Publications

2017
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.
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.
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.
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.
Liu Y, Wang Y, Huang C, Zeng D. "Estimating personalized diagnostic rules depending on individualized characteristics." Stat Med. 2017;36(7):1099-1117.
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.
Yan Y, Zhou H, Cai J. "Improving efficiency of parameter estimation in case-cohort studies with multivariate failure time data." Biometrics. 2017.
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.
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.
Deng Y, Zeng D, Zhao J, Cai J. "Proportional hazards model with a change point for clustered event data." Biometrics. 2017.
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.
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.
Mao L, Lin D-Y, Zeng D. "Semiparametric regression analysis of interval-censored competing risks data." Biometrics. 2017.
Liu Y, Wang Y, Zeng D. "Sequential multiple assignment randomization trials with enrichment design." Biometrics. 2017;73(2):378-390.
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.
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.
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.
Psioda M, Ibrahim JG. binDesignPP: Bayesian sample size for non-inferiority randomized trials with binary data with power prior (SAS)..; 2016.
Wang T. Biomarker Stratified Design Enriched by Auxiliary Biomarker.; 2016.
Zhang D, Sun JLena, Pieper K. "Bivariate Mixed Effects Analysis of Clustered Data with Large Cluster Sizes." Stat Biosci. 2016;8(2):220-233.
Psioda M, Ibrahim JG. BPower: Computes two versions of Bayesian power for normal models (SAS)..; 2016.
George SL, Wang X, Pang H. Cancer Clinical Trials: Current and Controversial Issues in Design and Analysis.. Boca Raton: Chapman & Hall / CRC Press; 2016.
Chen M, Lin H, Zhao H. "CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS." Ann Appl Stat. 2016;10(1):506-526.
Chen J, Liu Y, Zeng D, Song R, Zhao Y, Kosorok MR. "Comment." J Am Stat Assoc. 2016;111(515):942-947.
Guan Q, Laber EB, Reich BJ. "Comment." J Am Stat Assoc. 2016;111(515):936-942.
He K, Li Y, Zhu J, et al. "Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates." Bioinformatics. 2016;32(1):50-7.
Chen G, Liu Y, Shen D, Kosorok MR. "Composite large margin classifiers with latent subclasses for heterogeneous biomedical data." Stat Anal Data Min. 2016;9(2):75-88.
Zhang X, Wu Y, Wang L, Li R. "A Consistent Information Criterion for Support Vector Machines in Diverging Model Spaces." J Mach Learn Res. 2016;17(16):1-26.
Psioda M, Ibrahim JG. design_biomAR: Bayes adaptive randomization for the probit model (SAS)..; 2016.
Hung H, Lin Y-T, Chen P, Wang C-C, Huang S-Y, Tzeng J-Y. "Detection of gene-gene interactions using multistage sparse and low-rank regression." Biometrics. 2016;72(1):85-94.
Davidian M, Tsiatis AA, Laber EB. "Dynamic treatment regimes.". In: Cancer Clinical Trials: Current and Controversial Issues in Design and Analysis. Boca Raton: Chapman & Hall / CRC Press; 2016.
Boland MRegina. Electronic Health Records and Precision Medicine: Enabling Large-Scale Discoveries Using Phenome-Wide Approaches.; 2016.
George SL, Wang X, Pang H. "Endpoints for cancer clinical trials.". In: Cancer Clinical Trials: Current and Controversial Issues in Design and Analysis. Boca Raton: Chapman & Hall / CRC Press; 2016.
Tan Z, Qin G, Zhou H. "Estimation of a partially linear additive model for data from an outcome-dependent sampling design with a continuous outcome." Biostatistics. 2016;17(4):663-76.
Linn KA, Laber EB, Stefanski LA. "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. Philadelphia: ASA-SIAM; 2016:2.
Acharya CR, McCarthy JM, Owzar K, Allen AS. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics. 2016;17:257.
Psioda M, Ibrahim JG. fitRE: Bayesian superiority design for gamma frailty recurrent events model (SAS)..; 2016.
Li Z, Owzar K. "Fitting Cox Models with Doubly Censored Data Using Spline-Based Sieve Marginal Likelihood." Scand Stat Theory Appl. 2016;43(2):476-486.
