Publications

2018
Sun W, Bunn P, Jin C, et al. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res.. 2018;46(6):3009-3018.
Wang X, Zhou J, Wang T, George SL. "On Enrichment Strategies for Biomarker Stratified Clinical Trials." J Biopharm Stat. 2018;28(2):292-308.
Chen J, Fu H, He X, Kosorok MR, Liu Y. "Estimating individualized treatment rules for ordinal treatments." Biometrics. 2018.
Lin J, Sibley A, Truong T, Owzar K, Li Z. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed.; 2018.
Butler EL, Laber EB, Davis SM, Kosorok MR. "Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics. 2018;74(1):18-26.
Maity A, Zhao J, Sullivan PF, Tzeng J-Y. "Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet. Epidemiol.. 2018;42(1):64-79.
Lin J, Wu Y, Wang XF, Owzar K. intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R). 0.1.1 ed.; 2018.
Choi J, Zeng D, Olshan AF, Cai J. "Joint modeling of survival time and longitudinal outcomes with flexible random effects." Lifetime Data Anal. 2018;24(1):126-152.
Hibbard JC, Friedstat JS, Thomas SM, Edkins RE, C Hultman S, Kosorok MR. "LIBERTI: A SMART study in plastic surgery." Clin Trials. 2018:1740774518762435.
Yang S, Tsiatis AA, Blazing M. "Modeling survival distribution as a function of time to treatment discontinuation: A dynamic treatment regime approach." Biometrics. 2018.
Van den Berge K, Perraudeau F, Soneson C, et al. "Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol.. 2018;19(1):24.
Wang C, Chen M-H, Wu J, Yan J, Zhang Y, Schifano E. "Online updating method with new variables for big data streams." Can J Stat. 2018;46(1):123-146.
Zhou Q, Cai J, Zhou H. "Outcome-dependent sampling with interval-censored failure time data." Biometrics. 2018;74(1):58-67.
Jung S-H. "Phase II cancer clinical trials for biomarker-guided treatments." J Biopharm Stat. 2018;28(2):256-263.
Wang C, Tzeng J-Y, Wu P-Z, Preisig M, Hsiao CKate. "Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics. 2018;209(1):105-113.
Chen X, Cai J. "Reweighted estimators for additive hazard model with censoring indicators missing at random." Lifetime Data Anal. 2018;24(2):224-249.
Luo Y, Maity A, Wu MC, et al. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet. Epidemiol.. 2018;42(3):276-287.
2017
Leão WL, Abanto-Valle CA, Chen M-H. "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. 2017;10:529-541.
Eggleston BS, Ibrahim JG, Catellier D. "Bayesian clinical trial design using Markov models with applications to autoimmune disease." Contemp Clin Trials. 2017;63:73-83.
Lu Z-H, Khondker Z, Ibrahim JG, Wang Y, Zhu H. "Bayesian longitudinal low-rank regression models for imaging genetic data from longitudinal studies." Neuroimage. 2017;149:305-322.
Zhang D, Chen M-H, Ibrahim JG, Boye ME, Shen W. "Bayesian Model Assessment in Joint Modeling of Longitudinal and Survival Data with Applications to Cancer Clinical Trials." J Comput Graph Stat. 2017;26(1):121-133.
Ibrahim JG, Psioda M. BayesProp: Bayesian Clinical Trial Design for Regression Models Using Historical Data (SAS).; 2017.
bcSeq: Fast Sequence Alignment for High-Throughput shRNA and CRISPR Screens (R).; 2017.
Zhou Q, Zhou H, Cai J. "Case-cohort studies with interval-censored failure time data." Biometrika. 2017;104(1):17-29.
Fan A, Song R, Lu W. "Change-Plane Analysis for Subgroup Detection and Sample Size Calculation." J Am Stat Assoc. 2017;112(518):769-778.
Parke T, Marchenko O, Anisimov V, et al. "Comparing oncology clinical programs by use of innovative designs and expected net present value optimization: Which adaptive approach leads to the best result?" J Biopharm Stat. 2017;27(3):457-476.
Li Z. "Comparison of adaptive treatment strategies based on longitudinal outcomes in sequential multiple assignment randomized trials." Stat Med. 2017;36(3):403-415.
Chen Y, Liu Y, Ning J, Nie L, Zhu H, Chu H. "A composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews." Stat Methods Med Res. 2017;26(2):914-930.
