Publications

2015
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.
Chen, Tianle, Donglin Zeng, and Yuanjia Wang. "Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration." Biometrics 71, no. 4 (2015): 918-28.
Tao, Ran, Donglin Zeng, Nora Franceschini, Kari E. North, Eric Boerwinkle, and Dan-Yu Lin. MultiTDS: Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling (C++)., 2015.
Foster, Nathan R., Lindsay A. Renfro, Steven E. Schild, Mary W. Redman, Xiaofei F. Wang, Suzanne E. Dahlberg, Keyue Ding, Penelope A. Bradbury, Suresh S. Ramalingam, David R. Gandara et al. "Multitrial Evaluation of Progression-Free Survival as a Surrogate End Point for Overall Survival in First-Line Extensive-Stage Small-Cell Lung Cancer." J Thorac Oncol 10, no. 7 (2015): 1099-106.
Tzeng, Jung-Ying, Patrik K. E. Magnusson, Patrick F. Sullivan, and Jin P. Szatkiewicz. "A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
Zhao, Ying-Qi, Donglin Zeng, Eric B. Laber, and Michael R. Kosorok. "New Statistical Learning Methods for Estimating Optimal Dynamic Treatment Regimes." J Am Stat Assoc 110, no. 510 (2015): 583-598.
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.
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.
Brownstein, Naomi C., Jianwen Cai, Gary D. Slade, and Eric Bair. "Parameter estimation in Cox models with missing failure indicators and the OPPERA study." Stat Med 34, no. 30 (2015): 3984-96.
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.
Song, R, W Wang, D Zeng, and M R. Kosorok. "Penalized Q-Learning for Dynamic Treatment Regimens." Stat Sin 25, no. 3 (2015): 901-920.
Ibrahim, Joseph G., Ming-Hui Chen, Yeongjin Gwon, and Fang Chen. "The power prior: theory and applications." Stat Med 34, no. 28 (2015): 3724-49.
Kong, Dehan, Kelly S. Giovanello, Yalin Wang, Weili Lin, Eunjee Lee, Yong Fan, Murali P Doraiswamy, and Hongtu Zhu. "Predicting Alzheimer's Disease Using Combined Imaging-Whole Genome SNP Data." J Alzheimers Dis 46, no. 3 (2015): 695-702.
Hu, Yi-Juan, Wei Sun, Jung-Ying Tzeng, and Charles M. Perou. "Proper Use of Allele-Specific Expression Improves Statistical Power for -eQTL Mapping with RNA-Seq Data." J Am Stat Assoc 110, no. 511 (2015): 962-974.
Tan, Hung-Jui, Anne-Marie Meyer, Tzy-Mey Kuo, Angela B. Smith, Stephanie B. Wheeler, William R. Carpenter, and Matthew E. Nielsen. "Provider-based research networks and diffusion of surgical technologies among patients with early-stage kidney cancer." Cancer 121, no. 6 (2015): 836-43.
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.
Lachos, Victor H., Ming-Hui Chen, Carlos A. Abanto-Valle, and Caio L. N. Azevedo. "Quantile regression for censored mixed-effects models with applications to HIV studies." Stat Interface 8, no. 2 (2015): 203-215.
Pang, Herbert, Inyoung Kim, and Hongyu Zhao. "Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data." Stat Biosci 7, no. 2 (2015): 167-186.
Cao, Hongyuan, Donglin Zeng, and Jason P. Fine. "Regression analysis of sparse asynchronous longitudinal data." J R Stat Soc Series B Stat Methodol 77, no. 4 (2015): 755-776.
Zhu, Ruoqing, Donglin Zeng, and Michael R. Kosorok. "Reinforcement Learning Trees." J Am Stat Assoc 110, no. 512 (2015): 1770-1784.
Zhang, Baqun, Anastasios A. Tsiatis, Eric B. Laber, and Marie Davidian. "Response to reader reaction." Biometrics 71, no. 1 (2015): 267-273.
