Johns Hopkins University, Dept. of Biostatistics Working Papers

Papers from 2011
Flexible Distributed Lag Models using Random Functions with Application to Estimating Mortality Displacement from Heat-Related Deaths (December 14, 2011) Roger D. Peng
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CONSONANT MULTIPLE TESTING PROCEDURES FOR OVERALL AND SUBPOPULATION TREATMENT EFFECTS IN RANDOMIZED TRIALS (November 30, 2011) Michael Rosenblum
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Assessing Association for Bivariate Survival Data with Interval Sampling: A Copula Model Approach with Application to AIDS Study (November 16, 2011) Hong Zhu and Mei-Cheng Wang
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LONGITUDINAL HIGH-DIMENSIONAL DATA ANALYSIS (November 16, 2011) Vadim Zipunnikov, Sonja Greven, Brian Caffo, Daniel S. Reich, and Ciprian Crainiceanu
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CORRECTED CONFIDENCE BANDS FOR FUNCTIONAL DATA USING PRINCIPAL COMPONENTS (November 9, 2011) Jeff Goldsmith, Sonja Greven, and Ciprian M. Crainiceanu
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LIKELIHOOD BASED POPULATION INDEPENDENT COMPONENT ANALYSIS (November 9, 2011) Ani Eloyan, Ciprian M. Crainiceanu, and Brian S. Caffo
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LONGITUDINAL ANALYSIS OF SPATIOTEMPORAL PROCESSES: A CASE STUDY OF DYNAMIC CONTRAST-ENHANCED MAGNETIC RESONANCE IMAGING IN MULTIPLE SCLEROSIS (September 13, 2011) Russell T. Shinohara, Ciprian M. Crainiceanu, Brian S. Caffo, and Daniel S. Reich
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MOVELETS: A DICTIONARY OF MOVEMENT (August 31, 2011) Jiawei Bai, Jeff Goldsmith, Brian Caffo, Thomas A. Glass, and Ciprian M. Crainiceanu
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MODIFICATION BY FRAILTY STATUS OF AMBIENT AIR POLLUTION EFFECTS ON LUNG FUNCTION IN OLDER ADULTS IN THE CARDIOVASCULAR HEALTH STUDY (August 24, 2011) Sandrah P. Eckel, Thomas A. Louis, Paulo H.M. Chaves, Linda P. Fried, and Helene G. Margolis
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Reduced Bayesian Hierarchical Models: Estimating Health Effects of Simultaneous Exposure to Multiple Pollutants (July 12, 2011) Jennifer F. Bobb, Francesca Dominici, and Roger D. Peng
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REMOVING TECHNICAL VARIABILITY IN RNA-SEQ DATA USING CONDITIONAL QUANTILE NORMALIZATION (May 24, 2011) Kasper D. Hansen, Rafael A. Irizarry, and Zhijin Wu
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A BROAD SYMMETRY CRITERION FOR NONPARAMETRIC VALIDITY OF PARAMETRICALLY-BASED TESTS IN RANDOMIZED TRIALS (April 12, 2011) Russell T. Shinohara, Constantine E. Frangakis, and Constantine G.. Lyketos
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SIMPLE EXAMPLES OF ESTIMATING CAUSAL EFFECTS USING TARGETED MAXIMUM LIKELIHOOD ESTIMATION (March 3, 2011) Michael Rosenblum and Mark J. van der Laan
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STATISTICAL INFERENCE ON THE DIFFERENCE IN THE MEANS OF TWO CORRELATED FUNCTIONAL PROCESSES: AN APPLICATION TO SLEEP EEG POWER SPECTRA (February 8, 2011) Ciprian M. Crainiceanu, Ana-Maria Staicu, Shubankar Ray, and Naresh Punjabi
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POPULATION FUNCTIONAL DATA ANALYSIS OF GROUP ICA-BASED CONNECTIVITY MEASURES FROM fMRI (February 4, 2011) Shanshan Li, Brian S. Caffo, Suresh Joel, Stewart Mostofsky, James Pekar, and Susan Spear Bassett
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FUNCTIONAL PRINCIPAL COMPONENTS MODEL FOR HIGH-DIMENSIONAL BRAIN IMAGING (January 18, 2011) Vadim Zipunnikov, Brian S. Caffo, David M. Yousem, Christos Davatzikos, Brian S. Schwartz, and Ciprian Crainiceanu
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POPULATION-WIDE MODEL-FREE QUANTIFICATION OF BLOOD-BRAIN-BARRIER DYNAMICS IN MULTIPLE SCLEROSIS (January 7, 2011) Russell T. Shinohara, Ciprian Crainiceanu, Brian Caffo, María Inés Gaitán, and Daniel Reich
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Papers from 2010
MODELING FUNCTIONAL DATA WITH SPATIALLY HETEROGENEOUS SHAPE CHARACTERISTICS (October 13, 2010) Ana-Maria Staicu, Ciprian M. Crainiceanu, Daniel S. Reich, and David Ruppert
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POPULATION VALUE DECOMPOSITION, A FRAMEWORK FOR THE ANALYSIS OF IMAGE POPULATIONS (October 7, 2010) Ciprian M. Crainiceanu, Brian S. Caffo, Sheng Luo, and Vadim Zipunnikov
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MULTILEVEL FUNCTIONAL PRINCIPAL COMPONENT ANALYSIS FOR HIGH-DIMENSIONAL DATA (October 6, 2010) Vadim Zipunnikov, Brian Caffo, Ciprian Crainiceanu, David M. Yousem, Christos Davatzikos, and Brian S. Schwartz
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USING THE R PACKAGE crlmm FOR GENOTYPING AND COPY NUMBER ESTIMATION (September 29, 2010) Robert B. Scharpf, Rafael Irizarry, Walter Ritchie, Benilton Carvalho, and Ingo Ruczinski
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ESTIMATING TEMPORAL ASSOCIATIONS IN ELECTROCORTICOGRAPHIC (ECoG) TIME SERIES WITH FIRST ORDER PRUNING (September 29, 2010) Haley Hedlin, Dana Boatman, and Brian Caffo
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LONGITUDINAL PENALIZED FUNCTIONAL REGRESSION (September 9, 2010) Jeff Goldsmith, Ciprian M. Crainiceanu, Brian Caffo, and Daniel Reich
