Publications

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He, Qianchuan, and Dan-Yu Lin. GWASelect: A variable selection method for genomewide association studies (C++).., 2011.
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.
Zhu, Ruoqing, Ying-Qi Zhao, Guanhua Chen, Shuangge Ma, and Hongyu Zhao. "Greedy outcome weighted tree learning of optimal personalized treatment rules." Biometrics 73, no. 2 (2017): 391-400.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R)., 2017.
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.
Todem, D, J Fine, and L Peng. "A global sensitivity test for evaluating statistical hypotheses with nonidentifiable models." Biometrics 66, no. 2 (2010): 558-66.
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.
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.
Diao, Guoqing. GHREG: Semiparametric general hazards rate model for right-censored data (C).., 2013.
Ha, Min Jin, and Shannon T. Holloway. GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R).. 1.0 ed., 2016.
Almirall, D, and Susan A. Murphy. Getting SMART about developing individualized sequences of health interventions., 2012.
Chi, Eric. Getting High-throughput Arrays in Order with Convex Biclustering., 2016.
Chua, Katherina C., Chenling Xiong, Carol Ho, Taisei Mushiroda, Chen Jiang, Flora Mulkey, Dongbing Lai, Bryan P. Schneider, Sara R. Rashkin, John S. Witte et al. "Genomewide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy." Clin Pharmacol Ther 108, no. 3 (2020): 625-634.
R Baldwin, Michael, Kouros Owzar, Hitoshi Zembutsu, Aparna Chhibber, Michiaki Kubo, Chen Jiang, Dorothy Watson, Rachel J. Eclov, Joel Mefford, Howard L. McLeod et al. "A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res 18, no. 18 (2012): 5099-109.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Yazdani, Azam, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael R. Kosorok, Gita Dangol, and Ahmad Samiei. "Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics." BMC Genomics 20, no. 1 (2019): 395.
Tzeng, Jung-Ying. A gene-trait similarity regression method for gene-level pharmacogenetics analysis., 2011.
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.
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.
Wojcik, Genevieve L., Mariaelisa Graff, Katherine K. Nishimura, Ran Tao, Jeffrey Haessler, Christopher R. Gignoux, Heather M. Highland, Yesha M. Patel, Elena P. Sorokin, Christy L. Avery et al. "Genetic analyses of diverse populations improves discovery for complex traits." Nature 570, no. 7762 (2019): 514-518.
Pang, Herbert. geneSelRSF: Gene selection using iterative recursive feature elimination (R).. 1.0 ed., 2012.
Cruz-Garcia, Lourdes, Grainne O'Brien, Botond Sipos, Simon Mayes, Michael I. Love, Daniel J. Turner, and Christophe Badie. "Generation of a Transcriptional Radiation Exposure Signature in Human Blood Using Long-Read Nanopore Sequencing." Radiat Res 193, no. 2 (2020): 143-154.
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.
Lin, Dan-Yu, Donglin Zeng, and David Couper. "A general framework for integrative analysis of incomplete multiomics data." Genet Epidemiol 44, no. 7 (2020): 646-664.
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.
He, Qianchuan, Christy L. Avery, and Dan-Yu Lin. "A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
Tzeng, Jung-Ying, Wenbin Lu, and Fang-Chi Hsu. "GENE-LEVEL PHARMACOGENETIC ANALYSIS ON SURVIVAL OUTCOMES USING GENE-TRAIT SIMILARITY REGRESSION." Ann Appl Stat 8, no. 2 (2014): 1232-1255.
Mathur, Ravi, Daniel Rotroff, Jun Ma, Ali Shojaie, and Alison Motsinger-Reif. "Gene set analysis methods: a systematic comparison." BioData Min 11 (2018): 8.
Pang, Herbert, Stephen L. George, Ken Hui, and Tiejun Tong. "Gene selection using iterative feature elimination random forests for survival outcomes." IEEE/ACM Trans Comput Biol Bioinform 9, no. 5 (2012): 1422-31.
Lewis, Paul O.. Galax (C++)., 2016.
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Lin, Ja-an, Hongtu Zhu, Ahn Mihye, Wei Sun, and Joseph G. Ibrahim. "Functional-mixed effects models for candidate genetic mapping in imaging genetic studies." Genet Epidemiol 38, no. 8 (2014): 680-91.
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.
Laber, Eric B., and Ana-Maria Staicu. "Functional feature construction for individualized treatment regimes." J Am Stat Assoc 113, no. 523 (2017): 1219-1227.
Crews, Hugh B., Dennis D. Boos, and Leonard A. Stefanski. "FSR Methods for Second-Order Regression Models." Comput Stat Data Anal 55, no. 6 (2011): 2026-2037.
Luo, S, R Song, M Styner, J H. Gilmore, and H Zhu. "FSEM: Functional Structural Equation Models for Twin Functional Data." J Am Stat Assoc 114, no. 525 (2019): 344-357.