A Gould, Lawrence, Mark Ernest Boye, Michael J. Crowther, Joseph G. Ibrahim, George Quartey, Sandrine Micallef, and Frederic Y. Bois. "Responses to discussants of 'Joint modeling of survival and longitudinal non-survival data: current methods and issues. report of the DIA Bayesian joint modeling working group'." Stat Med 34, no. 14 (2015): 2202-3.
Zhu, Ruoqing, and Michael R. Kosorok. RLT: Reinforcement learning trees (R).. 2.0 ed., 2015.
Hua, Zhaowei, Hongtu Zhu, and David B. Dunson. "Semiparametric Bayes local additive models for longitudinal data." Stat Biosci 7, no. 1 (2015): 90-107.
Hu, Yi-Juan, Yun Li, Paul L. Auer, and Dan-Yu Lin. SEQGWAS: Integrative analysis of sequencing and GWAS data (C/C++).. 1.0 ed., 2015.
Cheng, Guang, Hao Helen Zhang, and Zuofeng Shang. "Sparse and Efficient Estimation for Partial Spline Models with Increasing Dimension." Ann Inst Stat Math 67, no. 1 (2015): 93-127.
Song, Rui, Michael Kosorok, Donglin Zeng, Yingqi Zhao, Eric Laber, and Ming Yuan. "On Sparse representation for Optimal Individualized Treatment Selection with Penalized Outcome Weighted Learning." Stat 4, no. 1 (2015): 59-68.
Guo, Ruixin, Mihye Ahn, and Hongtu Zhu. "Spatially Weighted Principal Component Analysis for Imaging Classification." J Comput Graph Stat 24, no. 1 (2015): 274-296.
Sun, Qiang, Hongtu Zhu, Yufeng Liu, and Joseph G. Ibrahim. "SPReM: Sparse Projection Regression Model For High-dimensional Linear Regression." J Am Stat Assoc 110, no. 509 (2015): 289-302.
Yu, Jichang, Yanyan Liu, Dale P. Sandler, and Haibo Zhou. "Statistical inference for the additive hazards model under outcome-dependent sampling." Can J Stat 43, no. 3 (2015): 436-453.
Jung, Sin-Ho. "Statistical issues for design and analysis of single-arm multi-stage phase II cancer clinical trials." Contemp Clin Trials 42 (2015): 9-17.
Huang, Hanwen, Yufeng Liu, Ming Yuan, and J S. Marron. "Statistical Significance of Clustering using Soft Thresholding." J Comput Graph Stat 24, no. 4 (2015): 975-993.
Cao, Hongyuan, Mathew M. Churpek, Donglin Zeng, Jason P. Fine, and Shannon T. Holloway. SurvLong: Analysis of proportional hazards model with sparse longitudinal covariates (R).. 1.0 ed., 2015.
Hung, Hung, Yu-Ting Lin, Penweng Chen, Chen-Chien Wang, Su-Yun Huang, and Jung-Ying Tzeng. TensorGxG: A sparse and low-rank screening based on the combination of a low-rank interaction model and the Lasso screening (Matlab).., 2015.
Song, Guochen. TRECASE_MLE: eQTL mapping based on total read count and allele-specific expression in RNA-Seq data with maximum-likelihood estimation (C/C++).., 2015.
Laber, E B., and Y Q. Zhao. "Tree-based methods for individualized treatment regimes." Biometrika 102, no. 3 (2015): 501-514.
Liu, Yulun, Yong Chen, and Haitao Chu. "A unification of models for meta-analysis of diagnostic accuracy studies without a gold standard." Biometrics 71, no. 2 (2015): 538-47.
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.
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.
Wang, Xiaofei, Lin Gu, Ying Zhang, Daniel J. Sargent, William Richards, Apar Kishor Ganti, Jeffery Crawford, Harvey Jay Cohen, Thomas Stinchcombe, Everett Vokes et al. "Validation of survival prognostic models for non-small-cell lung cancer in stage- and age-specific groups." Lung Cancer 90, no. 2 (2015): 281-7.