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Mixed effect Poisson log-linear models for clinical and epidemiological sleep hypnogram data (August 31, 2010) Bruce J. Swihart; Brian S. Caffo PhD; Ciprian Crainiceanu PhD; and Naresh M. Punjabi PhD, MD
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SURROGATE SCREENING MODELS FOR THE LOW PHYSICAL ACTIVITY CRITERION OF FRAILTY (August 16, 2010) Sandrah P. Eckel, Karen Bandeen-Roche, Paulo H.M. Chaves, Linda P. Fried, and Thomas A. Louis
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A unified approach to modeling multivariate binary data using copulas over partitions (July 15, 2010) Bruce J. Swihart, Brian Caffo, and Ciprian Crainiceanu
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A DECISION-THEORY APPROACH TO INTERPRETABLE SET ANALYSIS FOR HIGH-DIMENSIONAL DATA (July 1, 2010) Simina Maria Boca, Hector C. Bravo, Brian Caffo, Jeffrey T. Leek, and Giovanni Parmigiani
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THE USE OF PROPENSITY SCORES TO ASSESS THE GENERALIZABILITY OF RESULTS FROM RANDOMIZED TRIALS (May 13, 2010) Elizabeth A. Stuart, Stephen R. Cole, Catherine P. Bradshaw, and Philip J. Leaf
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ACCURATE GENOME-SCALE PERCENTAGE DNA METHYLATION ESTIMATES FROM MICROARRAY DATA (March 16, 2010) Martin J. Aryee, Zhijin Wu, Christine Ladd-Acosta, Brian Herb, Andrew P. Feinberg, Srinivasan Yegnasurbramanian, and Rafael A. Irizarry
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Likelihood Ratio Testing for Admixture Models with Application to Genetic Linkage Analysis (March 15, 2010) Chong-Zhi Di and Kung-Yee Liang
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MULTILEVEL SPARSE FUNCTIONAL PRINCIPAL COMPONENT ANALYSIS (March 2, 2010) Chong-Zhi Di and Ciprian M. Crainiceanu
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WAVELET BASED FUNCTIONAL MODELS FOR TRANSCRIPTOME ANALYSIS WITH TILING ARRAYS (February 3, 2010) Lieven Clement, Kristof DeBeuf, Ciprian Crainiceanu, Olivier Thas, Marnik Vuylsteke, and Rafael Irizarry
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PENALIZED FUNCTIONAL REGRESSION (January 21, 2010) Jeff Goldsmith, Jennifer Feder, Ciprian M. Crainiceanu, Brian Caffo, and Daniel Reich
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REGRESSION ADJUSTMENT AND STRATIFICATION BY PROPENSTY SCORE IN TREATMENT EFFECT ESTIMATION (January 19, 2010) Jessica A. Myers and Thomas A. Louis
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Papers from 2009
On the Behaviour of Marginal and Conditional Akaike Information Criteria in Linear Mixed Models (November 24, 2009) Sonja Greven and Thomas Kneib
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Analyzing Bivariate Survival Data with Interval Sampling and Application to Cancer Epidemiology (November 11, 2009) Hong Zhu and Mei-Cheng Wang
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Modeling multilevel sleep transitional data via Poisson log-linear multilevel models (November 3, 2009) Bruce J. Swihart, Brian Caffo, Ciprian Crainiceanu, and Naresh M. Punjabi
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BAYESIAN FUNCTIONAL DATA ANALYSIS USING WinBUGS (November 3, 2009) Ciprian M. Crainiceanu and A. Jeffrey Goldsmith
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LASAGNA PLOTS: A SAUCY ALTERNATIVE TO SPAGHETTI PLOTS (October 20, 2009) Bruce Swihart, Brian Caffo, Bryan D. James, Matthew Strand, Brian S. Schwartz, and Naresh M. Punjabi
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REDEFINING CpG ISLANDS USING A HIDEEN MARKOV MODEL (September 11, 2009) Hao Wu, Brain Caffo, Harris A. Jaffee, Andrew P. Feinberg, and Rafael A. Irizarry
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Estimating effects by combining instrumental variables with case-control designs: the role of principal stratification (September 9, 2009) Russell T. Shinohara, Constantine E. Frangakis, Elizabeth Platz, and Konstantinos Tsilidis
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MODEL-BASED QUALITY ASSESSMENT AND BASE-CALLING FOR SECOND-GENERATION SEQUENCING DATA (September 9, 2009) Rafael A. Irizarry and Hector Corrada Bravo
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COMBINATIONAL MIXTURES OF MULTIPARAMETER DISTRIBUTIONS (August 24, 2009) Valeria Edefonti and Giovanni Parmigiani
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TRIO LOGIC REGRESSION - DETECTION OF SNP - SNP INTERACTIONS IN CASE-PARENT TRIOS (July 1, 2009) Qing Li, Thomas A. Louis, M. Daniele Fallin, and Ingo Ruczinski
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A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS (June 29, 2009) Robert B. Scharpf, Ingo Ruczinski, Benilton Carvalho, Betty Doan, Aravinda Chakravarti, and Rafael A. Irizarry
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Caching and Visualizing Statistical Analyses (June 29, 2009) Roger D. Peng and Duncan Temple Lang
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A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS (June 29, 2009) Robert B. Scharpf, Ingo Ruczinski, Benilton Carvalho, Betty Doan, Aravinda Chakravarti, and Rafael A. Irizarry
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Subset Quantile Normalization using Negative Control Features (June 26, 2009) Zhijin Wu
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A Spatio-Temporal Approach for Estimating Chronic Effects of Air Pollution (June 24, 2009) Sonja Greven, Francesca Dominici, and Scott L. Zeger
