Publications

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C
Knickmeyer, Rebecca C., Jiaping Wang, Hongtu Zhu, Xiujuan Geng, Sandra Woolson, Robert M. Hamer, Thomas Konneker, Weili Lin, Martin Styner, and John H. Gilmore. "Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.
Goldberg, Yair, Rui Song, Donglin Zeng, and Michael R. Kosorok. "Comment on "Dynamic treatment regimes: technical challenges and applications"." Electron J Stat 8, no. 1 (2014): 1290-1300.
Goldberg, Yair, and Michael R. Kosorok. "Comment on "Adaptive Confidence Intervals for the Test Error in Classification"." J Am Stat Assoc 106, no. 495 (2011): 920-924.
Ivanova, A, K M. Anderson, Gary L. Rosner, and E Rubin. "Comment." Stat Biopharm Res 7, no. 4 (2015): 357-358.
Guan, Qian, Eric B. Laber, and Brian J. Reich. "Comment." J Am Stat Assoc 111, no. 515 (2016): 936-942.
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.
Yang, Shu, and Peng Ding. "Combining Multiple Observational Data Sources to Estimate Causal Effects." J Am Stat Assoc 115, no. 531 (2020): 1540-1554.
Lee, Mei-Hsien, Jung-Ying Tzeng, Su-Yun Huang, and Chuhsing Kate Hsiao. "Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies." BMC Genet 12 (2011): 48.
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.
Hu, Yi-Juan, Dan-Yu Lin, Wei Sun, and Donglin Zeng. CNVstat: Statistical association analysis of copy number variants (C).. 1.0 ed., 2012.
Rom, D. The Closure Principle Revisited., 2014.
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.
Sargent, Daniel J., and Stephen L. George. "Clinical trials data collection: when less is more." J Clin Oncol 28, no. 34 (2010): 5019-21.
Ganti, Apar Kishor, Xiaofei Wang, Thomas E. Stinchcombe, Yinpeng Wang, Jeffrey Bradley, Harvey J. Cohen, Karen Kelly, Rebecca Paulus, Suresh S. Ramalingam, Everett E. Vokes et al. "Clinical prognostic model for older patients with advanced non-small cell lung cancer." J Geriatr Oncol 10, no. 4 (2019): 555-559.
Gatsonis, C. Clinical Evaluation of Diagnostic Tests and Biomarkers in CER., 2012.
Mentz, Robert J., Phillip J. Schulte, Jerome L. Fleg, Mona Fiuzat, William E. Kraus, Ileana L. Piña, Steven J. Keteyian, Dalane W. Kitzman, David J. Whellan, Stephen J. Ellis et al. "Clinical characteristics, response to exercise training, and outcomes in patients with heart failure and chronic obstructive pulmonary disease: findings from Heart Failure and A Controlled Trial Investigating Outcomes of Exercise TraiNing (HF-ACTION)." Am Heart J 165, no. 2 (2013): 193-9.
Chen, Li, D Y. Lin, and Donglin Zeng. "Checking semiparametric transformation models with censored data." Biostatistics 13, no. 1 (2012): 18-31.
Huang, Ying, Eric B. Laber, and Holly Janes. "Characterizing expected benefits of biomarkers in treatment selection." Biostatistics 16, no. 2 (2015): 383-99.
Wei, Susan, and Michael R. Kosorok. "The Change-Plane Cox Model." Biometrika 105, no. 4 (2018): 891-903.
Fan, Ailin, Rui Song, and Wenbin Lu. "Change-Plane Analysis for Subgroup Detection and Sample Size Calculation." J Am Stat Assoc 112, no. 518 (2017): 769-778.
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.
Owzar, Kouros. Challenges in genome-wide association analysis of drug-induced toxicity data from clinical trials., 2012.
Song, Rui, Wenbin Lu, Shuangge Ma, and Jessie X Jeng. "Censored Rank Independence Screening for High-dimensional Survival Data." Biometrika 101, no. 4 (2014): 799-814.
