Papers to Appear in Biometrics

Vol. 67, No. 4
December 2011

Presidential Address

Presidential Address: XXV International Biometric Conference, Florianopolis, Brazil, December 2010 IBS: Transforming our Governance
Kaye E. Basford

Biometric Methodology

Split-plot designs for robotic serial dilution assays
Jeffrey S. Buzas, Carrie G. Wager and David M. Lansky

A multi-step protein lysate array quantification method and its statistical properties
Ji-Yeon Yang and Xuming He

Dynamic linear model for the identification of miRNAs in next-generation sequencing data
W. Evan Johnson, Noah C. Welker and Brenda L. Bass

BM-Map: Bayesian mapping of multireads for next-generation sequencing data
Yuan Ji, Yanxun Xu, Qiong Zhang, Kam-Wah Tsui, Yuan Yuan, Clift Norris, Shoudan Liang and Han Liang

Estimating effect sizes of differentially expressed genes for power and sample size assessments in microarray experiments
Shigeyuki Matsui and Hisashi Noma

Wilks' Lambda dissimilarity measures for gene clustering: an approach based on the identification of transcription modules
Alberto Roverato and F. Marta L. Di Lascio

Likelihood ratio testing for admixture models with application to genetic linkage analysis
Chong-Zhi Di and Kung-Yee Liang

Combining disease models to test for gene-environment interaction in nuclear families
Thomas J. Hoffmann, Stijn Vansteelandt, Christoph Lange, Edwin K. Silverman, Dawn L. DeMeo and Nan M. Laird

Powerful tests for detecting a gene effect in the presence of possible gene-gene interactions using garrote kernel machines
Arnab Maity and Xihong Lin

Penalized Gaussian process regression and classification for high-dimensional nonlinear data
G. Yi, J. Q. Shi and T. Choi

Stochastic functional data analysis: A diffusion model-based approach
Bin Zhu, Peter X.-K. Song and Jeremy M. G. Taylor

Robust estimation for ordinary differential equation models
J. Cao, L. Wang and J. Xu

Testing for interaction in two-way random and mixed effects models: The fully nonparametric approach
Trent Gaugler and Michael G. Akritas

Prediction of individual long-term outcomes in smoking cessation trials using frailty models
Yimei Li, E. Paul Wileyto and Daniel F. Heitjan

Smoothing spline ANOVA frailty model for recurrent event data
Pang Du, Yihua Jiang and Yuedong Wang

Additive mixed effect model for clustered failure time data
Jianwen Cai and Donglin Zeng

A new semiparametric estimation method for accelerated hazard model
Jiajia Zhang, Yingwei Peng and Ou Zhao

Explained variation in a fully specified model for data-grouped survival data
C. B. Pipper, C. Ritz and T. H. Scheike

Buckley-James-type estimator with right-censored and length-biased data
Jing Ning, Jing Qin and Yu Shen

On path restoration for censored outcomes
Brent A. Johnson, Qi Long and Matthias Chung

Graphical procedures for evaluating overall and subject-specific incremental values from new predictors with censored event time data
Hajime Uno, T. Cai, L. Tian and L. J. Wei

Inference for the effect of treatment on survival probability in randomized trials with noncompliance and administrative censoring
Hui Nie, Jing Cheng and Dylan S. Small

A new criterion for confounder selection
Tyler J. VanderWeele and Ilya Shpitser

Inference for causal interactions for continuous exposures under dichotomization
Tyler J. VanderWeele, Yu Chen and Habibul Ahsan

Reinforcement learning strategies for clinical trials in non-small cell lung cancer
Yufan Zhao, Donglin Zeng, Mark A. Socinski and Michael R. Kosorok

A shrinkage approach for estimating a treatment effect using intermediate biomarker data in clinical trials
Yun Li, Jeremy M. G. Taylor and Roderick J. A. Little

Comparing biomarkers as principal surrogate endpoints
Y. Huang and P. B. Gilbert

Multiple imputation methods for multivariate one-sided tests with missing data
Tao Wang and Lang Wu