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FROZEN ROBUST MULTI-ARRAY ANALYSIS (fRMA) (May 22, 2009) Matthew N. McCall, Benjamin M. Bolstad, and Rafael A. Irizarry
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A BAYESIAN SHRINKAGE MODEL FOR INCOMPLETE LONGITUDINAL BINARY DATA WITH APPLICATION TO THE BREAST CANCER PREVENTION TRIAL (May 22, 2009) C. Wang, M.J. Daniels, Daniel O. Scharfstein, and S. Land
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COVARIATE-ADJUSTED NONPARAMETRIC ANALYSIS OF MAGNETIC RESONANCE IMAGES USING MARKOV CHAIN MONTE CARLO (May 13, 2009) Haley Hedlin, Brian S. Caffo, Ziyad Mahfoud, and Susan Spear Bassett
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NONLINEAR TUBE-FITTING FOR THE ANALYSIS OF ANATOMICAL AND FUNCTIONAL STRUCTURES (April 21, 2009) Jeff Goldsmith, Brian S. Caffo, Ciprian Crainiceanu, Daniel Reich, Yong Du, and Craig Hendrix
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GENE SET ENRICHMENT ANALYSIS MADE SIMPLE (April 21, 2009) Rafael A. Irizarry, Chi Wang, Yun Zhou, and Terence P. Speed
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GENERALIZED LIQUID ASSOCIATION (April 8, 2009) Yen-Yi Ho, Leslie Cope, Thomas A. Louis, and Giovanni Parmigiani
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EFFICIENT EVALUATION OF RANKING PROCEDURES WHEN THE NUMBER OF UNITS IS LARGE WITH APPLICATION TO SNP IDENTIFICATION (February 11, 2009) Thomas A. Louis and Ingo Ruczinski
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ASSOCIATON TESTS THAT ACCOMMODATE GENOTYPING ERRORS (January 29, 2009) Ingo Ruczinski, Qing Li, Benilton Carvalho, M. Daniele Fallin, Rafael A. Irizarry, and Thomas A. Louis
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QUANTIFYING UNCERTAINTY IN GENOTYPE CALLS (January 29, 2009) Benilton Carvalho, Thomas A. Louis, and Rafael A. Irizarry
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Papers from 2008
LEARNING FROM NEAR MISSES IN MEDICATION ERRORS: A BAYESIAN APPROACH (December 17, 2008) Jessica A. Myers, Francesca Dominici, and Laura Morlock
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Bayesian Model Averaging for Clustered Data: Imputing Missing Daily Air Pollution Concentration (December 15, 2008) Howard H. Chang, Francesca Dominici, and Roger D. Peng
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Spatial Misalignment in time series studies of air pollution and health data (December 1, 2008) Roger D. Peng and Michelle L. Bell
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Multilevel Latent Class Models with Dirichlet Mixing Distribution (October 21, 2008) Chongzhi Di and Karen Bandeen-Roche
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GENERALIZED MULTILEVEL FUNCTIONAL REGRESSION (September 23, 2008) Ciprian M. Crainiceanu, Ana-Maria Staicu, and Chongzhi Di
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A NOVEL AND SIMPLE RULE OF THUMB FOR MULTIPLICITY CONTROL IN EQUIVALENCE TESTING USING TWO ONE-SIDED TESTS (July 23, 2008) Carolyn Lauzon and Brian S. Caffo
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Estimating the Causal Effect of Lower Tidal Volume Ventilation on Survival in Patients with Acute Lung Injury (July 11, 2008) Weiwei Wang, Daniel Scharfstein, Roy Brower, and Dale Needham
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BAYESIAN INFERENCE FOR SMOKING CESSATION WITH A LATENT CURE STATE (July 10, 2008) Sheng Luo, Ciprian M. Crainiceanu, Thomas A. Louis, and Nilanjan Chatterjee
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Causal Inference in Observational Studies with Outcome-Dependent Sampling (June 12, 2008) Weiwei Wang, Daniel Scharfstein, Zhiqiang Tan, and Ellen J. MacKenzie
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ANALYSIS OF SUBGROUP EFFECTS IN RANDOMIZED TRIALS WHEN SUBGROUP MEMBERSHIP IS INFORMATIVELY MISSING: APPLICATION TO THE MADIT II STUDY (June 12, 2008) Daniel O. Scharfstein, Georgiana Onicescu, and Steven Goodman
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Caching and Distributing Statistical Analyses in R (April 29, 2008) Roger D. Peng
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LIKELIHOOD ESTIMATION OF CONJUGACY RELATIONSHIPS IN LINEAR MODELS WITH APPLICATIONS TO HIGH-THROUGHPUT GENOMICS (April 7, 2008) 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 (March 31, 2008) Brian S. Caffo, B. Swihart, A. Laffan, C. Crainiceanu, and N. Punjabi
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A Method for Visualizing Multivariate Time Series Data (February 25, 2008) Roger D. Peng
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JOINTLY MODELING CONTINUOUS AND BINARY OUTCOMES FOR BOOLEAN OUTCOMES: AN APPLICATION TO MODELING HYPERTENSION (February 19, 2008) Xianbin Li, Brian S. Caffo, and Elizabeth Stuart
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MODEL SELECTION AND HEALTH EFFECT ESTIMATION IN ENVIRONMENTAL EPIDEMIOLOGY (January 30, 2008) Francesca Dominici, Chi Wang, Ciprian Crainiceanu, and Giovanni Parmigiani
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STATISTICAL METHODS FOR AUTOMATED DRUG SUSCEPTIBILITY TESTING: BAYESIAN MINIMUM INHIBITORY CONCENTRATION PREDICTION FROM GROWTH CURVES (January 18, 2008) Xi Zhou, Merlise A. Clyde, James Garrett, Viridiana Lourdes, Michael O'Connell, Giovanni Parmigiani, David J. Turner, and Tim Wiles
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A BAYESIAN APPROACH TO EFFECT ESTIMATION ACCOUNTING FOR ADJUSTMENT UNCERTAINTY (January 15, 2008) Chi Wang, Giovanni Parmigiani, Ciprian Crainiceanu, and Francesca Dominici
