The Division of Biostatistics is one of five divisions of the School of Public Health at the University of California, Berkeley. Its mission is the promotion of teaching and research of biostatistical methods by faculty and graduate students. Graduate students are admitted to M.A. and Ph.D. programs through the Group in Biostatistics which is a joint program of the School of Public Health and the Department of Statistics.

The Biostatistics Working Paper series includes articles on statistical methods and applications developed by faculty and visitors of the Division of Biostatistics. In general, articles dated 2001 and later are downloadable from this site. For earlier articles that have appeared in print, we have included an abstract with a citation. Articles that are not downloadable or are unavailable in print may be requested from

Nicholas P. Jewell
Chair, Group in Biostatistics
University of California, Berkeley
140 Warren Hall
Berkeley, CA 94720-7360

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Papers from 2014

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Adaptive Pair-Matching in the SEARCH Trial and Estimation of the Intervention Effect, Laura Balzer, Maya L. Petersen, and Mark J. van der Laan

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Targeted Covariate-Adjusted Response-Adaptive LASSO-Based Randomized Controlled Trials, Antoine Chambaz, Wenjing Zheng, and Mark J. van der Laan

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A New Approach to Variance Estimation for Time-ordered Dependent Data, Molly M. Davies and Mark J. van der Laan

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Deductive Derivation and Computerization of Compatible Semiparametric Efficient Estimation, Constantine E. Frangakis, Tianchen Qian, Zhenke Wu, and Ivan Diaz

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Super-Learning of an Optimal Dynamic Treatment Rule, Alexander R. Luedtke and Mark J. van der Laan

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A Scalable Supervised Subsemble Prediction Algorithm, Stephanie Sapp and Mark J. van der Laan

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Targeted Learning of the Mean Outcome Under an Optimal Dynamic Treatment Rule, Mark J. van der Laan and Alexander R. Luedtke

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Entering the Era of Data Science: Targeted Learning and the Integration of Statistics and Computational Data Analysis, Mark J. van der Laan and Richard J.C.M. Starmans

Papers from 2013

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Estimating Effects on Rare Outcomes: Knowledge is Power, Laura B. Balzer and Mark J. van der Laan

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Variable Importance and Prediction Methods for Longitudinal Problems with Missing Variables, Ivan Diaz, Alan E. Hubbard, Anna Decker, and Mitchell Cohen

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Targeted Data Adaptive Estimation of the Causal Dose Response Curve, Iván Díaz and Mark J. van der Laan

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An Application Of Machine Learning Methods To The Derivation Of Exposure-Response Curves For Respiratory Outcomes, Ekaterina Eliseeva, Alan E. Hubbard, and Ira B. Tager

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Testing the Relative Performance of Data Adaptive Prediction Algorithms: A Generalized Test of Conditional Risk Differences, Benjamin A. Goldstein, Eric Polley, Farren Briggs, and Mark J. van der Laan

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Vertically Shifted Mixture Models for Clustering Longitudinal Data by Shape, Brianna C. Heggeseth and Nicholas P. Jewell

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Adapting Data Adaptive Methods for Small, but High Dimensional Omic Data: Applications to GWAS/EWAS and More, Sara Kherad Pajouh, Alan E. Hubbard, and Martyn T. Smith

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Balancing Score Adjusted Targeted Minimum Loss-based Estimation, Samuel D. Lendle, Bruce Fireman, and Mark J. van der Laan

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Targeted Maximum Likelihood Estimation for Dynamic and Static Longitudinal Marginal Structural Working Models, Maya L. Petersen, Joshua Schwab, Susan Gruber, Nello Blaser, Michael Schomaker, and Mark J. van der Laan

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Subsemble: An Ensemble Method for Combining Subset-Specific Algorithm Fits, Stephanie Sapp, Mark J. van der Laan, and John Canny

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Targeted Estimation of Variable Importance Measures with Interval-Censored Outcomes, Stephanie Sapp, Mark J. van der Laan, and Kimberly Page

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Targeted Learning of an Optimal Dynamic Treatment, and Statistical Inference for its Mean Outcome, Mark J. van der Laan