Hamy, Anne-Sophie, Sandrine Tury, Xiaofei Wang, Junheng Gao, Jean-Yves Pierga, Sylvie Giacchetti, Etienne Brain, Barbara Pistilli, Michel Marty, Marc Espié et al. "Celecoxib With Neoadjuvant Chemotherapy for Breast Cancer Might Worsen Outcomes Differentially by COX-2 Expression and ER Status: Exploratory Analysis of the REMAGUS02 Trial." J Clin Oncol 37, no. 8 (2019): 624-635.
M Hodgson, Elizabeth, Andrew F. Olshan, Kari E. North, Charles L. Poole, Donglin Zeng, Chiu-Kit Tse, Tope O. Keku, Joseph Galanko, Robert Sandler, and Robert C. Millikan. "The case-only independence assumption: associations between genetic polymorphisms and smoking among controls in two population-based studies." Int J Mol Epidemiol Genet 3, no. 4 (2012): 333-60.
Zhou, Q, H Zhou, and J Cai. "Case-cohort studies with interval-censored failure time data." Biometrika 104, no. 1 (2017): 17-29.
Bondell, Howard D., and Shannon T. Holloway. CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R).. R 3.0 ed., 2013.
McLeod, Howard L.. "Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
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.
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Diao, Guoqing, Jun Dong, Donglin Zeng, and Joseph G. Ibrahim. BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++)., 2018.
Ibrahim, Joseph G., Yeongjin Gwon, and Ming-Hui Chen. BSMED: Bayesian survival meta-experimental design using historical data (SAS).. 1.0 ed., 2015.
Psioda, Matthew, and Joseph G. Ibrahim. BPower: Computes two versions of Bayesian power for normal models (SAS).., 2016.
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.
Chu, Haitao, Lei Nie, Yong Chen, Yi Huang, and Wei Sun. "Bivariate random effects models for meta-analysis of comparative studies with binary outcomes: methods for the absolute risk difference and relative risk." Stat Methods Med Res 21, no. 6 (2012): 621-33.
Chu, Haitao, Hongfei Guo, and Yijie Zhou. "Bivariate random effects meta-analysis of diagnostic studies using generalized linear mixed models." Med Decis Making 30, no. 4 (2010): 499-508.
Sargent, Daniel J.. Biomarker-based clinical trials., 2012.
Korn, E. Biomarker-adaptive clinical trial designs., 2011.
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.
Wang, Ting. Biomarker Stratified Design Enriched by Auxiliary Biomarker., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. binDesignPP: Bayesian sample size for non-inferiority randomized trials with binary data with power prior (SAS).., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. binDesign: Bayesian sample size for non-inferiority randomized trials with binary data (SAS).., 2016.
Huang, Hanwen, Yufeng Liu, and J S. Marron. "Bidirectional discrimination with application to data visualization." Biometrika 99, no. 4 (2012): 851-864.
Chen, Guanhua, Patrick F. Sullivan, and Michael R. Kosorok. "Biclustering with heterogeneous variance." Proc Natl Acad Sci U S A 110, no. 30 (2013): 12253-8.
Helgeson, Erika S., Qian Liu, Guanhua Chen, Michael R. Kosorok, and Eric Bair. "Biclustering via sparse clustering." Biometrics 76, no. 1 (2020): 348-358.
Wang, Xiaofei. Biased sampling and its applications in biomarker validation., 2011.
Lee, Eunjee, Hongtu Zhu, Dehan Kong, Yalin Wang, Kelly Sullivan Giovanello, and Joseph G. Ibrahim. "BFLCRM: A BAYESIAN FUNCTIONAL LINEAR COX REGRESSION MODEL FOR PREDICTING TIME TO CONVERSION TO ALZHEIMER'S DISEASE." Ann Appl Stat 9, no. 4 (2015): 2153-2178.
Psioda, Matthew, and Joseph G. Ibrahim. BetaBinPredProb: Compute predictive probabilities in Bayesian design for Phase IIA trials in a beta-binomial case (SAS).., 2016.