Chow S-M, Lu Z, Sherwood A, Zhu H. "Fitting Nonlinear Ordinary Differential Equation Models with Random Effects and Unknown Initial Conditions Using the Stochastic Approximation Expectation-Maximization (SAEM) Algorithm." Psychometrika. 2016;81(1):102-34.
Chi E. Getting High-throughput Arrays in Order with Convex Biclustering.; 2016.
Ha MJin, Holloway ST. GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R).. 1.0 ed.; 2016.
Wang X, Chen M, Yu X, et al. "Global copy number profiling of cancer genomes." Bioinformatics. 2016;32(6):926-8.
Ma X, Chen Y, Cole SR, Chu H. "A hybrid Bayesian hierarchical model combining cohort and case-control studies for meta-analysis of diagnostic tests: Accounting for partial verification bias." Stat Methods Med Res. 2016;25(6):3015-3037.
Nair S. Immune-based therapies.; 2016.
Kim S, Cai J, Couper D. "Improving the efficiency of estimation in the additive hazards model for stratified case-cohort design with multiple diseases." Stat Med. 2016;35(2):282-93.
Bunn P, Zeng D, Lin D-Y. IntCens: Nonparametric maximum likelihood estimation for a broad class of semiparametric regression models with general interval-censored data (R)..; 2016.
Wong KYau. Integration of Multiple High-dimensional Genomic Data Types for Survival Prediction.; 2016.
Acharya CR, McCarthy JM, Owzar K, Allen AS. JAGUAR: Joint analysis of genotype and group-specific variability using a novel score test approach to map expression quantitative trait loci (eQTL) (R). 3.0.1 ed.; 2016.
Zhang D, Chen M-H, Ibrahim JG, Boye ME, Shen W. "JMFit: A SAS Macro for Joint Models of Longitudinal and Survival Data." J Stat Softw. 2016;71(3).
Xiao W, Lu W, Zhang HHelen. "JOINT STRUCTURE SELECTION AND ESTIMATION IN THE TIME-VARYING COEFFICIENT COX MODEL." Stat Sin. 2016;26(2):547-567.
Lin J, Sibley A, Shterev ID, Owzar K. jtGWAS: Efficient Jonckheere-Terpstra test statistics (R).. 1.0 ed.; 2016.
Palumbo A, Michael Y, Hyslop T. "Latent class model characterization of neighborhood socioeconomic status." Cancer Causes Control. 2016;27(3):445-52.
Lin J, Sibley A, Truong T, et al. lclGWAS: Efficient estimation of discrete-time multivariate frailty model using exact likelihood function for grouped survival data (R)..; 2016.
Wang Y, Wu P, Liu Y, Weng C, Zeng D. "Learning Optimal Individualized Treatment Rules from Electronic Health Record Data." IEEE Int Conf Healthc Inform. 2016;2016:65-71.
Shortreed SM. Leveraging Electronic Medical Records to Better Target Suicide Prevention.; 2016.
Chang J, Tang CYong, Wu Y. "LOCAL INDEPENDENCE FEATURE SCREENING FOR NONPARAMETRIC AND SEMIPARAMETRIC MODELS BY MARGINAL EMPIRICAL LIKELIHOOD." Ann Stat. 2016;44(2):515-539.
Lee H, Hudgens MG, Cai J, Cole SR. "Marginal Structural Cox Models with Case-Cohort Sampling." Stat Sin. 2016;26(2):509-526.
Zeng D, Mao L, Lin DY. "Maximum likelihood estimation for semiparametric transformation models with interval-censored data." Biometrika. 2016;103(2):253-271.
Zhao L. Measures of Clinical Benefit in Immuno-Oncology Studies.; 2016.
Psioda M, Ibrahim JG. MultiARMSBinary: Simulates Bayes adaptive randomization of multiple arms in a beta-binomial simulation (SAS)..; 2016.
Lizotte DJ, Laber EB. "Multi-Objective Markov Decision Processes for Data-Driven Decision Support." J Mach Learn Res. 2016;17.
Xie J. Multiple Testing of General Dependence by Quantile-Based Contingency Tables with an Application in Identifying Gene Co-expression Network Change Associated with Cancer Survival.; 2016.
Xia F, George SL, Wang X. "A Multi-state Model for Designing Clinical Trials for Testing Overall Survival Allowing for Crossover after Progression." Stat Biopharm Res. 2016;8(1):12-21.
Ibrahim JG. Network Meta-analysis for Ordinal Outcomes: Applications in Comparing Crohn's Disease Treatments.; 2016.