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DESIGN AND ANALYSIS ISSUES IN GENOME-WIDE SOMATIC MUTATION STUDIES OF CANCER (January 10, 2008) Giovanni Parmigiani, Simina Boca, Jimmy Lin, Kenneth W. Kinzler, Victor E. Velculescu, and Bert Vogelstein
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ON THE MERITS OF VOXEL-BASED MORPHOMETRIC PATH-ANALYSIS FOR INVESTIGATING VOLUMETRIC MEDIATION OF A TOXICANT'S INFLUENCE ON COGNITIVE FUNCTION (January 8, 2008) Shu-chih Su, Brian S. Caffo, Lynn E. Eberly, Elizabeth Garrett-Mayer, Walter F. Stewart, Sining Chen, David Yousem, Christos Davatzikos, and Brian Schwartz
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GEOSTATISTICAL INFERENCE UNDER PREFERENTIAL SAMPLING (January 6, 2008) Peter J. Diggle, Raquel Menezes, and Ting-li Su
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Papers from 2007
Bayesian Analysis for Penalized Spline Regression Using Win BUGS (December 1, 2007) Ciprian M. Crainiceanu, David Ruppert, and M.P. Wand
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DECOMPOSITION OF REGRESSION ESTIMATORS TO EXPLORE THE INFLUENCE OF "UNMEASURED" TIME-VARYING CONFOUNDERS (November 21, 2007) Yun Lu and Scott L. Zeger
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A BAYESIAN MODEL FOR CROSS-STUDY DIFFERENTIAL GENE EXPRESSION (November 21, 2007) Robert B. Scharpf, Hakon Tjelemeland, Giovanni Parmigiani, and Andrew B. Nobel
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A SMOOTHING APPROACH TO DATA MASKING (October 11, 2007) Yijie Zhous, Francesca Dominici, and Thomas A. Louis
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STATISTICAL METHODS FOR THE ANALYSIS OF CANCER GENOME SEQUENCING DATA (October 11, 2007) Giovanni Parmigiani, J. Lin, Simina Boca, T. Sjoblom, K.W. Kinzler, V.E. Velculescu, and B. Vogelstein
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OPTIMAL PROPENSITY SCORE STRATIFICATION (October 5, 2007) Jessica A. Myers and Thomas A. Louis
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MULTIPLE MODEL EVALUATION ABSENT THE GOLD STANDARD VIA MODEL COMBINATION (October 3, 2007) Edwin J. Iversen, Jr.; Giovanni Parmigiani; and Sining Chen
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EFFECTIVE COMMUNICATION OF STANDARD ERRORS AND CONFIDENCE INTERVALS (August 22, 2007) Thomas A. Louis and Scott L. Zeger
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INFERENCE FOR SURVIVAL CURVES WITH INFORMATIVELY COARSENED DISCRETE EVENT-TIME DATA: APPLICATION TO ALIVE (August 16, 2007) Michelle Shardell, Daniel O. Scharfstein, David Vlahov, and Noya Galai
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RANDOM EFFECTS MODELS IN A META-ANALYSIS OF THE ACCURACY OF DIAGNOSTIC TESTS WITHIN A GOLD STANDARD IN THE PRESENCE OF MISSING DATA (June 22, 2007) Haitao Chu, Sining Chen, and Thomas A. Louis
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IDENTIFYING EFFECT MODIFIERS IN AIR POLLUTION TIME-SERIES STUDIES USING A TWO-STAGE ANALYSIS (June 18, 2007) Sandrah P. Eckel and Thomas A. Louis
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DISTRIBUTED REPRODUCIBLE RESEARCH USING CACHED COMPUTATIONS (June 11, 2007) Roger Peng and Sandrah P. Eckel
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The Integrative Correlation Coefficient: a Measure of Cross-study Reproducibility for Gene Expressionea Array Data (May 11, 2007) Leslie M. Cope, Liz Garrett-Mayer, Edward Gabrielson, and Giovanni Parmigiani
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RACIAL DISPARITIES IN MORTALITY RISKS IN A SAMPLE OF THE U.S. MEDICARE POPULATION (May 7, 2007) Yijie Zhou, Francesca Dominici, and Thomas A. Louis
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A CASE STUDY IN PHARMACOLOGIC IMAGING USING PRINCIPAL CURVES IN SINGLE PHOTON EMISSION COMPUTED TOMOGRAPHY (May 3, 2007) Brian S. Caffo, Ciprian M. Crainiceanu, Lijuan Deng, and Craig W. Hendrix
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A REPRODUCIBLE RESEARCH TOOLKIT FOR R (May 3, 2007) Roger Peng
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IS MRI-BASED VOLUME A MEDIATOR OF THE ASSOCIATION OF CUMULATIVE LEAD DOSE WITH COGNITIVE FUNCTION? (April 13, 2007) Brian S. Caffo, Sining Chen, Walter Stewart, Karen Bolla, David Yousem, Christos Davatzikos, and Brian S. Schwartz
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A BAYESIAN HIERARCHICAL FRAMEWORK FOR SPATIAL MODELING OF fMRI DATA (April 12, 2007) F. DuBois Bowman, Brian S. Caffo, Susan Spear Bassett, and Clinton Kilts
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TRENDS IN PARTICULATE MATTER AND MORTALITY: AN APPROACH TO THE ASSESSMENT OF UNMEASURED CONFOUNDING (March 30, 2007) Holly Janes, Francesca Dominici, and Scott Zeger
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FAST ADAPTIVE PENALIZED SPLINES (March 29, 2007) Tatyana Krivobokova, Ciprian M. Crainiceanu, and Goran Kauermann
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MODIFIED TEST STATISTICS BY INTER-VOXEL VARIANCE SHRINKAGE WITH AN APPLICATION TO fMRI (March 10, 2007) Shu-chih Su, Brian Caffo, Elizabeth Garrett-Mayer, and Susan Bassett
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SEMIPARAMETRIC BIVARIATE QUANTILE-QUANTILE REGRESSION FOR ANALYZING SEMI-COMPETING RISKS DATA (March 2, 2007) Daniel O. Scharfstein, James M. Robins, and Mark van der Laan
