Biostatistics creates and applies methods for quantitative research in the health sciences. Our faculty conduct research across the spectrum of statistical science from foundations of inference to the discovery of new methodology to health applications. Our designs and analytic methods enable health scientists and professionals in academia, government, pharmaceutical companies, medical research organizations and elsewhere to efficiently acquire knowledge and draw valid conclusions from their ever-expanding sources of information.

A collection of working papers and related research documents from the department faculty may be found here.

Further information about the department may be found at www.biostat.jhsph.edu.

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Papers from 2014

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LEVERAGING PROGNOSTIC BASELINE VARIABLES TO GAIN PRECISION IN RANDOMIZED TRIALS, Elizabeth Colantuoni and Michael Rosenblum

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ENHANCED PRECISION IN THE ANALYSIS OF RANDOMIZED TRIALS WITH ORDINAL OUTCOMES, Iván Díaz, Elizabeth Colantuoni, and Michael Rosenblum

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TARGETED MAXIMUM LIKELIHOOD ESTIMATION USING EXPONENTIAL FAMILIES, Iván Díaz and Michael Rosenblum

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INTERADAPT -- AN INTERACTIVE TOOL FOR DESIGNING AND EVALUATING RANDOMIZED TRIALS WITH ADAPTIVE ENROLLMENT CRITERIA, Aaron Joel Fisher, Harris Jaffee, and Michael Rosenblum

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COX REGRESSION MODELS WITH FUNCTIONAL COVARIATES FOR SURVIVAL DATA, Jonathan E. Gellar, Elizabeth Colantuoni, Dale M. Needham, and Ciprian M. Crainiceanu

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VARIABLE-DOMAIN FUNCTIONAL REGRESSION FOR MODELING ICU DATA, Jonathan E. Gellar, Elizabeth Colantuoni, Dale M. Needham, and Ciprian M. Crainiceanu

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A BAYESIAN APPROACH TO JOINT MODELING OF MENSTRUAL CYCLE LENGTH AND FECUNDITY, Kirsten J. Lum, Rajeshwari Sundaram, Germaine M. Buck-Louis, and Thomas A. Louis

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ADAPTIVE RANDOMIZED TRIAL DESIGNS THAT CANNOT BE DOMINATED BY ANY STANDARD DESIGN AT THE SAME TOTAL SAMPLE SIZE, Michael Rosenblum

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OPTIMAL, TWO STAGE, ADAPTIVE ENRICHMENT DESIGNS FOR RANDOMIZED TRIALS USING SPARSE LINEAR PROGRAMMING, Michael Rosenblum, Xingyuan Fang, and Han Liu

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Estimating population treatment effects from a survey sub-sample, Kara E. Rudolph, Ivan Diaz, Michael Rosenblum, and Elizabeth A. Stuart

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CROSS-DESIGN SYNTHESIS FOR EXTENDING THE APPLICABILITY OF TRIAL EVIDENCE WHEN TREATMENT EFFECT IS HETEROGENEOUS-I. METHODOLOGY, Ravi Varadhan and Carlos Weiss

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APPLYING MULTIPLE IMPUTATION FOR EXTERNAL CALIBRATION TO PROPENSTY SCORE ANALYSIS, Yenny Webb-Vargas, Kara E. Rudolph, D. Lenis, Peter Murakami, and Elizabeth A. Stuart

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CROSS-DESIGN SYNTHESIS FOR EXTENDING THE APPLICABILITY OF TRIAL EVIDENCE WHEN TREATMENT EFFECT IS HETEROGENEOUS. PART II. APPLICATION AND EXTERNAL VALIDATION, Carlos Weiss and Ravi Varadhan

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Partially-Latent Class Models (pLCM) for Case-Control Studies of Childhood Pneumonia Etiology, Zhenke Wu, Maria Deloria-Knoll, Laura L. Hammitt, and Scott L. Zeger

Papers from 2013

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Sparse Median Graphs Estimation in a High Dimensional Semiparametric Model, Fang Han, Han Liu, and Brian Caffo

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PREDICTING HUMAN MOVEMENT TYPE BASED ON MULTIPLE ACCELEROMETERS USING MOVELETS, Bing He, Jiawei Bai, Annemarie Koster, Casserotti Paolo, Nancy Glynn, Tamara B. Harris, and Ciprian Crainiceanu

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PENALIZED FUNCTION-ON-FUNCTION REGRESSION, Andrada E. Ivanescu, Ana-Maria Staicu, Fabian Scheipl, and Sonja Greven