Carpenter, William R., Anne-Marie Meyer, Amy P. Abernethy, Til Stürmer, and Michael R. Kosorok. "A framework for understanding cancer comparative effectiveness research data needs." J Clin Epidemiol 65, no. 11 (2012): 1150-8.
Bhattacharya, Arjun, Montserrat García-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, and Michael I. Love. "A framework for transcriptome-wide association studies in breast cancer in diverse study populations." Genome Biol 21, no. 1 (2020): 42.
Yuan, Ying, John H. Gilmore, Xiujuan Geng, Styner Martin, Kehui Chen, Jane-ling Wang, and Hongtu Zhu. "FMEM: functional mixed effects modeling for the analysis of longitudinal white matter Tract data." Neuroimage 84 (2014): 753-64.
Chen, Liddy M., Joseph G. Ibrahim, and Haitao Chu. "Flexible stopping boundaries when changing primary endpoints after unblinded interim analyses." J Biopharm Stat 24, no. 4 (2014): 817-33.
Lachos, Victor H., Larissa A. Matos, Luis M. Castro, and Ming-Hui Chen. "Flexible longitudinal linear mixed models for multiple censored responses data." Stat Med 38, no. 6 (2019): 1074-1102.
Kong, Dehan, Joseph G. Ibrahim, Eunjee Lee, and Hongtu Zhu. "FLCRM: Functional linear cox regression model." Biometrics 74, no. 1 (2018): 109-117.
Ibrahim, Joseph G., Ming-Hui Chen, Amy H Xia, and Thomas Liu. Fixed: Bayesian meta-experimental design (SAS).., 2012.
Ibrahim, Joseph G., Hongtu Zhu, Ramon I. Garcia, and Ruixin Guo. Fixed and random effects selection in mixed effects toolkit (R).., 2011.
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.
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.
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.
Li, Zhiguo. Fitting Cox models with doubly censored data using spline-based marginal likelihood., 2011.
Psioda, Matthew, and Joseph G. Ibrahim. fitRE: Bayesian superiority design for gamma frailty recurrent events model (SAS).., 2016.
Jiang, Yu, Yujun Han, Slavé Petrovski, Kouros Owzar, David B. Goldstein, and Andrew S. Allen. fitDNM: Test of de novo enrichment that incorporates functional information (R).. 1.0 ed., 2015.
Dasgupta, Sayan, Yair Goldberg, and Michael R. Kosorok. "FEATURE ELIMINATION IN KERNEL MACHINES IN MODERATELY HIGH DIMENSIONS." Ann Stat 47, no. 1 (2019): 497-526.
Marceau, Rachel, Wenbin Lu, Michèle M. Sale, Bradford B. Worrall, Stephen R. Williams, Fang-Chi Hsu, Jung-Ying Tzeng, and Shannon T. Holloway. FastKM: A fast multiple-kernel method based on a low-rank approximation (R).. 1.0 ed., 2015.
Lin, Jiaxing, Alexander Sibley, Ivo D. Shterev, and Kouros Owzar. fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies (R). 1.0.4 ed., 2017.
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.
Madar, V. Faster algorithm to control the Benjamini-Hochberg false discovery rate and its application for analysis of huge genomic data.., 2014.
Marceau, Rachel, Wenbin Lu, Shannon Holloway, Michèle M. Sale, Bradford B. Worrall, Stephen R. Williams, Fang-Chi Hsu, and Jung-Ying Tzeng. "A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction." Genet Epidemiol 39, no. 6 (2015): 456-68.
Chang, S-M, J-Y Tzeng, and R-B Chen. "Fast Bayesian Variable Screenings for Binary Response Regressions with Small Sample Size." J Stat Comput Simul 87, no. 14 (2017): 2708-2723.
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.
Ghosh, Lipika, Jiancheng Jiang, Yanqing Sun, and Haibo Zhou. "Failure time regression with continuous informative auxiliary covariates." J Stat Distrib Appl 2 (2015): 2.
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.
Post, Justin B., and Howard D. Bondell. "Factor selection and structural identification in the interaction ANOVA model." Biometrics 69, no. 1 (2013): 70-9.
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.
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Goldberg, Y, and M R. Kosorok. "An Exponential Bound for Cox Regression." Stat Probab Lett 82, no. 7 (2012): 1267-1272.
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.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. "An Expectation Maximization algorithm for fitting the generalized odds-rate model to interval censored data." Stat Med 36, no. 7 (2017): 1157-1171.
Wang, L. Evaluation of Viable Dynamic Treatment Regimes in a Sequentially Randomized Trial of Advanced Prostate Cancer., 2014.
Cao, Guanqun, David Todem, Lijian Yang, and Jason P. Fine. "Evaluating Statistical Hypotheses Using Weakly-Identifiable Estimating Functions." Scand Stat Theory Appl 40, no. 2 (2013): 256-273.
Laber, Eric B., and Min Qian. "Evaluating personalized treatment regimes." In Methods in Comparative Effectiveness Research. New York: Chapman and Hall/CRC, 2017.
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.
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.
Tamura, Roy N., Xiaohong Huang, and Dennis D. Boos. "Estimation of treatment effect for the sequential parallel design." Stat Med 30, no. 30 (2011): 3496-506.
