Publications

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Computer Simulation
Zhao, Yue, Benjamin R. Saville, Haibo Zhou, and Gary G. Koch. "Sensitivity analysis for missing outcomes in time-to-event data with covariate adjustment." J Biopharm Stat 26, no. 2 (2016): 269-79.
Wang, Xin, Daowen Zhang, and Jung-Ying Tzeng. "Pathway-guided identification of gene-gene interactions." Ann Hum Genet 78, no. 6 (2014): 478-91.
Miranda, Michelle F., Hongtu Zhu, and Joseph G. Ibrahim. "Bayesian spatial transformation models with applications in neuroimaging data." Biometrics 69, no. 4 (2013): 1074-83.
Li, Yimei, John H. Gilmore, Jiaping Wang, Martin Styner, Weili Lin, and Hongtu Zhu. "TwinMARM: two-stage multiscale adaptive regression methods for twin neuroimaging data." IEEE Trans Med Imaging 31, no. 5 (2012): 1100-12.
Li, Yimei, John H. Gilmore, Dinggang Shen, Martin Styner, Weili Lin, and Hongtu Zhu. "Multiscale adaptive generalized estimating equations for longitudinal neuroimaging data." Neuroimage 72 (2013): 91-105.
Guo, Ruixin, Hongtu Zhu, Sy-Miin Chow, and Joseph G. Ibrahim. "Bayesian lasso for semiparametric structural equation models." Biometrics 68, no. 2 (2012): 567-77.
Gao, Fei, Jun Dong, Donglin Zeng, Alan Rong, and Joseph G. Ibrahim. "Pattern mixture models for clinical validation of biomarkers in the presence of missing data." Stat Med 36, no. 19 (2017): 2994-3004.
Xue, Hongqi, Shuang Wu, Yichao Wu, Juan C. Ramirez Idarraga, and Hulin Wu. "Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks." Stat Med 37, no. 17 (2018): 2630-2644.
Jiang, Yu, Yujun Han, Slavé Petrovski, Kouros Owzar, David B. Goldstein, and Andrew S. Allen. "Incorporating Functional Information in Tests of Excess De Novo Mutational Load." Am J Hum Genet 97, no. 2 (2015): 272-83.
Wu, Jing, Ming-Hui Chen, Elizabeth D. Schifano, Joseph G. Ibrahim, and Jeffrey D. Fisher. "A new Bayesian joint model for longitudinal count data with many zeros, intermittent missingness, and dropout with applications to HIV prevention trials." Stat Med 38, no. 30 (2019): 5565-5586.
Luckett, Daniel J., Eric B. Laber, Samer S. El-Kamary, Cheng Fan, Ravi Jhaveri, Charles M. Perou, Fatma M. Shebl, and Michael R. Kosorok. "Receiver operating characteristic curves and confidence bands for support vector machines." Biometrics 77, no. 4 (2021): 1422-1430.
Acharya, Chaitanya R., Kouros Owzar, and Andrew S. Allen. "Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC Bioinformatics 18, no. 1 (2017): 455.
Baldoni, Pedro L., Naim U. Rashid, and Joseph G. Ibrahim. "Improved detection of epigenomic marks with mixed-effects hidden Markov models." Biometrics 75, no. 4 (2019): 1401-1413.
Skup, Martha, Hongtu Zhu, and Heping Zhang. "Multiscale adaptive marginal analysis of longitudinal neuroimaging data with time-varying covariates." Biometrics 68, no. 4 (2012): 1083-92.
Chen, Yong, Yulun Liu, Jing Ning, Lei Nie, Hongjian Zhu, and Haitao Chu. "A composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews." Stat Methods Med Res 26, no. 2 (2017): 914-930.
X Jeng, Jessie, Jacob Rhyne, Teng Zhang, and Jung-Ying Tzeng. "Effective SNP ranking improves the performance of eQTL mapping." Genet Epidemiol 44, no. 6 (2020): 611-619.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric regression analysis of interval-censored data with informative dropout." Biometrics 74, no. 4 (2018): 1213-1222.
Zeng, Donglin, Emil Cornea, Jun Dong, Jean Pan, and Joseph G. Ibrahim. "Assessing temporal agreement between central and local progression-free survival times." Stat Med 34, no. 5 (2015): 844-58.