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TRIAL DESIGNS THAT SIMULTANEOUSLY OPTIMIZE THE POPULATION ENROLLED AND THE TREATMENT ALLOCATION PROBABILITIES, Brandon S. Luber, Michael Rosenblum, and Antoine Chambaz

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Joint Estimation of Multiple Graphical Models from High Dimensional Time Series, Huitong Qiu, Fang Han, Han Liu, and Brian Caffo

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UNIFORMLY MOST POWERFUL TESTS FOR SIMULTANEOUSLY DETECTING A TREATMENT EFFECT IN THE OVERALL POPULATION AND AT LEAST ONE SUBPOPULATION, Michael Rosenblum

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OPTIMAL TESTS OF TREATMENT EFFECTS FOR THE OVERALL POPULATION AND TWO SUBPOPULATIONS IN RANDOMIZED TRIALS, USING SPARSE LINEAR PROGRAMMING, Michael Rosenblum, Han Liu, and En-Hsu Yen

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Adaptive, Group Sequential Designs that Balance the Benefits and Risks of Wider Inclusion Criteria, Michael Rosenblum, Richard E. Thompson, Brandon S. Luber, and Daniel F. Hanley

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Soft Null Hypotheses: A Case Study of Image Enhancement Detection in Brain Lesions, Haochang Shou, Russell T. Shinohara, Han Liu, Daniel Reich, and Ciprian Crainiceanu

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Structured Functional Principal Component Analysis, Haochang Shou, Vadim Zipunnikov, Ciprian Crainiceanu, and Sonja Greven

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RESTRICTED LIKELIHOOD RATIO TESTS FOR FUNCTIONAL EFFECTS IN THE FUNCTIONAL LINEAR MODEL, Bruce J. Swihart, Jeff Goldsmith, and Ciprian M. Crainiceanu

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FAST COVARIANCE ESTIMATION FOR HIGH-DIMENSIONAL FUNCTIONAL DATA, Luo Xiao, David Ruppert, Vadim Zipunnikov, and Ciprian Crainiceanu

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Homotopic Group ICA for Multi-Subject Brain Imaging Data, Juemin Yang, Ani Eloyan, Anita Barber, Mary Beth Nebel, Stewart Mostofsky, Jim Pekar, Ciprian Crainiceanu, and Brian Caffo

Papers from 2012

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BOOTSTRAP-BASED INFERENCE ON THE DIFFERENCE IN THE MEANS OF TWO CORRELATED FUNCTIONAL PROCESSES, Ciprian M. Crainiceanu, Ana-Maria Staicu, Shubankar Ray, and Naresh Punjabi

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ANALYTIC PROGRAMMING WITH fMRI DATA: A QUICK-START GUIDE FOR STATISTICIANS USING R, Ani Eloyan, Shanshan Li, John Muschelli, Jim Pekar, Stewart Mostofsky, and Brian S. Caffo

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AUTOMATED DIAGNOSES OF ATTENTION DEFICIT HYPERACTIVE DISORDER USING MAGNETIC RESONANCE IMAGING, Ani Eloyan, John Muschelli, Mary Beth Nebel, Han Liu, Fang Han, Tuo Zhao, Anita Barber, Suresh Joel, James J. Pekar, Stewart Mostofsky, and Brian Caffo

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LONGITUDINAL FUNCTIONAL MODELS WITH STRUCTURED PENALTIES, Madan G. Kundu, Jaroslaw Harezlak, and Timothy W. Randolph

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CONFIDENCE INTERVALS FOR THE SELECTED POPULATION IN RANDOMIZED TRIALS THAT ADAPT THE POPULATION ENROLLED, Michael Rosenblum

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LIKELIHOOD RATIO TESTS FOR THE MEAN STRUCTURE OF CORRELATED FUNCTIONAL PROCESSES, Ana-Maria Staicu, Yingxing Li, Ciprian Crainiceanu, and David M. Ruppert

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MODELING SLEEP FRAGMENTATION IN POPULATIONS OF SLEEP HYPNOGRAMS, Bruce J. Swihart, Naresh M. Punjabi, and Ciprian M. Crainiceanu

Papers from 2011

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MOVELETS: A DICTIONARY OF MOVEMENT, Jiawei Bai, Jeff Goldsmith, Brian Caffo, Thomas A. Glass, and Ciprian M. Crainiceanu

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Reduced Bayesian Hierarchical Models: Estimating Health Effects of Simultaneous Exposure to Multiple Pollutants, Jennifer F. Bobb, Francesca Dominici, and Roger D. Peng

