Our research involves developing statistical methods and theories for the analysis
of data as commonly arise in randomized controlled trials and observational studies. In
particular, we are concerned with methods dealing in proper ways with informative
censoring, confounding, the curse of dimensionality, multiple testing, and data adaptive
selection of models. Our philosophy is targeted learning, formalized by our recent work
on targeted maximum likelihood learning, and unified loss based learning. This
statistical approach aims to let the data speak for the purpose of answering a particular
scientific question of interest, and provide robust tests of null hypotheses of interest.
We are continuously concerned with bringing these methods into practice and benchmark
them by the practical performance on simulated and real data. 

Please note Web site for the new book, Targeted Learning: www.targetedlearningbook.com

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)
 

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)
 

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)
 

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)
 

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)
 

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)
 

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)
 

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)
 
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)
 

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)
 

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)
 

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)
 

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)
 

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)
 

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)
 

PDF

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)
 

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)
 

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)