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Statistical Inference for Data Adaptive Target Parameters, Mark J. van der Laan, Alan E. Hubbard, and Sara Kherad Pajouh

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Challenges in Estimating the Causal Effect of an Intervention with Pre-Post Data (Part 1): Definition & Identification of the Causal Parameter, Ann M. Weber, Mark J. van der Laan, and Maya L. Petersen

Papers from 2012

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Why Match in Individually and Cluster Randomized Trials?, Laura B. Balzer, Maya L. Petersen, and Mark J. van der Laan

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Targeted Learning of The Probability of Success of An In Vitro Fertilization Program Controlling for Time-dependent Confounders, Antoine Chambaz, Sherri Rose, Jean Bouyer, and Mark J. van der Laan

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Avoiding Boundary Estimates in Linear Mixed Models Through Weakly Informative Priors, Yeojin Chung, Sophia Rabe-Hesketh, Andrew Gelman, Jingchen Liu, and Vincent Dorie

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Optimal Spatial Prediction Using Ensemble Machine Learning, Molly M. Davies and Mark J. van der Laan

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Assessing the Causal Effect of Policies: An Approach Based on Stochastic Interventions, Iván Díaz and Mark J. van der Laan

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Sensitivity Analysis for Causal Inference Under Unmeasured Confounding and Measurement Error Problems, Iván Díaz and Mark J. van der Laan

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The Impact of Covariance Misspecification in Multivariate Gaussian Mixtures on Estimation and Inference: An Application to Longitudinal Modeling, Brianna C. Heggeseth and Nicholas P. Jewell

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Computationally Efficient Confidence Intervals for Cross-validated Area Under the ROC Curve Estimates, Erin LeDell, Maya L. Petersen, and Mark J. van der Laan

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Targeted Learning for Causality and Statistical Analysis in Medical Research, Sherri Rose, Richard J.C.M. Starmans, and Mark J. van der Laan

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Causal Inference for Networks, Mark J. van der Laan

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Statistical Inference when using Data Adaptive Estimators of Nuisance Parameters, Mark J. van der Laan

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Adaptive Matching in Randomized Trials and Observational Studies, Mark J. van der Laan, Laura Balzer, and Maya L. Petersen

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Causal Mediation in a Survival Setting with Time-Dependent Mediators, Wenjing Zheng and Mark J. van der Laan

Papers from 2011

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Estimation of a Non-Parametric Variable Importance Measure of a Continuous Exposure, Chambaz Antoine, Pierre Neuvial, and Mark J. van der Laan

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Targeted Maximum Likelihood Estimation for Dynamic Treatment Regimes in Sequential Randomized Controlled Trials, Paul Chaffee and Mark J. van der Laan

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Targeted Minimum Loss Based Estimation Based on Directly Solving the Efficient Influence Curve Equation, Paul Chaffee and Mark J. van der Laan

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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, Antoine Chambaz, Dominique Choudat, Catherine Huber, Jean-Claude Pairon, and Mark J. van der Laan

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Estimation and Testing in Targeted Group Sequential Covariate-adjusted Randomized Clinical Trials, Antoine Chambaz and Mark J. van der Laan

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Population Intervention Causal Effects Based on Stochastic Interventions, Ivan Diaz Munoz and Mark J. van der Laan

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Super Learner Based Conditional Density Estimation with Application to Marginal Structural Models, Ivan Diaz Munoz and Mark J. van der Laan

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A Generalized Approach for Testing the Association of a Set of Predictors with an Outcome: A Gene Based Test, Benjamin A. Goldstein, Alan E. Hubbard, and Lisa F. Barcellos

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Targeted Minimum Loss Based Estimator that Outperforms a given Estimator, Susan Gruber and Mark J. van der Laan

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tmle: An R Package for Targeted Maximum Likelihood Estimation, Susan Gruber and Mark J. van der Laan

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Identification and Efficient Estimation of the Natural Direct Effect Among the Untreated, Samuel D. Lendle and Mark J. van der Laan

