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 2008

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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

Papers from 2007

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Biomarker Discovery Using Targeted Maximum Likelihood Estimation: Application to the Treatment of Antiretroviral Resistant HIV Infection, Oliver Bembom, Maya L. Petersen , Soo-Yon Rhee , W. Jeffrey Fessel , Sandra E. Sinisi, Robert W. Shafer, and Mark J. van der Laan

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Analyzing Sequentially Randomized Trials Based on Causal Effect Models for Realistic Individualized Treatment Rules, Oliver Bembom and Mark J. van der Laan

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Estimating the Effect of Vigorous Physical Activity on Mortality in the Elderly Based on Realistic Individualized Treatment and Intention-to-Treat Rules, Oliver Bembom and Mark J. van der Laan

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The Causal Effect of Recent Leisure-Time Physical Activity on All-Cause Mortality Among the Elderly, Oliver Bembom, Mark J. van der Laan, and Ira B. Tager

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Resampling-Based Empirical Bayes Multiple Testing Procedures for Controlling Generalized Tail Probability and Expected Value Error Rates: , Sandrine Dudoit, Houston N. Gilbert, and Mark J. van der Laan

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Covariate Adjustment in Randomized Trials with Binary Outcomes: Targeted Maximum Likelihood Estimation, Kelly L. Moore and Mark J. van der Laan

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Detailed Version: Analyzing Direct Effects in Randomized Trials with Secondary Interventions: An Application to HIV Prevention Trials, Michael A. Rosenblum, Nicholas P. Jewell, Mark J. van der Laan, Stephen Shiboski, Ariane van der Straten, and Nancy Padian

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Analyzing Direct Effects in Randomized Trials with Secondary Interventions , Michael Rosenblum, Nicholas P. Jewell, Mark J. van der Laan, Stephen Shiboski, Ariane van der Straten, and Nancy Padian

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Empirical Efficiency Maximization, Daniel B. Rubin and Mark J. van der Laan

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Loss-Based Estimation with Evolutionary Algorithms and Cross-Validation, David Shilane, Richard H. Liang, and Sandrine Dudoit

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Time-Dependent Performance Comparison of Stochastic Optimization Algorithms, David Shilane, Jarno Martikainen, and Seppo Ovaska

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Super Learner, Mark J. van der Laan, Eric C. Polley, and Alan E. Hubbard

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A Note on Targeted Maximum Likelihood and Right Censored Data, Mark J. van der Laan and Daniel Rubin

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Regression Analysis of a Disease Onset Distribution Using Diagnosis Data, Jessica G. Young, Nicholas P. Jewell, and Steven J. Samuels

Papers from 2006

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

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

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

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

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A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting, Daniel Rubin, Sandrine Dudoit, and Mark J. van der Laan

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

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

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

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

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

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

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

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

Papers from 2005

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Colon Cancer Prognosis Prediction by Gene Expression Profiling, Alain Barrier, Sandrine Dudoit, and et al.

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Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling, Alain Barrier, Sandrine Dudoit, and et al.

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Application of a Multiple Testing Procedure Controlling the Proportion of False Positives to Protein and Bacterial Data, Merrill D. Birkner, Alan E. Hubbard, and Mark J. van der Laan

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Data Adaptive Pathway Testing, Merrill D. Birkner, Alan E. Hubbard, and Mark J. van der Laan

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Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data, Merrill D. Birkner, Alan E. Hubbard, Mark J. van der Laan, Christine F. Skibola, Christine M. Hegedus, and Martyn T. Smith

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Multiple Testing Procedures and Applications to Genomics, Merrill D. Birkner, Katherine S. Pollard, Mark J. van der Laan, and Sandrine Dudoit

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Application of a Variable Importance Measure Method to HIV-1 Sequence Data, Merrill D. Birkner and Mark J. van der Laan

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Optimization of the Architecture of Neural Networks Using a Deletion/Substitution/Addition Algorithm, Blythe Durbin, Sandrine Dudoit, and Mark J. van der Laan

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Survival Ensembles, Torsten Hothorn, Peter Buhlmann, Sandrine Dudoit, Annette M. Molinaro, and Mark J. van der Laan