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A HIDDEN MARKOV MODEL FOR JOINT ESTIMATION OF GENOTYPE AND COPY NUMBER IN HIGH-THROUGHPUT SNP CHIPS (February 28, 2007) Robert B. Scharpf, Giovanni Parmigiani, Jonathan Pevnser, and Ingo Ruczinski
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ASSESSING THE UNRELIABILITY OF THE MEDICAL LITERATURE: A RESPONSE TO "WHY MOST PUBLISHED RESEARCH FINDINGS ARE FALSE" (February 28, 2007) Steven Goodman and Sander Greenland
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MULTIPLE DISEASES IN CARRIER PROBABILITY ESTIMATION: ACCOUNTING FOR SURVIVING ALL CANCERS OTHER THAN BREAST AND OVARY IN BRCAPRO (February 20, 2007) Hormuzd A. Katki, Amanda Blackford, Sining Chen, and Giovanni Parmigiani
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A SURVEY OF THE LIKELIHOOD APPROACH TO BIOEQUIVALENCE TRIALS (February 6, 2007) Leena Choi, Brian S. Caffo, and Charles Rohde
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MORTALITY IN THE MEDICARE POPULATION AND CHRONIC EXPOSURE TO FINE PARTICULATE AIR POLLUTION (January 25, 2007) Scott L. Zeger, Francesca Dominici, Aidan McDermott, and Jonathan M. Samet
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TRAB: TESTING WHETHER MUTATION FREQUENCIES ARE ABOVE AN UNKNOWN BACKGROUND (January 19, 2007) Giovanni Parmigiani, Sining Chen, and Victor E. Velculescu
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FORECASTING THE GLOBAL BURDEN OF ALZHEIMER'S DISEASE (January 19, 2007) Ron Brookmeyer, Elizabeth Johnson, Kathryn Ziegler-Graham, and H. Michael Arrighi
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OPTIMIZED CROSS-STUDY ANALYSIS OF MICROARRAY-BASED PREDICTORS (January 11, 2007) Xiaogang Zhong, Luigi Marchionni, Leslie Cope, Edwin S. Iversen, Elizabeth S. Garrett-Mayer, Edward Gabrielson, and Giovanni Parmigiani
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A BAYESIAN HIERARCHICAL MODEL FOR CONSTRAINED DISTRIBUTED LAG FUNCTIONS: ESTIMATING THE TIME COURSE OF HOSPITALIZATION ASSOCIATED WITH AIR POLLUTION EXPOSURE (January 3, 2007) Roger Peng, Francesca Dominici, and Leah J. Welty
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Papers from 2006
INTERACTING WITH LOCAL AND REMOTE DATA RESPOSITORIES USING THE stashR PACKAGE (December 20, 2006) Sandrah P. Eckel and Roger Peng
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USE OF HIDDEN MARKOV MODELS FOR QTL MAPPING (December 5, 2006) Karl W. Broman
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GAMMA SHAPE MIXTURES FOR HEAVY-TAILED DISTRIBUTIONS (December 1, 2006) Sergio Venturini, Francesca Dominici, and Giovanni Parmigiani
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PENALIZED LIKELIHOOD AND BAYESIAN METHODS FOR SPARSE CONTINGENCY TABLES: AN ANALYSIS OF ALTERNATIVE SPLICING IN FULL-LENGTH cDNA LIBRARIES (November 7, 2006) Corinne Dahinden, Giovanni Parmigiani, Mark C. Emerick, and Peter Buhlmann
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ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS (October 25, 2006) Wenyi Wang , Benilton Caravalho, Nate Miller, Jonathan Pevsner, Aravinda Chakravarti, and Rafael A. Irizarry
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A Comparative Analysis of the Chronic Effects of Fine Particulate Matter (October 13, 2006) Sorina E. Eftim, Holly Janes, Aidan McDermott, Jonathan M. Samet, and Francesca Dominici
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COX MODELS WITH NONLINEAR EFFECT OF COVARIATES MEASURED WITH ERROR: A CASE STUDY OF CHRONIC KIDNEY DISEASE INCIDENCE (September 19, 2006) Ciprian M. Crainiceanu, David Ruppert, and Josef Coresh
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Adjustment Uncertainty in Effect Estimation (August 28, 2006) Ciprian M. Crainiceanu, Francesca Dominici, and Giovanni Parmigiani
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FDR and Bayesian Multiple Comparisons Rules (July 18, 2006) Peter Muller, Giovanni Parmigiani, and Kenneth Rice
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A FLEXIBLE GENERAL CLASS OF MARGINAL AND CONDITIONAL RANDOM INTERCEPT MODELS FOR BINARY OUTCOMES USING MIXTURES OF NORMALS (July 13, 2006) Brian Caffo, Ming-Wen An, and Charles A. Rohde
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INVESTIGATING MEDIATION WHEN COUNTERFACTUALS ARE NOT METAPHYSICAL: DOES SUNLIGHT UVB EXPOSURE MEDIATE THE EFFECT OF EYEGLASSES ON CATARACTS? (July 12, 2006) Brian Egleston, Daniel O. Scharfstein, Beatriz Munoz, and Sheila West
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ON THE POTENTIAL FOR ILL-LOGIC WITH LOGICALLY DEFINED OUTCOMES (July 7, 2006) Xianbin Li, Brian S. Caffo, and Daniel O. Scharfstein
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EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA (July 3, 2006) Benilton Carvalho, Terence P. Speed, and Rafael A. Irizarry
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MULTIVARIATE ANALYSIS AND VISUALIZATION OF SPLICING CORRELATIONS IN SINGLE-GENE TRANSCRIPTOMES (June 23, 2006) Mark C. Emerick, Giovanni Parmigiani, and William S. Agnew
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INTERACTING WITH DATA USING THE FILEHASH PACKAGE FOR R (June 1, 2006) Roger Peng
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PRINCIPAL STRATIFICATION DESIGNS TO ESTIMATE INPUT DATA MISSING DUE TO DEATH (May 16, 2006) Constantine E. Frangakis, Donald B. Rubin, Ming-Wen An, and Ellen MacKenzie
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RECURRENT EVENT MODELS IN THE PRESENCE OF A TERMINAL EVENT: COMPARISON, INFERENCE AND DATA ANALYSIS (April 13, 2006) Xianghua Luo and Mei-Cheng Wang