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The Relative Performance of Targeted Maximum Likelihood Estimators, Kristin E. Porter, Susan Gruber, Mark J. van der Laan, and Jasjeet S. Sekhon

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GC-Content Normalization for RNA-Seq Data, Davide Risso, Katja Schwartz, Gavin Sherlock, and Sandrine Dudoit

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Variable Importance Analysis with the multiPIM R Package, Stephan J. Ritter, Nicholas P. Jewell, and Alan E. Hubbard

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A General Implementation of TMLE for Longitudinal Data Applied to Causal Inference in Survival Analysis, Ori M. Stitelman, Victor De Gruttola, and Mark J. van der Laan

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Targeted Maximum Likelihood Estimation of Conditional Relative Risk in a Semi-parametric Regression Model, Cathy Tuglus, Kristin E. Porter, and Mark J. van der Laan

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Targeted Minimum Loss Based Estimation of an Intervention Specific Mean Outcome, Mark J. van der Laan and Susan Gruber

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Targeted Methods for Finding Quantitative Trait Loci, Hui Wang, Sherri Rose, and Mark J. van der Laan

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Targeted Maximum Likelihood Estimation of Natural Direct Effect, Wenjing Zheng and Mark J. van der Laan

Papers from 2010

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Permutation-based Pathway Testing using the Super Learner Algorithm, Paul Chaffee, Alan E. Hubbard, and Mark L. van der Laan

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Targeting The Optimal Design In Randomized Clinical Trials With Binary Outcomes And No Covariate, Antoine Chambaz and Mark J. van der Laan

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Targeted Bayesian Learning, Ivan Diaz Munoz, Alan E. Hubbard, and Mark J. van der Laan

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A Targeted Maximum Likelihood Estimator of a Causal Effect on a Bounded Continuous Outcome, Susan Gruber and Mark J. van der Laan

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Gains in Power from Structured Two-Sample Tests of Means on Graphs, Laurent Jacob, Pierre Neuvial, and Sandrine Dudoit

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Observational Study and Individualized Antiretroviral Therapy Initiation Rules for Reducing Cancer Incidence in HIV-Infected Patients, Romain Neugebauer, Michael J. Silverberg, and Mark J. van der Laan

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Diagnosing and Responding to Violations in the Positivity Assumption, Maya L. Petersen, Kristin Porter, Susan Gruber, Yue Wang, and Mark J. van der Laan

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Super Learner In Prediction, Eric C. Polley and Mark J. van der Laan

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Optimizing Randomized Trial Designs to Distinguish which Subpopulations Benefit from Treatment, Michael Rosenblum and Mark J. van der Laan

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Simple, Efficient Estimators of Treatment Effects in Randomized Trials Using Generalized Linear Models to Leverage Baseline Variables, Michael Rosenblum and Mark J. van der Laan

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Simple Examples of Estimating Causal Effects Using Targeted Maximum Likelihood Estimation, Michael Rosenblum and Mark J. van der Laan

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Targeted Maximum Likelihood Estimation of the Parameter of a Marginal Structural Model, Michael Rosenblum and Mark J. van der Laan

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The Impact Of Coarsening The Explanatory Variable Of Interest In Making Causal Inferences: Implicit Assumptions Behind Dichotomizing Variables, Ori M. Stitelman, Alan E. Hubbard, and Nicholas P. Jewell

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Collaborative Targeted Maximum Likelihood For Time To Event Data, Ori M. Stitelman and Mark J. van der Laan

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Targeted Maximum Likelihood Method for Repeated Measures Semiparametric Regression: Discovery for Transcription Factor Activity, Catherine Tuglus and Mark J. van der Laan

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Estimation of Causal Effects of Community Based Interventions, Mark J. van der Laan

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Targeted Maximum Likelihood Based Causal Inference, Mark J. van der Laan

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Asymptotic Theory for Cross-validated Targeted Maximum Likelihood Estimation, Wenjing Zheng and Mark J. van der Laan