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Population Intervention Models in Causal Inference, Alan E. Hubbard and Mark J. van der Laan

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Correspondences between Regression Models for Complex Binary Outcomes and Those for Structured Multivariate Survival Analyses, Nicholas P. Jewell

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Nonparametric Estimation of the Case Fatality Ratio with Competing Risks Data: An Application to Severe Acute Respiratory Syndome (SARS) , Nicholas P. Jewell, Xiudong Lei, A. C. Ghani, C. A. Donnelly, G. M. Leung, L. M. Ho, B. Cowling, and A. J. Hedley

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Efficacy Studies of Malaria Treatments in Africa: Efficient Estimation with Missing Indicators of Failure, Rhoderick N. Machekano, Grant Dorsey, and Alan E. Hubbard

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Cross-Validating and Bagging Partitioning Algorithms with Variable Importance, Annette M. Molinaro and Mark J. van der Laan

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Survival Point Estimate Prediction in Matched and Non-Matched Case-Control Subsample Designed Studies, Annette M. Molinaro, Mark J. van der Laan, Dan H. Moore, and Karla Kerlikowske

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G-computation Estimation of Nonparametric Causal Effects on Time-Dependent Mean Outcomes in Longitudinal Studies, Romain Neugebauer and Mark J. van der Laan

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Causal Inference in Longitudinal Studies with History-Restricted Marginal Structural Models, Romain Neugebauer, Mark J. van der Laan, and Ira B. Tager

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History-Adjusted Marginal Structural Models to Estimate Time-Varying Effect Modification , Maya L. Petersen, Steven G. Deeks, Jeffrey N. Martin, and Mark J. van der Laan

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Estimation of Direct Causal Effects, Maya L. Petersen and Mark J. van der Laan

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History-Adjusted Marginal Structural Models: Optimal Treatment Strategies, Maya L. Petersen and Mark J. van der Laan

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History-Adjusted Marginal Structural Models: Time-Varying Effect Modification, Maya L. Petersen and Mark J. van der Laan

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Test Statistics Null Distributions in Multiple Testing: Simulation Studies and Applications to Genomics, Katherine S. Pollard, Merrill D. Birkner, Mark J. van der Laan, and Sandrine Dudoit

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Cluster Analysis of Genomic Data with Applications in R, Katherine S. Pollard and Mark J. van der Laan

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A General Imputation Methodology for Nonparametric Regression with Censored Data, Dan Rubin and Mark J. van der Laan

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Cross-validated Bagged Prediction of Survival, Sandra E. Sinisi, Romain Neugebauer, and Mark J. van der Laan

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Statistical Inference for Variable Importance, Mark J. van der Laan

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Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives, Mark J. van der Laan, Merrill D. Birkner, and Alan E. Hubbard

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Quantile-Function Based Null Distribution in Resampling Based Multiple Testing, Mark J. van der Laan and Alan E. Hubbard

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Direct Effect Models, Mark J. van der Laan and Maya L. Petersen

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Estimating Function Based Cross-Validation and Learning, Mark J. van der Laan and Daniel Rubin

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Cross-validated Bagged Learning, Mark J. van der Laan, Sandra E. Sinisi, and Maya L. Petersen

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A Fine-Scale Linkage Disequilibrium Measure Based on Length of Haplotype Sharing, Yan Wang, Lue Ping Zhao, and Sandrine Dudoit

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A Causal Inference Approach for Constructing Transcriptional Regulatory Networks, Biao Xing and Mark J. van der Laan

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A Note on the Construction of Counterfactuals and the G-computation Formula, Zhuo Yu and Mark J. van der Laan

Papers from 2004

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Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data, Merrill D. Birkner, Sandra E. Sinisi, and Mark J. van der Laan

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Linear Life Expectancy Regression with Censored Data, Ying Qing Chen and Su-Chun Cheng

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Mean Response Models of Repeated Measurements in Presence of Varying Effectiveness Onset, Ying Qing Chen and Su-Chun Cheng

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Semiparametric Regression Analysis of Mean Residual Life with Censored Survival Data, Ying Qing Chen and Su-Chun Cheng