Fan C, Lu W, Song R, Zhou Y. "Concordance-Assisted Learning for Estimating Optimal Individualized Treatment Regimes." J R Stat Soc Series B Stat Methodol. 2017;79(5):1565-1582.
Jung S-H. CTD Systems (Java).; 2017.
Ibrahim JG, Psioda M. CureBayes: Bayesian phase 3 design using the cure rate model. (SAS and R).; 2017.
Jung S-H. "Design of Phase II Non-inferiority Trials." Contemp Clin Trials Commun. 2017;7:23-27.
Chiuzan C, Shtaynberger J, Manji GA, et al. "Dose-finding designs for trials of molecularly targeted agents and immunotherapies." J Biopharm Stat. 2017;27(3):477-494.
Jiang R, Lu W, Song R, Hudgens MG, Naprvavnik S. "DOUBLY ROBUST ESTIMATION OF OPTIMAL TREATMENT REGIMES FOR SURVIVAL DATA-WITH APPLICATION TO AN HIV/AIDS STUDY." Ann Appl Stat. 2017;11(3):1763-1786.
Laber EB, Davidian M. "Dynamic treatment regimes, past, present, and future: A conversation with experts." Stat Methods Med Res. 2017;26(4):1605-1610.
Holloway ST, Laber EB, Linn KA, Zhang B, Davidian M, Tsiatis AA. DynTxRegime: A comprehensive package for analysis of dynamic treatment regimes (R).. v3.1 ed.; 2017.
Kang S, Lu W, Liu M. "Efficient estimation for accelerated failure time model under case-cohort and nested case-control sampling." Biometrics. 2017;73(1):114-123.
Mao L, Lin DY. "Efficient Estimation of Semiparametric Transformation Models for the Cumulative Incidence of Competing Risks." J R Stat Soc Series B Stat Methodol. 2017;79(2):573-587.
Tao R, Zeng D, Lin D-Y. "Efficient Semiparametric Inference Under Two-Phase Sampling, With Applications to Genetic Association Studies." J Am Stat Assoc. 2017;112(520):1468-1476.
Liu Y, Wang Y, Huang C, Zeng D. "Estimating personalized diagnostic rules depending on individualized characteristics." Stat Med. 2017;36(7):1099-1117.
Jiang R, Lu W, Song R, Davidian M. "On Estimation of Optimal Treatment Regimes For Maximizing -Year Survival Probability." J R Stat Soc Series B Stat Methodol. 2017;79(4):1165-1185.
Chang S-M, Tzeng J-Y, Chen R-B. "Fast Bayesian Variable Screenings for Binary Response Regressions with Small Sample Size." J Stat Comput Simul. 2017;87(14):2708-2723.
Lin J, Sibley A, Shterev ID, Owzar K. fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies (R). 1.0.4 ed.; 2017.
Zhou J, Zhang J, Lu W. GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R).; 2017.
Zhu R, Zhao Y-Q, Chen G, Ma S, Zhao H. "Greedy outcome weighted tree learning of optimal personalized treatment rules." Biometrics. 2017;73(2):391-400.
Zhou J, Zhang J, Lu W. ICGOR: Fit Generalized Odds Rate Hazards Model with Interval Censored Data (R). 2.0 ed.; 2017.
Yan Y, Zhou H, Cai J. "Improving efficiency of parameter estimation in case-cohort studies with multivariate failure time data." Biometrics. 2017;73(3):1042-1052.
Linn KA, Laber EB, Stefanski LA. "Interactive Q-learning for Quantiles." J Am Stat Assoc. 2017;112(518):638-649.
Acharya CR, Owzar K, Allen AS. "Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC Bioinformatics. 2017;18(1):455.
Zeng D, Gao F, Lin DY. "Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data." Biometrika. 2017;104(3):505-525.
Abanto-Valle CA, Langrock R, Chen M-H, Cardoso MV. "Maximum likelihood estimation for stochastic volatility in mean models with heavy-tailed distributions." Appl Stoch Models Bus Ind. 2017;33(4):394-408.
Bai X, Tsiatis AA, Lu W, Song R. "Optimal treatment regimes for survival endpoints using a locally-efficient doubly-robust estimator from a classification perspective." Lifetime Data Anal. 2017;23(4):585-604.
