Publications

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Journal Article
Yu, Jichang, Haibo Zhou, and Jianwen Cai. "Accelerated failure time model for data from outcome-dependent sampling." Lifetime Data Anal 27, no. 1 (2021): 15-37.
Ruppert, A S., J Yin, M Davidian, A A. Tsiatis, J C. Byrd, J A. Woyach, and S J. Mandrekar. "Application of a sequential multiple assignment randomized trial (SMART) design in older patients with chronic lymphocytic leukemia." Ann Oncol 30, no. 4 (2019): 542-550.
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.
Zhao, Junlong, Guan Yu, and Yufeng Liu. "ASSESSING ROBUSTNESS OF CLASSIFICATION USING ANGULAR BREAKDOWN POINT." Ann Stat 46, no. 6B (2018): 3362-3389.
Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
Chen, Ming-Hui, Joseph G. Ibrahim, Peter Lam, Alan Yu, and Yuanye Zhang. "Bayesian design of noninferiority trials for medical devices using historical data." Biometrics 67, no. 3 (2011): 1163-70.
Chow, Sy-Miin, Niansheng Tang, Ying Yuan, Xinyuan Song, and Hongtu Zhu. "Bayesian estimation of semiparametric nonlinear dynamic factor analysis models using the Dirichlet process prior." Br J Math Stat Psychol 64, no. Pt 1 (2011): 69-106.
Yao, Hui, Sungduk Kim, Ming-Hui Chen, Joseph G. Ibrahim, Arvind K. Shah, and Jianxin Lin. "Bayesian Inference for Multivariate Meta-regression with a Partially Observed Within-Study Sample Covariance Matrix." J Am Stat Assoc 110, no. 510 (2015): 528-544.
Yang, Hou-Cheng, Guanyu Hu, and Ming-Hui Chen. "Bayesian Variable Selection for Pareto Regression Models with Latent Multivariate Log Gamma Process with Applications to Earthquake Magnitudes." Geosciences (Basel) 9, no. 4 (2019).
Yang, Shu, and Peng Ding. "Combining Multiple Observational Data Sources to Estimate Causal Effects." J Am Stat Assoc 115, no. 531 (2020): 1540-1554.
Yu, Fang, Ming-Hui Chen, Lynn Kuo, Heather Talbott, and John S. Davis. "Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications." BMC Bioinformatics 16 (2015): 245.
Yimit, Askar, Ogun Adebali, Aziz Sancar, and Yuchao Jiang. "Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs." Nat Commun 10, no. 1 (2019): 309.
Yang, Shu, Jae Kwang Kim, and Rui Song. "Doubly robust inference when combining probability and non-probability samples with high dimensional data." J R Stat Soc Series B Stat Methodol 82, no. 2 (2020): 445-465.
Zhao, Y Q., D Zeng, E B. Laber, R Song, M Yuan, and M R. Kosorok. "Doubly Robust Learning for Estimating Individualized Treatment with Censored Data." Biometrika 102, no. 1 (2015): 151-168.
Yao, F, E Lei, and Y Wu. "Effective dimension reduction for sparse functional data." Biometrika 102, no. 2 (2015): 421-437.
Diao, Guoqing, Donglin Zeng, and Song Yang. "Efficient semiparametric estimation of short-term and long-term hazard ratios with right-censored data." Biometrics 69, no. 4 (2013): 840-9.
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.
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.
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.
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.
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.
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.
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.
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.
Gao, Hao, Chris R. Kelsey, John Boyle, Tianyi Xie, Suzanne Catalano, Xiaofei Wang, and Fang-Fang Yin. "Impact of Esophageal Motion on Dosimetry and Toxicity With Thoracic Radiation Therapy." Technol Cancer Res Treat 18 (2019): 1533033819849073.
Yan, Ying, Haibo Zhou, and Jianwen Cai. "Improving efficiency of parameter estimation in case-cohort studies with multivariate failure time data." Biometrics 73, no. 3 (2017): 1042-1052.
Yuan, Ying, Hongtu Zhu, Weili Lin, and J S. Marron. "Local Polynomial Regression for Symmetric Positive Definite Matrices." J R Stat Soc Series B Stat Methodol 74, no. 4 (2012): 697-719.
Huang, Jianguo, Mohit Sachdeva, Eric Xu, Timothy J. Robinson, Lixia Luo, Yan Ma, Nerissa T. Williams, Omar Lopez, Lisa D. Cervia, Fan Yuan et al. "The Long Noncoding RNA Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways." Mol Cancer Res 18, no. 10 (2020): 1534-1544.
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.
Liu, Yanyan, Zhongshang Yuan, Jianwen Cai, and Haibo Zhou. "Marginal hazard regression for correlated failure time data with auxiliary covariates." Lifetime Data Anal 18, no. 1 (2012): 116-38.
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.
Rashid, Naim U., Quefeng Li, Jen Jen Yeh, and Joseph G. Ibrahim. "Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction." J Am Stat Assoc 115, no. 531 (2020): 1125-1138.
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.
Bompard, Lucile, Shun Xu, Martin Styner, Beatriz Paniagua, Mihye Ahn, Ying Yuan, Valerie Jewells, Wei Gao, Dinggang Shen, Hongtu Zhu et al. "Multivariate longitudinal shape analysis of human lateral ventricles during the first twenty-four months of life." PLoS One 9, no. 9 (2014): e108306.
Appell, Malin L., Jonathan Berg, John Duley, William E. Evans, Martin A. Kennedy, Lynne Lennard, Tony Marinaki, Howard L. McLeod, Mary V. Relling, Elke Schaeffeler et al. "Nomenclature for alleles of the thiopurine methyltransferase gene." Pharmacogenet Genomics 23, no. 4 (2013): 242-8.