Kang, Suhyun, Wenbin Lu, and Mengling Liu. "Efficient estimation for accelerated failure time model under case-cohort and nested case-control sampling." Biometrics 73, no. 1 (2017): 114-123.
Cai, Jianwen, and Donglin Zeng. "Additive mixed effect model for clustered failure time data." Biometrics 67, no. 4 (2011): 1340-51.
Kang, Sangwook, Jianwen Cai, and Lloyd Chambless. "Marginal additive hazards model for case-cohort studies with multiple disease outcomes: an application to the Atherosclerosis Risk in Communities (ARIC) study." Biostatistics 14, no. 1 (2013): 28-41.
Zhou, Yi-Hui, and Fred A. Wright. "Hypothesis testing at the extremes: fast and robust association for high-throughput data." Biostatistics 16, no. 3 (2015): 611-25.
Zou, Baiming, Bo Jin, Gary G. Koch, Haibo Zhou, Stephen E. Borst, Sandeep Menon, and Jonathan J. Shuster. "On model selections for repeated measurement data in clinical studies." Stat Med 34, no. 10 (2015): 1621-33.
Laber, Eric B., Ying-Qi Zhao, Todd Regh, Marie Davidian, Anastasios Tsiatis, Joseph B. Stanford, Donglin Zeng, Rui Song, and Michael R. Kosorok. "Using pilot data to size a two-arm randomized trial to find a nearly optimal personalized treatment strategy." Stat Med 35, no. 8 (2016): 1245-56.
Zhu, Hongtu, Martin Styner, Yimei Li, Linglong Kong, Yundi Shi, Weili Lin, Christopher Coe, and John H. Gilmore. "Multivariate varying coefficient models for DTI tract statistics." Med Image Comput Comput Assist Interv 13, no. Pt 1 (2010): 690-7.
Chen, Liddy M., Joseph G. Ibrahim, and Haitao Chu. "Sample size and power determination in joint modeling of longitudinal and survival data." Stat Med 30, no. 18 (2011): 2295-309.
Chen, Ming-Hui, Joseph G. Ibrahim, Arvind K. Shah, Jianxin Lin, and Hui Yao. "Meta-analysis methods and models with applications in evaluation of cholesterol-lowering drugs." Stat Med 31, no. 28 (2012): 3597-616.
Potthoff, Richard F., and Susan Halabi. "A novel test to compare two treatments based on endpoints involving both nonfatal and fatal events." Pharm Stat 14, no. 4 (2015): 273-83.
Kwak, Minjung, Jinseog Kim, and Sin-Ho Jung. "Optimal estimation for regression models on τ-year survival probability." J Biopharm Stat 25, no. 3 (2015): 539-47.
Choi, Jaeun, Donglin Zeng, Andrew F. Olshan, and Jianwen Cai. "Joint modeling of survival time and longitudinal outcomes with flexible random effects." Lifetime Data Anal 24, no. 1 (2018): 126-152.
Hu, Y J., and D Y. Lin. "Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
Maity, Arnab, Jing Zhao, Patrick F. Sullivan, and Jung-Ying Tzeng. "Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet Epidemiol 42, no. 1 (2018): 64-79.
Psioda, Matthew A., and Joseph G. Ibrahim. "Bayesian clinical trial design using historical data that inform the treatment effect." Biostatistics 20, no. 3 (2019): 400-415.
Pang, Herbert, Tiejun Tong, and Michael Ng. "Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol 12, no. 3 (2013): 347-59.
Potthoff, Richard F.. "Differential losses to follow-up that are outcome-dependent can vitiate a clinical trial: Simulation results." J Biopharm Stat 28, no. 4 (2018): 633-644.
West, Rachel Marceau, Wenbin Lu, Daniel M. Rotroff, Melaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches et al. "Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
Zhang, Min, Anastasios A. Tsiatis, Marie Davidian, Karen S. Pieper, and Kenneth W. Mahaffey. "Inference on treatment effects from a randomized clinical trial in the presence of premature treatment discontinuation: the SYNERGY trial." Biostatistics 12, no. 2 (2011): 258-69.
Pan, Yinghao, Jianwen Cai, Sangmi Kim, and Haibo Zhou. "Regression analysis for secondary response variable in a case-cohort study." Biometrics 74, no. 3 (2018): 1014-1022.
