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 2007
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
Regulatory Motif Finding by Logic Regression, Sunduz Keles, Mark J. van der Laan, and Chris Vulpe
Deletion/Substitution/Addition Algorithm for Partitioning the Covariate Space in Prediction, Annette Molinaro and Mark J. van der Laan
Multiple Testing Procedures: R multtest Package and Applications to Genomics, Katherine S. Pollard, Sandrine Dudoit, and Mark J. van der Laan
GLLAMM Manual, Sophia Rabe-Hesketh, Anders Skrondal, and Andrew Pickles
Loss-Based Cross-Validated Deletion/Substitution/Addition Algorithms in Estimation, Sandra E. Sinisi and Mark J. van der Laan
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
The Cross-Validated Adaptive Epsilon-Net Estimator, Mark J. van der Laan, Sandrine Dudoit, and Aad W. van der Vaart
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
Estimation of Direct and Indirect Causal Effects in Longitudinal Studies, Mark J. van der Laan and Maya L. Petersen
History-Adjusted Marginal Structural Models and Statically-Optimal Dynamic Treatment Regimes, Mark J. van der Laan and Maya L. Petersen
Estimating a Survival Distribution with Current Status Data and High-Dimensional Covariates, Mark J. van der Laan and Aad van der Vaart
Quantification and Visualization of LD Patterns and Identification of Haplotype Blocks, Yan Wang and Sandrine Dudoit
Data Adaptive Estimation of the Treatment Specific Mean, Yue Wang, Oliver Bembom, and Mark J. van der Laan
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
A Semiparametric Model Selection Criterion with Applications to the Marginal Structural Model, M. Alan Brookhart and Mark J. van der Laan
Rank Regression in Stability Analysis, Ying Qing Chen, Annpey Pong, and Biao Xing
IBD Configuration Transition Matrices and Linkage Score Tests for Unilineal Relative Pairs, Sandrine Dudoit
Asymptotics of Cross-Validated Risk Estimation in Estimator Selection and Performance Assessment, Sandrine Dudoit and Mark J. van der Laan
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
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
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
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
Asymptotically Optimal Model Selection Method with Right Censored Outcomes, Sunduz Keles, Mark J. van der Laan, and Sandrine Dudoit
Supervised Detection of Regulatory Motifs in DNA Sequences, Sunduz Keles, Mark J. van der Laan, Sandrine Dudoit, Biao Xing, and Michael B. Eisen
Tree-based Multivariate Regression and Density Estimation with Right-Censored Data , Annette M. Molinaro, Sandrine Dudoit, and Mark J. van der Laan
Locally Efficient Estimation of Nonparametric Causal Effects on Mean Outcomes in Longitudinal Studies, Romain Neugebauer and Mark J. van der Laan
Resampling-based Multiple Testing: Asymptotic Control of Type I Error and Applications to Gene Expression Data, Katherine S. Pollard and Mark J. van der Laan
Unified Cross-Validation Methodology For Selection Among Estimators and a General Cross-Validated Adaptive Epsilon-Net Estimator: Finite Sample Oracle Inequalities and Examples, Mark J. van der Laan and Sandrine Dudoit
Asymptotic Optimality of Likelihood Based Cross-Validation, Mark J. van der Laan, Sandrine Dudoit, and Sunduz Keles
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate, Mark J. van der Laan, Sandrine Dudoit, and Katherine S. Pollard
Double Robust Estimation in Longitudinal Marginal Structural Models, Zhuo Yu and Mark J. van der Laan
Measuring Treatment Effects Using Semiparametric Models, Zhuo Yu and Mark J. van der Laan
Papers from 2002
Locally Efficient Estimation of Regression Parameters Using Current Status Data, Chris Andrews, Mark J. van der Laan, and James M. Robins
Analysis of Longitudinal Marginal Structural Models , Jennifer F. Bryan, Zhuo Yu, and Mark J. van der Laan
Accelerated Hazards Model: Method, Theory and Applications, Ying Qing Chen, Nicholas P. Jewell, and Jingrong Yang
Regression Analysis of Recurrent Gap Times with Time-Dependent Covariates, Ying Qing Chen, Mei-Cheng Wang, and Yijian Huang
Semiparametric Regression Analysis on Longitudinal Pattern of Recurrent Gap Times, Ying Qing Chen, Mei-Cheng Wang, and Yijian Huang
Inference for Proportional Mean Residual Life Model in the Presence of Censoring, Ying Q. Chen and Nicholas P. Jewell
Multiple Hypothesis Testing in Microarray Experiments, Sandrine Dudoit, Juliet Popper Shaffer, and Jennifer C. Boldrick
An Empirical Study of Marginal Structural Models for Time-Independent Treatment, Tanya A. Henneman and Mark J. van der Laan
Estimating Causal Parameters in Marginal Structural Models with Unmeasured Confounders Using Instrumental Variables, Tanya A. Henneman, Mark Johannes van der Laan, and Alan E. Hubbard
Case-Control Current Status Data, Nicholas P. Jewell and Mark J. van der Laan