2016
Zhang, Guosheng, Kuan-Chieh Huang, Zheng Xu, Jung-Ying Tzeng, Karen N. Conneely, Weihua Guan, Jian Kang, and Yun Li. "Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression." Genet Epidemiol 40, no. 4 (2016): 333-40.
Minsker, Stanislav, Ying-Qi Zhao, and Guang Cheng. "Active Clinical Trials for Personalized Medicine." J Am Stat Assoc 111, no. 514 (2016): 875-887.
Shin, Sunyoung, Jason Fine, and Yufeng Liu. "Adaptive Estimation with Partially Overlapping Models." Stat Sin 26, no. 1 (2016): 235-253.
Cornea, Emil, Hongtu Zhu, Peter Kim, and Joseph G. Ibrahim. ADNI_RMRSS: Regression Models on Riemannian Symmetric Spaces (MATLAB)., 2016.
X Jeng, Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. AFNC: Adaptive false negative control (R)., 2016.
Roe, Matthew T., Derek D. Cyr, Debra Eckart, Phillip J. Schulte, Michael A. Morse, Kimberly L. Blackwell, Neal E. Ready, Yousuf S Zafar, Anne W. Beaven, John H. Strickler et al. "Ascertainment, classification, and impact of neoplasm detection during prolonged treatment with dual antiplatelet therapy with prasugrel vs. clopidogrel following acute coronary syndrome." Eur Heart J 37, no. 4 (2016): 412-22.
Murphy, Susan A.. Assessing Time-Varying Causal Interactions and Treatment Effects with Applications to Mobile Health., 2016.
Chen, Mengjie, Zhao Ren, Hongyu Zhao, and Harrison Zhou. "Asymptotically Normal and Efficient Estimation of Covariate-Adjusted Gaussian Graphical Model." J Am Stat Assoc 111, no. 513 (2016): 394-406.
Song, Rui, Moulinath Banerjee, and Michael R. Kosorok. "ASYMPTOTICS FOR CHANGE-POINT MODELS UNDER VARYING DEGREES OF MIS-SPECIFICATION." Ann Stat 44, no. 1 (2016): 153-182.
Cao, Hongyuan, Donglin Zeng, Jason P. Fine, and Shannon T. Holloway. AsynchLong: Regression analysis of sparse asynchronous longitudinal data (R).. 2.0 ed., 2016.
DE Castro, Mário, Ming-Hui Chen, and Y Zhang. "Bayesian frailty models for multi-state survival data." In Statistical Applications from Clinical Trials and Personalized Medicine to Finance and Business Analytics. New York: Springer, 2016.
Psioda, Matthew, and Joseph G. Ibrahim. BetaBinPredProb: Compute predictive probabilities in Bayesian design for Phase IIA trials in a beta-binomial case (SAS).., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. binDesign: Bayesian sample size for non-inferiority randomized trials with binary data (SAS).., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. binDesignPP: Bayesian sample size for non-inferiority randomized trials with binary data with power prior (SAS).., 2016.
Wang, Ting. Biomarker Stratified Design Enriched by Auxiliary Biomarker., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. BPower: Computes two versions of Bayesian power for normal models (SAS).., 2016.
George, Stephen L., Xiaofei Wang, and Herbert Pang. Cancer Clinical Trials: Current and Controversial Issues in Design and Analysis.. Boca Raton: Chapman & Hall / CRC Press, 2016.
Chen, Mengjie, Haifan Lin, and Hongyu Zhao. "CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS." Ann Appl Stat 10, no. 1 (2016): 506-526.
Wang, Xuefeng, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy R. Zhang, Scott R Powers, and Michael Krauthammer. CLOSE: A toolkit for CNA/LOH analysis with Sequencing data., 2016.
Chen, Jingxiang, Yufeng Liu, Donglin Zeng, Rui Song, Yingqi Zhao, and Michael R. Kosorok. "Comment." J Am Stat Assoc 111, no. 515 (2016): 942-947.
Guan, Qian, Eric B. Laber, and Brian J. Reich. "Comment." J Am Stat Assoc 111, no. 515 (2016): 936-942.
