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
Papers from 2010
Asymptotic Theory for Cross-validated Targeted Maximum Likelihood Estimation, Wenjing Zheng and Mark J. van der Laan
Papers from 2009
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
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
Joint Multiple Testing Procedures for Graphical Model Selection with Applications to Biological Networks, Houston N. Gilbert, Mark J. van der Laan, and Sandrine Dudoit
Targeted Maximum Likelihood Estimation: A Gentle Introduction, Susan Gruber and Mark J. van der Laan
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
Causal Inference in Epidemiological Studies with Strong Confounding, Kelly L. Moore, Romain S. Neugebauer, Mark J. van der Laan, and Ira B. Tager
Application of Time-to-Event Methods in the Assessment of Safety in Clinical Trials, Kelly L. Moore and Mark J. van der Laan
Selecting Optimal Treatments Based on Predictive Factors, Eric C. Polley and Mark J. van der Laan
Causal Inference for Nested Case-Control Studies using Targeted Maximum Likelihood Estimation, Sherri Rose and Mark J. van der Laan
Collaborative Targeted Maximum Likelihood Estimation, Mark J. van der Laan and Susan Gruber
Readings in Targeted Maximum Likelihood Estimation, Mark J. van der Laan, Sherri Rose, and Susan Gruber
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
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
Data-adaptive selection of the truncation level for Inverse-Probability-of-Treatment-Weighted estimators, Oliver Bembom and Mark J. van der Laan
Supervised Distance Matrices: Theory and Applications to Genomics, Katherine S. POLLARD and Mark J. van der Laan
Confidence Intervals for the Population Mean Tailored to Small Sample Sizes, with Applications to Survey Sampling, Michael Rosenblum and Mark J. van der Laan
Using Regression Models to Analyze Randomized Trials: Asymptotically Valid Hypothesis Tests Despite Incorrectly Specified Models, Michael Rosenblum and Mark J. van der Laan
A Guide to Causal Parameters in Case-Control Designs: Targeted Maximum Likelihood Estimation, Sherri Rose and Mark J. van der Laan
A Note on Risk Prediction for Case-Control Studies, Sherri Rose and Mark J. van der Laan
Why Match? Investigating Matched Case-Control Study Designs with Causal Effect Estimation, Sherri Rose and Mark J. van der Laan
A Small Sample Correction for Estimating Attributable Risk in Case-Control Studies, Daniel B. Rubin
Covariate Adjustment for the Intention-to-Treat Parameter with Empirical Efficiency Maximization, Daniel B. Rubin and Mark J. van der Laan
Doubly Robust Ecological Inference, Daniel B. Rubin and Mark J. van der Laan
Confidence Intervals for Negative Binomial Random Variables of High Dispersion, David Shilane, Alan E. Hubbard, and S N. Evans
FDR Controlling Procedure for Multi-stage Analyses, Catherine Tuglus and Mark J. van der Laan
Targeted Methods for Biomarker Discovery, the Search for a Standard, Catherine Tuglus and Mark J. van der Laan
Estimation Based on Case-Control Designs with Known Incidence Probability, Mark J. van der Laan
The Construction and Analysis of Adaptive Group Sequential Designs, Mark J. van der Laan
Papers from 2007
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
Analyzing Sequentially Randomized Trials Based on Causal Effect Models for Realistic Individualized Treatment Rules, Oliver Bembom and Mark J. van der Laan
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
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
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
Covariate Adjustment in Randomized Trials with Binary Outcomes: Targeted Maximum Likelihood Estimation, Kelly L. Moore and Mark J. van der Laan
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
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
Empirical Efficiency Maximization, Daniel B. Rubin and Mark J. van der Laan
Loss-Based Estimation with Evolutionary Algorithms and Cross-Validation, David Shilane, Richard H. Liang, and Sandrine Dudoit
Time-Dependent Performance Comparison of Stochastic Optimization Algorithms, David Shilane, Jarno Martikainen, and Seppo Ovaska
Super Learner, Mark J. van der Laan, Eric C. Polley, and Alan E. Hubbard
A Note on Targeted Maximum Likelihood and Right Censored Data, Mark J. van der Laan and Daniel Rubin
Regression Analysis of a Disease Onset Distribution Using Diagnosis Data, Jessica G. Young, Nicholas P. Jewell, and Steven J. Samuels
Papers from 2006
Supervised Detection of Conserved Motifs in DNA Sequences with cosmo, Oliver Bembom, Sunduz Keles, and Mark J. van der Laan
Multiple Tests of Association with Biological Annotation Metadata, Sandrine Dudoit, Sunduz Keles, and Mark J. van der Laan
Empirical Bayes Approach to Controlling Familywise Error: An Application to HIV Resistance Data, Rhoderick N. Machekano and Alan E. Hubbard
Individualized Treatment Rules: Generating Candidate Clinical Trials, Maya L. Petersen, Steven G. Deeks, and Mark J. van der Laan
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting, Daniel Rubin, Sandrine Dudoit, and Mark J. van der Laan
Doubly Robust Censoring Unbiased Transformations, Daniel Rubin and Mark J. van der Laan
Extending Marginal Structural Models through Local, Penalized, and Additive Learning, Daniel Rubin and Mark J. van der Laan
A General Framework for Statistical Performance Comparison of Evolutionary Computation Algorithms, David Shilane, Jarno Martikainen, Sandrine Dudoit, and Seppo Ovaska
Super Learning: An Application to Prediction of HIV-1 Drug Susceptibility, Sandra E. Sinisi, Maya L. Petersen, and Mark J. van der Laan
Causal Effect Models for Intention to Treat and Realistic Individualized Treatment Rules, Mark J. van der Laan
Statistical Learning of Origin-Specific Statically Optimal Individualized Treatment Rules, Mark J. van der Laan and Maya L. Petersen
Targeted Maximum Likelihood Learning, Mark J. van der Laan and Daniel Rubin
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
Colon Cancer Prognosis Prediction by Gene Expression Profiling, Alain Barrier, Sandrine Dudoit, and et al.