Kwak M, Jung S-H. "Optimal two-stage log-rank test for randomized phase II clinical trials." J Biopharm Stat. 2017;27(4):639-658.
Kelleher SA, Dorfman CS, Vilardaga JCPlumb, et al. "Optimizing delivery of a behavioral pain intervention in cancer patients using a sequential multiple assignment randomized trial SMART." Contemp Clin Trials. 2017;57:51-57.
Chen H, Zeng D, Wang Y. "Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression." Biometrics. 2017;73(4):1343-1354.
Musolino A, Campone M, Neven P, et al. "Phase II, randomized, placebo-controlled study of dovitinib in combination with fulvestrant in postmenopausal patients with HR, HER2 breast cancer that had progressed during or after prior endocrine therapy." Breast Cancer Res.. 2017;19(1):18.
Jung S-H. "Phase II Trials for Heterogeneous Patient Populations with a Time-to-Event Endpoint." Med Res Arch. 2017;5(7).
Stinchcombe TE, Zhang Y, Vokes EE, et al. "Pooled Analysis of Individual Patient Data on Concurrent Chemoradiotherapy for Stage III Non-Small-Cell Lung Cancer in Elderly Patients Compared With Younger Patients Who Participated in US National Cancer Institute Cooperative Group Studies." J. Clin. Oncol.. 2017;35(25):2885-2892.
Tang Z-Z, Bunn P, Tao R, Liu Z, Lin D-Y. "PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics. 2017;18(1):160.
Liu Z, Song R, Zeng D, Zhang J. "Principal Components Adjusted Variable Screening." Comput Stat Data Anal. 2017;110:134-144.
Deng Y, Zeng D, Zhao J, Cai J. "Proportional hazards model with a change point for clustered event data." Biometrics. 2017;73(3):835-845.
Blau SR, Davis LM, Gorney AM, et al. "Quantifying center of pressure variability in chondrodystrophoid dogs." Vet. J.. 2017;226:26-31.
Zhao J, Li D, Seo J, Allen AS, Gordân R. "Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding." Res Comput Mol Biol. 2017;10229:336-352.
Ding J, Lu T-S, Cai J, Zhou H. "Recent progresses in outcome-dependent sampling with failure time data." Lifetime Data Anal. 2017;23(1):57-82.
Pan Y, Cai J, Kim S, Zhou H. "Regression analysis for secondary response variable in a case-cohort study." Biometrics. 2017.
Cornea E, Zhu H, Kim P, Ibrahim JG. "Regression Models on Riemannian Symmetric Spaces." J R Stat Soc Series B Stat Methodol. 2017;79(2):463-482.
Ni A, Cai J. "A regularized variable selection procedure in additive hazards model with stratified case-cohort design." Lifetime Data Anal. 2017.
Kong D, Maity A, Hsu F-C, Tzeng J-Y. "Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"." Biometrics. 2017.
Yao XI, Wang X, Speicher PJ, et al. "Reporting and Guidelines in Propensity Score Analysis: A Systematic Review of Cancer and Cancer Surgical Studies." J. Natl. Cancer Inst.. 2017;109(8).
Zhou X, Mayer-Hamblett N, Khan U, Kosorok MR. "Residual Weighted Learning for Estimating Individualized Treatment Rules." J Am Stat Assoc. 2017;112(517):169-187.
Jia X, Ivanova A, Lee SM. "Selection of the initial design for the two-stage continual reassessment method." J Biopharm Stat. 2017;27(3):495-506.
Gao F, Zeng D, Lin D-Y. "Semiparametric estimation of the accelerated failure time model with partly interval-censored data." Biometrics. 2017;73(4):1161-1168.
Mao L, Lin D-Y, Zeng D. "Semiparametric regression analysis of interval-censored competing risks data." Biometrics. 2017;73(3):857-865.
Liang B, Tong X, Zeng D, Wang Y. "SEMIPARAMETRIC REGRESSION ANALYSIS OF REPEATED CURRENT STATUS DATA." Stat Sin. 2017;27(3):1079-1100.
Song R, Luo S, Zeng D, Zhang HHelen, Lu W, Li Z. "Semiparametric Single-Index Model for Estimating Optimal Individualized Treatment Strategy." Electron J Stat. 2017;11(1):364-384.
Liu Y, Wang Y, Zeng D. "Sequential multiple assignment randomization trials with enrichment design." Biometrics. 2017;73(2):378-390.
