Publications

2019
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.
Xiao, W, H H. Zhang, and W Lu. "Robust regression for optimal individualized treatment rules." Stat Med 38, no. 11 (2019): 2059-2073.
Wong, Kin Yau, Donglin Zeng, and D Y. Lin. "Robust Score Tests With Missing Data in Genomics Studies." J Am Stat Assoc 114, no. 528 (2019): 1778-1786.
Yang, Yuchen, Ruth Huh, Houston W. Culpepper, Yuan Lin, Michael I. Love, and Yun Li. "SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data." Bioinformatics 35, no. 8 (2019): 1269-1277.
Gao, Fei, Donglin Zeng, David Couper, and D Y. Lin. "Semiparametric Regression Analysis of Multiple Right- and Interval-Censored Events." J Am Stat Assoc 114, no. 527 (2019): 1232-1240.
Wu, Yuan, Christina D. Chambers, and Ronghui Xu. "Semiparametric sieve maximum likelihood estimation under cure model with partly interval censored and left truncated data for application to spontaneous abortion." Lifetime Data Anal 25, no. 3 (2019): 507-528.
Lin, Dan-Yu. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
Yang, Yanyan, Jinchuan Hu, Christopher P. Selby, Wentao Li, Askar Yimit, Yuchao Jiang, and Aziz Sancar. "Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J Biol Chem 294, no. 1 (2019): 210-217.
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.
Shi, Chengchun, Rui Song, and Wenbin Lu. "ON TESTING CONDITIONAL QUALITATIVE TREATMENT EFFECTS." Ann Stat 47, no. 4 (2019): 2348-2377.
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.
Olby, Natasha J., Ji-Hey Lim, Nikki Wagner, Natalia Zidan, Peter J. Early, Christopher L. Mariani, Karen R. Muñana, and Eric Laber. "Time course and prognostic value of serum GFAP, pNFH, and S100β concentrations in dogs with complete spinal cord injury because of intervertebral disc extrusion." J Vet Intern Med 33, no. 2 (2019): 726-734.
Schild, Steven E., Wen Fan, Thomas E. Stinchcombe, Everett E. Vokes, Suresh S. Ramalingam, Jeffrey D. Bradley, Karen Kelly, Herbert H. Pang, and Xiaofei Wang. "Toxicity Related to Radiotherapy Dose and Targeting Strategy: A Pooled Analysis of Cooperative Group Trials of Combined Modality Therapy for Locally Advanced Non-Small Cell Lung Cancer." J Thorac Oncol 14, no. 2 (2019): 298-303.
Zhou, Jie, Jiajia Zhang, Alexander C. Mclain, Wenbin Lu, Xuemei Sui, and James W. Hardin. "A varying-coefficient generalized odds rate model with time-varying exposure: An application to fitness and cardiovascular disease mortality." Biometrics 75, no. 3 (2019): 853-863.
Bellach, Anna, Michael R. Kosorok, Ludger Rüschendorf, and Jason P. Fine. "Weighted NPMLE for the Subdistribution of a Competing Risk." J Am Stat Assoc 114, no. 525 (2019): 259-270.
2018
Fu, Sheng, Sanguo Zhang, and Yufeng Liu. "Adaptively weighted large-margin angle-based classifiers." J Multivar Anal 166 (2018): 282-299.
Wang, Ting. AEBSD: Sample size of AEBSD and Comparison with BSD (R)., 2018.
Burbank, Allison J., Krista Todoric, Pamela Steele, Jonathan Rosen, Haibo Zhou, Marcia Frye, Ceila E. Loughlin, Sally Ivins, Katherine Mills, Lauren Dembnicki Massey et al. "Age and African-American race impact the validity and reliability of the asthma control test in persistent asthmatics." Respir Res 19, no. 1 (2018): 152.
Kim, Soyoung, Donglin Zeng, and Jianwen Cai. "Analysis of multiple survival events in generalized case-cohort designs." Biometrics 74, no. 4 (2018): 1250-1260.
Zhu, Anqi, Joseph G. Ibrahim, and Michael I. Love. apeglm: Approximate posterior estimation for GLM coefficients (R)., 2018.
Wu, Jing, Mário DE Castro, Elizabeth D. Schifano, and Ming-Hui Chen. "Assessing covariate effects using Jeffreys-type prior in the Cox model in the presence of a monotone partial likelihood." J Stat Theory Pract 12, no. 1 (2018): 23-41.
Zhao, Junlong, Guan Yu, and Yufeng Liu. "ASSESSING ROBUSTNESS OF CLASSIFICATION USING ANGULAR BREAKDOWN POINT." Ann Stat 46, no. 6B (2018): 3362-3389.
Liu, Yang, Qianchuan He, and Wei Sun. "Association analysis using somatic mutations." PLoS Genet 14, no. 11 (2018): e1007746.
