Papers to Appear in Biometrics

Vol. 73, No. 3
September 2017

Editorial: Biometrics, JABES and the International Biometric Society



A risk-based measure of time-varying prognostic discrimination for survival models
C. Jason Liang and Patrick J. Heagerty

Discussion on "A risk-based measure of time-varying prognostic discrimination for survival models"
H. Michael and L. Tian

Discussion on "A risk-based measure of time-varying prognostic discrimination for survival models"
T. A. Gerds and Martin Schumacher

Discussion on "A risk-based measure of time-varying prognostic discrimination for survival models"
Layla Parast and Carolyn M. Rutter

Rejoinder to "A risk-based measure of time-varying prognostic discrimination for survival models"
C. Jason Liang and Patrick J. Heagerty

A space-time skew-t model for threshold exceedances
Samuel A. Morris, Brian J. Reich, Emeric Thibaud, and Daniel Cooley

Modeling nonstationarity in space and time
Lyndsay Shand and Bo Li

On joint estimation of Gaussian graphical models for spatial and temporal data
Zhixiang Lin, Tao Wang, Can Yang, and Hongyu Zhao

Hypothesis testing of matrix graph model with application to brain connectivity analysis
Yin Xia and Lexin Li

A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms
Tao Wang and Hongyu Zhao

Parametric functional principal component analysis
Peijun Sang, Liangliang Wang, and Jiguo Cao

Statistical significance for hierarchical clustering
Patrick K. Kimes, Yufeng Liu, D. Neil Hayes, and J. S. Marron

Pearson's Chi-square test and rank correlation inferences for clustered data
Joanna H. Shih and Michael P. Fay

Proportional hazards model with a change point for clustered event data
Yu Deng, Donglin Zeng, Jinying Zhao, and Jianwen Cai

Selection of effects in Cox frailty models by regularization methods
Andreas Groll, Trevor Hastie, and Gerhard Tutz

Semiparametric regression analysis of interval-censored competing risks data
Lu Mao, D. Y. Lin, and Donglin Zeng

On estimation of time-dependent attributable fraction from population-based case-control studies
Wei Zhao, Ying Qing Chen, and Li Hsu

Sequence robust association test for familial data
Wei Dai, Ming Yang, Chaolong Wang, and Tianxi Cai

Estimation of the relatedness coefficients from biallelic markers, application in plant mating designs
Fabien Laporte, Alain Charcosset, and Tristan Mary-Huard

Conditional estimation in two-stage adaptive designs
Per Broberg and Frank Miller

Bayesian response-adaptive designs for basket trials
Steffan Ventz, William T. Barry, Giovanni Parmigiani, and Lorenzo Trippa

Maximin optimal designs for cluster randomized trials
Sheng Wu, Weng Kee Wong, and Catherine M. Crespi

Optimum designs for non-linear mixed effects models in the presence of covariates
Barbara Bogacka, A. H. M. Mahbub Latif, Steven Gilmour, and Kuresh Youdim

A penalized framework for distributed lag non-linear models
Antonio Gasparrini, Fabian Scheipl, Ben Armstrong, and Michael G. Kenward

Estimating varying coefficients for partial differential equation models
Xinyu Zhang, Jiguo Cao, and Raymond J. Carroll

A generalized Levene's scale test for variance heterogeneity in the presence of sample correlation and group uncertainty
David Soave and Lei Sun

Order-restricted inference for means with missing values
Heng Wang and Ping-Shou Zhong


Direct estimation for adaptive treatment length Policies: Methods and application to evaluating the effect of delayed PEG insertion
Xin Lu and Brent A. Johnson

Combining item response theory with multiple imputation to equate health assessment questionnaires
Chenyang Gu and Roee Gutman

A multi-dimensional functional principal components analysis of EEG data
Kyle Hasenstab, Aaron Scheffler, Donatello Telesca, Catherine A. Sugar, Shafali Jeste, Charlotte DiStefano, and Damla Senturk

Estimation and testing problems in auditory neuroscience via clustering
Youngdeok Hwang, Samantha Wright, and Bret M. Hanlon