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Semiparametric Quantitative-Trait-Locus Mapping: II. on Censored Age-at-Onset, Ying Qing Chen, Chengcheng Hu, and Rongling Wu

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Semiparametric Quantitative-Trait-Locus Mapping: I. on Functional Growth Curves, Ying Qing Chen and Rongling Wu

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A Note on Empirical Likelihood Inference of Residual Life Regression, Ying Qing Chen and Yichuan Zhao

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Multiple Testing Procedures for Controlling Tail Probability Error Rates, Sandrine Dudoit, Mark J. van der Laan, and Merrill D. Birkner

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Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data, Nicholas P. Jewell, Mark J. van der Laan, and Stephen Shiboski

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Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data, Sunduz Keles, Mark J. van der Laan, Sandrine Dudoit, and Simon E. Cawley

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Regulatory Motif Finding by Logic Regression, Sunduz Keles, Mark J. van der Laan, and Chris Vulpe

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Deletion/Substitution/Addition Algorithm for Partitioning the Covariate Space in Prediction, Annette Molinaro and Mark J. van der Laan

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Multiple Testing Procedures: R multtest Package and Applications to Genomics, Katherine S. Pollard, Sandrine Dudoit, and Mark J. van der Laan

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GLLAMM Manual, Sophia Rabe-Hesketh, Anders Skrondal, and Andrew Pickles

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Loss-Based Cross-Validated Deletion/Substitution/Addition Algorithms in Estimation, Sandra E. Sinisi and Mark J. van der Laan

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Multiple Testing. Part III. Procedures for Control of the Generalized Family-Wise Error Rate and Proportion of False Positives, Mark J. van der Laan, Sandrine Dudoit, and Katherine S. Pollard

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The Cross-Validated Adaptive Epsilon-Net Estimator, Mark J. van der Laan, Sandrine Dudoit, and Aad W. van der Vaart

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Estimation of Treatment Effects in Randomized Trials with Noncompliance and a Dichotomous Outcome , Mark J. van der Laan, Alan E. Hubbard, and Nicholas P. Jewell

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Estimation of Direct and Indirect Causal Effects in Longitudinal Studies, Mark J. van der Laan and Maya L. Petersen

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History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimes, Mark J. van der Laan and Maya L. Petersen

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Estimating a Survival Distribution with Current Status Data and High-Dimensional Covariates, Mark J. van der Laan and Aad van der Vaart

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Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks, Yan Wang and Sandrine Dudoit

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Data Adaptive Estimation of the Treatment Specific Mean, Yue Wang, Oliver Bembom, and Mark J. van der Laan

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A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data , Biao Xing and Mark J. van der Laan

Papers from 2003

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A Semiparametric Model Selection Criterion with Applications to the Marginal Structural Model, M. Alan Brookhart and Mark J. van der Laan

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Rank Regression in Stability Analysis, Ying Qing Chen, Annpey Pong, and Biao Xing

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IBD Configuration Transition Matrices and Linkage Score Tests for Unilineal Relative Pairs, Sandrine Dudoit

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Asymptotics of Cross-Validated Risk Estimation in Estimator Selection and Performance Assessment, Sandrine Dudoit and Mark J. van der Laan

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Loss-Based Estimation with Cross-Validation: Applications to Microarray Data Analysis and Motif Finding, Sandrine Dudoit, Mark J. van der Laan, Sunduz Keles, Annette M. Molinaro, Sandra E. Sinisi, and Siew Leng Teng

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Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates, Sandrine Dudoit, Mark J. van der Laan, and Katherine S. Pollard

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Temporal Stability and Geographic Variation in Cumulative Case Fatality Rates and Average Doubling Times of SARS Epidemics, Alison P. Galvani, Xiudong Lei, and Nicholas P. Jewell

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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, Thaddeus Haight, Romain Neugebauer, Ira B. Tager, and Mark J. van der Laan

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Asymptotically Optimal Model Selection Method with Right Censored Outcomes, Sunduz Keles, Mark J. van der Laan, and Sandrine Dudoit

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Supervised Detection of Regulatory Motifs in DNA Sequences, Sunduz Keles, Mark J. van der Laan, Sandrine Dudoit, Biao Xing, and Michael B. Eisen