Blackwell, Kimberly, Roman Donskih, Michael C Jones, Allen Nixon, Maria J. Vidal, Roumen Nakov, Pritibha Singh, Gregor Schaffar, Pere Gascón, and Nadia Harbeck. "A Comparison of Proposed Biosimilar LA-EP2006 and Reference Pegfilgrastim for the Prevention of Neutropenia in Patients With Early-Stage Breast Cancer Receiving Myelosuppressive Adjuvant or Neoadjuvant Chemotherapy: Pegfilgrastim Randomized Oncology (Supp." Oncologist 21, no. 7 (2016): 789-94.
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.
Chen, Guanhua, Yufeng Liu, Dinggang Shen, and Michael R. Kosorok. "Composite large margin classifiers with latent subclasses for heterogeneous biomedical data." Stat Anal Data Min 9, no. 2 (2016): 75-88.
Zhang, Xiang, Yichao Wu, Lan Wang, and Runze Li. "A Consistent Information Criterion for Support Vector Machines in Diverging Model Spaces." J Mach Learn Res 17, no. 16 (2016): 1-26.
Psioda, Matthew, and Joseph G. Ibrahim. design_biomAR: Bayes adaptive randomization for the probit model (SAS).., 2016.
Chen, Ting-Huei, Wei Sun, and Jason P. Fine. "Designing penalty functions in high dimensional problems: The role of tuning parameters." Electron J Stat 10, no. 2 (2016): 2312-2328.
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.
Wang, Xiaofei, Ming-Hui Chen, R C. Kuo, and Dipak K. Dey. "Dynamic spatial pattern recognition in count data." In New Developments in Statistical Modeling, Inference and Application, 185-202. New York: Springer, 2016.
Davidian, Marie, Anastasios A. Tsiatis, and Eric B. Laber. "Dynamic treatment regimes." In Cancer Clinical Trials: Current and Controversial Issues in Design and Analysis. Boca Raton: Chapman & Hall / CRC Press, 2016.
Boland, Mary Regina. Electronic Health Records and Precision Medicine: Enabling Large-Scale Discoveries Using Phenome-Wide Approaches., 2016.
S Farber, Harrison, Vadim Tsvankin, Jessica L. Narloch, Grace J. Kim, April K. S. Salama, Gordana Vlahovic, Kimberly L. Blackwell, John P. Kirkpatrick, and Peter E. Fecci. "Embracing rejection: Immunologic trends in brain metastasis." Oncoimmunology 5, no. 7 (2016): e1172153.
George, Stephen L., Xiaofei Wang, and Herbert Pang. "Endpoints for cancer clinical trials." In Cancer Clinical Trials: Current and Controversial Issues in Design and Analysis. Boca Raton: Chapman & Hall / CRC Press, 2016.
Pang, Herbert H., Xiaofei Wang, Thomas E. Stinchcombe, Melisa L. Wong, Perry Cheng, Apar Kishor Ganti, Daniel J. Sargent, Ying Zhang, Chen Hu, Sumithra J. Mandrekar et al. "Enrollment Trends and Disparity Among Patients With Lung Cancer in National Clinical Trials, 1990 to 2012." J Clin Oncol 34, no. 33 (2016): 3992-3999.
Lewis, Paul O., Ming-Hui Chen, Lynn Kuo, Louise A. Lewis, Karolina Fučíková, Suman Neupane, Yu-Bo Wang, and Daoyuan Shi. "Estimating Bayesian Phylogenetic Information Content." Syst Biol 65, no. 6 (2016): 1009-1023.
Tan, Ziwen, Guoyou Qin, and Haibo Zhou. "Estimation of a partially linear additive model for data from an outcome-dependent sampling design with a continuous outcome." Biostatistics 17, no. 4 (2016): 663-76.
Linn, Kristin A., Eric B. Laber, and Leonard A. Stefanski. "Estimation of dynamic treatment regimes for complex outcomes: Balancing benefits and risks." In Adaptive Treatment Strategies in Practice: Planning Trials and Analyzing Data for Personalized Medicine, 249-262. Philadelphia: ASA-SIAM, 2016.
Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
Psioda, Matthew, and Joseph G. Ibrahim. fitRE: Bayesian superiority design for gamma frailty recurrent events model (SAS).., 2016.
Li, Zhiguo, and Kouros Owzar. "Fitting Cox Models with Doubly Censored Data Using Spline-Based Sieve Marginal Likelihood." Scand Stat Theory Appl 43, no. 2 (2016): 476-486.
Chow, Sy-Miin, Zhaohua Lu, Andrew Sherwood, and Hongtu Zhu. "Fitting Nonlinear Ordinary Differential Equation Models with Random Effects and Unknown Initial Conditions Using the Stochastic Approximation Expectation-Maximization (SAEM) Algorithm." Psychometrika 81, no. 1 (2016): 102-34.
Lewis, Paul O.. Galax (C++)., 2016.
Chi, Eric. Getting High-throughput Arrays in Order with Convex Biclustering., 2016.
Ha, Min Jin, and Shannon T. Holloway. GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R).. 1.0 ed., 2016.
Wang, Xuefeng, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy R. Zhang, Scott R Powers, and Michael Krauthammer. "Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
Ma, Xiaoye, Yong Chen, Stephen R. Cole, and Haitao Chu. "A hybrid Bayesian hierarchical model combining cohort and case-control studies for meta-analysis of diagnostic tests: Accounting for partial verification bias." Stat Methods Med Res 25, no. 6 (2016): 3015-3037.
Nair, Smita. Immune-based therapies., 2016.
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.
Bunn, Paul, Donglin Zeng, and Dan-Yu Lin. IntCens: Nonparametric maximum likelihood estimation for a broad class of semiparametric regression models with general interval-censored data (R).., 2016.
Wong, Kin Yau. Integration of Multiple High-dimensional Genomic Data Types for Survival Prediction., 2016.
Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. JAGUAR: Joint analysis of genotype and group-specific variability using a novel score test approach to map expression quantitative trait loci (eQTL) (R). 3.0.1 ed., 2016.
Zhang, Danjie, Ming-Hui Chen, Joseph G. Ibrahim, Mark E. Boye, and Wei Shen. "JMFit: A SAS Macro for Joint Models of Longitudinal and Survival Data." J Stat Softw 71, no. 3 (2016).
Xiao, Wei, Wenbin Lu, and Hao Helen Zhang. "JOINT STRUCTURE SELECTION AND ESTIMATION IN THE TIME-VARYING COEFFICIENT COX MODEL." Stat Sin 26, no. 2 (2016): 547-567.
Lin, Jiaxing, Alexander Sibley, Ivo D. Shterev, and Kouros Owzar. jtGWAS: Efficient Jonckheere-Terpstra test statistics (R).. 1.0 ed., 2016.
Palumbo, Aimee, Yvonne Michael, and Terry Hyslop. "Latent class model characterization of neighborhood socioeconomic status." Cancer Causes Control 27, no. 3 (2016): 445-52.
Lin, Jiaxing, Alexander Sibley, Trach Truong, Nancy Cox, Eileen Dolan, Yu Jiang, Janice M. McCarthy, Andrew S. Allen, Kouros Owzar, and Zhiguo Li. lclGWAS: Efficient estimation of discrete-time multivariate frailty model using exact likelihood function for grouped survival data (R).., 2016.
Wang, Yuanjia, Peng Wu, Ying Liu, Chunhua Weng, and Donglin Zeng. "Learning Optimal Individualized Treatment Rules from Electronic Health Record Data." IEEE Int Conf Healthc Inform 2016 (2016): 65-71.
Shortreed, Susan M.. Leveraging Electronic Medical Records to Better Target Suicide Prevention., 2016.
Chang, Jinyuan, Cheng Yong Tang, and Yichao Wu. "LOCAL INDEPENDENCE FEATURE SCREENING FOR NONPARAMETRIC AND SEMIPARAMETRIC MODELS BY MARGINAL EMPIRICAL LIKELIHOOD." Ann Stat 44, no. 2 (2016): 515-539.

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