Papers to Appear in Biometrics


Vol. 73, No. 1
March 2017

Report of the Co-Editors - 2016

BIOMETRIC METHODOLOGY

Convex biclustering
Eric C. Chi, Genevera I. Allen, and Richard G. Baraniuk

Towards an objective and reproducible model choice via variable selection deviation
Wenjing Yang and Yuhong Yang

Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering
Jinyuan Chang, Wen Zhou, Wen-Xin Zhou, and Lan Wang

A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data
Rong Fu, Pei Wang, Ayumu Taguchi, Chee-Hong Wong, Qing Zhang, Adi Gazdar, Samir M. Hanash, Qinghua Zhou, and Ziding Feng

A random effect model for reconstruction of spatial chromatin structure
Jincheol Park and Shili Lin

Diagnosing misspecification of the random-effects distribution in mixed models
Reza Drikvandi, Geert Verbeke, and Geert Molenberghs

Joint partially linear model for longitudinal data with informative drop-outs
Sehee Kim, Donglin Zeng, and Jeremy M. G. Taylor

On longitudinal prediction with time-to-event outcome: Comparison of modeling options
Marlena Maziarz, Patrick Heagerty, Tianxi Cai, and Yingye Zheng

Multiple imputation for cure rate quantile regression with censored data
Yuanshan Wu and Guosheng Yin

Nonparametric analysis of competing risks data with event category missing at random
Natalia A. Gouskova, Feng-Chang Lin, and Jason P. Fine

Efficient estimation for accelerated failure time model under case-cohort and nested case-control sampling
Suhyun Kang, Wenbin Lu, and Mengling Liu

Doubly robust estimator for net survival rate in analyses of cancer registry data
Sho Komukai and Satoshi Hattori

Estimating the average treatment effect on survival based on observational data and using partly conditional modeling
Qi Gong and Douglas E. Schaubel

Adaptive contrast weighted learning for multi-stage multi-treatment decision-making
Yebin Tao and Lu Wang

Alternative measures of between-study heterogeneity in meta-analysis: Reducing the impact of outlying studies
Lifeng Lin, Haitao Chu, and James S. Hodges

Petersen estimator, Chapman adjustment, list effects and heterogeneity
Chang Xuan Mao, Ruochen Huang, and Sijia Zhang

Robustifying Bayesian nonparametric mixtures for count data
Antonio Canale and Igor Prunster

The LZIP: A Bayesian latent factor model for correlated zero-inflated counts
Brian Neelon and Dongjun Chung

Likelihood ratio tests for a dose-response effect using multiple nonlinear regression models
Georg Gutjahr and Björn Bornkamp

On the combination of c- and D-optimal designs: General approaches and applications in dose response studies
Tim Holland-Letz

Ordinal probability effect measures for group comparisons in multinomial cumulative link models
Alan Agresti and Maria Kateri

BIOMETRIC PRACTICE

Sufficient dimension reduction for censored predictors
Diego Tomassi, Liliana Forzani, Efstathia Bura, and Ruth Pfeiffer

Multivariate Bayesian variable selection exploiting dependence structure among outcomes: application to air pollution effects on DNA methylation
Kyu Ha Lee, Mahlet G. Tadesse, Andrea A. Bacarelli, Joel Schwartz, and Brent A. Coull

Adaptive prior weighting in generalized regression
Leonhard Held and Rafael Sauter

Nonparametric inference on quantile lost lifespan
Lauren Balmert and Jong-Hyeon Jeong

Tumor dormancy and frailty models: a novel approach
Paola M. V. Rancoita, Morten Valberg, Romano Demicheli, Elia Biganzoli and Clelia Di Serio

Modelling of successive cancer risks in Lynch Syndrome families in the presence of competing risks using copulas
Yun-Hee Choi, Laurent Briollais, Aung K. Win, John Hopper, Dan Buchanan, Mark Jenkins, and Lajmi Lakhal Chaieb

Time series modeling of pathogen-specific disease probabilities with subsampled data
Leigh Fisher, Jon Wakefield, Cici Bauer, and Steve Self

Dynamic models for estimating the effect of HAART on CD4 in observational studies: application to the Aquitaine Cohort and the Swiss HIV Cohort Study
M. Prague, D. Commenges, J. M. Gran, B. Ledergerber, J. Young, H. Furrer and R. Thiebaut

Using the SAEM algorithm for mechanistic joint models characterizing the relationship between nonlinear PSA kinetics and survival in prostate cancer patients
Solene Desmee, France Mentre, Christine Veyrat-Follet, Bernard Sebastien, and Jeremie Guedj

Hidden Markov latent variable models for multivariate longitudinal data
Xin-Yuan Song, Ye-Mao Xia, and Hongtu Zhu

Clustering multivariate functional data with phase variation
Juhyun Park and Jeongyoun Ahn

Assessment of DPOAE test-retest difference curves via hierarchical Gaussian processes
Junshu Bao, Timothy Hanson, Garnett McMillan, and Kristin Knight