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Liu, Ying, Yuanjia Wang, Michael R. Kosorok, Yingqi Zhao, and Donglin Zeng. "Augmented outcome-weighted learning for estimating optimal dynamic treatment regimens." Stat Med 37, no. 26 (2018): 3776-3788.
Wang, Ting, Xiaofei Wang, Haibo Zhou, Jianwen Cai, and Stephen L. George. "Auxiliary variable-enriched biomarker-stratified design." Stat Med 37, no. 30 (2018): 4610-4635.
Eggleston, Barry S., Doug Wilson, Becky McNeil, Joseph G. Ibrahim, and Diane Catellier. BayesCTDesign: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data (R)., 2018.
Psioda, Matthew A., and Joseph G. Ibrahim. "Bayesian design of a survival trial with a cured fraction using historical data." Stat Med 37, no. 26 (2018): 3814-3831.
Li, Wenqing, Ming-Hui Chen, Xiaojing Wangy, and Dipak K. Dey. "Bayesian Design of Non-Inferiority Clinical Trials via the Bayes Factor." Stat Biosci 10, no. 2 (2018): 439-459.
Wu, Jing, Joseph G. Ibrahim, Ming-Hui Chen, Elizabeth D. Schifano, and Jeffrey D. Fisher. "Bayesian Modeling and Inference for Nonignorably Missing Longitudinal Binary Response Data with Applications to HIV Prevention Trials." Stat Sin 28 (2018): 1929-1963.
Lin, Jiaxing, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S. Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan et al. "bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics 34, no. 20 (2018): 3581-3583.
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.
Diao, Guoqing, Jun Dong, Donglin Zeng, and Joseph G. Ibrahim. BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++)., 2018.
Wei, Susan, and Michael R. Kosorok. "The Change-Plane Cox Model." Biometrika 105, no. 4 (2018): 891-903.
Jiang, Yuchao, and Nancy R. Zhang. CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R)., 2018.
Jiang, Yuchao, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson, and Nancy R. Zhang. "CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing." Genome Biol 19, no. 1 (2018): 202.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. "Computationally Efficient Estimation for the Generalized Odds Rate Mixture Cure Model with Interval-Censored Data." J Comput Graph Stat 27, no. 1 (2018): 48-58.
Liang, Shuhan, Wenbin Lu, and Rui Song. "Deep advantage learning for optimal dynamic treatment regime." Stat Theory Relat Fields 2, no. 1 (2018): 80-88.
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.
Lawson, Michael T., Hunyong Cho, Arkopal Choudhury, Yifan Cui, Xiaotong Jiang, Teeranan Pokaprakarn, and Michael R. Kosorok. "Discussion of Laber et al. "Optimal treatment allocations in space and time for on-line control of an emerging infectious disease"." J R Stat Soc Ser C Appl Stat 67, no. 4 (2018): 779-780.
Lin, D Y.. "Discussion of the Paper by R. L. Prentice and Y. Huang - Optimal Designs and Efficient Inference for Biomarker Studies." Stat Theory Relat Fields 2, no. 1 (2018): 21-22.
Chen, Jingxiang, Chong Zhang, Michael R. Kosorok, and Yufeng Liu. "Double Sparsity Kernel Learning with Automatic Variable Selection and Data Extraction." Stat Interface 11, no. 3 (2018): 401-420.
Liu, Ying, Yuanjia Wang, and Donglin Zeng. DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R). 1.3 ed., 2018.
Wong, Kin Yau, Donglin Zeng, and D Y. Lin. "Efficient Estimation for Semiparametric Structural Equation Models With Censored Data." J Am Stat Assoc 113, no. 522 (2018): 893-905.
Gong, Siliang, Kai Zhang, and Yufeng Liu. "Efficient test-based variable selection for high-dimensional linear models." J Multivar Anal 166 (2018): 17-31.
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.
Chen, Jingxiang, Haoda Fu, Xuanyao He, Michael R. Kosorok, and Yufeng Liu. "Estimating individualized treatment rules for ordinal treatments." Biometrics 74, no. 3 (2018): 924-933.
Gao, Fei, Donglin Zeng, Helen Wei, Xuena Wang, and Joseph G. Ibrahim. "Estimating Treatment Effects for Recurrent Events in the Presence of Rescue Medications: An Application to the Immune Thrombocytopenia Study." Stat Biosci 10, no. 2 (2018): 473-489.
Kang, Suhyun, Wenbin Lu, and Jiajia Zhang. "ON ESTIMATION OF THE OPTIMAL TREATMENT REGIME WITH THE ADDITIVE HAZARDS MODEL." Stat Sin 28, no. 3 (2018): 1539-1560.