Bayesian genome- and epigenome-wide association studies with gene level dependence
E. F. Lock and D. B. Dunson

Visualizations for genetic assignment analyses using the saddlepoint approximation method
L. F. McMillan and R. M. Fewster

Improving efficiency of parameter estimation in case-cohort studies with multivariate failure time data
Ying Yan, Haibo Zhou, and Jianwen Cai


Correction to "Nonparametric analysis of competing risks data with event category missing at random," by Natalia Gouskova, Feng-Chang Lin, and Jason Fine; 73, 104-113, March 2017

Book Reviews

Papers to appear in future issues of Biometrics

BayesCAT: Bayesian co-estimation of alignment and tree
Heejung Shim and Bret Larget

Quantifying publication bias in meta-analysis
Lifeng Lin and Haitao Chu

Discussion on "Quantifying publication bias in meta-analysis"
Nancy L. Geller

Discussion on "Quantifying publication bias in meta-analysis"
Dan Jackson

Discussion on "Quantifying publication bias in meta-analysis"
Christopher H. Schmid

Rejoinder to "Quantifying publication bias in meta-analysis"
Lifeng Lin and Haitao Chu

Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression
Huaihou Chen, Donglin Zeng, and Yuanjia Wang

A simple correction to completer analyses and improvement on baseline observation carried forward
David Petroff

Controlling the false discoveries in LASSO
Hanwen Huang

Stagewise Generalized Estimating Equations with grouped variables
Gregory Vaughan, Robert Aseltine, Kun Chen, and Jun Yan

A generalized Fellner-Schall method for smoothing parameter optimization with application to Tweedie location, scale and shape models
Simon N. Wood and Matteo Fasiolo

A general instrumental variable framework for regression analysis with outcome missing not at random
Eric J. Tchetgen Tchetgen and Kathleen E. Wirth

Data-driven confounder selection via Markov and Bayesian networks
Jenny Haggstrom

Discussion on "Data-driven confounder selection via Markov and Bayesian networks"
Edward H. Kennedy and Sivaraman Balakrishnany

Discussion on "Data-driven confounder selection via Markov and Bayesian networks"
Thomas S. Richardson, James M. Robins, and Linbo Wang

Rejoinder to "Data-driven confounder selection via Markov and Bayesian networks"
Jenny Haggstrom

A general statistical framework for subgroup identification and comparative treatment scoring
Shuai Chen, Lu Tian, Tianxi Cai, and Menggang Yu

Nonparametric Bayesian covariate-adjusted estimation of the Youden index
Vanda Inacio de Carvalho, Miguel de Carvalho, and Adam J. Branscum

Parametric modeling of quantile regression coefficient functions with censored and truncated data
Paolo Frumento and Matteo Bottai

Weighted pseudolikelihood for SNP set analysis with multiple secondary outcomes in case-control genetic association studies
Tamar Sofer, Elizabeth D. Schifano, David C. Christiani, and Xihong Lin

Modeling and analyzing respondent-driven sampling as a counting process
Yakir Berchenko, Jonathan D. Rosenblatt, and Simon D. W. Frost

Design and monitoring of multi-arm multi-stage clinical trials
Pranab Ghosh, Lingyun Liu, P. Senchaudhuri, Ping Gao, and Cyrus R. Mehta

Augmented estimation for t-year survival with censored regression models
Yu Zheng and Tianxi Cai

Outcome-adaptive lasso: variable selection for causal inference
Susan M. Shortreed and Ashkan Ertefai

Learning gene regulatory networks from next generation sequencing data
Bochao Jia, Suwa Xu, Guanghua Xiao, Vishal Lamba, and Faming Liang

A model for paired-multinomial data and its application to analysis of data on a taxonomic tree
Pixu Shi and Hongzhe Li

Bayesian population finding with biomarkers in a randomized clinical trial
Satoshi Morita and Peter Mueller

Estimating time-varying directed gene regulation networks
Yunlong Nie, LiangLiang Wang, and Jiguo Cao