Prognosis of Stage II Colon Cancer by Non-Neoplastic Mucosa Gene Expresssion Profiling, Alain Barrier, Sandrine Dudoit, and et al.
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
Data Adaptive Pathway Testing, Merrill D. Birkner, Alan E. Hubbard, and Mark J. van der Laan
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
Multiple Testing Procedures and Applications to Genomics, Merrill D. Birkner, Katherine S. Pollard, Mark J. van der Laan, and Sandrine Dudoit
Application of a Variable Importance Measure Method to HIV-1 Sequence Data, Merrill D. Birkner and Mark J. van der Laan
Optimization of the Architecture of Neural Networks Using a Deletion/Substitution/Addition Algorithm, Blythe Durbin, Sandrine Dudoit, and Mark J. van der Laan
Survival Ensembles, Torsten Hothorn, Peter Buhlmann, Sandrine Dudoit, Annette M. Molinaro, and Mark J. van der Laan
Population Intervention Models in Causal Inference, Alan E. Hubbard and Mark J. van der Laan
Correspondences between Regression Models for Complex Binary Outcomes and Those for Structured Multivariate Survival Analyses, Nicholas P. Jewell
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
Efficacy Studies of Malaria Treatments in Africa: Efficient Estimation with Missing Indicators of Failure, Rhoderick N. Machekano, Grant Dorsey, and Alan E. Hubbard
Cross-Validating and Bagging Partitioning Algorithms with Variable Importance, Annette M. Molinaro and Mark J. van der Laan
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
G-computation Estimation of Nonparametric Causal Effects on Time-Dependent Mean Outcomes in Longitudinal Studies, Romain Neugebauer and Mark J. van der Laan
Causal Inference in Longitudinal Studies with History-Restricted Marginal Structural Models, Romain Neugebauer, Mark J. van der Laan, and Ira B. Tager
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
Estimation of Direct Causal Effects, Maya L. Petersen and Mark J. van der Laan
History-Adjusted Marginal Structural Models: Optimal Treatment Strategies, Maya L. Petersen and Mark J. van der Laan
History-Adjusted Marginal Structural Models: Time-Varying Effect Modification, Maya L. Petersen and Mark J. van der Laan
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
Cluster Analysis of Genomic Data with Applications in R, Katherine S. Pollard and Mark J. van der Laan
A General Imputation Methodology for Nonparametric Regression with Censored Data, Dan Rubin and Mark J. van der Laan
Cross-validated Bagged Prediction of Survival, Sandra E. Sinisi, Romain Neugebauer, and Mark J. van der Laan
Statistical Inference for Variable Importance, Mark J. van der Laan
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
Quantile-Function Based Null Distribution in Resampling Based Multiple Testing, Mark J. van der Laan and Alan E. Hubbard
Direct Effect Models, Mark J. van der Laan and Maya L. Petersen
Estimating Function Based Cross-Validation and Learning, Mark J. van der Laan and Daniel Rubin
Cross-validated Bagged Learning, Mark J. van der Laan, Sandra E. Sinisi, and Maya L. Petersen
A Fine-Scale Linkage Disequilibrium Measure Based on Length of Haplotype Sharing, Yan Wang, Lue Ping Zhao, and Sandrine Dudoit
A Causal Inference Approach for Constructing Transcriptional Regulatory Networks, Biao Xing and Mark J. van der Laan
A Note on the Construction of Counterfactuals and the G-computation Formula, Zhuo Yu and Mark J. van der Laan
Papers from 2004
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
Linear Life Expectancy Regression with Censored Data, Ying Qing Chen and Su-Chun Cheng
Mean Response Models of Repeated Measurements in Presence of Varying Effectiveness Onset, Ying Qing Chen and Su-Chun Cheng
Semiparametric Regression Analysis of Mean Residual Life with Censored Survival Data, Ying Qing Chen and Su-Chun Cheng
Semiparametric Quantitative-Trait-Locus Mapping: II. on Censored Age-at-Onset, Ying Qing Chen, Chengcheng Hu, and Rongling Wu
Semiparametric Quantitative-Trait-Locus Mapping: I. on Functional Growth Curves, Ying Qing Chen and Rongling Wu
A Note on Empirical Likelihood Inference of Residual Life Regression, Ying Qing Chen and Yichuan Zhao
Multiple Testing Procedures for Controlling Tail Probability Error Rates, Sandrine Dudoit, Mark J. van der Laan, and Merrill D. Birkner
Choice of Monitoring Mechanism for Optimal Nonparametric Functional Estimation for Binary Data, Nicholas P. Jewell, Mark J. van der Laan, and Stephen Shiboski
Multiple Testing Methods For ChIP-Chip High Density Oligonucleotide Array Data, Sunduz Keles, Mark J. van der Laan, Sandrine Dudoit, and Simon E. Cawley