Ivanova A, Deal A. Simon’s like design with relaxed futility stopping (Web).; 2017.
Phanstiel DH, Van Bortle K, Spacek D, et al. "Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development." Mol. Cell. 2017;67(6):1037-1048.e6.
Diao G, Zeng D, Ibrahim JG, et al. "Statistical design of noninferiority multiple region clinical trials to assess global and consistent treatment effects." J Biopharm Stat. 2017;27(6):933-944.
Laber EB, Shedden K. "Statistical Significance and the Dichotomization of Evidence: The Relevance of the for Statisticians." J Am Stat Assoc. 2017;112(519):902-904.
Kimes PK, Liu Y, Hayes DNeil, Marron JStephen. "Statistical significance for hierarchical clustering." Biometrics. 2017;73(3):811-821.
Kang S, Lu W, Song R. "Subgroup detection and sample size calculation with proportional hazards regression for survival data." Stat Med. 2017;36(29):4646-4659.
Vock DM, Durheim MT, Tsuang WM, et al. "Survival Benefit of Lung Transplantation in the Modern Era of Lung Allocation." Ann Am Thorac Soc. 2017;14(2):172-181.
Silva GO, Siegel MB, Mose LE, et al. "SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol.. 2017;18(1):66.
Diéras V, Miles D, Verma S, et al. "Trastuzumab emtansine versus capecitabine plus lapatinib in patients with previously treated HER2-positive advanced breast cancer (EMILIA): a descriptive analysis of final overall survival results from a randomised, open-label, phase 3 trial." Lancet Oncol.. 2017;18(6):732-742.
Cui Y, Zhu R, Kosorok M. "Tree based weighted learning for estimating individualized treatment rules with censored data." Electron J Stat. 2017;11(2):3927-3953.
Shook-Sa BE, Chen D-G, Zhou H. "Using Structural Equation Modeling to Assess the Links between Tobacco Smoke Exposure, Volatile Organic Compounds, and Respiratory Function for Adolescents Aged 6 to 18 in the United States." Int J Environ Res Public Health. 2017;14(10).
Wang X, Wang X, Hodgson L, et al. "Validation of Progression-Free Survival as a Surrogate Endpoint for Overall Survival in Malignant Mesothelioma: Analysis of Cancer and Leukemia Group B and North Central Cancer Treatment Group (Alliance) Trials." Oncologist. 2017;22(2):189-198.
Jusakul A, Cutcutache I, Yong CHan, et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov. 2017;7(10):1116-1135.
2016
Zhang G, Huang K-C, Xu Z, et al. "Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression." Genet. Epidemiol.. 2016;40(4):333-40.
Minsker S, Zhao Y-Q, Cheng G. "Active Clinical Trials for Personalized Medicine." J Am Stat Assoc. 2016;111(514):875-887.
Shin S, Fine J, Liu Y. "Adaptive Estimation with Partially Overlapping Models." Stat Sin. 2016;26(1):235-253.
X Jeng J, Daye ZJohn, Lu W, Tzeng J-Y. AFNC: Adaptive false negative control (R).; 2016.
Roe MT, Cyr DD, Eckart D, 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.. 2016;37(4):412-22.
Murphy SA. Assessing Time-Varying Causal Interactions and Treatment Effects with Applications to Mobile Health.; 2016.
Chen M, Ren Z, Zhao H, Zhou H. "Asymptotically Normal and Efficient Estimation of Covariate-Adjusted Gaussian Graphical Model." J Am Stat Assoc. 2016;111(513):394-406.
Song R, Banerjee M, Kosorok MR. "ASYMPTOTICS FOR CHANGE-POINT MODELS UNDER VARYING DEGREES OF MIS-SPECIFICATION." Ann Stat. 2016;44(1):153-182.
Cao H, Zeng D, Fine JP, Holloway ST. AsynchLong: Regression analysis of sparse asynchronous longitudinal data (R).. 2.0 ed.; 2016.
Psioda M, Ibrahim JG. BetaBinPredProb: Compute predictive probabilities in Bayesian design for Phase IIA trials in a beta-binomial case (SAS)..; 2016.
Psioda M, Ibrahim JG. binDesign: Bayesian sample size for non-inferiority randomized trials with binary data (SAS)..; 2016.

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