Hager, Rebecca, Anastasios A. Tsiatis, and Marie Davidian. "Optimal two-stage dynamic treatment regimes from a classification perspective with censored survival data." Biometrics 74, no. 4 (2018): 1180-1192.
Esserman, Denise, Yingqi Zhao, Yiyun Tang, and Jianwen Cai. "Sample size estimation in educational intervention trials with subgroup heterogeneity in only one arm." Stat Med 32, no. 12 (2013): 2140-54.
Wang, Charlotte, Jung-Ying Tzeng, Pei-Zhen Wu, Martin Preisig, and Chuhsing Kate Hsiao. "Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics 209, no. 1 (2018): 105-113.
Hu, Yi-Juan, Sonja I. Berndt, Stefan Gustafsson, Andrea Ganna, Joel Hirschhorn, Kari E. North, Erik Ingelsson, and Dan-Yu Lin. "Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet 93, no. 2 (2013): 236-48.
Liu, Jianyu, Wei Sun, and Yufeng Liu. "Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics 75, no. 1 (2019): 36-47.
Maitra, Poulami, Leila D. A. F. Amorim, and Jianwen Cai. "Multiplicative rates model for recurrent events in case-cohort studies." Lifetime Data Anal 26, no. 1 (2020): 134-157.
Reich, Brian J., and Howard D. Bondell. "A spatial dirichlet process mixture model for clustering population genetics data." Biometrics 67, no. 2 (2011): 381-90.
Kang, Chaeryon, Bahjat Qaqish, Jane Monaco, Stacey L. Sheridan, and Jianwen Cai. "Kappa statistic for clustered dichotomous responses from physicians and patients." Stat Med 32, no. 21 (2013): 3700-19.
Yang, Shu, Anastasios A. Tsiatis, and Michael Blazing. "Modeling survival distribution as a function of time to treatment discontinuation: A dynamic treatment regime approach." Biometrics 74, no. 3 (2018): 900-909.
Psioda, Matthew A., Kuolung Hu, Yang Zhang, Jean Pan, and Joseph G. Ibrahim. "Bayesian design of biosimilars clinical programs involving multiple therapeutic indications." Biometrics 76, no. 2 (2020): 630-642.
Zeng, Donglin, Fei Gao, Kuolung Hu, Catherine Jia, and Joseph G. Ibrahim. "Hypothesis testing for two-stage designs with over or under enrollment." Stat Med 34, no. 16 (2015): 2417-26.
Neely, Megan L., Howard D. Bondell, and Jung-Ying Tzeng. "A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies." Biometrics 71, no. 2 (2015): 529-37.
Xue, Xiaoqiang, Matthew C. Foster, and Anastasia Ivanova. "Rapid enrollment design for finding the optimal dose in immunotherapy trials with ordered groups." J Biopharm Stat 29, no. 4 (2019): 625-634.
Pang, Herbert, Michael Hauser, and Stéphane Minvielle. "Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
Lin, Jiaxing, Alexander Sibley, Ivo Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan, and Kouros Owzar. "fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies." BMC Bioinformatics 20, no. 1 (2019): 333.
Kang, Suhyun, Wenbin Lu, and Rui Song. "Subgroup detection and sample size calculation with proportional hazards regression for survival data." Stat Med 36, no. 29 (2017): 4646-4659.
Jeng, Xinge Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
Tang, Zheng-Zheng, and Dan-Yu Lin. "Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs." Am J Hum Genet 97, no. 1 (2015): 35-53.
Chen, Qingxia, Fan Zhang, Ming-Hui Chen, and Xiuyu Julie Cong. "Estimation of treatment effects and model diagnostics with two-way time-varying treatment switching: an application to a head and neck study." Lifetime Data Anal 26, no. 4 (2020): 685-707.
Ha, Min Jin, and Wei Sun. "Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation." Biometrics 70, no. 3 (2014): 765-73.
Liu, Bo, Wenbin Lu, and Jiajia Zhang. "Accelerated intensity frailty model for recurrent events data." Biometrics 70, no. 3 (2014): 579-87.
Yuan, Ying, John H. Gilmore, Xiujuan Geng, Martin A. Styner, Kehui Chen, Jane-ling Wang, and Hongtu Zhu. "A longitudinal functional analysis framework for analysis of white matter tract statistics." Inf Process Med Imaging 23 (2013): 220-31.