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POOR PERFORMANCE OF BOOTSTRAP CONFIDENCE INTERVALS FOR THE LOCATION OF A QUANTITATIVE TRAIT LOUCS (March 24, 2006) Ani Manichaikul, Josee Dupuis, Saunak Sen, and Karl W. Broman
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BIVARIATE BINOMIAL SPATIAL MODELLING LOA loa PREVALENCE IN TROPICAL AFRICA (March 21, 2006) Ciprian M. Crainiceanu, Peter J. Diggle, and Barry Rowlingson
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FEATURE-LEVEL EXPLORATION OF THE CHOE ET AL. AFFYMETRIX GENECHIP CONTROL DATASET (March 17, 2006) Rafael A. Irizarry, Leslie Cope, and Zhijin Wu
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ON THE EQUIVALENCE OF CASE-CROSSOVER AND TIME SERIES METHODS IN ENVIRONMENTAL EPIDEMIOLOGY (March 13, 2006) Yun Lu and Scott L. Zeger
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Papers from 2005
ON THE USE OF NON-EUCLIDEAN ISOTROPY IN GEOSTATISTICS (December 5, 2005) Frank C. Curriero
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THE ROLE OF AN EXPLICIT CAUSAL FRAMEWORK IN AFFECTED SIB PAIR DESIGNS WITH COVARIATES (December 1, 2005) Constantine E. Frangakis, Fan Li, and Betty Q. Doan
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NONPARAMETRIC ESTIMATION OF BIVARIATE FAILURE TIME ASSOCIATIONS IN THE PRESENCE OF A COMPETING RISK (November 17, 2005) Karen Bandeen-Roche and Jing Ning
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MODELING DIFFERENTIATED TREATMENT EFFECTS FOR MULTIPLE OUTCOMES DATA (November 11, 2005) Hongfei Guo and Karen Bandeen-Roche
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Analyzing Panel Count Data with Informative Observation Times (October 28, 2005) Chiung-Yu Huang, Mei-Cheng Wang, and Ying Zhang
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Additive Hazards Models with Latent Treatment Effectiveness Lag Time (October 13, 2005) Ying Qing Chen, Charles A. Rohde, and Mei-Cheng Wang
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Estimation and Projection of Indicence and Prevalence Based on Doubly Truncated Data with Application to Pharmacoepidemiological Databases (October 1, 2005) Henrik Stovring and Mei-Cheng Wang
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Comparison of Affymetrix GeneChip Expression Measures (September 1, 2005) Rafael A. Irizarry, Zhijin Wu, and Harris A. Jaffee
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A User-Friendly Introduction to Link-Probit-Normal Models (August 18, 2005) Brian S. Caffo and Michael Griswold
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Analysis of Affymetrix GeneChip Data Using Amplified RNA (August 1, 2005) Leslie Cope, Scott M. Hartman, Hinrich W.H. Gohlmann, Jay P. Tiesman, and Rafael A. Irizarry
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Does the Effect of Micronutrient Supplementation on Neonatal Survival Vary with Respect to the Percentiles of the Birth Weight Distribution? (July 20, 2005) Francesca Dominici, Scott L. Zeger, Giovanni Parmigiani, Joanne Katz, and Parul Christian
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When Should One Substract Background Fluorescence in Two Color Microarrays? (July 20, 2005) Robert B. Scharpf, Christine A. Iacobuzio-Donahue, Julie B. Sneddon, and Giovanni Parmigiani
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Spatio-temporal Point Processes: Methods and Applications (June 27, 2005) Peter J. Diggle
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A Mechanistic Latent Variable Model for Estimating Drug Concentrations in the Male Genital Tract (June 23, 2005) Leena Choi, Brian Caffo, Charles A. Rohde, Themba T. Ndovi, and Craig W. Hendrix
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A Partial Likelihood for Spatio-temporal Point Processes (June 21, 2005) Peter J. Diggle
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Polydesigns and Causal Inference (June 15, 2005) Fan Li and Constantine E. Frangakis
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Model Choice in Time Series Studies of Air Pollution and Mortality (June 1, 2005) Roger D. Peng, Francesca Dominici, and Thomas A. Louis
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Searching for Differentially Expressed Gene Combinations (March 25, 2005) Marcel Dettling, Edward Gabrielson, and Giovanni Parmigiani
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Understanding the Continual Reassessment Method for Dose Finding Studies: An Overview for Non-Statisticians (March 3, 2005) Elizabeth Garrett-Mayer
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A Statistical Framework for the Analysis of Microarray Probe-Level Data (March 1, 2005) Zhijin Wu and Rafael A. Irizarry
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Fixed-Width Output Analysis for Markov Chain Monte Carlo (February 9, 2005) Galin L. Jones, Murali Haran, Brian S. Caffo, and Ronald Neath
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Designs in Partially Controlled Studies: Messages from a Review (February 1, 2005) Fan Li and Constantine E. Frangakis
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Papers from 2004
Clustering and Classification Methods for Gene Expression Data Analysis (December 23, 2004) Elizabeth Garrett-Mayer and Giovanni Parmigiani
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Estimating Percentile-Specific Causal Effects: A Case Study of Micronutrient Supplementation, Birth Weight, and Infant Mortality (December 16, 2004) Francesca Dominici, Scott L. Zeger, Giovanni Parmigiani, Joanne Katz, and Parul Christian