Sibley, Alexander, Zhiguo Li, Yu Jiang, Yi-Ju Li, Cliburn Chan, Andrew Allen, and Kouros Owzar. "Facilitating the Calculation of the Efficient Score Using Symbolic Computing." Am Stat 72, no. 2 (2018): 199-205.
Xie, Jichun, and Ruosha Li. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates." J R Stat Soc Series B Stat Methodol 80, no. 5 (2018): 1015-1034.
Kong, Dehan, Joseph G. Ibrahim, Eunjee Lee, and Hongtu Zhu. "FLCRM: Functional linear cox regression model." Biometrics 74, no. 1 (2018): 109-117.
Li, Tengfei, Fengchang Xie, Xiangnan Feng, Joseph G. Ibrahim, and Hongtu Zhu. "Functional Linear Regression Models for Nonignorable Missing Scalar Responses." Stat Sin 28, no. 4 (2018): 1867-1886.
Mathur, Ravi, Daniel Rotroff, Jun Ma, Ali Shojaie, and Alison Motsinger-Reif. "Gene set analysis methods: a systematic comparison." BioData Min 11 (2018): 8.
Innocenti, Federico, Chen Jiang, Alexander B. Sibley, Amy S. Etheridge, Ace J. Hatch, Stefanie Denning, Donna Niedzwiecki, Ivo D. Shterev, Jiaxing Lin, Yoichi Furukawa et al. "Genetic variation determines VEGF-A plasma levels in cancer patients." Sci Rep 8, no. 1 (2018): 16332.
Hidalgo, Sebastian J. Teran, Michael C. Wu, Stephanie M. Engel, and Michael R. Kosorok. "Goodness-Of-Fit Test for Nonparametric Regression Models: Smoothing Spline ANOVA Models as Example." Comput Stat Data Anal 122 (2018): 135-155.
Lin, Jiaxing, Alexander Sibley, Tracy Truong, Kouros Owzar, and Zhiguo Li. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed., 2018.
Shi, Chengchun, Alin Fan, Rui Song, and Wenbin Lu. "HIGH-DIMENSIONAL A-LEARNING FOR OPTIMAL DYNAMIC TREATMENT REGIMES." Ann Stat 46, no. 3 (2018): 925-957.
X Jeng, Jessie, Wenbin Lu, and Huimin Peng. "High-Dimensional Inference for Personalized Treatment Decision." Electron J Stat 12, no. 1 (2018): 2074-2089.
Laber, Eric B., Fan Wu, Catherine Munera, Ilya Lipkovich, Salvatore Colucci, and Steve Ripa. "Identifying optimal dosage regimes under safety constraints: An application to long term opioid treatment of chronic pain." Stat Med 37, no. 9 (2018): 1407-1418.
Butler, Emily L., Eric B. Laber, Sonia M. Davis, and Michael R. Kosorok. "Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics 74, no. 1 (2018): 18-26.
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.
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.
Lin, Jiaxing, Yuan Wu, Xiaofei F. Wang, and Kouros Owzar. intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R). 0.1.1 ed., 2018.
Urrutia, Eugene, Hao Chen, Zilu Zhou, Nancy R. Zhang, and Yuchao Jiang. "Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics 34, no. 12 (2018): 2126-2128.
Pietryk, Edward W., Kiristin Clement, Marwa Elnagheeb, Ryan Kuster, Kayla Kilpatrick, Michael I. Love, and Folami Y. Ideraabdullah. "Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol 78 (2018): 9-19.
Zhang, Yichi, Eric B. Laber, Marie Davidian, and Anastasios A. Tsiatis. "Interpretable Dynamic Treatment Regimes." J Am Stat Assoc 113, no. 524 (2018): 1541-1549.
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.
Hibbard, Jonathan C., Jonathan S. Friedstat, Sonia M. Thomas, Renee E. Edkins, Scott C Hultman, and Michael R. Kosorok. "LIBERTI: A SMART study in plastic surgery." Clin Trials 15, no. 3 (2018): 286-293.
Urrutia, Eugene, Hao Chen, Zilu Zhou, Nancy R. Zhang, and Yuchao Jiang. MARATHON: Integrates Multiple Related Statistical Software for Copy Number Profiling and Downstream Analyses (R)., 2018.
Shi, Chengchun, Wenbin Lu, and Rui Song. "A Massive Data Framework for M-Estimators with Cubic-Rate." J Am Stat Assoc 113, no. 524 (2018): 1698-1709.
Shi, Chengchun, Rui Song, Wenbin Lu, and Bo Fu. "Maximin Projection Learning for Optimal Treatment Decision with Heterogeneous Individualized Treatment Effects." J R Stat Soc Series B Stat Methodol 80, no. 4 (2018): 681-702.
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.