A moment adjusted imputation method for measurement error models
Laine Thomas, Leonard Stefanski and Marie Davidian

Differential measurement errors in zero-truncated regression models for count data
Yih-Huei Huang, Wen-Han Hwang and Fei-Yin Chen

Nonparametric tests for homogeneity of species assemblages: A data depth approach
Jun Li, Jifei Ban and Louis S. Santiago

Estimating species richness from quadrat sampling data: a general approach
Jerome Dupuis and Michel Goulard

Smoothing population size estimates for time-stratified mark-recapture experiments using Bayesian P-splines
Simon J. Bonner and Carl J. Schwarz

Detecting disease outbreaks using local spatiotemporal methods
Yingqi Zhao, Donglin Zeng, Amy H. Herring, Amy Ising, Anna Waller, David Richardson and Michael R. Kosorok

Variance estimation for systematic designs in spatial surveys
R. M. Fewster

A general probabilistic model for group independent component analysis and its estimation methods
Ying Guo

Dose-response curve estimation: A semiparametric mixture approach
Ying Yuan and Guosheng Yin

Continual reassessment method for partial ordering
Nolan A. Wages, Mark R. Conaway and John O'Quigley

Biometric Practice

Insights on the robust variance estimator under recurrent-events model
Hussein R. Al-Khalidi, Yili Hong, Thomas R. Fleming and Terry M. Therneau

A hot-deck multiple imputation procedure for gaps in longitudinal recurrent event histories
Chia-Ning Wang, Roderick Little, Bin Nan and Sioban D. Harlow

Outcome dependent sampling from existing cohorts with longitudinal binary response data: study planning and analysis
Jonathan S. Schildcrout and Patrick J. Heagerty

Linear and non-linear mixed-effects models for censored HIV viral loads using normal/independent distributions
Victor H. Lachos, Dipankar Bandyopadhyay and Dipak K. Dey

A Bayesian model averaging approach for estimating the relative risk of mortality associated with heat waves in 105 U.S. cities
Jennifer F. Bobb, Francesca Dominici and Roger D. Peng

An empirical Bayes approach to joint analysis of multiple microarray gene expression studies
Lingyan Ruan and Ming Yuan

Bayesian modeling for genetic anticipation in presence of mutational heterogeneity: A case-study in Lynch Syndrome
Philip S. Boonstra, Bhramar Mukherjee, Jeremy M. G. Taylor, Mef Nilbert, Victor M. Moreno and Stephen B. Gruber

Optimizing the concentration and bolus of a drug delivered by continuous infusion
Peter F. Thall, Aniko Szabo, Hoang Q. Nguyen, Catherine M. Amlie-Lefond and Osama O. Zaidat

Extraction of food consumption systems by non-negative matrix factorization (NMF) for the assessment of food choices
Melanie Zetlaoui, Max Feinberg, Philippe Verger and Stephan Clemencon

Heterogeneous capture-recapture models with covariates: A partial likelihood approach for closed populations
Jakub Stoklosa, Wen-Han Hwang, Sheng-Hai Wu and Richard Huggins

Reader Reaction

A note on monotonicity assumptions for exact unconditional tests in binary matched-pairs designs
Xiaochun Li, Mengling Liu and Judith D. Goldberg

Correspondence

Letter to the Editor of Biometrics on "Joint regression analysis for discrete longitudinal data" by Madsen and Fang
Roy T. Sabo and N. Rao Chaganty

Rejoinder to Letter
L. Madsen and Y. Fang

Papers to appear in future issues of Biometrics

Bayesian effect estimation accounting for adjustment uncertainty
Chi Wang, Giovanni Parmigiani and Francesca Dominici

Discussion of Bayesian effect estimation accounting for adjustment uncertainty
R. Gutman and D. B. Rubin; S. Vansteelandt; L. McCandless

