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