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.
Schifano, Elizabeth D., Jing Wu, Chun Wang, Jun Yan, and Ming-Hui Chen. "Online Updating of Statistical Inference in the Big Data Setting." Technometrics 58, no. 3 (2016): 393-403.
Wang, Wenjie, Ming-Hui Chen, Sy Han Chiou, Hui-Chuan Lai, Xiaojing Wang, Jun Yan, and Zhumin Zhang. "Onset of persistent pseudomonas aeruginosa infection in children with cystic fibrosis with interval censored data." BMC Med Res Methodol 16, no. 1 (2016): 122.
Yu, Jichang, Yanyan Liu, Jianwen Cai, Dale P. Sandler, and Haibo Zhou. "Outcome-Dependent Sampling Design and Inference for Cox's Proportional Hazards Model." J Stat Plan Inference 178 (2016): 24-36.
Anderson, Gray R., Suzanne E. Wardell, Merve Cakir, Lorin Crawford, Jim C. Leeds, Daniel P. Nussbaum, Pallavi S. Shankar, Ryan S. Soderquist, Elizabeth M. Stein, Jennifer P. Tingley et al. "PIK3CA mutations enable targeting of a breast tumor dependency through mTOR-mediated MCL-1 translation." Sci Transl Med 8, no. 369 (2016): 369ra175.
Jung, Sin-Ho, and Stanley S Young. "Power and sample size calculation for microarray studies." J Biopharm Stat 22, no. 1 (2012): 30-42.
Rashid, Naim U., Xianlu L. Peng, Chong Jin, Richard A. Moffitt, Keith E. Volmar, Brian A. Belt, Roheena Z. Panni, Timothy M. Nywening, Silvia G. Herrera, Kristin J. Moore et al. "Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer." Clin Cancer Res 26, no. 1 (2020): 82-92.
Yan, Kang K., Xiaofei Wang, Wendy W. T. Lam, Varut Vardhanabhuti, Anne W. M. Lee, and Herbert H. Pang. "Radiomics analysis using stability selection supervised component analysis for right-censored survival data." Comput Biol Med 124 (2020): 103959.
Yao, Xiaoxin I., Xiaofei Wang, Paul J. Speicher, Shelley E Hwang, Perry Cheng, David H. Harpole, Mark F. Berry, Deborah Schrag, and Herbert H. Pang. "Reporting and Guidelines in Propensity Score Analysis: A Systematic Review of Cancer and Cancer Surgical Studies." J Natl Cancer Inst 109, no. 8 (2017).
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.
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.
Yuan, Jiacheng, Herbert Pang, Tiejun Tong, Dong Xi, Wenzhao Guo, and Peter Mesenbrink. "Seamless Phase IIa/IIb and enhanced dose-finding adaptive design." J Biopharm Stat 26, no. 5 (2016): 912-23.
Yang, S, K Pieper, and F Cools. "Semiparametric estimation of structural failure time models in continuous-time processes." Biometrika 107, no. 1 (2020): 123-136.
Zhang, Hong, Donglin Zeng, Sylviane Olschwang, and Kai Yu. "Semiparametric inference on the penetrances of rare genetic mutations based on a case-family design." J Stat Plan Inference 143, no. 2 (2013): 368-377.
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.
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.
Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar. "SNPpy--database management for SNP data from genome wide association studies." PLoS One 6, no. 10 (2011): e24982.
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.
Rao, Shangbang, Joseph G. Ibrahim, Jian Cheng, Pew-Thian Yap, and Hongtu Zhu. "SR-HARDI: Spatially Regularizing High Angular Resolution Diffusion Imaging." J Comput Graph Stat 25, no. 4 (2016): 1195-1211.
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.
Wang, Chun, Ming-Hui Chen, Elizabeth Schifano, Jing Wu, and Jun Yan. "Statistical methods and computing for big data." Stat Interface 9, no. 4 (2016): 399-414.
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.
Kass, Robert E., Brian S. Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu, and Nancy Reid. "Ten Simple Rules for Effective Statistical Practice." PLoS Comput Biol 12, no. 6 (2016): e1004961.
Yuan, Shuai, Hao Helen Zhang, and Marie Davidian. "Variable selection for covariate-adjusted semiparametric inference in randomized clinical trials." Stat Med 31, no. 29 (2012): 3789-804.
Yuan, Ying, Hongtu Zhu, Martin Styner, John H. Gilmore, and J S. Marron. "VARYING COEFFICIENT MODEL FOR MODELING DIFFUSION TENSORS ALONG WHITE MATTER TRACTS." Ann Appl Stat 7, no. 1 (2013): 102-125.
Song, Rui, Feng Yi, and Hui Zou. "On Varying-coefficient Independence Screening for High-dimensional Varying-coefficient Models." Stat Sin 24, no. 4 (2014): 1735-1752.
Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
Software
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.
Jung, Sin-Ho, and Stanley S Young. Power and sample size calculation for microarray studies (Fortran).., 2012.
Yi, Chanhee, Alexander Sibley, and Kouros Owzar. RSNPset: Genome-wide SNP set analysis on the basis of efficient scores (R).. v0.2 ed., 2014.
Yi, Chanhee, Alexander Sibley, and Kouros Owzar. snplist: Tools to create gene sets (R).. 0.12 ed., 2013.
Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar. SNPpy: Database management for SNP data from genome wide association studies.., 2011.
Jung, Sin-Ho, and Stanley S Young. survSNP: Power and sample size calculations for SNP association studies with censored time-to-event outcomes (R).., 2012.