Papers to Appear in Biometrics

Vol. 68, No. 1
March 2012

Report of the Co-Editors - 2011

Biometric Methodology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


Biometric Practice

Discussion Papers

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

Discussion of Bayesian enrichment strategies for randomized discontinuation trials
Mithat Gonen

Discussion of Bayesian enrichment strategies for randomized discontinuation trials
Inna Perevozskaya

Discussion of Bayesian enrichment strategies for randomized discontinuation trials
Andy Grieve

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

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 modeling
Geert Molenberghs

Discussion of Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modeling
Ed Korn

Discussion of Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modeling
Vance W. Berger, Grant Izmirlian, Diana Knoll

Discussion of Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modeling
John O'Quigley and Philippe Flandre

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Rejoinder to "A note on two-sample tests for comparing intra-individual genetic sequence diversity between populations"
Peter B. Gilbert, A. J. Rossini and Raj Shankarappa

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

Efficient estimation for rank-based regression with clustered data
Liya Fu and You-Gan Wang

A method of moments estimator for random effect multivariate meta-analysis
Han Chen, Alisa K. Manning and Josee Dupuis

A robust Bayesian random effects model for nonlinear calibration problems
Y. Fong, J. Wakefield, S. De Rosa and N. Frahm

Bayesian model selection For incomplete data using the posterior predictive distribution
Michael J. Daniels, Arkendu S. Chatterjee and Chenguang Wang

Bayesian inference for the causal effect of mediation
M. J. Daniels, J. Roy, C. Kim, J. W. Hogan and M. G. Perri

A robust method for estimating optimal treatment regimes
Baqun Zhang, Anastasios A. Tsiatis, Eric B. Laber and Marie Davidian

Multiscale adaptive marginal analysis of longitudinal neuroimaging data with time-varying covariates
Martha Skup, Hongtu Zhu and Heping Zhang for the Alzheimer's Disease Neuroimaging Initiative

Natural direct and indirect effects on the exposed: effect decomposition under weaker assumptions
Stijn Vansteelandt and Tyler VanderWeele

Bayesian meta-analysis of the accuracy of a test for tuberculous pleuritis in the absence of a gold-standard reference
Nandini Dendukuri, Ian Schiller, Lawrence Joseph and Madhukar Pai

Semiparametric Bayesian survival analysis using models with log-linear median
Jianchang Lin, Debajyoti Sinha, Stuart Lipsitz and Adriano Polpo

A hierarchical semiparametric model for incorporating inter-gene information for analysis of genomic data
Long Qu, Dan Nettleton and Jack C. M. Dekkers

Predicting the geographic distribution of a species from presence-only data subject to detection errors
Robert M. Dorazio

Bivariate marker measurements and ROC analysis
Mei-Cheng Wang and Shanshan Li

Spatial-temporal modeling of the association between air pollution exposure and preterm birth: identifying critical windows of exposure
Joshua Warren, Montserrat Fuentes, Amy Herring and Peter Langlois

Evaluating the predictive value of biomarkers with stratified case-cohort design
Dandan Liu, Tianxi Cai and Yingye Zheng

Analysis of longitudinal clinical trials with missing data using multiple imputation in conjunction with robust regression
Devan V. Mehrotra, Xiaoming Li, Jiajun Lu and Kaifeng Lu

Robust Gaussian graphical modeling via l1 penalization
Hokeun Sun and Hongzhe Li

The use of two-way linear mixed models in multi-treatment meta-analysis
H. P. Piepho, E. R. Williams and L. V. Madden

Compliance mixture modelling with a zero effect complier class and missing data
Michael E. Sobel and Bengt Muthen

A general class of semiparametric transformation frailty models for nonproportional hazards survival data
Sangbum Choi and Xuelin Huang

Mapping cancer risk in Southwestern Ontario with changing census boundaries
P. Nguyen, P. E. Brown and J. Stafford

Bayesian latent factor regression for functional and longitudinal data
Silvia Montagna, Surya T. Tokdar, Brian Neelon and David B. Dunson