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.
Jiang, Runchao, Wenbin Lu, Rui Song, and Marie Davidian. "On Estimation of Optimal Treatment Regimes For Maximizing -Year Survival Probability." J R Stat Soc Series B Stat Methodol 79, no. 4 (2017): 1165-1185.
Zhao, Yingqi. Estimation of Optimal Dynamic Treatment Regimes., 2014.
Zhao, Ying-Qi, and Eric B. Laber. "Estimation of optimal dynamic treatment regimes." Clin Trials 11, no. 4 (2014): 400-407.
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.
Wang, Xiaofei, Junling Ma, Stephen George, and Haibo Zhou. "Estimation of AUC or Partial AUC under Test-Result-Dependent Sampling." Stat Biopharm Res 4, no. 4 (2012): 313-323.
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.
Milanzi, Elasma, Geert Molenberghs, Ariel Alonso, Michael G. Kenward, Anastasios A. Tsiatis, Marie Davidian, and Geert Verbeke. "Estimation After a Group Sequential Trial." Stat Biosci 7, no. 2 (2015): 187-205.
Zeng, Donglin, Qingxia Chen, Ming-Hui Chen, and Joseph G. Ibrahim. "Estimating treatment effects with treatment switching via semicompeting risks models: an application to a colorectal cancer study." Biometrika 99, no. 1 (2012): 167-184.
Zeng, Donglin. Estimating treatment effects with treatment switching via semi-competing risks models: An application to a colorectal cancer study., 2011.
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.
Chen, Qingxia, Donglin Zeng, Joseph G. Ibrahim, Mouna Akacha, and Heinz Schmidli. "Estimating time-varying effects for overdispersed recurrent events data with treatment switching." Biometrika 100, no. 2 (2013): 339-354.
Joshi, Neha, Jason Fine, Rong Chu, and Anastasia Ivanova. "Estimating the subgroup and testing for treatment effect in a post-hoc analysis of a clinical trial with a biomarker." J Biopharm Stat 29, no. 4 (2019): 685-695.
Liu, Ying, Yuanjia Wang, Chaorui Huang, and Donglin Zeng. "Estimating personalized diagnostic rules depending on individualized characteristics." Stat Med 36, no. 7 (2017): 1099-1117.
Zhang, Baqun, Anastasios A. Tsiatis, Marie Davidian, Min Zhang, and Eric Laber. "Estimating Optimal Treatment Regimes from a Classification Perspective." Stat 1, no. 1 (2012): 103-114.
Zhao, Yingqi. Estimating Individualized Treatment Rules Using Outcome Weighted Learning., 2011.
Zhao, Yingqi, Donglin Zeng, John A Rush, and Michael R. Kosorok. "Estimating Individualized Treatment Rules Using Outcome Weighted Learning." J Am Stat Assoc 107, no. 449 (2012): 1106-1118.
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.
Nguyen, Crystal T., Daniel J. Luckett, Anna R. Kahkoska, Grace E. Shearrer, Donna Spruijt-Metz, Jaimie N. Davis, and Michael R. Kosorok. "Estimating individualized treatment regimes from crossover designs." Biometrics 76, no. 3 (2020): 778-788.
Ding, Jieli, Haibo Zhou, Yanyan Liu, Jianwen Cai, and Matthew P. Longnecker. "Estimating effect of environmental contaminants on women's subfecundity for the MoBa study data with an outcome-dependent sampling scheme." Biostatistics 15, no. 4 (2014): 636-50.
Luckett, Daniel J., Eric B. Laber, Anna R. Kahkoska, David M. Maahs, Elizabeth Mayer-Davis, and Michael R. Kosorok. "Estimating Dynamic Treatment Regimes in Mobile Health Using V-learning." J Am Stat Assoc 115, no. 530 (2020): 692-706.
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.
Zhang, Aijing, Jung-Ying Tzeng, and Shein-Chung Chow. "Establishment of reference standards in biosimilar studies." GaBI J 2, no. 4 (2013): 173-177.
Xia, Kai, Yang Yu, Mihye Ahn, Hongtu Zhu, Fei Zou, John H. Gilmore, and Rebecca C. Knickmeyer. "Environmental and genetic contributors to salivary testosterone levels in infants." Front Endocrinol (Lausanne) 5 (2014): 187.
Jiang, Binyan, Rui Song, Jialiang Li, and Donglin Zeng. "Entropy Learning for Dynamic Treatment Regimes." Stat Sin 29, no. 4 (2019): 1633-1655.
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.
Song, Guochen, and Anastasia Ivanova. "Enrollment and Stopping Rules for Managing Toxicity Requiring Long Follow-Up in Phase II Oncology Trials." J Biopharm Stat 25, no. 6 (2015): 1206-14.
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.
Wang, Xiaofei, Jianwen Cai, and Stephen L. George. Enriched biomarker-driven clinical trials. In Wiley StatsRef: Statistics Reference Online. Wiley, 2019.
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.

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