Chow, Shein-Chung. Benefits, Challenges and Obstacles of Adaptive Clinical Trial Designs., 2012.
bcSeq: Fast Sequence Alignment for High-Throughput shRNA and CRISPR Screens (R)., 2017.
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.
Ibrahim, Joseph G., and Matthew Psioda. BayesProp: Bayesian Clinical Trial Design for Regression Models Using Historical Data (SAS)., 2017.
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).
DE Castro, Mário, Ming-Hui Chen, Joseph G. Ibrahim, and John P. Klein. "Bayesian Transformation Models for Multivariate Survival Data." Scand Stat Theory Appl 41, no. 1 (2014): 187-199.
Miranda, Michelle F., Hongtu Zhu, and Joseph G. Ibrahim. "Bayesian spatial transformation models with applications in neuroimaging data." Biometrics 69, no. 4 (2013): 1074-83.
Chen, Ming-Hui, Joseph G. Ibrahim, Amy H Xia, Thomas Liu, and Violeta Hennessey. "Bayesian sequential meta-analysis design in evaluating cardiovascular risk in a new antidiabetic drug development program." Stat Med 33, no. 9 (2014): 1600-18.
Zhu, Hongtu, Joseph G. Ibrahim, and Niansheng Tang. "Bayesian Sensitivity Analysis of Statistical Models with Missing Data." Stat Sin 24, no. 2 (2014): 871-896.
Ibrahim, Joseph G., Ming-Hui Chen, Mani Lakshminarayanan, Guanghan F. Liu, and Joseph F. Heyse. "Bayesian probability of success for clinical trials using historical data." Stat Med 34, no. 2 (2015): 249-64.
DE Castro, Mário, Ming-Hui Chen, and Yuanye Zhang. "Bayesian path specific frailty models for multi-state survival data with applications." Biometrics 71, no. 3 (2015): 760-71.
Guan, Qian, Brian J. Reich, Eric B. Laber, and Dipankar Bandyopadhyay. "Bayesian Nonparametric Policy Search with Application to Periodontal Recall Intervals." J Am Stat Assoc 115, no. 531 (2020): 1066-1078.
Ibrahim, Joseph G., Sungduk Kim, Ming-Hui Chen, Arvind K. Shah, and Jianxin Lin. "Bayesian multivariate skew meta-regression models for individual patient data." Stat Methods Med Res 28, no. 10-11 (2019): 3415-3436.
DE Castro, Mário, Ming-Hui Chen, Yuanye Zhang, and Anthony V. D'Amico. "A Bayesian multi-risks survival (MRS) model in the presence of double censorings." Biometrics 76, no. 4 (2020): 1297-1309.
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.
Chen, Qingxia, Ming-Hui Chen, David Ohlssen, and Joseph G. Ibrahim. "Bayesian modeling and inference for clinical trials with partial retrieved data following dropout." Stat Med 32, no. 24 (2013): 4180-95.
Zhang, Danjie, Ming-Hui Chen, Joseph G. Ibrahim, Mark E. Boye, and Wei Shen. "Bayesian Model Assessment in Joint Modeling of Longitudinal and Survival Data with Applications to Cancer Clinical Trials." J Comput Graph Stat 26, no. 1 (2017): 121-133.
Ibrahim, Joseph G., Ming-Hui Chen, and Haitao Chu. "Bayesian methods in clinical trials: a Bayesian analysis of ECOG trials E1684 and E1690." BMC Med Res Methodol 12 (2012): 183.
Ibrahim, Joseph G., Ming-Hui Chen, Amy H Xia, Thomas Liu, and V Henessey. "Bayesian meta-experimental design for evaluating cardiovascular risk." In Quantitative Evaluation if Safety in Drug Development: Design, Analysis and Reporting, 13-38. Boca Raton: Chapman & Hall / CRC Press, 2014.
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.