Isogai, Yoh, Zheng Wu, Michael I. Love, Michael Ho- Young Ahn, Dhananjay Bambah-Mukku, Vivian Hua, Karolina Farrell, and Catherine Dulac. "Multisensory Logic of Infant-Directed Aggression by Males." Cell 175, no. 7 (2018): 1827-1841.e17.
Wang, Yu-Bo, Ming-Hui Chen, Lynn Kuo, and Paul O. Lewis. "A New Monte Carlo Method for Estimating Marginal Likelihoods." Bayesian Anal 13, no. 2 (2018): 311-333.
Chen, G, Michael R. Kosorok, and X Zhou. Nonconvex Optimization. In Wiley StatsRef: Statistics Reference Online., 2018.
Van den Berge, Koen, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit, and Lieven Clement. "Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol 19, no. 1 (2018): 24.
Wang, Chun, Ming-Hui Chen, Jing Wu, Jun Yan, Yuping Zhang, and Elizabeth Schifano. "Online updating method with new variables for big data streams." Can J Stat 46, no. 1 (2018): 123-146.
Laber, Eric B., Nick J. Meyer, Brian J. Reich, Krishna Pacifici, Jaime A. Collazo, and John M. Drake. "Optimal treatment allocations in space and time for on-line control of an emerging infectious disease." J R Stat Soc Ser C Appl Stat 67, no. 4 (2018): 743-770.
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.
Zhou, Qingning, Jianwen Cai, and Haibo Zhou. "Outcome-dependent sampling with interval-censored failure time data." Biometrics 74, no. 1 (2018): 58-67.
Chung, Yunro, Anastasia Ivanova, Michael G. Hudgens, and Jason P. Fine. "Partial likelihood estimation of isotonic proportional hazards models." Biometrika 105, no. 1 (2018): 133-148.
Jung, Sin-Ho. "Phase II cancer clinical trials for biomarker-guided treatments." J Biopharm Stat 28, no. 2 (2018): 256-263.
Davenport, Clemontina A., Arnab Maity, Patrick F. Sullivan, and Jung-Ying Tzeng. "A Powerful Test for SNP Effects on Multivariate Binary Outcomes using Kernel Machine Regression." Stat Biosci 10, no. 1 (2018): 117-138.
Psioda, Matthew A., Mat Soukup, and Joseph G. Ibrahim. "A practical Bayesian adaptive design incorporating data from historical controls." Stat Med 37, no. 27 (2018): 4054-4070.
Naqa, Issam El, Michael R. Kosorok, Judy Jin, Michelle Mierzwa, and Randall K. Ten Haken. "Prospects and challenges for clinical decision support in the era of big data." JCO Clin Cancer Inform 2 (2018).
Laber, Eric B., E Rose, Marie Davidian, and Anastasios A. Tsiatis. Q-Learning. In Wiley StatsRef: Statistics Reference Online. Wiley, 2018.
Wang, Lan, Yu Zhou, Rui Song, and Ben Sherwood. "Quantile-Optimal Treatment Regimes." J Am Stat Assoc 113, no. 523 (2018): 1243-1254.
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.
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.
Ni, Ai, and Jianwen Cai. "A regularized variable selection procedure in additive hazards model with stratified case-cohort design." Lifetime Data Anal 24, no. 3 (2018): 443-463.
Kong, Dehan, Arnab Maity, Fang-Chi Hsu, and Jung-Ying Tzeng. "Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"." Biometrics 74, no. 2 (2018): 767-768.
Chen, Xiaolin, and Jianwen Cai. "Reweighted estimators for additive hazard model with censoring indicators missing at random." Lifetime Data Anal 24, no. 2 (2018): 224-249.
Zhang, Chong, Minh Pham, Sheng Fu, and Yufeng Liu. "Robust Multicategory Support Vector Machines using Difference Convex Algorithm." Math Program 169, no. 1 (2018): 277-305.
Liu, Yang, Wei Sun, and Qianchuan He. SAME: Somatic mutation Association test with Measurement Errors (R)., 2018.
Li, Zhiguo, Xiaofei Wang, Yuan Wu, and Kouros Owzar. "Sample size calculation for studies with grouped survival data." Stat Med 37, no. 27 (2018): 3904-3917.
Pan, Yinghao, Jianwen Cai, Matthew P. Longnecker, and Haibo Zhou. "Secondary outcome analysis for data from an outcome-dependent sampling design." Stat Med 37, no. 15 (2018): 2321-2337.
Zeng, Donglin, Noorie Hyun, and Jianwen Cai. "Semiparametric Additive Model for Estimating Risk Difference in Multicenter Studies." Biostat Epidemiol 2, no. 1 (2018): 84-98.
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.
Hao, Botao, Will Wei Sun, Yufeng Liu, and Guang Cheng. "Simultaneous Clustering and Estimation of Heterogeneous Graphical Models." J Mach Learn Res 18 (2018).

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