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MODIFICATION BY FRAILTY STATUS OF AMBIENT AIR POLLUTION EFFECTS ON LUNG FUNCTION IN OLDER ADULTS IN THE CARDIOVASCULAR HEALTH STUDY, Sandrah P. Eckel, Thomas A. Louis, Paulo H.M. Chaves, Linda P. Fried, and Helene G. Margolis

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LIKELIHOOD BASED POPULATION INDEPENDENT COMPONENT ANALYSIS, Ani Eloyan, Ciprian M. Crainiceanu, and Brian S. Caffo

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CORRECTED CONFIDENCE BANDS FOR FUNCTIONAL DATA USING PRINCIPAL COMPONENTS, Jeff Goldsmith, Sonja Greven, and Ciprian M. Crainiceanu

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REMOVING TECHNICAL VARIABILITY IN RNA-SEQ DATA USING CONDITIONAL QUANTILE NORMALIZATION, Kasper D. Hansen, Rafael A. Irizarry, and Zhijin Wu

Component extraction of Complex Biomedical signal and performance analysis based on different algorithm, hemant pasusangai kasturiwale

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POPULATION FUNCTIONAL DATA ANALYSIS OF GROUP ICA-BASED CONNECTIVITY MEASURES FROM fMRI, Shanshan Li, Brian S. Caffo, Suresh Joel, Stewart Mostofsky, James Pekar, and Susan Spear Bassett

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Flexible Distributed Lag Models using Random Functions with Application to Estimating Mortality Displacement from Heat-Related Deaths, Roger D. Peng

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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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POPULATION-WIDE MODEL-FREE QUANTIFICATION OF BLOOD-BRAIN-BARRIER DYNAMICS IN MULTIPLE SCLEROSIS, Russell T. Shinohara, Ciprian Crainiceanu, Brian Caffo, María Inés Gaitán, and Daniel Reich

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LONGITUDINAL ANALYSIS OF SPATIOTEMPORAL PROCESSES: A CASE STUDY OF DYNAMIC CONTRAST-ENHANCED MAGNETIC RESONANCE IMAGING IN MULTIPLE SCLEROSIS, Russell T. Shinohara, Ciprian M. Crainiceanu, Brian S. Caffo, and Daniel S. Reich

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A BROAD SYMMETRY CRITERION FOR NONPARAMETRIC VALIDITY OF PARAMETRICALLY-BASED TESTS IN RANDOMIZED TRIALS, Russell T. Shinohara, Constantine E. Frangakis, and Constantine G.. Lyketos

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Assessing Association for Bivariate Survival Data with Interval Sampling: A Copula Model Approach with Application to AIDS Study, Hong Zhu and Mei-Cheng Wang

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FUNCTIONAL PRINCIPAL COMPONENTS MODEL FOR HIGH-DIMENSIONAL BRAIN IMAGING, Vadim Zipunnikov, Brian S. Caffo, David M. Yousem, Christos Davatzikos, Brian S. Schwartz, and Ciprian Crainiceanu

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LONGITUDINAL HIGH-DIMENSIONAL DATA ANALYSIS, Vadim Zipunnikov, Sonja Greven, Brian Caffo, Daniel S. Reich, and Ciprian Crainiceanu

Papers from 2010

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ACCURATE GENOME-SCALE PERCENTAGE DNA METHYLATION ESTIMATES FROM MICROARRAY DATA, Martin J. Aryee, Zhijin Wu, Christine Ladd-Acosta, Brian Herb, Andrew P. Feinberg, Srinivasan Yegnasurbramanian, and Rafael A. Irizarry

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A DECISION-THEORY APPROACH TO INTERPRETABLE SET ANALYSIS FOR HIGH-DIMENSIONAL DATA, Simina Maria Boca, Hector C. Bravo, Brian Caffo, Jeffrey T. Leek, and Giovanni Parmigiani

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WAVELET BASED FUNCTIONAL MODELS FOR TRANSCRIPTOME ANALYSIS WITH TILING ARRAYS, Lieven Clement, Kristof DeBeuf, Ciprian Crainiceanu, Olivier Thas, Marnik Vuylsteke, and Rafael Irizarry

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POPULATION VALUE DECOMPOSITION, A FRAMEWORK FOR THE ANALYSIS OF IMAGE POPULATIONS, Ciprian M. Crainiceanu, Brian S. Caffo, Sheng Luo, and Vadim Zipunnikov

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MULTILEVEL SPARSE FUNCTIONAL PRINCIPAL COMPONENT ANALYSIS, Chong-Zhi Di and Ciprian M. Crainiceanu

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Likelihood Ratio Testing for Admixture Models with Application to Genetic Linkage Analysis, Chong-Zhi Di and Kung-Yee Liang