He, Qianchuan, and Dan-Yu Lin. "A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
Maity, Arnab, Patrick F. Sullivan, and Jun-Ying Tzeng. "Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
Kim, Soyoung, Jianwen Cai, and David Couper. "Improving the efficiency of estimation in the additive hazards model for stratified case-cohort design with multiple diseases." Stat Med 35, no. 2 (2016): 282-93.
Martinez, Kara, Arnab Maity, Robert H. Yolken, Patrick F. Sullivan, and Jung-Ying Tzeng. "Robust kernel association testing (RobKAT)." Genet Epidemiol 44, no. 3 (2020): 272-282.
Kwak, Minjung, Sang-Won Um, and Sin-Ho Jung. "Comparison of operational characteristics for binary tests with clustered data." Stat Med 34, no. 15 (2015): 2325-33.
Zhu, Hongtu, Linglong Kong, Runze Li, Martin Styner, Guido Gerig, Weili Lin, and John H. Gilmore. "FADTTS: functional analysis of diffusion tensor tract statistics." Neuroimage 56, no. 3 (2011): 1412-25.
Chen, Yong, Yulun Liu, Haitao Chu, Mei-Ling Ting Lee, and Christopher H. Schmid. "A simple and robust method for multivariate meta-analysis of diagnostic test accuracy." Stat Med 36, no. 1 (2017): 105-121.
Sohn, Insuk, Kouros Owzar, Stephen L. George, Sujong Kim, and Sin-Ho Jung. "Robust test method for time-course microarray experiments." BMC Bioinformatics 11 (2010): 391.
Jung, Sin-Ho, Myron N. Chang, and Sun J. Kang. "Phase II cancer clinical trials with heterogeneous patient populations." J Biopharm Stat 22, no. 2 (2012): 312-28.
Wang, Xin, Michael P. Epstein, and Jung-Ying Tzeng. "Analysis of gene-gene interactions using gene-trait similarity regression." Hum Hered 78, no. 1 (2014): 17-26.
Wang, Zhi, Arnab Maity, Chuhsing Kate Hsiao, Deepak Voora, Rima Kaddurah-Daouk, and Jung-Ying Tzeng. "Module-based association analysis for omics data with network structure." PLoS One 10, no. 3 (2015): e0122309.
Ibrahim, Joseph G., Hongtu Zhu, Ramon I. Garcia, and Ruixin Guo. "Fixed and random effects selection in mixed effects models." Biometrics 67, no. 2 (2011): 495-503.
Hu, Wenrong, Jianwen Cai, and Donglin Zeng. "Sample size/power calculation for stratified case-cohort design." Stat Med 33, no. 23 (2014): 3973-85.
Chakraborty, Bibhas, Eric B. Laber, and Yingqi Zhao. "Inference for optimal dynamic treatment regimes using an adaptive m-out-of-n bootstrap scheme." Biometrics 69, no. 3 (2013): 714-23.
Zhou, Qingning, Jianwen Cai, and Haibo Zhou. "Outcome-dependent sampling with interval-censored failure time data." Biometrics 74, no. 1 (2018): 58-67.
Li, Jialiang, Binyan Jiang, and Jason P. Fine. "Multicategory reclassification statistics for assessing improvements in diagnostic accuracy." Biostatistics 14, no. 2 (2013): 382-94.
Mao, Lu, and D Y. Lin. "Semiparametric regression for the weighted composite endpoint of recurrent and terminal events." Biostatistics 17, no. 2 (2016): 390-403.
Zhou, Yi-Hui, William T. Barry, and Fred A. Wright. "Empirical pathway analysis, without permutation." Biostatistics 14, no. 3 (2013): 573-85.
Helgeson, Erika S., Qian Liu, Guanhua Chen, Michael R. Kosorok, and Eric Bair. "Biclustering via sparse clustering." Biometrics 76, no. 1 (2020): 348-358.
Luo, Yiwen, Arnab Maity, Michael C. Wu, Chris Smith, Qing Duan, Yun Li, and Jung-Ying Tzeng. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
Dong, Lin, Eric Laber, Yair Goldberg, Rui Song, and Shu Yang. "Ascertaining properties of weighting in the estimation of optimal treatment regimes under monotone missingness." Stat Med 39, no. 25 (2020): 3503-3520.
He, Qianchuan, Hao Helen Zhang, Christy L. Avery, and D Y. Lin. "Sparse meta-analysis with high-dimensional data." Biostatistics 17, no. 2 (2016): 205-20.