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Ranking USRDS Provider-Specific SMRs from 1998-2001 (December 14, 2004) Rongheng Lin, Thomas A. Louis, Susan M. Paddock, and Greg Ridgeway
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Semiparametric Regression in Capture-Recapture Modelling (December 8, 2004) O. Gimenez, C. Barbraud, Ciprian M. Crainiceanu, S. Jenouvrier, and B.T. Morgan
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Cross-study Validation and Combined Analysis of Gene Expression Microarray Data (December 2, 2004) Elizabeth Garrett-Mayer, Giovanni Parmigiani, Xiaogang Zhong, Leslie Cope, and Edward Gabrielson
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The Proportional Odds Model for Assessing Rater Agreement with Multiple Modalities (December 2, 2004) Elizabeth Garrett-Mayer, Steven N. Goodman, and Ralph H. Hruban
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Multiple Lab Comparison of Microarray Platforms (November 30, 2004) Rafael A. Irizarry et al.
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Squared Extrapolation Methods (SQUAREM): A New Class of Simple and Efficient Numerical Schemes for Accelerating the Convergence of the EM Algorithm (November 19, 2004) Ravi Varadhan and Ch. Roland
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ON MARGINALIZED MULTILEVEL MODELS AND THEIR COMPUTATION (November 15, 2004) Michael E. Griswold and Scott L. Zeger
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Spatially Adaptive Bayesian P-Splines with Heteroscedastic Errors (November 1, 2004) Ciprian M. Crainiceanu, David Ruppert, and Raymond J. Carroll
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Bayesian Hierarchical Distributed Lag Models for Summer Ozone Exposure and Cardio-Respiratory Mortality (October 31, 2004) Yi Huang, Francesca Dominici, and Michelle L. Bell
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A Hypothesis Test for the End of a Common Source Outbreak (September 20, 2004) Ron Brookmeyer and Xiaojun You
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Optimal Sampling Times in Bioequivalence Studies Using a Simulated Annealing Algorithm (September 17, 2004) Leena Choi, Brian Caffo, and Charles Rohde
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Effect of Misreported Family History on Mendelian Mutation Prediction Models (September 13, 2004) Hormuzd A. Katki
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On Time Series Analysis of Public Health and Biomedical Data (September 1, 2004) Scott L. Zeger, Rafael A. Irizarry, and Roger D. Peng
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MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data (August 27, 2004) Leslie Cope, Xiaogang Zhong, Elizabeth S. Garrett-Mayer, and Giovanni Parmigiani
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A Hierarchical Multivariate Two-Part Model for Profiling Providers' Effects on Healthcare Charges (August 26, 2004) John W. Robinson, Scott L. Zeger, and Christopher B. Forrest
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Studying Effects of Primary Care Physicians and Patients on the Trade-Off Between Charges for Primary Care and Specialty Care Using a Hierarchical Multivariate Two-Part Model (August 26, 2004) John W. Robinson, Scott L. Zeger, and Christopher B. Forrest
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BayesMendel: An R Environment for Mendelian Risk Prediction (August 26, 2004) Sining Chen, Wenyi Wang, Karl Broman, Hormuzd A. Katki, and Giovanni Parmigiani
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The Genomes of Recombinant Inbred Lines: The Gory Details (August 2, 2004) Karl W. Broman
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Ozone and Mortality: A Meta-Analysis of Time-Series Studies and Comparison to a Multi-City Study (The National Morbidity, Mortality, and Air Pollution Study) (July 19, 2004) Michelle L. Bell, Jonathan M. Samet, and Francesca Dominici
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Quantitative Methods for Tracking Cognitive Change 3 Years After Coronary Artery Bypass Surgery (June 28, 2004) Sarah Barry; Scott L. Zeger; Ola A. Selnes; Maura A. Grega; Louis M. Borowicz, Jr.; and Guy M. McKhann
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The National Morbidity, Mortality, and Air Pollution Study Database in R (June 25, 2004) Roger D. Peng, Leah J. Welty, and Aidan McDermott
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Accuracy of MSI Testing in Predicting Germline Mutations of MSH2 and MLH1: A Case Study in Bayesian Meta-Analysis of Diagnostic Tests Without a Gold Standard (June 24, 2004) Sining Chen, Patrice Watson, and Giovanni Parmigiani
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Bayesian Geostatistical Design (June 15, 2004) Peter J. Diggle and Soren Lophaven
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A Model Based Background Adjustment for Oligonucleotide Expression Arrays (May 28, 2004) Zhijin Wu, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez Murillo, and Forrest Spencer
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Seasonal Analyses of Air Pollution and Mortality in 100 U.S. Cities (May 27, 2004) Roger D. Peng, Francesca Dominici, Roberto Pastor-Barriuso, Scott L. Zeger, and Jonathan M. Samet