Lu, Zhao-Hua, Zakaria Khondker, Joseph G. Ibrahim, Yue Wang, and Hongtu Zhu. "Bayesian longitudinal low-rank regression models for imaging genetic data from longitudinal studies." Neuroimage 149 (2017): 305-322.
Guo, Ruixin, Hongtu Zhu, Sy-Miin Chow, and Joseph G. Ibrahim. Bayesian Lasso for semiparametric structural equation models toolkit (C++).., 2011.
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.
Zhu, Hongtu, Joseph G. Ibrahim, Yueh-Yun Chi, and Niansheng Tang. "Bayesian influence measures for joint models for longitudinal and survival data." Biometrics 68, no. 3 (2012): 954-64.
Zhu, Hongtu, Joseph G. Ibrahim, and Niansheng Tang. "Bayesian influence analysis: a geometric approach." Biometrika 98, no. 2 (2011): 307-323.
Chen, Yong, Sheng Luo, Haitao Chu, and Peng Wei. "Bayesian inference on risk differences: an application to multivariate meta-analysis of adverse events in clinical trials." Stat Biopharm Res 5, no. 2 (2013): 142-155.
Sinha, Arijit, Zhiyi Chi, and Ming-Hui Chen. "BAYESIAN INFERENCE OF HIDDEN GAMMA WEAR PROCESS MODEL FOR SURVIVAL DATA WITH TIES." Stat Sin 25, no. 4 (2015): 1613-1635.
Li, Hao, Ming-Hui Chen, Joseph G. Ibrahim, Sungduk Kim, Arvind K. Shah, Jianxin Lin, and Andrew M. Tershakovec. "Bayesian inference for network meta-regression using multivariate random effects with applications to cholesterol lowering drugs." Biostatistics 20, no. 3 (2019): 499-516.
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.
Kim, Sungduk, Ming-Hui Chen, Joseph G. Ibrahim, Arvind K. Shah, and Jianxin Lin. "Bayesian inference for multivariate meta-analysis Box-Cox transformation models for individual patient data with applications to evaluation of cholesterol-lowering drugs." Stat Med 32, no. 23 (2013): 3972-90.
Zhu, Hongtu, Zakaria Khondker, Zhaohua Lu, and Joseph G. Ibrahim. "Bayesian Generalized Low Rank Regression Models for Neuroimaging Phenotypes and Genetic Markers." J Am Stat Assoc 109, no. 507 (2014): 997-990.
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.
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.
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.
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.
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.
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.
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.
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.
Eggleston, Barry S., Joseph G. Ibrahim, and Diane Catellier. "Bayesian clinical trial design using Markov models with applications to autoimmune disease." Contemp Clin Trials 63 (2017): 73-83.
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.
Zhu, Hongtu, Joseph G. Ibrahim, and Qingxia Chen. "Bayesian Case-deletion Model Complexity and Information Criterion." Stat Interface 7, no. 4 (2014): 531-542.
Zhu, Hongtu, Joseph G. Ibrahim, Hyunsoon Cho, and Niansheng Tang. "Bayesian Case Influence Measures for Statistical Models with Missing Data." J Comput Graph Stat 21, no. 1 (2012): 253-271.
Chen, Yong, Haitao Chu, Sheng Luo, Lei Nie, and Sining Chen. "Bayesian analysis on meta-analysis of case-control studies accounting for within-study correlation." Stat Methods Med Res 24, no. 6 (2015): 836-55.
Leão, William L., Carlos A. Abanto-Valle, and Ming-Hui Chen. "Bayesian analysis of stochastic volatility-in-mean model with leverage and asymmetrically heavy-tailed error using generalized hyperbolic skew Student's t-distribution." Stat Interface 10 (2017): 529-541.
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.
Ibrahim, Joseph G., Haitao Chu, and Liddy M. Chen. "Basic concepts and methods for joint models of longitudinal and survival data." J Clin Oncol 28, no. 16 (2010): 2796-801.
Wahed, AS. Baseline Covariate Adjustment in SMART Studies via Artificial Randomization., 2014.

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