Rejoinder by Chi Wang, Giovanni Parmigiani and Francesca Dominici

Predictive cross-validation for the choice of linear mixed-effects models with application to data from the Swiss HIV Cohort Study
Julia Braun, Leonhard Held and Bruno Ledergerber

Robust estimation of mean and dispersion functions in extended generalized additive models
C. Croux, I. Gijbels and I. Prosdocimi

A powerful and robust test statistic for randomization inference in group-randomized trials with matched pairs of groups
Kai Zhang, Mikhail Traskin and Dylan S. Small

A Bayesian model for estimating population means using a link-tracing sampling design
Katherine St. Clair and Daniel O'Connell

Augmented cross-sectional studies with abbreviated follow-up for estimating HIV incidence
Brian Claggett, Stephen W. Lagakos and Rui Wang

Dynamic logistic regression and dynamic model averaging for binary classification
Tyler H. McCormick, Adrian E. Raftery, David Madigan and Randall S. Burd

Bayesian enrichment strategies for randomized discontinuation trials
Lorenzo Trippa, Gary L. Rosner and Peter Mueller

Discussion of Bayesian enrichment strategies for randomized discontinuation trials
Heinz Schmidli and Beat Neuenschwander; Mithat Gonen; Inna Perevozskaya; and Andy Grieve

Rejoinder by Lorenzo Trippa, Gary L. Rosner and Peter Mueller

Letter to the Editor "Out of the frying pan and in to the fire?"
Vance W. Berger

Rejoinder to Letter to the Editor "Out of the frying pan and in to the fire?"
M. Proschan, E. Brittain, and L. Kammerman

Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modelling
Debashis Ghosh, Jeremy M. G. Taylor and Daniel J. Sargent

Discussion of Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modelling
Geert Molenberghs; Ed Korn; Vance W. Berger, Grant Izmirlian, Diana Knoll; and John O'Quigley and Philippe Flandre

Rejoinder by Debashis Ghosh, Jeremy M. G. Taylor and Daniel J. Sargent

Modeling adverse birth outcomes via confirmatory factor quantile regression
Lane F. Burgette and Jerome P. Reiter

On estimation of relative survival
Maja Pohar Perme, Janez Stare and Jacques Esteve

A Bayesian adjustment for multiplicative measurement errors for a calibration problem with application to a stem cell study
Peng Zhang, Juxin Liu, Jianhu Dong, Jelena L. Holovati, Brenda Letcher and Locksley E. McGann

Reader Reaction to "Using regression models to analyze randomized trials: asymptotically valid hypothesis tests despite incorrectly specified models"
Jane Paik

A broad symmetry criterion for nonparametric validity of parametrically-based tests in randomized trials
Russell T. Shinohara, Constantine E. Frangakis and Constantine G. Lyketsos

Multiple loci mapping via model-free variable selection
Wei Sun and Lexin Li

Local multiplicity adjustment for the spatial scan statistic using the Gumbel distribution
Ronald E. Gangnon

Informative Dorfman screening
Christopher S. McMahan, Joshua M. Tebbs and Christopher R. Bilder

Predicting treatment effect from surrogate endpoints and historical trials: an extrapolation involving probabilities of a binary outcome or survival to a specific time
Stuart G. Baker, Daniel J. Sargent, Marc Buyse and Tomasz Burzykowski

Bayesian adaptive trial design for a newly validated surrogate endpoint
Lindsay A. Renfro, Bradley P. Carlin and Daniel J. Sargent

High-dimensional heteroscedastic regression with an application to eQTL data analysis
Z. John Daye, Jinbo Chen and Hongzhe Li

Constructing normalcy and discrepancy indexes for birth weight and gestational age using a threshold regression mixture model
G. A. Whitmore, Guangyu Zhang and Mei-Ling Ting Lee

Isotonized CDF estimation from judgment post-stratification data with empty strata
Xinlei Wang, Ke Wang and Johan Lim

A composite likelihood approach to latent multivariate Gaussian modeling of SNP data with application to genetic association testing
Fang Han and Wei Pan