Sensitivity analysis for matched pair analysis of binary data: From worst case to average case analysis
R. Hasegawa and D. Small

A fast small-sample kernel independence test for microbiome community-level association analysis
Xiang Zhan, Anna Plantinga, Ni Zhao, and Michael C. Wu

Groupwise envelope models for imaging genetic analysis
Yeonhee Park, Zhihua Su, and Hongtu Zhu

Analysis of multiple diverse phenotypes via semiparametric canonical correlation analysis
Denis Agniel and Tianxi Cai

Joint modeling of zero-inflated panel count and severity outcomes
E. Juarez-Colunga, G. L. Silva, and C. B. Dean

Pointwise influence matrices for functional-response regression
Philip T. Reiss, Lei Huang, Pei-Shien Wu, Huaihou Chen, and Stan Colcombe

Simulation-based hypothesis testing of high dimensional means under covariance heterogeneity
Jinyuan Chang, Chao Zheng, Wen-Xin Zhou, and Wen Zhou

Parametric overdispersed frailty models for current status data
Steven Abrams, Marc Aerts, Geert Molenberghs, and Niel Hens

Second-order quasi-likelihood for spatial point processes
Chong Deng, Yongtao Guan, Rasmus P. Waagepetersen, and Jingfei Zhang

Joint modeling of longitudinal, recurrent events and failure time data for survivor's population
Qing Cai, Mei-Cheng Wang, and Kwun Chuen Gary Chan

Accelerated failure time models for semi-competing risks data in the presence of complex censoring
Kyu Ha Lee, Virginie Rondeau, and Sebastien Haneuse

Instrumental variables estimation of exposure effects on a time-to-event endpoint using structural cumulative survival models
Torben Martinussen, Stijn Vansteelandt, Eric J. Tchetgen Tchetgen, and David M. Zucker

Hidden Markov models for extended batch data
L. L. E. Cowen, P. Besbeas, B. J. T. Morgan, C. J. Schwarz

Incorporating covariates into integrated factor analysis of multi-view data
Gen Li and Sungkyu Jung

Semiparametric estimation of the accelerated failure time model with partly interval-censored data
Fei Gao, Donglin Zeng, and D. Y. Lin

On the multiple imputation variance estimator for control-based and delta-adjusted pattern mixture models
Yongqiang Tang

Doubly robust estimation of generalized partial linear models for longitudinal data with dropouts
Huiming Lin, Bo Fu, Guoyou Qin, and Zhongyi Zhu

Bayesian regression for group testing data
Christopher S. McMahan, Joshua M. Tebbs, Timothy E. Hanson, and Christopher R. Bilder

Efficient Bayesian hierarchical functional data analysis with basis function approximations using Gaussian-Wishart processes
Jingjing Yang, Dennis D. Cox, Jong Soo Lee, Peng Ren, and Taeryon Choi

Functional multiple indicators, multiple causes measurement error models
Carmen D. Tekwe, Roger S. Zoh, Fuller W. Bazer, Guoyao Wu, and Raymond J. Carroll

A note on marginalization of regression parameters from mixed models of binary outcomes
Donald Hedeker, Stephen du Toit, Hakan Demirtas, and Robert D. Gibbons

Semiparametric probit models with univariate and bivariate current-status data
Hao Liu and Jing Qin

Estimating the probability of clonal relatedness of pairs of tumors in cancer patients
Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya, and Colin B. Begg

Computation of ancestry scores with mixed families and unrelated individuals
Yi-Hui Zhou, J. S. Marron, and Fred A. Wright

Inferring network structure in non-normal and mixed discrete-continuous genomic data
Anindya Bhadra, Arvind Rao, and Veerabhadran Baladandayuthapani

Conditional adaptive Bayesian spectral analysis of nonstationary biomedical time series
Scott A. Bruce, Martica H. Hall, Daniel J. Buysse, and Robert T. Krafty

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information
Sandra. E. Safo, Shuzhao Li, and Qi Long