Psioda M, Ibrahim JG. NormalMean_BSS: Calculates the Bayesian sample size based on ACC, ALC, and WOC for normal model (SAS)..; 2016.
Psioda M, Ibrahim JG. normDesign: Bayesian sample size for non-inferiority randomized trials with normal data (SAS)..; 2016.
Psioda M, Ibrahim JG. normDesignPP: Bayesian sample size for non-inferiority randomized trials with normal data with power prior (SAS)..; 2016.
Schifano ED, Wu J, Wang C, Yan J, Chen M-H. "Online Updating of Statistical Inference in the Big Data Setting." Technometrics. 2016;58(3):393-403.
Wang W, Chen M-H, Chiou SHan, et al. "Onset of persistent pseudomonas aeruginosa infection in children with cystic fibrosis with interval censored data." BMC Med Res Methodol. 2016;16(1):122.
Davidian M, Tsiatis AA, Laber EB. Optimal dynamic treatment regimes.; 2016. Optimal dynamic treatment regimes.
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. 2016.
Lu W, Zhang HHelen, Zeng D, Geng Y, Holloway ST. OTRselect: Variable selection for optimal treatment decision (R).. 1.0 ed. CRAN Repository; 2016.
Yu J, Liu Y, Cai J, Sandler DP, Zhou H. "Outcome-Dependent Sampling Design and Inference for Cox's Proportional Hazards Model." J Stat Plan Inference. 2016;178:24-36.
Chen G, Zeng D, Kosorok MR. "Personalized Dose Finding Using Outcome Weighted Learning." J Am Stat Assoc. 2016;111(516):1509-1521.
Huang Y, Laber E. "Personalized Evaluation of Biomarker Value: A Cost-Benefit Perspective." Stat Biosci. 2016;8:43-65.
Chen M, Gao C, Zhao H. "Posterior Contraction Rates of the Phylogenetic Indian Buffet Processes." Bayesian Anal. 2016;11(2):477-497.
Milanzi E, Molenberghs G, Alonso A, et al. "Properties of Estimators in Exponential Family Settings with Observation-based Stopping Rules." J Biom Biostat. 2016;7(1).
Joeng H-K, Chen M-H, Kang S. "Proportional exponentiated link transformed hazards (ELTH) models for discrete time survival data with application." Lifetime Data Anal. 2016;22(1):38-62.
Zhang C, Liu Y, Wu Y. "On Quantile Regression in Reproducing Kernel Hilbert Spaces with Data Sparsity Constraint." J Mach Learn Res. 2016;17(40):1-45.
Ou F-S, Zeng D, Cai J. "Quantile Regression Models for Current Status Data." J Stat Plan Inference. 2016;178:112-127.
Cobran EK, Chen RC, Overman R, et al. "Racial Differences in Diffusion of Intensity-Modulated Radiation Therapy for Localized Prostate Cancer." Am J Mens Health. 2016;10(5):399-407.
Zhang C, Liu Y, Holloway ST. RAMSVM: Reinforced angle-based multicategory support vector machines (R).. 2.0 ed.; 2016.
Ivanova A, Wang Y, Foster MC. "The rapid enrollment design for Phase I clinical trials." Stat Med. 2016;35(15):2516-24.
Jeng XJessie, Daye ZJohn, Lu W, Tzeng J-Y. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput. Biol.. 2016;12(6):e1004993.
Zhang C, Liu Y, Wang J, Zhu H. "Reinforced Angle-based Multicategory Support Vector Machines." J Comput Graph Stat. 2016;25(3):806-825.
Wang X, Berry MF. "Risk calculators are useful but...." J. Thorac. Cardiovasc. Surg.. 2016;151(3):706-7.
Ibrahim JG, Gwon Y, Chen M-H. "SAS Macro BSMED: Bayesian survival meta-experimental design using historical data.". In: Pharmaceutical Statistics Using SAS. Cary: SAS Institute Inc; 2016.
Yuan J, Pang H, Tong T, Xi D, Guo W, Mesenbrink P. "Seamless Phase IIa/IIb and enhanced dose-finding adaptive design." J Biopharm Stat. 2016;26(5):912-23.
Mao L, Lin DY. "Semiparametric regression for the weighted composite endpoint of recurrent and terminal events." Biostatistics. 2016;17(2):390-403.

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