Identifiability of causal effects for binary variables with baseline data missing due to death
Wei Yan, Yaqin Hu and Zhi Geng

Inverse Batschelet distributions for circular data
M. C. Jones and Arthur Pewsey

G-estimation and artificial censoring: problems, challenges, and applications
Marshall M. Joffe, Wei Peter Yang and Harold Feldman

A statistical framework for eQTL mapping using RNA-seq data
Wei Sun

Letter to the Editor "Comment on Nie et al (2001), Biometrics, early view"
Stuart G. Baker

Rejoinder to Letter to the Editor "Comment on Nie et al (2001), Biometrics, early view"
Hui Nie, Jing Chen and Dylan S. Small

Efficient algorithms for optimal designs with correlated observations in pharmacokinetics and dose finding studies
Tim Holland-Letz, Holger Dette and Didier Renard

Some alternatives to asymptotic tests for the analysis of pharmacogenetic data using nonlinear mixed effects models
Julie Bertrand, Emmanuelle Comets, Marylore Chenel and France Mentre

Combining multiple imputation and inverse-probability weighting
Shaun Seaman, Ian White, Andrew Copas and Leah Li

Quantile regression for doubly censored data
Shuang Ji, Limin Peng, Yu Cheng and HuiChuan Lai

Goodness-of-fit diagnostics for Bayesian hierarchical models
Ying Yuan and Valen E. Johnson

Modeling functional data with spatially heterogeneous shape characteristics
Ana-Maria Staicu, Ciprian M. Crainiceanu, Daniel S. Reich and David Ruppert

Computationally efficient marginal models for clustered recurrent event data
Dandan Liu, Douglas E. Schaubel and John D. Kalbfleisch

A latent variable approach to study of gene-environment interactions in the presence of multiple correlated exposures
Brisa N. Sanchez, Shan Kang and Bhramar Mukherjee

Evaluating prognostic accuracy of biomarkers under competing risk
Yingye Zheng, Tianxi Cai, Yuying Jin and Ziding Feng

Penalized generalized estimating equations for high-dimensional longitudinal data analysis
Lan Wang, Jianhui Zhou and Annie Qu

Simple estimation and test procedures in capture-mark-recapture mixed models
Jean-Dominique Lebreton, Remi Choquet and Olivier Gimenez

Identification of partially linear structure in additive models with an application to gene expression prediction from sequence
Heng Lian, Xin Chen and Jian-Yi Yang

Pooling designs for outcomes under a Gaussian random effects model
Yaakov Malinovsky, Paul S. Albert and Enrique F. Schisterman

A framework for the joint modeling of longitudinal diagnostic outcome data and latent infection status: application to investigating the temporal relationship between infection and disease
G. Jones, W. O. Johnson, W. D. Vink and N. French

Group testing for case identification with correlated responses
Samuel D. Lendle, Michael G. Hudgens and Bahjat F. Qaqish

Evaluating correlation based metric for surrogate marker qualification within a causal correlation framework
Yue Wang, Robin Mogg and Jared Lunceford

Permutation tests for random effects in linear mixed models
Oliver Lee and Thomas M. Braun

A space-time conditional intensity model for invasive meningococcal disease occurrence
Sebastian Meyer, Johannes Elias and Michael Hohle

Bayesian meta-experimental design: evaluating cardiovascular risk in new antidiabetic therapies to treat Type 2 diabetes
Joseph G. Ibrahim, Ming-Hui Chen, H. Amy Xia and Thomas Liu

Logistic Bayesian LASSO for identifying association with rare haplotypes and application to age-related macular degeneration
Swati Biswas and Shili Lin

Semiparametric frailty models for clustered failure time data
Zhangsheng Yu, Xihong Lin and Wanzhu Tu

An empirical Bayesian approach for identifying differential co-expression in high-throughput experiments
John A. Dawson and Christina Kendziorski

Population intervention causal effects based on stochastic interventions
Ivan Diaz Munoz and Mark van der Laan