Brownstein, Naomi C., and Jianwen Cai. "Tests of trend between disease outcomes and ordinal covariates discretized from underlying continuous variables: simulation studies and applications to NHANES 2007-2008." BMC Med Res Methodol 19, no. 1 (2019): 2.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric estimation of the accelerated failure time model with partly interval-censored data." Biometrics 73, no. 4 (2017): 1161-1168.
Zhang, Yuanye, Ming-Hui Chen, Joseph G. Ibrahim, Donglin Zeng, Qingxia Chen, Zhiying Pan, and Xiaodong Xue. "Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching." Lifetime Data Anal 20, no. 1 (2014): 76-105.
Wang, Xiaofei, Jingzhu Zhou, Ting Wang, and Stephen L. George. "On Enrichment Strategies for Biomarker Stratified Clinical Trials." J Biopharm Stat 28, no. 2 (2018): 292-308.
Hyun, Jung Won, Yimei Li, John H. Gilmore, Zhaohua Lu, Martin Styner, and Hongtu Zhu. "SGPP: spatial Gaussian predictive process models for neuroimaging data." Neuroimage 89 (2014): 70-80.
Wang, Rujin, Dan-Yu Lin, and Yuchao Jiang. "SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
Zhou, Haibo, Yuanshan Wu, Yanyan Liu, and Jianwen Cai. "Semiparametric inference for a 2-stage outcome-auxiliary-dependent sampling design with continuous outcome." Biostatistics 12, no. 3 (2011): 521-34.
Cai, Na, Wenbin Lu, and Hao Helen Zhang. "Time-varying latent effect model for longitudinal data with informative observation times." Biometrics 68, no. 4 (2012): 1093-102.
Huque, Md Hamidul, Howard D. Bondell, Raymond J. Carroll, and Louise M. Ryan. "Spatial regression with covariate measurement error: A semiparametric approach." Biometrics 72, no. 3 (2016): 678-86.
Wu, Yuan, Xiaofei Wang, Jiaxing Lin, Beilin Jia, and Kouros Owzar. "Predictive accuracy of markers or risk scores for interval censored survival data." Stat Med 39, no. 18 (2020): 2437-2446.
Hung, Hung, Yu-Ting Lin, Penweng Chen, Chen-Chien Wang, Su-Yun Huang, and Jung-Ying Tzeng. "Detection of gene-gene interactions using multistage sparse and low-rank regression." Biometrics 72, no. 1 (2016): 85-94.
Zeng, Donglin, Ming-Hui Chen, Joseph G. Ibrahim, Rachel Wei, Beiying Ding, Chunlei Ke, and Qi Jiang. "A counterfactual p-value approach for benefit-risk assessment in clinical trials." J Biopharm Stat 25, no. 3 (2015): 508-24.
Chen, Stephanie T., Luo Xiao, and Ana-Maria Staicu. "A smoothing-based goodness-of-fit test of covariance for functional data." Biometrics 75, no. 2 (2019): 562-571.
Bai, Xiaofei, Anastasios A. Tsiatis, Wenbin Lu, and Rui Song. "Optimal treatment regimes for survival endpoints using a locally-efficient doubly-robust estimator from a classification perspective." Lifetime Data Anal 23, no. 4 (2017): 585-604.
Hu, Y J., D Y. Lin, and D Zeng. "A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics 11, no. 4 (2010): 583-98.
Shin, Seung Jun, Yichao Wu, Hao Helen Zhang, and Yufeng Liu. "Probability-enhanced sufficient dimension reduction for binary classification." Biometrics 70, no. 3 (2014): 546-55.
Chen, Yasheng, Songbai Ji, Xunlei Wu, Hongyu An, Hongtu Zhu, Dinggang Shen, and Weili Lin. "Simulation of brain mass effect with an arbitrary Lagrangian and Eulerian FEM." Med Image Comput Comput Assist Interv 13, no. Pt 2 (2010): 274-81.
He, Kevin, Yanming Li, Ji Zhu, Hongliang Liu, Jeffrey E. Lee, Christopher I. Amos, Terry Hyslop, Jiashun Jin, Huazhen Lin, Qinyi Wei et al. "Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates." Bioinformatics 32, no. 1 (2016): 50-7.

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