Estimating the size of an open population using sparse capture-recapture data
Richard Huggins, Jakub Stoklosa, Cameron Roach, and Paul Yip

A profile likelihood approach for longitudinal data analysis
Ziqi Chen, Man-Lai Tang, and Wei Gao

Multi-subgroup gene screening using semi-parametric hierarchical mixture models and the optimal discovery procedure: Application to a randomized
clinical trial in multiple myeloma

Shigeyuki Matsui, Hisashi Noma, Pingping Qu, Yoshio Sakai, Kota Matsui, Christoph Heuck, and John Crowley

Spatial Bayesian latent factor regression modeling of coordinate-based meta-analysis data
Silvia Montagna, Tor Wager, Lisa Feldman Barrett, Timothy D. Johnson, and Thomas E. Nichols

FPCA-based method to select optimal sampling schedules that capture between-subject variability in longitudinal studies
Meihua Wu, Ana Diez-Roux, Trivellore E. Ragunathan, and Brisa N. Sanchez

A Bayesian screening approach for hepatocellular carcinoma using multiple longitudinal biomarkers
Nabihah Tayob, Francesco Stingo, Kim-Anh Do, Anna S. F. Lok, and Ziding Feng

Why you can't transform your way out of trouble for small counts
David I. Warton

Simple and fast overidentified rank estimation for right-censored length-biased data and backward recurrence time
Yifei Sun, Kwun Chuen Gary Chan, and Jing Qin

Global sensitivity analysis for repeated measures studies with informative drop-out: A semi-parametric approach
Daniel Scharfstein, Aidan McDermott, Ivan Diaz, Marco Carone, Nicola Lunardon, and Ibrahim Turkoz

N mixture models vs Poisson regression
Richard J. Barker, Matthew R. Schofield, William A. Link, and John R, Sauer

A gatekeeping procedure to test a primary and a secondary endpoint in a group sequential design with multiple interim looks
Ajit C. Tamhane, Jiangtao Gou, Christopher Jennison, Cyrus R. Mehta, and Teresa Curto

Robust mislabel logistic regression without modeling mislabel probabilities
Hung Hung, Zhi-Yu Jou, and Su-Yun Huang

Model based bootstrapping when correcting for measurement error with application to logistic regression
John P. Buonaccorsi, Giovanni Romeo, and Magne Thoresen

Fast approximation of small p-values in permutation tests by partitioning the permutations
Brian Segal, Thomas Braun, Michael Elliott, and Hui Jiang

A local agreement pattern measure based on hazard functions for survival outcomes
Tian Dai, Ying Guo, Limin Peng, and Amita K. Manatunga

Correction to "Nonparametric analysis of competing risks data with event category missing at random,"
by Natalia Gouskova, Feng-Chang Lin, and Jason Fine; 73, 104-113, March 2017

Multiple phenotype association tests using summary statistics in genome-wide association studies
Zhonghua Liu and Xihong Lin

Covariate selection with group lasso and doubly robust estimation of causal effects
Brandon Koch, David M. Vock, and Julian Wolfson

Covariate-adjusted response-adaptive randomization for multi-arm clinical trials using a modified forward looking Gittins index rule
Sofia S. Villar and William F. Rosenberger

Evaluating center performance in the competing risks setting: Application to outcomes of wait-listed end-stage renal disease patients
Sai H. Dharmarajan, Douglas E. Schaubel, and Rajiv Saran

Joint principal trend analysis for longitudinal high-dimensional data
Yuping Zhang and Zhengqing Ouyang

Multivariate association analysis with somatic mutation data
Qianchuan He, Yang Liu, Ulrike Peters, and Li Hsu

Evaluating principal surrogate markers in vaccine trials in the presence of multiphase sampling
Ying Huang

Profiling the effects of short time-course cold ischemia on tumor protein phosphorylation using a Bayesian approach
You Wu, Jeremy Gaskins, Maiying Kong, and Susmita Datta

Cox regression with dependent error in covariates
Yijian Huang and C. Y. Wang

Incorporating patient preferences into estimation of optimal individualized treatment rules
Emily L. Butler, Eric B. Laber, Sonia M. Davis, and Michael R. Kosorok