Borrowing strength with non-exchangeable priors over subpopulations
L. G. Leon-Novelo, B. Nebiyou Bekele, P. Mueller, F. Quintana and K. Wathen

A Bayesian semiparametric approach for incorporating longitudinal information on exposure history for inference in case-control studies
Dhiman Bhadra, Michael J. Daniels, Sungduk Kim, Malay Ghosh and Bhramar Mukherjee

When do latent class models overstate accuracy for diagnostic and other classifiers in the absence of a gold standard?
Bruce D. Spencer

Abundance estimation of long-diving animals using line transect methods
Hiroshi Okamura, Shingo Minamikawa, Hans Julius Skaug and Toshiya Kishiro

Optimal matching with minimal deviation from fine balance in a study of obesity and surgical outcomes
Dan Yang, Dylan Small, Jeffrey H. Silber and Paul R. Rosenbaum

An omnibus consistent adaptive percentile modified Wilcoxon rank sum test with applications in gene expression studies
Olivier Thas, Lieven Clement, John C. W. Rayner, Beatriz Carvalho and Wim Van Criekinge

Hazard ratio estimation for biomarker-calibrated dietary exposures
Pamela A. Shaw and Ross L. Prentice

Empirical likelihood for cumulative hazard ratio estimation with covariate adjustment
Bin Dong and David E. Matthews

Estimating absolute and relative case fatality ratios from infectious disease surveillance data
Nicholas G. Reich, Justin Lessler, Derek A. T. Cummings and Ron Brookmeyer

Estimating incident population distribution from prevalent data
Kwun Chen Gary Chan and Mei-Cheng Wang

Model selection for Cox models with time-varying coefficients
Jun Yan and Jian Huang

Spatially balanced sampling through the Pivotal method
Anton Grafström, Niklas L. P. Lundstrom and Lina Schelin

Likelihood approach for detecting imprinting and in utero maternal effects using general pedigrees from prospective family-based association studies
Jingyuan Yang and Shili Lin

Bayesian Lasso for semiparametric structural equation models
Ruixin Guo, Hongtu Zhu, Sy-Miin Chow and Joseph G. Ibrahim

Numerical discretization-based estimation methods for ordinary differential equation models via penalized spline smoothing with applications in biomedical research
Hulin Wu, Hongqi Xue and Arun Kumar

Choice of prognostic estimators in joint models by estimating differences of expected conditional Kullback-Leibler risks
Daniel Commenges, Benoit Liquet and Cecile Proust-Lima

Two-component mixture cure rate model with spline estimated nonparametric components
Lu Wang, Pang Du and Hua Liang

Causal inference on quantiles with an obstetric application
Zhiwei Zhang, Zhen Chen, James F. Troendle and Jun Zhang

A geostatistical approach to large-scale disease mapping with temporal misalignment
Lauren Hund, Jarvis T. Chen, Nancy Krieger and Brent Coull

A joint mixed effects dispersion model for menstrual cycle length and time-to-pregnancy
Alexander McLain, Kirsten J. Lum and Rajeshwari Sundaram

Rapid testing of SNPs and gene-environment interactions in case-parent trio data based on exact analytic parameter estimation
Holger Schwender, Margaret A. Taub, Terri H. Beaty, Mary L. Marazita and Ingo Ruczinski

Discretized and aggregated: Modeling dive depth of harbor seals from ordered categorical data with temporal autocorrelation
Megan D. Higgs and Jay M. Ver Hoef

Chain binomial models and binomial autoregressive processes
Christian H. Weiß and Philip K. Pollett

Assessing the impact of a movement network on the spatio-temporal spread of infectious diseases
Birgit Schrodle, Leonhard Held and Havard Rue

Multilevel functional clustering analysis
Nicoleta Serbana and Huijing Jiang

A time series DDP for functional proteomics profiles
Luis E. Nieto-Barajas, Peter Mueller, Yuan Ji, Yiling Lu and Gordon B. Mills

