Publications

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Computer Simulation
Diao, Guoqing, Jun Dong, Donglin Zeng, Chunlei Ke, Alan Rong, and Joseph G. Ibrahim. "Biomarker threshold adaptive designs for survival endpoints." J Biopharm Stat 28, no. 6 (2018): 1038-1054.
Barry, William T., Charles M. Perou, Kelly P Marcom, Lisa A. Carey, and Joseph G. Ibrahim. "The use of Bayesian hierarchical models for adaptive randomization in biomarker-driven phase II studies." J Biopharm Stat 25, no. 1 (2015): 66-88.
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.
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.
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.
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.
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.
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.
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.
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.
Li, Meng, Ana-Maria Staicu, and Howard D. Bondell. "Incorporating covariates in skewed functional data models." Biostatistics 16, no. 3 (2015): 413-26.
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.
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.
Zou, Baiming, Jianwen Cai, Gary G. Koch, Haibo Zhou, and Fei Zou. "A model-based conditional power assessment for decision making in randomized controlled trial studies." Stat Med 36, no. 30 (2017): 4765-4776.
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.
Chen, Qingxia, Donglin Zeng, Joseph G. Ibrahim, Ming-Hui Chen, Zhiying Pan, and Xiaodong Xue. "Quantifying the average of the time-varying hazard ratio via a class of transformations." Lifetime Data Anal 21, no. 2 (2015): 259-79.
Hu, Y J., and D Y. Lin. "Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
Zhang, Yichi, Eric B. Laber, Anastasios Tsiatis, and Marie Davidian. "Using decision lists to construct interpretable and parsimonious treatment regimes." Biometrics 71, no. 4 (2015): 895-904.
Kong, Dehan, Arnab Maity, Fang-Chi Hsu, and Jung-Ying Tzeng. "Testing and estimation in marker-set association study using semiparametric quantile regression kernel machine." Biometrics 72, no. 2 (2016): 364-71.
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.
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.
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.
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.
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.
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.
Joeng, Hee-Koung, Ming-Hui Chen, and Sangwook Kang. "Proportional exponentiated link transformed hazards (ELTH) models for discrete time survival data with application." Lifetime Data Anal 22, no. 1 (2016): 38-62.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Li, Zhiguo, Marcia Valenstein, Paul Pfeiffer, and Dara Ganoczy. "A global logrank test for adaptive treatment strategies based on observational studies." Stat Med 33, no. 5 (2014): 760-71.
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.
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.
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.
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.
Helgeson, Erika S., Qian Liu, Guanhua Chen, Michael R. Kosorok, and Eric Bair. "Biclustering via sparse clustering." Biometrics 76, no. 1 (2020): 348-358.
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.
Zhou, Qingning, Jianwen Cai, and Haibo Zhou. "Outcome-dependent sampling with interval-censored failure time data." Biometrics 74, no. 1 (2018): 58-67.
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.
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, 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.
Geng, Yuan, Hao Helen Zhang, and Wenbin Lu. "On optimal treatment regimes selection for mean survival time." Stat Med 34, no. 7 (2015): 1169-84.
Chen, Ming-Hui, Joseph G. Ibrahim, Donglin Zeng, Kuolung Hu, and Catherine Jia. "Bayesian design of superiority clinical trials for recurrent events data with applications to bleeding and transfusion events in myelodyplastic syndrome." Biometrics 70, no. 4 (2014): 1003-13.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
He, Qianchuan, and Dan-Yu Lin. "A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
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.
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.
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.
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.
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.
Wang, Xin, Daowen Zhang, and Jung-Ying Tzeng. "Pathway-guided identification of gene-gene interactions." Ann Hum Genet 78, no. 6 (2014): 478-91.
Daniel, Rhian M., and Anastasios A. Tsiatis. "Efficient estimation of the distribution of time to composite endpoint when some endpoints are only partially observed." Lifetime Data Anal 19, no. 4 (2013): 513-46.
Zhang, Baqun, Anastasios A. Tsiatis, Eric B. Laber, and Marie Davidian. "A robust method for estimating optimal treatment regimes." Biometrics 68, no. 4 (2012): 1010-8.
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.
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.
Zhou, Yi-Hui, William T. Barry, and Fred A. Wright. "Empirical pathway analysis, without permutation." Biostatistics 14, no. 3 (2013): 573-85.
Chen, Xiaolin, Qihua Wang, Jianwen Cai, and Viswanathan Shankar. "Semiparametric additive marginal regression models for multiple type recurrent events." Lifetime Data Anal 18, no. 4 (2012): 504-27.
Li, Jialiang, Binyan Jiang, and Jason P. Fine. "Multicategory reclassification statistics for assessing improvements in diagnostic accuracy." Biostatistics 14, no. 2 (2013): 382-94.
Ibrahim, Joseph G., Ming-Hui Chen, Amy H Xia, and Thomas Liu. "Bayesian meta-experimental design: evaluating cardiovascular risk in new antidiabetic therapies to treat type 2 diabetes." Biometrics 68, no. 2 (2012): 578-86.
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.
Tsiatis, Anastasios A., Marie Davidian, and Weihua Cao. "Improved doubly robust estimation when data are monotonely coarsened, with application to longitudinal studies with dropout." Biometrics 67, no. 2 (2011): 536-45.
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.
Liu, Yang, Xiwen Ma, Donghui Zhang, Lijiang Geng, Xiaojing Wang, Wei Zheng, and Ming-Hui Chen. "Look before you leap: systematic evaluation of tree-based statistical methods in subgroup identification." J Biopharm Stat 29, no. 6 (2019): 1082-1102.
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.
Lin, Dan-Yu, and Zheng-Zheng Tang. "A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet 89, no. 3 (2011): 354-67.
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.
Koehler, Megan L., Howard D. Bondell, and Jung-Ying Tzeng. "Evaluating haplotype effects in case-control studies via penalized-likelihood approaches: prospective or retrospective analysis?" Genet Epidemiol 34, no. 8 (2010): 892-911.
Post, Justin B., and Howard D. Bondell. "Factor selection and structural identification in the interaction ANOVA model." Biometrics 69, no. 1 (2013): 70-9.
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.
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
Diao, Guoqing, Guanghan F. Liu, Donglin Zeng, William Wang, Xianming Tan, Joseph F. Heyse, and Joseph G. Ibrahim. "Efficient methods for signal detection from correlated adverse events in clinical trials." Biometrics 75, no. 3 (2019): 1000-1008.
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.
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.
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.
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.
Pang, Herbert, and Sin-Ho Jung. "Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes." Genet Epidemiol 37, no. 3 (2013): 276-82.
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.
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.
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.

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