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SURROGATE SCREENING MODELS FOR THE LOW PHYSICAL ACTIVITY CRITERION OF FRAILTY, Sandrah P. Eckel, Karen Bandeen-Roche, Paulo H.M. Chaves, Linda P. Fried, and Thomas A. Louis

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LONGITUDINAL PENALIZED FUNCTIONAL REGRESSION, Jeff Goldsmith, Ciprian M. Crainiceanu, Brian Caffo, and Daniel Reich

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PENALIZED FUNCTIONAL REGRESSION, Jeff Goldsmith, Jennifer Feder, Ciprian M. Crainiceanu, Brian Caffo, and Daniel Reich

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ESTIMATING TEMPORAL ASSOCIATIONS IN ELECTROCORTICOGRAPHIC (ECoG) TIME SERIES WITH FIRST ORDER PRUNING, Haley Hedlin, Dana Boatman, and Brian Caffo

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REGRESSION ADJUSTMENT AND STRATIFICATION BY PROPENSTY SCORE IN TREATMENT EFFECT ESTIMATION, Jessica A. Myers and Thomas A. Louis

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USING THE R PACKAGE crlmm FOR GENOTYPING AND COPY NUMBER ESTIMATION, Robert B. Scharpf, Rafael Irizarry, Walter Ritchie, Benilton Carvalho, and Ingo Ruczinski

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MODELING FUNCTIONAL DATA WITH SPATIALLY HETEROGENEOUS SHAPE CHARACTERISTICS, Ana-Maria Staicu, Ciprian M. Crainiceanu, Daniel S. Reich, and David Ruppert

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THE USE OF PROPENSITY SCORES TO ASSESS THE GENERALIZABILITY OF RESULTS FROM RANDOMIZED TRIALS, Elizabeth A. Stuart, Stephen R. Cole, Catherine P. Bradshaw, and Philip J. Leaf

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A unified approach to modeling multivariate binary data using copulas over partitions, Bruce J. Swihart, Brian Caffo, and Ciprian Crainiceanu

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Mixed effect Poisson log-linear models for clinical and epidemiological sleep hypnogram data, Bruce J. Swihart; Brian S. Caffo PhD; Ciprian Crainiceanu PhD; and Naresh M. Punjabi PhD, MD

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MULTILEVEL FUNCTIONAL PRINCIPAL COMPONENT ANALYSIS FOR HIGH-DIMENSIONAL DATA, Vadim Zipunnikov, Brian Caffo, Ciprian Crainiceanu, David M. Yousem, Christos Davatzikos, and Brian S. Schwartz

Papers from 2009

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QUANTIFYING UNCERTAINTY IN GENOTYPE CALLS, Benilton Carvalho, Thomas A. Louis, and Rafael A. Irizarry

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BAYESIAN FUNCTIONAL DATA ANALYSIS USING WinBUGS, Ciprian M. Crainiceanu and A. Jeffrey Goldsmith

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COMBINATIONAL MIXTURES OF MULTIPARAMETER DISTRIBUTIONS, Valeria Edefonti and Giovanni Parmigiani

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NONLINEAR TUBE-FITTING FOR THE ANALYSIS OF ANATOMICAL AND FUNCTIONAL STRUCTURES, Jeff Goldsmith, Brian S. Caffo, Ciprian Crainiceanu, Daniel Reich, Yong Du, and Craig Hendrix

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A Spatio-Temporal Approach for Estimating Chronic Effects of Air Pollution, Sonja Greven, Francesca Dominici, and Scott L. Zeger

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On the Behaviour of Marginal and Conditional Akaike Information Criteria in Linear Mixed Models, Sonja Greven and Thomas Kneib

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COVARIATE-ADJUSTED NONPARAMETRIC ANALYSIS OF MAGNETIC RESONANCE IMAGES USING MARKOV CHAIN MONTE CARLO, Haley Hedlin, Brian S. Caffo, Ziyad Mahfoud, and Susan Spear Bassett

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GENERALIZED LIQUID ASSOCIATION, Yen-Yi Ho, Leslie Cope, Thomas A. Louis, and Giovanni Parmigiani

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MODEL-BASED QUALITY ASSESSMENT AND BASE-CALLING FOR SECOND-GENERATION SEQUENCING DATA, Rafael A. Irizarry and Hector Corrada Bravo

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GENE SET ENRICHMENT ANALYSIS MADE SIMPLE, Rafael A. Irizarry, Chi Wang, Yun Zhou, and Terence P. Speed