A pseudo Bayesian shrinkage approach to regression with missing covariates
Nanhua Zhang and Roderick J. Little

Bayesian semiparametric nonlinear mixed-effects joint models for data with skewness, missing responses, and measurement errors in covariates
Yangxin Huang and Getachew Dagne

Improving the flexibility and efficiency of phase II designs for oncology trials
Stefan Englert and Meinhard Kieser

Analyzing multiple-probe microarray: estimation and application of gene expression indexes
Mehdi Maadooliat, Jianhua Z. Huang and Jianhua Hu

Space-time data fusion under error in computer model output: an application to modeling air quality
Veronica J. Berrocal, Alan E. Gelfand and David M. Holland

Assessing treatment-selection markers using a potential outcomes framework
Ying Huang, Peter B. Gilbert and Holly Janes

Median tests for censored survival data; a contingency table approach
Shaowu Tang and Jong-Hyeon Jeong

Two-dimensional informative array testing
Christopher S. McMahan, Joshua M. Tebbs and Christopher R. Bilder

Semiparametric maximum likelihood methods for analyzing genetic and environmental effects with case-control mother-child pair data
Jinbo Chen, Dongyu Lin and Hagit Hochner

The k-ZIG: flexible modeling for zero-inflated counts
Souparno Ghosh, Alan E. Gelfand, Kai Zhu and James S. Clark

Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation
Pei Fen Kuan and Derek Y. Chiang

A Bayesian approach to improved estimation of causal effect predictiveness for a principal surrogate endpoint
Corwin M. Zigler and Thomas R. Belin

On the efficiency of score tests for homogeneity in two-component parametric models for discrete data
David Todem, Wei-Wen Hsu and KyungMann Kim

A note on two-sample tests for comparing intra-individual genetic sequence diversity between populations
E. E. Giorgi and T. Bhattacharya

Impact of time to start treatment following infection with application to initiating HAART in HIV-positive patients
Judith J. Lok and Victor DeGruttola

Evolutionary factor analysis of replicated time series
G. Motta and H. Ombao

Bayesian influence measures for joint models for longitudinal and survival data
Hongtu Zhu, Joseph G. Ibrahim, Yueh-Yun Chi and Niansheng Tang

Nonparametric lower bounds for species richness and shared species richness under sampling without replacement
Anne Chao and Chih-Wei Lin

Reader Reaction to "Using regression models to analyze randomized trials: asymptotically valid hypothesis tests despite incorrectly specified models
Jane Paik

Functional uniform priors for nonlinear modelling
Björn Bornkamp

A network-based analysis of the 1861 Hagelloch Measles Data
Chris Groendyke, David Welch and David R. Hunter

Estimating propensity scores and causal survival functions using prevalent survival data
Yu-Jen Cheng and Mei-Cheng Wang

Treatment monitoring of HIV infected patients based on mechanistic models
Melanie Prague, Daniel Commenges, Julia Drylewicz and Rodolphe Thiebaut

Nonparametric inference for median costs with censored data
Hongwei Zhao, Chen Zuo, Shuai Chen and Heejung Bang

A partitioning deletion/substitution/addition algorithm for creating survival risk groups
Karen Lostritto, Robert L. Strawderman and Annette M. Molinaro

Improved estimation of the noncentrality parameter distribution from a large number of t-statistics, with applications to false discovery rate estimation in microarray data analysis
Long Qu, Dan Nettleton and Jack C. M. Dekkers

Robust classification of functional and quantitative image data using functional mixed models
Hongxiao Zhu, Philip J. Brown and Jeffrey S. Morris

A hybrid EM and Monte Carlo EM algorithm and its application to analysis of transmission of infectious diseases
Yang Yang, Ira M. Longini, Jr., M. Elizabeth Halloran and Valerie Obenchain

Model selection for generalized estimating equations accommodating dropout missingness
Chung-Wei Shen and Yi-Hau Chen

Double-robust semiparametric estimator for differences in restricted mean lifetimes in observational studies
Min Zhang and Douglas E. Schaubel