Outcome-dependent sampling with interval-censored failure time data
Qingning Zhou, Jianwen Cai, and Haibo Zhou

A pairwise likelihood augmented Cox estimator for left-truncated data
Fan Wu, Sehee Kim, Jing Qin, Rajiv Saran, and Yi Li

A GLM-based latent variable ordination method for microbiome samples
Michael Sohn and Hongzhe Li

FLCRM: Functional Linear Cox Regression Model
Dehan Kong, Joseph G. Ibrahim, Eunjee Lee, and Hongtu Zhu

Risk prediction for heterogeneous populations with application to hospital admission prediction
Jared Huling, Menggang Yu, Muxuan Liang, and Maureen Smith

Augmented and doubly robust G-estimation of causal effects under a structural nested failure time model
Karl Mertens and Stijn Vansteelandt

Single index methods for evaluation of marker-guided treatment rules based on multivariate marker panels
Veronika Skrivankova and Patrick J. Heagerty

Model-free scoring system for risk prediction with application to hepatocellular carcinoma study
Weining Shen, Jing Ning, Ying Yuan, Anna S. Lok, and Ziding Feng

A C-index for recurrent event data: Application to hospitalizations among dialysis patients
Sehee Kim, Douglas E. Schaubel, and Keith P. McCullough

A matrix-based method of moments for fitting multivariate network meta-analysis models with multiple outcomes and random inconsistency effects
Dan Jackson, Sylwia Bujkiewicz, Martin Law, Richard D. Riley, and Ian R. White

Regularity of a renewal process estimated from binary data
John D. Rice, Robert L. Strawderman, and Brent A. Johnson

Sample size determination for multilevel hierarchical designs using generalized linear mixed models
A. Amatya and D. Bhaumik

Eigenvalue significance testing for genetic association
Yi-Hui Zhou, J. S. Marron, and Fred A. Wright

Continuous-time capture-recapture in closed populations
Matthew R. Schofield, Richard J. Barker, and Nicholas Gelling

Spatial capture-mark-resight estimation of animal population density
Murray G. Efford and Christine M. Hunter

Monte Carlo methods for nonparametric regression with heteroscedastic measurement error
Julie McIntyre, Brent A. Johnson, and Stephen M. Rappaport

A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine
Xiang Zhan and Michael C. Wu

Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"
Dehan Kong, Arnab Maity, Fang-Chi Hsu, and Jung-Ying Tzeng

Case-only approach to identifying markers predicting treatment effects on the relative risk scale
James Y. Dai, Jason Liang, Michael LeBlanc, Ross L. Prentice, and Holly Janes

Inverse probability weighted Cox regression for doubly truncated data
Micha Mandel, Jacobo de Una-Alvarez, David K. Simon, and Rebecca A. Betensky

Efficiency of two sample tests via the restricted mean survival time for analyzing event time observations
Lu Tian, Haoda Fu, Stephen J. Ruberg, Hajime Uno, and L. J. Wei

Analysis of restricted mean survival time for length-biased data
Chi Hyun Lee, Jing Ning, and Yu Shen

Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data
Iris Ivy M. Gauran, Junyong Park, Johan Lim, DoHwan Park, John Zylstra, Thomas Peterson, Maricel Kann, and John L. Spouge

Estimation and evaluation of linear individualized treatment rules to guarantee performance
Xin Qiu, Donglin Zeng, and Yuanjia Wang

Experimental designs for multi-drug combination studies using signaling networks
Hengzhen Huang, Hong-Bin Fang, and Ming T. Tan

Fully-Bayesian spectral methods for imaging data
Brian J. Reich, Joseph Guinness, Simon N. Vandekar, Russell T. Shinohara, and Ana-Maria Staicu

A semiparametric likelihood-based method for regression analysis of mixed panel-count data
Liang Zhu, Ying Zhang, Yimei Li, Jianguo Sun, and Leslie L. Robison

