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.
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.
Jung S-H. CTD Systems.; 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.
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.
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 t-Year Survival Probability." J R Stat Soc Series B Stat Methodol. 2017;79(4):1165-1185.
Lin J, Sibley A, Shterev ID, Owzar K. fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies. 1.0.4 ed.; 2017.
Zhu R, Zhao Y, 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;73(3):1042-1052.
Butler EL, Laber EB, Davis SM, Kosorok MR. "Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics. 2017.
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.
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.
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.
Jung S-H. "Phase II Cancer Clinical Trials for Biomarker-Guided Treatments." J Biopharm Stat. 2017.
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.
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.
Ni A, Cai J. "A regularized variable selection procedure in additive hazards model with stratified case-cohort design." Lifetime Data Anal. 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.
Chen X, Cai J. "Reweighted estimators for additive hazard model with censoring indicators missing at random." Lifetime Data Anal. 2017.
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;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.
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.
Kang S, Lu W, Song R. "Subgroup detection and sample size calculation with proportional hazards regression for survival data." Stat Med. 2017.
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.
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, Cheng G. "Active Clinical Trials for Personalized Medicine." J Am Stat Assoc. 2016;111(514):875-887.
Shin S, Fine JP, 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.
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.
Blackwell K, Donskih R, C Jones M, et al. "A Comparison of Proposed Biosimilar LA-EP2006 and Reference Pegfilgrastim for the Prevention of Neutropenia in Patients With Early-Stage Breast Cancer Receiving Myelosuppressive Adjuvant or Neoadjuvant Chemotherapy: Pegfilgrastim Randomized Oncology (Supp." Oncologist. 2016;21(7):789-94.
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.
S Farber H, Tsvankin V, Narloch JL, et al. "Embracing rejection: Immunologic trends in brain metastasis." Oncoimmunology. 2016;5(7):e1172153.
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.
Pang HH, Wang X, Stinchcombe TE, et al. "Enrollment Trends and Disparity Among Patients With Lung Cancer in National Clinical Trials, 1990 to 2012." J. Clin. Oncol.. 2016.
Lewis PO, Chen M-H, Kuo L, et al. "Estimating Bayesian Phylogenetic Information Content." Syst. Biol.. 2016;65(6):1009-1023.
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.
Harnden KK, Blackwell KL. "Increased Fiber Intake Decreases Premenopausal Breast Cancer Risk." Pediatrics. 2016;137(3):e20154376.
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 MErnest, 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.

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