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Screening for Differentially Expressed Genes: Are Multilevel Models Helpful? (April 16, 2004) Dongmei Liu, Giovanni Parmigiani, and Brian Caffo
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A Cox Model for Biostatistics of the Future (March 2, 2004) Scott L. Zeger, Peter J. Diggle, and Kung-Yee Liang
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Self-Reported Memory Symptoms with Coronary Artery Disease: A Prospective of CABG Patients and Nonsurgical Controls (March 1, 2004) Ola A. Selnes; Maura A. Grega; Louis M. Borowicz, Jr.; Sarah Barry; Scott L. Zeger; and Guy M. McKhann
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Point Process Methodology for On-line Spatio-temporal Disease Surveillance (February 17, 2004) Peter J. Diggle, Barry Rowlingson, and Ting-li Su
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Choosing Smoothness Parameters for Smoothing Splines by Minimizing and Estimate of Risk (February 3, 2004) Rafael A. Irizarry
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Optimal Sample Size for Multiple Testing: the Case of Gene Expression Microarrays (February 2, 2004) Peter Muller, Giovanni Parmigiani, Christian Robert, and Judith Rousseau
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Inequity Measures for Evaluations of Environmental Justice: A Case Study of Close Proximity to Highways in NYC (January 21, 2004) Jerry O. Jacobson, Nicolas W. Hengartner, and Thomas A. Louis
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Power and Robustness of Linkage Tests for Quantitative Traits in General Pedigrees (January 5, 2004) Weimin Chen, Karl Broman, and Kung-Yee Liang
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Papers from 2003
Uncertainty and the Value of Diagnostic Information With Application to Axillary Lymph Node Dissection in Breast Cancer (December 22, 2003) Giovanni Parmigiani
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Kernel Estimation of Rate Function for Recurrent Event Data (December 2, 2003) Chin-Tsang Chiang, Mei-Cheng Wang, and Chiung-Yu Huang
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Modeling the Incubation Period of Anthrax (December 1, 2003) Ron Brookmeyer, Elizabeth Johnson, and Sarah Barry
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Optimization of Breast Cancer Screening Modalities (December 1, 2003) Yu Shen and Giovanni Parmigiani
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Underestimation of Standard Errors in Multi-Site Time Series Studies (November 21, 2003) Michael Daniels, Francesca Dominici, and Scott L. Zeger
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Smooth Quantile Ratio Estimation with Regression: Estimating Medical Expenditures for Smoking Attributable Diseases (November 18, 2003) Francesca Dominici and Scott L. Zeger
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Time-Series Studies of Particulate Matter (November 18, 2003) Michelle L. Bell, Jonathan M. Samet, and Francesca Dominici
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Loss Function Based Ranking in Two-Stage, Hierarchical Models (November 10, 2003) Rongheng Lin, Thomas A. Louis, Susan M. Paddock, and Greg Ridgeway
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Joint Modeling and Estimation for Recurrent Event Processes and Failure Time Data (November 1, 2003) Chiung-Yu Huang and Mei-Cheng Wang
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Unification of Variance Components and Haseman-Elston Regression for Quantitative Trait Linkage Analysis (October 29, 2003) Wei-Min Chen, Karl W. Broman, and Kung-Yee Liang
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Hierarchical Bivariate Time Series Models: A Combined Analysis of the Effects of Particulate Matter on Morbidity and Mortality (October 28, 2003) Francesca Dominici, Antonella Zanobetti, Scott L. Zeger, Joel Schwartz, and Jonathan M. Samet
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Smooth Quantile Ratio Estimation (October 28, 2003) Francesca Dominici, Leslie Cope, Daniel Q. Naiman, and Scott L. Zeger
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Nonparametric Estimation of the Bivariate Recurrence Time Distribution (October 20, 2003) Chiung-Yu Huang and Mei-Cheng Wang
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A Nested Unsupervised Approach to Identifying Novel Molecular Subtypes (October 6, 2003) Elizabeth Garrett and Giovanni Parmigiani
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Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays (September 29, 2003) Zhijin Wu, Richard LeBlanc, and Rafael A. Irizarry
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Cross-Calibration of Stroke Disability Measures: Bayesian Analysis of Longitudinal Ordinal Categorical Data Using Negative Dependence (August 29, 2003) Giovanni Parmigiani, Heidi W. Ashih, Gregory P. Samsa, Pamela W. Duncan, Sue Min Lai, and David B. Matchar
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Checking Assumptions in Latent Class Regression Models via a Markov Chain Monte Carlo Estimation Approach: An Application to Depression and Socio-Economic Status (January 15, 2003) Elizabeth Garrett, Richard Miech, Pamela Owens, William W. Eaton, and Scott L. Zeger
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Papers from 2002
Estimating the Number of Essential Genes in a Genome by Random Transposon Mutagenesis (July 29, 2002) Natalie J. Blades and Karl W. Broman
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