Papers from 2009

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Evaluation of Statistical Methods for Normalization and Differential Expression in mRNA-Seq Experiments, James H. Bullard, Elizabeth A. Purdom, Kasper D. Hansen, and Sandrine Dudoit

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Resampling-Based Multiple Hypothesis Testing with Applications to Genomics: New Developments in the R/Bioconductor Package multtest, Houston N. Gilbert, Katherine S. Pollard, Mark J. van der Laan, and Sandrine Dudoit

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Joint Multiple Testing Procedures for Graphical Model Selection with Applications to Biological Networks, Houston N. Gilbert, Mark J. van der Laan, and Sandrine Dudoit

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Targeted Maximum Likelihood Estimation: A Gentle Introduction, Susan Gruber and Mark J. van der Laan

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Nonparametric population average models: deriving the form of approximate population average models estimated using generalized estimating equations, Alan E. Hubbard and Mark J. van der Laan

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Causal Inference in Epidemiological Studies with Strong Confounding, Kelly L. Moore, Romain S. Neugebauer, Mark J. van der Laan, and Ira B. Tager

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Application of Time-to-Event Methods in the Assessment of Safety in Clinical Trials, Kelly L. Moore and Mark J. van der Laan

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Selecting Optimal Treatments Based on Predictive Factors, Eric C. Polley and Mark J. van der Laan

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Causal Inference for Nested Case-Control Studies using Targeted Maximum Likelihood Estimation, Sherri Rose and Mark J. van der Laan

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Collaborative Targeted Maximum Likelihood Estimation, Mark J. van der Laan and Susan Gruber

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Readings in Targeted Maximum Likelihood Estimation, Mark J. van der Laan, Sherri Rose, and Susan Gruber

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A Machine-Learning Algorithm for Estimating and Ranking the Impact of Environmental Risk Factors in Exploratory Epidemiological Studies, Jessica G. Young, Alan E. Hubbard, B Eskenazi, and Nicholas P. Jewell

Papers from 2008

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Data-adaptive Selection Of The Adjustment Set In Variable Importance Estimation, Oliver Bembom, Jeffrey W. Fessel, Robert W. Shafer, and Mark J. van der Laan

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Data-adaptive selection of the truncation level for Inverse-Probability-of-Treatment-Weighted estimators, Oliver Bembom and Mark J. van der Laan

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Supervised Distance Matrices: Theory and Applications to Genomics, Katherine S. POLLARD and Mark J. van der Laan

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Confidence Intervals for the Population Mean Tailored to Small Sample Sizes, with Applications to Survey Sampling, Michael Rosenblum and Mark J. van der Laan

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Using Regression Models to Analyze Randomized Trials: Asymptotically Valid Hypothesis Tests Despite Incorrectly Specified Models, Michael Rosenblum and Mark J. van der Laan

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A Guide to Causal Parameters in Case-Control Designs: Targeted Maximum Likelihood Estimation, Sherri Rose and Mark J. van der Laan

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A Note on Risk Prediction for Case-Control Studies, Sherri Rose and Mark J. van der Laan

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Why Match? Investigating Matched Case-Control Study Designs with Causal Effect Estimation, Sherri Rose and Mark J. van der Laan

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A Small Sample Correction for Estimating Attributable Risk in Case-Control Studies, Daniel B. Rubin

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Covariate Adjustment for the Intention-to-Treat Parameter with Empirical Efficiency Maximization, Daniel B. Rubin and Mark J. van der Laan

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Doubly Robust Ecological Inference, Daniel B. Rubin and Mark J. van der Laan

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Confidence Intervals for Negative Binomial Random Variables of High Dispersion, David Shilane, Alan E. Hubbard, and S N. Evans

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FDR Controlling Procedure for Multi-stage Analyses, Catherine Tuglus and Mark J. van der Laan

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Targeted Methods for Biomarker Discovery, the Search for a Standard, Catherine Tuglus and Mark J. van der Laan

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Estimation Based on Case-Control Designs with Known Incidence Probability, Mark J. van der Laan

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The Construction and Analysis of Adaptive Group Sequential Designs, Mark J. van der Laan