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.
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.
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.
Guan Q, Laber EB, Reich BJ. "Comment." J Am Stat Assoc. 2016;111(515):936-942.
Chen J, Liu Y, Zeng D, Song R, Zhao Y, Kosorok MR. "Comment." J Am Stat Assoc. 2016;111(515):942-947.
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.
Zhu R, Zhao Y-Q, Chen G, Ma S, Zhao H. "Greedy outcome weighted tree learning of optimal personalized treatment rules." Biometrics. 2016.
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.
Zhao Y, Saville BR, Zhou H, Koch GG. "Sensitivity analysis for missing outcomes in time-to-event data with covariate adjustment." J Biopharm Stat. 2016;26(2):269-79.

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