Boland, Mary Regina. Electronic Health Records and Precision Medicine: Enabling Large-Scale Discoveries Using Phenome-Wide Approaches., 2016.
Zhao, Yingqi. Estimating Individualized Treatment Rules Using Outcome Weighted Learning., 2011.
Zeng, Donglin. Estimating treatment effects with treatment switching via semi-competing risks models: An application to a colorectal cancer study., 2011.
Zhao, Yingqi. Estimation of Optimal Dynamic Treatment Regimes., 2014.
Wang, L. Evaluation of Viable Dynamic Treatment Regimes in a Sequentially Randomized Trial of Advanced Prostate Cancer., 2014.
Madar, V. Faster algorithm to control the Benjamini-Hochberg false discovery rate and its application for analysis of huge genomic data.., 2014.
Li, Zhiguo. Fitting Cox models with doubly censored data using spline-based marginal likelihood., 2011.
Tzeng, Jung-Ying. A gene-trait similarity regression method for gene-level pharmacogenetics analysis., 2011.
Chi, Eric. Getting High-throughput Arrays in Order with Convex Biclustering., 2016.
Almirall, D, and Susan A. Murphy. Getting SMART about developing individualized sequences of health interventions., 2012.
Gou, J, and AC Tamhane. Hochberg Multiple Test Procedure Under Negative Dependence., 2014.
Nair, Smita. Immune-based therapies., 2016.
Sarkar, S. Improving Holm's procedure using pairwise dependencies., 2014.
Benjamini, Y. In Hochberg’s tradition: Selective Inference for Clinical Trials., 2014.
Wong, Kin Yau. Integration of Multiple High-dimensional Genomic Data Types for Survival Prediction., 2016.
Zhang, Yichi. Interpretable treatment regimes., 2014.
Linn, Kristin A.. IQ-Learning., 2012.
Shortreed, Susan M.. Leveraging Electronic Medical Records to Better Target Suicide Prevention., 2016.
Zhao, Luping. Measures of Clinical Benefit in Immuno-Oncology Studies., 2016.
Murphy, Susan A.. Micro-Randomized Trials & mHealth., 2014.
Xie, Jichun. 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.
Ibrahim, Joseph G.. Network Meta-analysis for Ordinal Outcomes: Applications in Comparing Crohn's Disease Treatments., 2016.
Ivanova, Anastasia. Oncology Phase II trials with ordinal outcome., 2012.
Rosenblum, M. Optimal, Two Stage, Adaptive Enrichment Designs for Randomized Trials, using Sparse Linear Programming., 2014.
Fine, Jason P.. An overview of competing risks data, with applications in clinical trials., 2011.
Heyse, Joseph F.. An Overview of Multiple Testing Procedures for Categorical Data., 2014.
Song, Rui. Penalized Q-Learning for Dynamic Treatment Regimes., 2012.
Auman, Todd. Pharmacogenomic interrogation of colorectal cancer using next-generation whole exome sequencing., 2011.
Bobashev, G. Prediction of the Best Treatment Assignment Using Random Forest with Regression in the Nodes., 2012.
Davidian, Marie. A robust method for estimating optimal treatment regimes., 2011.
Levenson, M. Safety decision-making with multiple sources and different types of studies—recent examples from FDA Advisory Committees., 2011.
Laber, Eric B.. Sizing a trial for estimation of an optimal treatment regime., 2014.
Thall, PF. SMART Design, Conduct, and Analysis in Oncology., 2014.
Kang, Suhyun. Subgroup Detection and Sample Size Calculation with Proportional Hazards Regression for Survival Data., 2016.
Almirall, D. Tutorial: Getting SMART about Dynamic Treatment Regimes: A Conceptual Introduction., 2014.
Bretz, F. Tutorial: Introduction to Multiplicity in Clinical Trials., 2014.
Hung, H M. James. Utilities and challenges of adaptive designs in drug development., 2011.
Davidian, Marie, Michael R. Kosorok, Eric B. Laber, and Anastasios A. Tsiatis. Workshop on Personalized Medicine and Dynamic Treatment Regimes., 2012.
Zhu, Ruoqing, Donglin Zeng, and Michael R. Kosorok. Reinforcement learning trees In The University of North Carolina at Chapel Hill Department of Biostatistics Technical Report Series. UNC at Chapel Hill. Chapel Hill: The University of North Carolina, 2012.
Cornea, Emil, Hongtu Zhu, Peter Kim, and Joseph G. Ibrahim. ADNI_RMRSS: Regression Models on Riemannian Symmetric Spaces (MATLAB)., 2016.
Wang, Ting. AEBSD: Sample size of AEBSD and Comparison with BSD (R)., 2018.
X Jeng, Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. AFNC: Adaptive false negative control (R)., 2016.
Zhu, Anqi, Joseph G. Ibrahim, and Michael I. Love. apeglm: Approximate posterior estimation for GLM coefficients (R)., 2018.
Wang, WeiBo, Wei Wang, Wei Sun, James J. Crowley, and Jin P. Szatkiewicz. ASGENSENG: Detect Allele Specific CNV from Both WGS and WES Data (Python/Shell)., 2015.
Cao, Hongyuan, Donglin Zeng, Jason P. Fine, and Shannon T. Holloway. AsynchLong: Regression analysis of sparse asynchronous longitudinal data (R).. 2.0 ed., 2016.
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.
Guo, Ruixin, Hongtu Zhu, Sy-Miin Chow, and Joseph G. Ibrahim. Bayesian Lasso for semiparametric structural equation models toolkit (C++).., 2011.
Ibrahim, Joseph G., and Matthew Psioda. 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.
Psioda, Matthew, and Joseph G. Ibrahim. BetaBinPredProb: Compute predictive probabilities in Bayesian design for Phase IIA trials in a beta-binomial case (SAS).., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. binDesign: Bayesian sample size for non-inferiority randomized trials with binary data (SAS).., 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. BPower: Computes two versions of Bayesian power for normal models (SAS).., 2016.
Ibrahim, Joseph G., Yeongjin Gwon, and Ming-Hui Chen. BSMED: Bayesian survival meta-experimental design using historical data (SAS).. 1.0 ed., 2015.
Diao, Guoqing, Jun Dong, Donglin Zeng, and Joseph G. Ibrahim. BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++)., 2018.
Bondell, Howard D., and Shannon T. Holloway. CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R).. R 3.0 ed., 2013.
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.
Hu, Yi-Juan, Dan-Yu Lin, Wei Sun, and Donglin Zeng. CNVstat: Statistical association analysis of copy number variants (C).. 1.0 ed., 2012.
Jiang, Yuchao, and Nancy R. Zhang. CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R)., 2018.
Brucker, Amanda, Shannon T. Holloway, and Jung-Ying Tzeng. CONCUR: Kernel-based association test for copy number variation (CNV) aggregate analysis (R)., 2020.
Cornea, Emil, Bahjat Qaqish, and Joseph G. Ibrahim. CR: Power calculation for weighted log-rank tests in cure rate models (R).., 2012.
Bayar, Mohamed, Anastasia Ivanova, and Gwenael Le Teuff. CRM2DIM: Dual-Agent Bayesian Continual Reassessment Method (SAS). 1.0 ed., 2019.
Li, Meng, Ana-Maria Staicu, and Howard D. Bondell. cSFM: Covariate-adjusted skewed functional model (R).. 1.1 ed., 2014.
Jung, Sin-Ho. CTD Systems (Java)., 2017.
Ibrahim, Joseph G., and Matthew Psioda. CureBayes: Bayesian phase 3 design using the cure rate model. (SAS and R)., 2017.
Psioda, