randomized Clinical Trials With Binary Outcomes And No Covariate (with Antoine Chambaz), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 
Targeted Maximum Likelihood Based Causal Inference: Part I, The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Based Causal Inference: Part II, The International Journal of Biostatistics (2010)
 

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Application of Time-to-Event Methods in the Assessment of Safety in Clinical Trials (with Kelly L. Moore), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials (with Michael Rosenblum, Nicholas P. Jewell, Steven Shiboski, Ariane van der Straten, and Nancy Padian), Journal of the Royal Statistical Society, Series A, (Statistics in Society) (2009)
 

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Selecting Optimal Treatments Based on Predictive Factors (with Eric C. Polley), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Targeted Methods for Biomarker Discovery, the Search for a Standard (with Catherine Tuglus), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Covariate Adjustment for the Intention-to-Treat Parameter with Empirical Efficiency Maximization (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Individualized treatment rules: Generating candidate clinical trials (with Maya Petersen and Steven G. Deeks), Statistics in Medicine (2007)
 

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Empirical Efficiency Maximization (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Diaphragm and lubricant gel for prevention of HIV acquisition in southern African women: a randomised controlled trial (with Nancy Padian, Ariane van der Straten, Gita Ramjee, Tsungai Chipato, Guy de Bruyn, Kelly Blanchard, Stephen Shiboski, Elizabeth T. Montgomery, Heidi Fancher, Helen Cheng, Michael Rosenblum, Nicholas Jewell, and James McIntyre), The Lancet (2007)
 

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Analyzing Sequentially Randomized Trials Based on Causal Effect Models for Realistic Individualized Treatment Rules (with Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 
Analyzing Direct Effects in Randomized Trials with Secondary Interventions (with Michael Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), Nicholas P. Jewell (2007)
 
Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome (with Alan E. Hubbard and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome (with Alan E. Hubbard and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimation of Direct and Indirect Causal Effects in Longitudinal Studies (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Comparison of the Inverse Probability of Treatment Weighted (IPTW) Estimator With a Naïve Estimator in the Analysis of Longitudinal Data With Time-Dependent Confounding: A Simulation Study (with Thaddeus Haight, Romain Neugebauer, and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Measuring Treatment Effects Using Semiparametric Models (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Estimating Causal Parameters in Marginal Structural Models with Unmeasured Confounders Using Instrumental Variables (with Tanya A. Henneman and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

Computational Biology/Bioinformatics

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Permutation-based Pathway Testing using the Super Learner Algorithm (with Paul Chaffee and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Resampling-Based Multiple Hypothesis Testing with Applications to Genomics: New Developments in the R/Bioconductor Package multtest (with Houston N. Gilbert, Katherine S. Pollard, and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Joint Multiple Testing Procedures for Graphical Model Selection with Applications to Biological Networks (with Houston N. Gilbert and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 
Supervised Distance Matrices (with Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2008)
 
A Comparison of Methods to Control Type I Errors in Microarray Studies (with Jinsong Chen, Martyn T. Smith, and Alan E. Hubbard), Statistical Applications in Genetics and Molecular Biology (2007)
 
Super Learner (with Eric C. Polley and Alan E. Hubbard), Statistical Applications in Genetics and Molecular Biology (2007)
 
Super Learning: An Application to the Prediction of HIV-1 Drug Resistance (with Sandra E. Sinisi, Eric C. Polley, Maya L. Petersen, and Soo-Yon Rhee), Statistical Applications in Genetics and Molecular Biology (2007)
 
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (with Oliver Bembom and Sunduz Keles), Statistical Applications in Genetics and Molecular Biology (2007)
 
Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data. (with Merrill D. Birkner and Sandra E. Sinisi), Statistical Applications in Genetics and Molecular Biology (2006)
 
Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics (with Sandra E. Sinisi), Statistical Applications in Genetics and Molecular Biology (2006)
 
Supervised Detection of Regulatory Motifs in DNA Sequences (with Sunduz Keles, Sandrine Dudoit, Biao Xing, and Michael B. Eisen), Statistical Applications in Genetics and Molecular Biology (2006)
 

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Super Learning: an Application to Prediction of HIV-1 Drug Susceptibility (with Sandra E. Sinisi and Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Data Adaptive Pathway Testing (with Merrill D. Birkner and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Cluster Analysis of Genomic Data with Applications in R (with Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Statistical Inference for Simultaneous Clustering of Gene Expression Data (with Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Paired and Unpaired Comparisons and Clustering with Gene Expression Data (with Jennifer F. Bryan and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Hybrid Clustering of Gene Expression Data with Visualization and the Bootstrap (with Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Gene Expression Analysis with the Parametric Bootstrap (with Jennifer F. Bryan), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 

Epidemiology

Targeted Maximum Likelihood Estimation of Natural Direct Effects (with Wenjing Zheng), The International Journal of Biostatistics (2012)
 
Antihypertensive Medication Use and Change in Kidney Function in Elderly Adults: A Marginal Structural Model Analysis (with Michelle C. Odden, Ira B. Tager, Joseph A.C. Delaney, Carmen A. Peralta, Ronit Katz, Mark J. Sarnak, Bruce M. Psaty, and Michael G. Shlipak), The International Journal of Biostatistics (2012)
 

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Threshold Regression Models Adapted to Case-Control Studies, and the Risk of Lung Cancer Due to Occupational Exposure to Asbestos in France (with Antoine Chambaz, Dominique Choudat, Catherine Huber, and Jean-Claude Pairon), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 
A Targeted Maximum Likelihood Estimator for Two-Stage Designs (with Sherri Rose), The International Journal of Biostatistics (2011)
 

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Causal Inference in Epidemiological Studies with Strong Confounding (with Kelly L. Moore, Romain S. Neugebauer, and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Causal Inference for Nested Case-Control Studies using Targeted Maximum Likelihood Estimation (with Sherri Rose), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 
Why Match? Investigating Matched Case-Control Study Designs with Causal Effect Estimation (with Sherri Rose), The International Journal of Biostatistics (2009)
 

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A Note on Risk Prediction for Case-Control Studies (with Sherri Rose), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Doubly Robust Ecological Inference (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Estimation Based on Case-Control Designs with Known Incidence Probability, U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Targeted Methods for Biomarker Discovery, the Search for a Standard (with Catherine Tuglus), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 
Estimation Based on Case-Control Designs with Known Prevalence Probability, The International Journal of Biostatistics (2008)
 
Simple Optimal Weighting of Cases and Controls in Case-Control Studies (with Sherri Rose), The International Journal of Biostatistics (2008)
 
History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification (with Maya Petersen, Steven Deeks, and Jefferey Martin), American Journal of Epidemiology (2007)
 

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Empirical Efficiency Maximization (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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The Causal Effect of Recent Leisure-Time Physical Activity on All-Cause Mortality Among the Elderly (with Oliver Bembom and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 
Analyzing Direct Effects in Randomized Trials with Secondary Interventions (with Michael Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), Nicholas P. Jewell (2007)
 
History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimens (with Maya L. Petersen and Marshall M. Joffe), The International Journal of Biostatistics (2006)
 

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Extending Marginal Structural Models through Local, Penalized, and Additive Learning (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Estimation of direct causal effects. (with Maya L. Petersen and Sandra E. Sinisi), Epidemiology (2006)
 

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History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification (with Maya L. Petersen, Steven G. Deeks, and Jeffrey N. Martin), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Population Intervention Models in Causal Inference (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Estimation of Direct Causal Effects (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Direct Effect Models (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Causal Inference in Longitudinal Studies with History-Restricted Marginal Structural Models (with Romain Neugebauer and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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History-Adjusted Marginal Structural Models: Optimal Treatment Strategies (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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History-Adjusted Marginal Structural Models: Time-Varying Effect Modification (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Data Adaptive Estimation of the Treatment Specific Mean (with Yue Wang and Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimes (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome (with Alan E. Hubbard and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome (with Alan E. Hubbard and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimation of Direct and Indirect Causal Effects in Longitudinal Studies (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (with Sunduz Keles, Sandrine Dudoit, and Simon E. Cawley), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Analysis of Longitudinal Marginal Structural Models (with Jennifer F. Bryan and Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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An Empirical Study of Marginal Structural Models for Time-Independent Treatment (with Tanya A. Henneman), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Case-Control Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Case-Control Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Current Status Data: Review, Recent Developments and Open Problems (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Current Status Data: Review, Recent Developments and Open Problems (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Estimating Causal Parameters in Marginal Structural Models with Unmeasured Confounders Using Instrumental Variables (with Tanya A. Henneman and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Efficient Estimation of the Lifetime and Disease Onset Distribution (with Nicholas P. Jewell and Derick R. Peterson), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 

HIV

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Observational Study and Individualized Antiretroviral Therapy Initiation Rules for Reducing Cancer Incidence in HIV-Infected Patients (with Romain Neugebauer and Michael J. Silverberg), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials (with Michael Rosenblum, Nicholas P. Jewell, Steven Shiboski, Ariane van der Straten, and Nancy Padian), Journal of the Royal Statistical Society, Series A, (Statistics in Society) (2009)
 
Biomarker discovery using targeted maximum-likelihood estimation: Application to the treatment of antiretroviral-resistant HIV infection (with Oliver Bembom, Maya L. Petersen, Soo-Yon Rhee, W Jeffrey Fessel, Sandra E. Sinisi, and Robert W. Shafer), Statstics in Medicine (2008)
 
Long-term consequences of the delay between virologic failure of highly active antiretroviral therapy and regimen modification (with Maya L. Petersen, Napravnik Sonia, Joseph J. Eron, Richard G. Moore, and Steven G. Deeks), AIDS (2008)
 
History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification (with Maya Petersen, Steven Deeks, and Jefferey Martin), American Journal of Epidemiology (2007)
 

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Individualized treatment rules: Generating candidate clinical trials (with Maya Petersen and Steven G. Deeks), Statistics in Medicine (2007)
 

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Pillbox Organizers are Associated with Improved Adherence to HIV Antiretroviral Therapy and Viral Suppression: A Marginal Structural Model Analysis. (with Maya Petersen, Yue Wang, David Guzman, Elise Riley, and David Bangsberg), Clinical Infectious Diseases (2007)
 

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Biomarker Discovery Using Targeted Maximum Likelihood Estimation: Application to the Treatment of Antiretroviral Resistant HIV Infection (with Oliver Bembom, Maya L. Petersen , Soo-Yon Rhee , W. Jeffrey Fessel , Sandra E. Sinisi, and Robert W. Shafer), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Diaphragm and lubricant gel for prevention of HIV acquisition in southern African women: a randomised controlled trial (with Nancy Padian, Ariane van der Straten, Gita Ramjee, Tsungai Chipato, Guy de Bruyn, Kelly Blanchard, Stephen Shiboski, Elizabeth T. Montgomery, Heidi Fancher, Helen Cheng, Michael Rosenblum, Nicholas Jewell, and James McIntyre), The Lancet (2007)
 

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Virologic Efficacy of Boosted Double vs. Boosted Single Protease Inhibitor Therapy. (with Maya Petersen, Yue Wang, Soo-Yon Rhee, Robert Shafer, and W. Jefferey Fessel), AIDS (2007)
 

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Identifying important explanatory variables for time-varying outcomes. (with Oliver Bembom and Maya L. Petersen), Fundamentals of Data Mining in Genomics and Proteomics (2006)
 

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Super Learning: an Application to Prediction of HIV-1 Drug Susceptibility (with Sandra E. Sinisi and Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Application of a Variable Importance Measure Method to HIV-1 Sequence Data (with Merrill D. Birkner), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

Longitudinal Data Analysis and Time Series

Targeted Minimum Loss Based Estimation of Causal Effects of Multiple Time Point Interventions (with Susan Gruber), The International Journal of Biostatistics (2012)
 

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Targeted Maximum Likelihood Estimation for Dynamic Treatment Regimes in Sequential Randomized Controlled Trials (with Paul Chaffee), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 
Biomarker discovery using targeted maximum-likelihood estimation: Application to the treatment of antiretroviral-resistant HIV infection (with Oliver Bembom, Maya L. Petersen, Soo-Yon Rhee, W Jeffrey Fessel, Sandra E. Sinisi, and Robert W. Shafer), Statstics in Medicine (2008)
 
Long-term consequences of the delay between virologic failure of highly active antiretroviral therapy and regimen modification (with Maya L. Petersen, Napravnik Sonia, Joseph J. Eron, Richard G. Moore, and Steven G. Deeks), AIDS (2008)
 
History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification (with Maya Petersen, Steven Deeks, and Jefferey Martin), American Journal of Epidemiology (2007)
 

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Individualized treatment rules: Generating candidate clinical trials (with Maya Petersen and Steven G. Deeks), Statistics in Medicine (2007)
 

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Detailed Version: Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials (with Michael A. Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Analyzing Direct Effects in Randomized Trials with Secondary Interventions (with Michael Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Identifying important explanatory variables for time-varying outcomes. (with Oliver Bembom and Maya L. Petersen), Fundamentals of Data Mining in Genomics and Proteomics (2006)
 
History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimens (with Maya L. Petersen and Marshall M. Joffe), The International Journal of Biostatistics (2006)
 

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Individualized Treatment Rules: Generating Candidate Clinical Trials (with Maya L. Petersen and Steven G. Deeks), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Direct Effect Models (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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G-computation Estimation of Nonparametric Causal Effects on Time-Dependent Mean Outcomes in Longitudinal Studies (with Romain Neugebauer), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Causal Inference in Longitudinal Studies with History-Restricted Marginal Structural Models (with Romain Neugebauer and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Estimation of Direct and Indirect Causal Effects in Longitudinal Studies (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Comparison of the Inverse Probability of Treatment Weighted (IPTW) Estimator With a Naïve Estimator in the Analysis of Longitudinal Data With Time-Dependent Confounding: A Simulation Study (with Thaddeus Haight, Romain Neugebauer, and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Locally Efficient Estimation of Nonparametric Causal Effects on Mean Outcomes in Longitudinal Studies (with Romain Neugebauer), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Double Robust Estimation in Longitudinal Marginal Structural Models (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Construction of Counterfactuals and the G-computation Formula (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Analysis of Longitudinal Marginal Structural Models (with Jennifer F. Bryan and Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Estimating Causal Parameters in Marginal Structural Models with Unmeasured Confounders Using Instrumental Variables (with Tanya A. Henneman and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Locally Efficient Estimation of a Multivariate Survival Function in Longitudinal Studies (with Alan E. Hubbard and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 
Estimation with Interval Censored Data in Longitudinal Studies, U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Locally Efficient Estimation of the Survival Distribution with Right Censored Data and Covariates When Collection of Data is Delayed (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Locally Efficient Estimation with Current Status Data and Time-Dependent Covariates (with James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 

Loss-Based Estimation with Cross-Validation

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A deletion/substitution/addition algorithm for classification neural networks, with applications to biomedical data (with Blythe Durbin and Sandrine Dudoit), Journal of Statistical Planning and Inference (2008)
 
Asymptotic Optimality of Likelihood-Based Cross-Validation (with Sandrine Dudoit and Sunduz Keles), Statistical Applications in Genetics and Molecular Biology (2006)
 

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Oracle inequalities for multi-fold cross validation (with Aad W. van der Vaart and Sandrine Dudoit), Statistics & Decisions (2006)
 

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The cross-validated adaptive epsilon-net estimator (with Sandrine Dudoit and Aad W. van der Vaart), Statistics & Decisions (2006)
 

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Estimating Function Based Cross-Validation and Learning (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Survival Ensembles (with Torsten Hothorn, Peter Buhlmann, Sandrine Dudoit, and Annette M. Molinaro), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Optimization of the Architecture of Neural Networks Using a Deletion/Substitution/Addition Algorithm (with Blythe Durbin and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
The Cross-Validated Adaptive Epsilon-Net Estimator (with Sandrine Dudoit and Aad W. van der Vaart), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding (with Sandrine Dudoit, Sunduz Keles, Annette M. Molinaro, Sandra E. Sinisi, and Siew Leng Teng), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 
Asymptotically Optimal Model Selection Method with Right Censored Outcomes (with Sunduz Keles and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 
Tree-based Multivariate Regression and Density Estimation with Right-Censored Data (with Annette M. Molinaro and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 
Asymptotic Optimality of Likelihood Based Cross-Validation (with Sandrine Dudoit and Sunduz Keles), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 
Asymptotics of Cross-Validated Risk Estimation in Estimator Selection and Performance Assessment (with Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

Multiple Hypothesis Testing

Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (with Sandrine Dudoit and Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates (with Sandrine Dudoit and Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives (with Sandrine Dudoit and Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2006)
 
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (with Daniel Rubin and Sandrine Dudoit), Statistical Applications in Genetics and Molecular Biology (2006)
 
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (with Daniel Rubin and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Test statistics null distributions in multiple testing: Simulation studies and applications to genomics (with Katherine S. Pollard, Merrill D. Birkner, and Sandrine Dudoit), Journal de la Société Française de Statistique (2005)
 
Test Statistics Null Distributions in Multiple Testing: Simulation Studies and Applications to Genomics (with Katherine S. Pollard, Merrill D. Birkner, and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Multiple Testing Procedures and Applications to Genomics (with Merrill D. Birkner, Katherine S. Pollard, and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 
Multiple Testing Procedures for Controlling Tail Probability Error Rates (with Sandrine Dudoit and Merrill D. Birkner), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Multiple Testing Procedures: R multtest Package and Applications to Genomics (with Katherine S. Pollard and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (with Sunduz Keles, Sandrine Dudoit, and Simon E. Cawley), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Multiple Testing. Part III. Procedures for Control of the Generalized Family-Wise Error Rate and Proportion of False Positives (with Sandrine Dudoit and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (with Sandrine Dudoit and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 
Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates (with Sandrine Dudoit and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

Software

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tmle: An R Package for Targeted Maximum Likelihood Estimation (with Susan Gruber), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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bias.pboot (with Susan Gruber, Kristin Porter, Maya Petersen, and Yue Wang), Susan Gruber (2010)
 

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tmle: an R package for targeted maximum likelihood estimation (with Susan Gruber), Susan Gruber (2010)
 
Multiple Testing Procedures: R multtest Package and Applications to Genomics (with Katherine S. Pollard and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

Statistical Theory and Methods

Targeted Minimum Loss Based Estimation of Causal Effects of Multiple Time Point Interventions (with Susan Gruber), The International Journal of Biostatistics (2012)
 
Targeted Maximum Likelihood Estimation of Natural Direct Effects (with Wenjing Zheng), The International Journal of Biostatistics (2012)
 
Targeted Maximum Likelihood Estimation of Effect Modification Parameters in Survival Analysis (with Ori M. Stitelman, C. William Wester, and Victor De Gruttola), The International Journal of Biostatistics (2012)
 

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Estimation and Testing in Targeted Group Sequential Covariate-adjusted Randomized Clinical Trials (with Antoine Chambaz), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Targeted Maximum Likelihood Estimation for Dynamic Treatment Regimes in Sequential Randomized Controlled Trials (with Paul Chaffee), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 
Targeting the Optimal Design in Randomized Clinical Trials with Binary Outcomes and No Covariate: Simulation Study (with Antoine Chambaz), The International Journal of Biostatistics (2011)
 
Collaborative Targeted Maximum Likelihood for Time to Event Data (with Ori M. Stitelman), The International Journal of Biostatistics (2011)
 
Targeting the Optimal Design in Randomized Clinical Trials with Binary Outcomes and No Covariate: Theoretical Study (with Antoine Chambaz), The International Journal of Biostatistics (2011)
 

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SIMPLE EXAMPLES OF ESTIMATING CAUSAL EFFECTS USING TARGETED MAXIMUM LIKELIHOOD ESTIMATION (with Michael Rosenblum), Johns Hopkins University, Dept. of Biostatistics Working Papers (2011)
 
A Targeted Maximum Likelihood Estimator for Two-Stage Designs (with Sherri Rose), The International Journal of Biostatistics (2011)
 

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Asymptotic Theory for Cross-validated Targeted Maximum Likelihood Estimation (with Wenjing Zheng), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Observational Study and Individualized Antiretroviral Therapy Initiation Rules for Reducing Cancer Incidence in HIV-Infected Patients (with Romain Neugebauer and Michael J. Silverberg), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Finding quantitative trait loci genes with collaborative targeted maximum likelihood learning (with Hui Wang and Sherri Rose), Statistics & Probability Letters (2010)
 
Diagnosing and responding to violations in the positivity assumption (with Maya L. Petersen, Kristin Porter, Susan Gruber, and Yue Wang), Statistical Methods in Medical Research (2010)
 

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Targeted Bayesian Learning (with Ivan Diaz-Munoz and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Diagnosing and Responding to Violations in the Positivity Assumption (with Maya L. Petersen, Kristin Porter, Susan Gruber, and Yue Wang), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Estimation of Causal Effects of Community Based Interventions, U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Optimizing Randomized Trial Designs to Distinguish which Subpopulations Benefit from Treatment (with Michael Rosenblum), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Super Learner In Prediction (with Eric C. Polley), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Simple Examples of Estimating Causal Effects Using Targeted Maximum Likelihood Estimation (with Michael Rosenblum), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Targeted Maximum Likelihood Method for Repeated Measures Semiparametric Regression: Discovery for Transcription Factor Activity (with Catherine Tuglus), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Targeted Maximum Likelihood Based Causal Inference, U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 
An Application of Collaborative Targeted Maximum Likelihood Estimation in Causal Inference and Genomics (with Susan Gruber), The International Journal of Biostatistics (2010)
 
A Targeted Maximum Likelihood Estimator of a Causal Effect on a Bounded Continuous Outcome (with Susan Gruber), The International Journal of Biostatistics (2010)
 
Collaborative Double Robust Targeted Maximum Likelihood Estimation (with Susan Gruber), The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Based Causal Inference: Part I, The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Based Causal Inference: Part II, The International Journal of Biostatistics (2010)
 
Targeted Maximum Likelihood Estimation of the Parameter of a Marginal Structural Model (with Michael Rosenblum), The International Journal of Biostatistics (2010)
 

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Readings in Targeted Maximum Likelihood Estimation (with Sherri Rose and Susan Gruber), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Causal Inference for Nested Case-Control Studies using Targeted Maximum Likelihood Estimation (with Sherri Rose), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Targeted Maximum Likelihood Estimation: A Gentle Introduction (with Susan Gruber), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Resampling-Based Multiple Hypothesis Testing with Applications to Genomics: New Developments in the R/Bioconductor Package multtest (with Houston N. Gilbert, Katherine S. Pollard, and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Collaborative Targeted Maximum Likelihood Estimation (with Susan Gruber), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 

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Joint Multiple Testing Procedures for Graphical Model Selection with Applications to Biological Networks (with Houston N. Gilbert and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 
Confidence Intervals for the Population Mean Tailored to Small Sample Sizes, with Applications to Survey Sampling (with Michael A. Rosenblum), The International Journal of Biostatistics (2009)
 
Modified FDR Controlling Procedure for Multi-Stage Analyses (with Catherine Tuglus), Statistical Applications in Genetics and Molecular Biology (2009)
 
Why Match? Investigating Matched Case-Control Study Designs with Causal Effect Estimation (with Sherri Rose), The International Journal of Biostatistics (2009)
 

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A Note on Risk Prediction for Case-Control Studies (with Sherri Rose), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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FDR Controlling Procedure for Multi-stage Analyses (with Catherine Tuglus), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Supervised Distance Matrices: Theory and Applications to Genomics (with Katherine S. POLLARD), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Doubly Robust Ecological Inference (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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A Guide to Causal Parameters in Case-Control Designs: Targeted Maximum Likelihood Estimation (with Sherri Rose), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Estimation Based on Case-Control Designs with Known Incidence Probability, U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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The Construction and Analysis of Adaptive Group Sequential Designs, U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Data-adaptive Selection Of The Adjustment Set In Variable Importance Estimation (with Oliver Bembom, Jeffrey W. Fessel, and Robert W. Shafer), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Data-adaptive selection of the truncation level for Inverse-Probability-of-Treatment-Weighted estimators (with Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Covariate Adjustment for the Intention-to-Treat Parameter with Empirical Efficiency Maximization (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 

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Using Regression Models to Analyze Randomized Trials: Asymptotically Valid Hypothesis Tests Despite Incorrectly Specified Models (with Michael Rosenblum), U.C. Berkeley Division of Biostatistics Working Paper Series (2008)
 
Biomarker discovery using targeted maximum-likelihood estimation: Application to the treatment of antiretroviral-resistant HIV infection (with Oliver Bembom, Maya L. Petersen, Soo-Yon Rhee, W Jeffrey Fessel, Sandra E. Sinisi, and Robert W. Shafer), Statstics in Medicine (2008)
 
Estimation Based on Case-Control Designs with Known Prevalence Probability, The International Journal of Biostatistics (2008)
 
Rejoinder to Tan (with Daniel B. Rubin), The International Journal of Biostatistics (2008)
 
Simple Optimal Weighting of Cases and Controls in Case-Control Studies (with Sherri Rose), The International Journal of Biostatistics (2008)
 
Supervised Distance Matrices (with Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2008)
 

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Resampling-Based Empirical Bayes Multiple Testing Procedures for Controlling Generalized Tail Probability and Expected Value Error Rates: (with Sandrine Dudoit and Houston N. Gilbert), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Individualized treatment rules: Generating candidate clinical trials (with Maya Petersen and Steven G. Deeks), Statistics in Medicine (2007)
 

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A Note on Targeted Maximum Likelihood and Right Censored Data (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Detailed Version: Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials (with Michael A. Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Analyzing Direct Effects in Randomized Trials with Secondary Interventions (with Michael Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Biomarker Discovery Using Targeted Maximum Likelihood Estimation: Application to the Treatment of Antiretroviral Resistant HIV Infection (with Oliver Bembom, Maya L. Petersen , Soo-Yon Rhee , W. Jeffrey Fessel , Sandra E. Sinisi, and Robert W. Shafer), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Empirical Efficiency Maximization (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Analyzing Sequentially Randomized Trials Based on Causal Effect Models for Realistic Individualized Treatment Rules (with Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Covariate Adjustment in Randomized Trials with Binary Outcomes: Targeted Maximum Likelihood Estimation (with Kelly L. Moore), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 
A Doubly Robust Censoring Unbiased Transformation (with Daniel Rubin), The International Journal of Biostatistics (2007)
 
Analyzing Direct Effects in Randomized Trials with Secondary Interventions (with Michael Rosenblum, Nicholas P. Jewell, Stephen Shiboski, Ariane van der Straten, and Nancy Padian), Nicholas P. Jewell (2007)
 
Super Learner (with Eric C. Polley and Alan E. Hubbard), Statistical Applications in Genetics and Molecular Biology (2007)
 
Super Learning: An Application to the Prediction of HIV-1 Drug Resistance (with Sandra E. Sinisi, Eric C. Polley, Maya L. Petersen, and Soo-Yon Rhee), Statistical Applications in Genetics and Molecular Biology (2007)
 
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo (with Oliver Bembom and Sunduz Keles), Statistical Applications in Genetics and Molecular Biology (2007)
 

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Identifying important explanatory variables for time-varying outcomes. (with Oliver Bembom and Maya L. Petersen), Fundamentals of Data Mining in Genomics and Proteomics (2006)
 
Statistical Inference for Variable Importance, The International Journal of Biostatistics (2006)
 
Quantile-Function Based Null Distribution in Resampling Based Multiple Testing (with Alan E. Hubbard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (with Sandrine Dudoit and Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates (with Sandrine Dudoit and Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Estimating a Survival Distribution with Current Status Data and High-dimensional Covariates (with Aad van der Vaart), The International Journal of Biostatistics (2006)
 
Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives. (with Merrill D. Birkner and Alan E. Hubbard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives (with Sandrine Dudoit and Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2006)
 
Asymptotic Optimality of Likelihood-Based Cross-Validation (with Sandrine Dudoit and Sunduz Keles), Statistical Applications in Genetics and Molecular Biology (2006)
 
Application of a Variable Importance Measure Method (with Merrill D. Birkner), The International Journal of Biostatistics (2006)
 
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (with Daniel Rubin and Sandrine Dudoit), Statistical Applications in Genetics and Molecular Biology (2006)
 

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Targeted Maximum Likelihood Learning (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Diagnosing Bias in the Inverse Probability of Treatment Weighted Estimator Resulting from Violation of Experimental Treatment Assignment (with Yue Wang, Maya L. Petersen, and David Bangsberg), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Extending Marginal Structural Models through Local, Penalized, and Additive Learning (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Statistical Learning of Origin-Specific Statically Optimal Individualized Treatment Rules (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Supervised Detection of Conserved Motifs in DNA Sequences with cosmo (with Oliver Bembom and Sunduz Keles), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Doubly Robust Censoring Unbiased Transformations (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting (with Daniel Rubin and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Causal Effect Models for Intention to Treat and Realistic Individualized Treatment Rules, U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Multiple Tests of Association with Biological Annotation Metadata (with Sandrine Dudoit and Sunduz Keles), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data (with Merrill D. Birkner, Alan E. Hubbard, Christine F. Skibola, Christine M. Hegedus, and Martyn T. Smith), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Quantile-Function Based Null Distribution in Resampling Based Multiple Testing (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Application of a Variable Importance Measure Method to HIV-1 Sequence Data (with Merrill D. Birkner), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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A General Imputation Methodology for Nonparametric Regression with Censored Data (with Dan Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Population Intervention Models in Causal Inference (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Direct Effect Models (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Statistical Inference for Variable Importance, U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Application of a Multiple Testing Procedure Controlling the Proportion of False Positives to Protein and Bacterial Data (with Merrill D. Birkner and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Cross-Validating and Bagging Partitioning Algorithms with Variable Importance (with Annette M. Molinaro), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Test Statistics Null Distributions in Multiple Testing: Simulation Studies and Applications to Genomics (with Katherine S. Pollard, Merrill D. Birkner, and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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A Note on the Construction of Counterfactuals and the G-computation Formula (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Cross-validated Bagged Learning (with Sandra E. Sinisi and Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Estimating Function Based Cross-Validation and Learning (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Causal Inference in Longitudinal Studies with History-Restricted Marginal Structural Models (with Romain Neugebauer and Ira B. Tager), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives (with Merrill D. Birkner and Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Optimization of the Architecture of Neural Networks Using a Deletion/Substitution/Addition Algorithm (with Blythe Durbin and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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A Causal Inference Approach for Constructing Transcriptional Regulatory Networks (with Biao Xing), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Multiple Testing Procedures and Applications to Genomics (with Merrill D. Birkner, Katherine S. Pollard, and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Multiple Testing Procedures for Controlling Tail Probability Error Rates (with Sandrine Dudoit and Merrill D. Birkner), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Multiple Testing Procedures: R multtest Package and Applications to Genomics (with Katherine S. Pollard and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Multiple Testing Procedures: R multtest Package and Applications to Genomics (with Katherine S. Pollard and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data (with Nicholas P. Jewell and Stephen Shiboski), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data (with Nicholas P. Jewell and Stephen Shiboski), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Deletion/Substitution/Addition Algorithm for Partitioning the Covariate Space in Prediction (with Annette Molinaro), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data (with Merrill D. Birkner and Sandra E. Sinisi), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Data Adaptive Estimation of the Treatment Specific Mean (with Yue Wang and Oliver Bembom), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimes (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimating a Survival Distribution with Current Status Data and High-Dimensional Covariates (with Aad van der Vaart), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome (with Alan E. Hubbard and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome (with Alan E. Hubbard and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimation of Direct and Indirect Causal Effects in Longitudinal Studies (with Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data (with Sunduz Keles, Sandrine Dudoit, and Simon E. Cawley), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data (with Biao Xing), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Loss-Based Cross-Validated Deletion/Substitution/Addition Algorithms in Estimation (with Sandra E. Sinisi), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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The Cross-Validated Adaptive Epsilon-Net Estimator (with Sandrine Dudoit and Aad W. van der Vaart), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Multiple Testing. Part III. Procedures for Control of the Generalized Family-Wise Error Rate and Proportion of False Positives (with Sandrine Dudoit and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate (with Sandrine Dudoit and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates (with Sandrine Dudoit and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding (with Sandrine Dudoit, Sunduz Keles, Annette M. Molinaro, Sandra E. Sinisi, and Siew Leng Teng), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Measuring Treatment Effects Using Semiparametric Models (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Asymptotically Optimal Model Selection Method with Right Censored Outcomes (with Sunduz Keles and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Tree-based Multivariate Regression and Density Estimation with Right-Censored Data (with Annette M. Molinaro and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Locally Efficient Estimation of Nonparametric Causal Effects on Mean Outcomes in Longitudinal Studies (with Romain Neugebauer), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Resampling-based Multiple Testing: Asymptotic Control of Type I Error and Applications to Gene Expression Data (with Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Double Robust Estimation in Longitudinal Marginal Structural Models (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Supervised Detection of Regulatory Motifs in DNA Sequences (with Sunduz Keles, Sandrine Dudoit, Biao Xing, and Michael B. Eisen), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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A Semiparametric Model Selection Criterion with Applications to the Marginal Structural Model (with M. Alan Brookhart), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Asymptotic Optimality of Likelihood Based Cross-Validation (with Sandrine Dudoit and Sunduz Keles), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Asymptotics of Cross-Validated Risk Estimation in Estimator Selection and Performance Assessment (with Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Recurrent Events Analysis in the Presence of Time Dependent Covariates and Dependent Censoring (with Maja Miloslavsky, Sunduz Keles, and Steve Butler), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Construction of Counterfactuals and the G-computation Formula (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Locally Efficient Estimation with Bivariate Right Censored Data (with Christopher M. Quale and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Locally Efficient Estimation of Regression Parameters Using Current Status Data (with Chris Andrews and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Case-Control Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Case-Control Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Why Prefer Double Robust Estimates? Illustration with Causal Point Treatment Studies (with Romain Neugebauer), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Bivariate Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Bivariate Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Current Status Data: Review, Recent Developments and Open Problems (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Current Status Data: Review, Recent Developments and Open Problems (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures (with Sunduz Keles and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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A Method to Identify Significant Clusters in Gene Expression Data (with Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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A New Partitioning Around Medoids Algorithm (with Katherine S. Pollard and Jennifer Bryan), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Locally Efficient Estimation with Bivariate Right Censored Data (with Christopher M. Quale and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Nonparametric Estimation from Current Status Data with Competing Risks (with Nicholas P. Jewell and Tanya Henneman), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Nonparametric Estimation from Current Status Data with Competing Risks (with Nicholas P. Jewell and Tanya Henneman), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 

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Statistical Inference for Simultaneous Clustering of Gene Expression Data (with Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Paired and Unpaired Comparisons and Clustering with Gene Expression Data (with Jennifer F. Bryan and Katherine S. Pollard), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Current Status and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Current Status and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Smooth Estimation of a Monotone Density (with Aad W. van der Vaart), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Fitting of Mixtures with Unspecified Number of Components Using Cross Validation Distance Estimate (with Maja Miloslavsky), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Gene Expression Analysis with the Parametric Bootstrap (with Jennifer F. Bryan), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 
Locally Efficient Estimation in Censored Data Models: Theory and Examples (with Richard D. Gill and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 
Locally Efficient Estimation of a Multivariate Survival Function in Longitudinal Studies (with Alan E. Hubbard and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 
The NPMLE in the Uniform Doubly Censored Current Status Data Model (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1999)
 
Nonparametric Efficient Estimation with Current Status Data and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Nonparametric Efficient Estimation with Current Status Data and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Estimation with Interval Censored Data in Longitudinal Studies, U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
The Nonparametric Maximum Likelihood Estimator in a Class of Doubly Censored Current Status Data Models with Application to Partner Studies (with Chris Andrews), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Inference with Bivariate Truncated Data (with Christopher M. Quale), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Locally Efficient Estimation of the Quality Adjusted Lifetime Distribution with Right-Censored Data and Covariates (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Nonparametric Locally Efficient Estimation of the Treatment Specific Survival Distribution with Right Censored Data and Covariates in Observational Studies (with Alan E. Hubbard and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Efficient Estimation from Right-Censored Data When Failure Indicators are Missing at Random (with Ian W. McKeague), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Efficient Estimation from Right-Censored Data When Failure Indicators are Missing at Random (with Ian W. McKeague), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Efficient Estimation of the Lifetime and Disease Onset Distribution (with Nicholas P. Jewell and Derick R. Peterson), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Efficient Estimation of the Lifetime and Disease Onset Distribution (with Nicholas P. Jewell and Derick R. Peterson), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Smooth Estimation and Inference with Interval Censored Data (with Derick R. Peterson), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Locally Efficient Estimation of the Survival Distribution with Right Censored Data and Covariates When Collection of Data is Delayed (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Locally Efficient Estimation with Current Status Data and Time-Dependent Covariates (with James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Estimation with Interval Censored Data and Covariates (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (1996)
 
Singly and Doubly Censored Current Status Data With Extensions to Multi-State Counting Processes (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1996)
 
Singly and Doubly Censored Current Status Data With Extensions to Multi-State Counting Processes (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1996)
 
Locally Efficient Estimation with Current Status Data and High Dimensional Covariates, U.C. Berkeley Division of Biostatistics Working Paper Series (1995)
 
The Two-Interval Line-Segment Problem, U.C. Berkeley Division of Biostatistics Working Paper Series (1995)
 
Efficiency of the Sieved-NPMLE in CAR-Missing Data Models, U.C. Berkeley Division of Biostatistics Working Paper Series (1995)
 
Nonparametric Estimation of the Bivariate Survival Function with Truncated Data, U.C. Berkeley Division of Biostatistics Working Paper Series (1995)
 
Singly and Doubly Censored Current Status Data: Estimation, Asymptotics and Regression (with Peter J. Bickel and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 
Singly and Doubly Censored Current Status Data: Estimation, Asymptotics and Regression (with Peter J. Bickel and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 
Efficient and Ad Hoc Estimation in the Bivariate Censoring Model, U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 
Generalizations of Current Status Data With Applications (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 
Generalizations of Current Status Data With Applications (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 
Proving Efficiency of NPMLE and Identities, U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 

Survival Analysis

Targeted Minimum Loss Based Estimation of Causal Effects of Multiple Time Point Interventions (with Susan Gruber), The International Journal of Biostatistics (2012)
 
Targeted Maximum Likelihood Estimation of Effect Modification Parameters in Survival Analysis (with Ori M. Stitelman, C. William Wester, and Victor De Gruttola), The International Journal of Biostatistics (2012)
 
Collaborative Targeted Maximum Likelihood for Time to Event Data (with Ori M. Stitelman), The International Journal of Biostatistics (2011)
 

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Threshold Regression Models Adapted to Case-Control Studies, and the Risk of Lung Cancer Due to Occupational Exposure to Asbestos in France (with Antoine Chambaz, Dominique Choudat, Catherine Huber, and Jean-Claude Pairon), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Collaborative Targeted Maximum Likelihood For Time To Event Data (with Ori M. Stitelman), U.C. Berkeley Division of Biostatistics Working Paper Series (2010)
 

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Selecting Optimal Treatments Based on Predictive Factors (with Eric C. Polley), U.C. Berkeley Division of Biostatistics Working Paper Series (2009)
 
Supervised Distance Matrices (with Katherine S. Pollard), Statistical Applications in Genetics and Molecular Biology (2008)
 

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A Note on Targeted Maximum Likelihood and Right Censored Data (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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Empirical Efficiency Maximization (with Daniel B. Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2007)
 

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SEMIPARAMETRIC BIVARIATE QUANTILE-QUANTILE REGRESSION FOR ANALYZING SEMI-COMPETING RISKS DATA (with Daniel O. Scharfstein and James M. Robins), Johns Hopkins University, Dept. of Biostatistics Working Papers (2007)
 
A Doubly Robust Censoring Unbiased Transformation (with Daniel Rubin), The International Journal of Biostatistics (2007)
 
Cross-Validated Bagged Prediction of Survival (with Sandra E. Sinisi and Romain Neugebauer), Statistical Applications in Genetics and Molecular Biology (2006)
 
Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data (with Nicholas P. Jewell and Stephen Shiboski), The International Journal of Biostatistics (2006)
 

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Doubly Robust Censoring Unbiased Transformations (with Daniel Rubin), U.C. Berkeley Division of Biostatistics Working Paper Series (2006)
 

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Cross-validated Bagged Prediction of Survival (with Sandra E. Sinisi), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Survival Point Estimate Prediction in Matched and Non-Matched Case-Control Subsample Designed Studies (with Annette M. Molinaro, Dan H. Moore, and Karla Kerlikowske), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Survival Ensembles (with Torsten Hothorn, Peter Buhlmann, Sandrine Dudoit, and Annette M. Molinaro), U.C. Berkeley Division of Biostatistics Working Paper Series (2005)
 

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Multiple Testing Procedures: R multtest Package and Applications to Genomics (with Katherine S. Pollard and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data (with Nicholas P. Jewell and Stephen Shiboski), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 
Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data (with Nicholas P. Jewell and Stephen Shiboski), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Deletion/Substitution/Addition Algorithm for Partitioning the Covariate Space in Prediction (with Annette Molinaro), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Estimating a Survival Distribution with Current Status Data and High-Dimensional Covariates (with Aad van der Vaart), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Loss-Based Cross-Validated Deletion/Substitution/Addition Algorithms in Estimation (with Sandra E. Sinisi), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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The Cross-Validated Adaptive Epsilon-Net Estimator (with Sandrine Dudoit and Aad W. van der Vaart), U.C. Berkeley Division of Biostatistics Working Paper Series (2004)
 

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Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding (with Sandrine Dudoit, Sunduz Keles, Annette M. Molinaro, Sandra E. Sinisi, and Siew Leng Teng), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Asymptotically Optimal Model Selection Method with Right Censored Outcomes (with Sunduz Keles and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Tree-based Multivariate Regression and Density Estimation with Right-Censored Data (with Annette M. Molinaro and Sandrine Dudoit), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Double Robust Estimation in Longitudinal Marginal Structural Models (with Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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A Semiparametric Model Selection Criterion with Applications to the Marginal Structural Model (with M. Alan Brookhart), U.C. Berkeley Division of Biostatistics Working Paper Series (2003)
 

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Recurrent Events Analysis in the Presence of Time Dependent Covariates and Dependent Censoring (with Maja Miloslavsky, Sunduz Keles, and Steve Butler), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Analysis of Longitudinal Marginal Structural Models (with Jennifer F. Bryan and Zhuo Yu), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Locally Efficient Estimation with Bivariate Right Censored Data (with Christopher M. Quale and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Locally Efficient Estimation of Regression Parameters Using Current Status Data (with Chris Andrews and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Case-Control Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Case-Control Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Why Prefer Double Robust Estimates? Illustration with Causal Point Treatment Studies (with Romain Neugebauer), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Bivariate Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Bivariate Current Status Data (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Current Status Data: Review, Recent Developments and Open Problems (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Current Status Data: Review, Recent Developments and Open Problems (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 

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Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures (with Sunduz Keles and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2002)
 
Nonparametric Estimation from Current Status Data with Competing Risks (with Nicholas P. Jewell and Tanya Henneman), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Nonparametric Estimation from Current Status Data with Competing Risks (with Nicholas P. Jewell and Tanya Henneman), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Current Status and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Current Status and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (2001)
 
Locally Efficient Estimation in Censored Data Models: Theory and Examples (with Richard D. Gill and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 
Locally Efficient Estimation of a Multivariate Survival Function in Longitudinal Studies (with Alan E. Hubbard and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (2000)
 
The NPMLE in the Uniform Doubly Censored Current Status Data Model (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1999)
 
Nonparametric Efficient Estimation with Current Status Data and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Nonparametric Efficient Estimation with Current Status Data and Right-Censored Data Structures When Observing a Marker at the Censoring Time (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Subset Selection Based on Order Statistics from Logistic Populations (with Paul van der Laan), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Locally Efficient Estimation of the Quality Adjusted Lifetime Distribution with Right-Censored Data and Covariates (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Nonparametric Locally Efficient Estimation of the Treatment Specific Survival Distribution with Right Censored Data and Covariates in Observational Studies (with Alan E. Hubbard and James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (1998)
 
Efficient Estimation of the Lifetime and Disease Onset Distribution (with Nicholas P. Jewell and Derick R. Peterson), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Smooth Estimation and Inference with Interval Censored Data (with Derick R. Peterson), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Locally Efficient Estimation of the Survival Distribution with Right Censored Data and Covariates When Collection of Data is Delayed (with Alan E. Hubbard), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Locally Efficient Estimation with Current Status Data and Time-Dependent Covariates (with James M. Robins), U.C. Berkeley Division of Biostatistics Working Paper Series (1997)
 
Singly and Doubly Censored Current Status Data With Extensions to Multi-State Counting Processes (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1996)
 
Singly and Doubly Censored Current Status Data With Extensions to Multi-State Counting Processes (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1996)
 
Singly and Doubly Censored Current Status Data: Estimation, Asymptotics and Regression (with Peter J. Bickel and Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 
Generalizations of Current Status Data With Applications (with Nicholas P. Jewell), U.C. Berkeley Division of Biostatistics Working Paper Series (1994)
 

Media Publications

Prediction

Disease Modeling

Targeted Maximum Likelihood Estimation of Effect Modification Parameters in Survival Analysis (with Ori M. Stitelman, C. William Wester, and Victor De Gruttola), The International Journal of Biostatistics (2012)
 

Design of Experiments and Sample Surveys

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Estimation and Testing in Targeted Group Sequential Covariate-adjusted Randomized Clinical Trials (with Antoine Chambaz), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

Biology

General Biostatistics

Targeted Minimum Loss Based Estimation of Causal Effects of Multiple Time Point Interventions (with Susan Gruber), The International Journal of Biostatistics (2012)
 
Targeted Maximum Likelihood Estimation of Natural Direct Effects (with Wenjing Zheng), The International Journal of Biostatistics (2012)
 

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Targeted Methods for Finding Quantitative Trait Loci (with Hui Wang and Sherri Rose), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Targeted Maximum Likelihood, Conditional Relative Risk, Semi-parametric, Multiplicative Model, Partial Linear Model (with Cathy Tuglus and Kristin E. Porter), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Super Learner Based Conditional Density Estimation with Application to Marginal Structural Models (with Ivan Diaz), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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A General Implementation of TMLE for Longitudinal Data Applied to Causal Inference in Survival Analysis (with Ori M. Stitelman and Victor De Gruttola), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Targeted Minimum Loss Based Estimator that Outperforms a given Estimator (with Susan Gruber), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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The Relative Performance of Targeted Maximum Likelihood Estimators (with Kristin E. Porter, Susan Gruber, and Jasjeet S. Sekhon), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Estimation and Testing in Targeted Group Sequential Covariate-adjusted Randomized Clinical Trials (with Antoine Chambaz), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

Statistical Models

Targeted Minimum Loss Based Estimation of Causal Effects of Multiple Time Point Interventions (with Susan Gruber), The International Journal of Biostatistics (2012)
 

Stochastic Interventions

Computation

Targeted Minimum Loss Based Estimation of Causal Effects of Multiple Time Point Interventions (with Susan Gruber), The International Journal of Biostatistics (2012)
 

Genetics

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Estimation of a Non-Parametric Variable Importance Measure of a Continuous Exposure (with Chambaz Antoine and Pierre Neuvial), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

No subject area

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Why Match in Individually and Cluster Randomized Trials? (with Laura B. Balzer and Maya L. Petersen), U.C. Berkeley Division of Biostatistics Working Paper Series (2012)
 

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Identification and Efficient Estimation of the Natural Direct Effect Among the Untreated (with Samuel D. Lendle), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Targeted Maximum Likelihood Estimation of Natural Direct Effect (with Wenjing Zheng), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)
 

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Targeted Minimum Loss Based Estimation Based on Directly Solving the Efficient Influence Curve Equation (with Paul Chaffee), U.C. Berkeley Division of Biostatistics Working Paper Series (2011)