Detecting rare and common haplotype-environment interaction under uncertainty of gene-environment independence assumption
Yuan Zhang, Shili Lin, and Swati Biswas

Book Reviews


Papers to appear in future issues of Biometrics

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"
Layla Parast and Carolyn M. Rutter

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

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

Reader Reaction on Estimation of Treatment Effects in All-Comers Randomized Clinical Trials with a Predictive Marker
Edward L. Korn and Boris Freidlin

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

A framework for Bayesian nonparametric inference for causal effects of mediation
Chanmin Kim, Michael J. Daniels, Bess H. Marcus, and Jason A. Roy

Sequential multiple assignment randomization trials with enrichment design
Ying Liu, Yuanjia Wang, and Donglin Zeng

Estimation of diagnostic accuracy of a combination of continuous biomarkers allowing for conditional dependence between the biomarkers and the imperfect reference-test
Leandro García Barrado, Els Coart, and Tomasz Burzykowski

Structured ordinary least squares: a sufficient dimension reduction approach for regressions with partitioned predictors and heterogeneous units
Yang Liu, Francesca Chiaromonte, and Bing Li

Quantile association for bivariate survival data
Ruosha Li, Yu Cheng, Qingxia Chen, and Jason Fine

On standardized relative survival
Peter Sasieni and Adam R. Brentnall

A Bayesian hierarchical model for prediction of latent health states from multiple data sources with application to active surveillance of prostate cancer
R. Yates Coley, Aaron J. Fisher, Mufaddal Mamawala, H. Ballentine Carter, Kenneth J. Pienta, and Scott L. Zeger

Semiparametric time-to-event modeling in the presence of a latent progression event
John D. Rice and Alex Tsodikov

Distance sampling detection functions: 2D or not 2D?
D. L. Borchers and M. J. Cox

Survival model construction guided by fit and predictive strength
Cecile Chauvel and John O'Quigley

Screening and clustering of sparse regressions with finite non-Gaussian mixtures
Jian Zhang

Multiple testing with heterogeneous multinomial distributions
Joshua Habiger, David Watts, and Michael Anderson

Residual-based model diagnosis methods for mixture cure models
Yingwei Peng and Jeremy M. G. Taylor

A Bayesian integrative approach for multi-platform genomic data: A kidney cancer case study
Thierry Chekouo, Francesco C. Stingo, James D. Doecke, and Kim-Anh Do

A joint modeling approach for multivariate survival data with random length
Shuling Liu, Amita K. Manatunga, Limin Peng, and Michele Marcus

A semiparametric model for vQTL mapping
Chuan Hong, Yang Ning, Peng Wei, Ying Cao, and Yong Chen

Hierarchical group testing for multiple infections
Peijie Hou, Joshua M. Tebbs, Christopher R. Bilder, and Christopher S. McMahan

Testing violations of exponential assumption in cancer clinical trials with survival endpoints
Gang Han, Michael J. Schell, Heping Zhang, Daniel Zelterman, Lajos Pusztai, Kerin Adelson, and Christos Hatzis

Greedy outcome weighted tree learning of optimal personalized treatment rules
Ruoqing Zhu, Ying-Qi Zhao, Guanhua Chen, Shuangge Ma, and Hongyu Zhao

Inference in randomized trials with death and missingness
Chenguang Wang, Daniel O. Scharfstein, Elizabeth Colantuoni, Timothy D. Girard, and Ying Yan

An adaptive Mantel-Haenszel test for sensitivity analysis in observational studies
Paul R. Rosenbaum and Dylan S. Small

Alternating logistic regressions with improved finite sample properties
Jamie Perin and John S. Preisser

A subgroup cluster based Bayesian adaptive design for precision medicine
Wentian Guo, Yuan Ji, and Daniel V. T. Catenacci

Estimation of the optimal regime in treatment of prostate cancer recurrence from observational data using flexible weighting models
Jincheng Shen, Lu Wang, and Jeremy M. G. Taylor

Model averaged double robust estimation
Matthew Cefalu, Francesca Dominici, Nils Arnold, and Giovanni Parmigiani

Bayesian variable selection for post-analytic interrogation of susceptibility loci
Siying Chen, Sara Nunez, Muredach P. Reilly, and Andrea S. Foulkes

Generalized semiparametric varying-coefficient model for longitudinal data with applications to adaptive treatment randomizations
Li Qi, Yanqing Sun, and Peter B. Gilbert

Integrative genetic risk prediction using nonparametric empirical Bayes classification
Sihai Dave Zhao

Hypothesis testing in functional linear models
Yu-Ru Su, Chong-Zhi Di, and Li Hsu

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

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

Model-robust inference for continuous threshold regression models
Youyi Fong, Chongzhi Di, Ying Huang, and Peter B. Gilbert

Multi-parameter regression survival modelling: An alternative to proportional hazards
K. Burke and G. MacKenzie

Assessing quantile prediction with censored quantile regression models
Ruosha Li and Limin Peng

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Modeling nonstationarity in space and time
Lyndsay Shand and Bo Li

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

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

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

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

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

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