Adaptive designs for the one-sample log-rank test
Rene Schmidt, Andreas Faldum, and Robert Kwiecien

Clustering distributions with the marginalized nested Dirichlet process
Daiane Aparecida Zuanetti, Peter Mueller, Yitan Zhu, Shengjie Yang, and Yuan Ji

Optimal treatment assignment to maximize expected outcome with multiple treatments
Zhilan Lou, Jun Shao, and Menggang Yu

Modeling the causal effect of treatment initiation time on survival: Application to HIV/TB co-infection
Liangyuan Hu, Joseph W. Hogan, Ann W. Mwangi, and Abraham Siika

Modeling associations between latent event processes governing time series of pulsing hormones
Huayu Liu, Nichole E. Carlson, Gary K. Grunwald, and Alex J. Polotsky

A two-stage model for wearable device data
Jiawei Bai, Yifei Sun, Jennifer A. Schrack, Ciprian M. Crainiceanu, and Mei-Cheng Wang

Heterogeneous reciprocal graphical models
Yang Ni, Peter Mueller, Yitan Zhu, and Yuan Ji

Estimation of cis-eQTL effect sizes using a log of linear model
John Palowitch, Andrey Shabalin, Yihui Zhou, Andrew B. Nobel, and Fred A. Wright

Cox regression model with doubly truncated data
Lior Rennert and Sharon X. Xie

On the fast small-sample kernel independence test for microbiome community-level association analysis
Bin Guo and Baolin Wu

Bayesian variable selection for multistate Markov models with interval-censored data in an ecological momentary assessment study of smoking cessation
Matthew D. Koslovsky, Michael D. Swartz, Wenyaw Chan, Luis Leon-Novelo, Anna V. Wilkinson, Darla E. Kendzor, and Michael S. Businelle

Testing for gene-environment interaction under exposure misspecification
Ryan Sun, Raymond J. Carroll, David C. Christiani, and Xihong Lin

Improved dynamic predictions from joint models of longitudinal and survival data with time-varying effects using P-splines
E. R. Andrinopoulou, P. H. C. Eilers, J. J. M. Takkenberg, and D. Rizopoulos

Covariate-adjusted Spearman's rank correlation with probability-scale residuals
Qi Liu, Chun Li, Valentine Wanga, and Bryan E. Shepherd

Statistical inference in a growth curve quantile regression model for longitudinal data
Hyunkeun Ryan Cho

Integrated powered density: screening ultrahigh dimensional covariates with survival outcomes
Hyokyoung G. Hong, Xuerong Chen, David C. Christiani, and Yi Li

A regression framework for assessing covariate effects on the reproducibility of high-throughput experiments
Qunhua Li and Feipeng Zhang

C-learning: a new classification framework to estimate optimal dynamic treatment regimes
Baqun Zhang and Min Zhang

New semiparametric method for predicting high-cost patients
Adam Maidman and Lan Wang

Toward a diagnostic toolkit for linear models with Gaussian-process distributed random effects
Maitreyee Bose, James S. Hodges, and Sudipto Banerjee

Dynamic borrowing through empirical power priors that control type I error
Stavros Nikolakopoulos, Ingeborg van der Tweel, and Kit C. B. Roes

Sieve analysis using the number of infecting pathogens
Dean Follmann and Chiung-Yu Huang

Detecting treatment differences in group sequential longitudinal studies with covariate adjustment
Neal O. Jeffries, James F. Troendle, and Nancy L. Geller

A multi-source adaptive platform design for testing sequential combinatorial therapeutic strategies
Alexander M. Kaizer, Brian P. Hobbs, and Joseph S. Koopmeiners

Time-dynamic profiling with application to hospital readmission among patients on dialysis
Jason P. Estes, Danh V. Nguyen, Yanjun Chen, Lorien S. Dalrymple, Connie M. Rhee, Kamyar Kalantar-Zadeh, and Damla Senturk

Semiparametric estimation of the accelerated mean model with panel count data under informative examination times
Sy Han Chiou, Gongjun Xu, Jun Yan, and Chiung-Yu Huang