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TRIO LOGIC REGRESSION - DETECTION OF SNP - SNP INTERACTIONS IN CASE-PARENT TRIOS, Qing Li, Thomas A. Louis, M. Daniele Fallin, and Ingo Ruczinski

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EFFICIENT EVALUATION OF RANKING PROCEDURES WHEN THE NUMBER OF UNITS IS LARGE WITH APPLICATION TO SNP IDENTIFICATION, Thomas A. Louis and Ingo Ruczinski

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FROZEN ROBUST MULTI-ARRAY ANALYSIS (fRMA), Matthew N. McCall, Benjamin M. Bolstad, and Rafael A. Irizarry

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Caching and Visualizing Statistical Analyses, Roger D. Peng and Duncan Temple Lang

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ASSOCIATON TESTS THAT ACCOMMODATE GENOTYPING ERRORS, Ingo Ruczinski, Qing Li, Benilton Carvalho, M. Daniele Fallin, Rafael A. Irizarry, and Thomas A. Louis

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A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS, Robert B. Scharpf, Ingo Ruczinski, Benilton Carvalho, Betty Doan, Aravinda Chakravarti, and Rafael A. Irizarry

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A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS, Robert B. Scharpf, Ingo Ruczinski, Benilton Carvalho, Betty Doan, Aravinda Chakravarti, and Rafael A. Irizarry

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Estimating effects by combining instrumental variables with case-control designs: the role of principal stratification, Russell T. Shinohara, Constantine E. Frangakis, Elizabeth Platz, and Konstantinos Tsilidis

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LASAGNA PLOTS: A SAUCY ALTERNATIVE TO SPAGHETTI PLOTS, Bruce Swihart, Brian Caffo, Bryan D. James, Matthew Strand, Brian S. Schwartz, and Naresh M. Punjabi

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Modeling multilevel sleep transitional data via Poisson log-linear multilevel models, Bruce J. Swihart, Brian Caffo, Ciprian Crainiceanu, and Naresh M. Punjabi

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A BAYESIAN SHRINKAGE MODEL FOR INCOMPLETE LONGITUDINAL BINARY DATA WITH APPLICATION TO THE BREAST CANCER PREVENTION TRIAL, C. Wang, M.J. Daniels, Daniel O. Scharfstein, and S. Land

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REDEFINING CpG ISLANDS USING A HIDEEN MARKOV MODEL, Hao Wu, Brain Caffo, Harris A. Jaffee, Andrew P. Feinberg, and Rafael A. Irizarry

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Subset Quantile Normalization using Negative Control Features, Zhijin Wu

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Analyzing Bivariate Survival Data with Interval Sampling and Application to Cancer Epidemiology, Hong Zhu and Mei-Cheng Wang

Papers from 2008

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LIKELIHOOD ESTIMATION OF CONJUGACY RELATIONSHIPS IN LINEAR MODELS WITH APPLICATIONS TO HIGH-THROUGHPUT GENOMICS, Brian S. Caffo, Liu Dongmei, Robert Scharpf, and Giovanni Parmigiani

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AN OVERVIEW OF OBSERVATIONAL SLEEP RESEARCH WITH APPLICATION TO SLEEP STAGE TRANSITIONING, Brian S. Caffo, B. Swihart, A. Laffan, C. Crainiceanu, and N. Punjabi

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Bayesian Model Averaging for Clustered Data: Imputing Missing Daily Air Pollution Concentration, Howard H. Chang, Francesca Dominici, and Roger D. Peng

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GENERALIZED MULTILEVEL FUNCTIONAL REGRESSION, Ciprian M. Crainiceanu, Ana-Maria Staicu, and Chongzhi Di

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Multilevel Latent Class Models with Dirichlet Mixing Distribution, Chongzhi Di and Karen Bandeen-Roche

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GEOSTATISTICAL INFERENCE UNDER PREFERENTIAL SAMPLING, Peter J. Diggle, Raquel Menezes, and Ting-li Su

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MODEL SELECTION AND HEALTH EFFECT ESTIMATION IN ENVIRONMENTAL EPIDEMIOLOGY, Francesca Dominici, Chi Wang, Ciprian Crainiceanu, and Giovanni Parmigiani

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A NOVEL AND SIMPLE RULE OF THUMB FOR MULTIPLICITY CONTROL IN EQUIVALENCE TESTING USING TWO ONE-SIDED TESTS, Carolyn Lauzon and Brian S. Caffo

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JOINTLY MODELING CONTINUOUS AND BINARY OUTCOMES FOR BOOLEAN OUTCOMES: AN APPLICATION TO MODELING HYPERTENSION, Xianbin Li, Brian S. Caffo, and Elizabeth Stuart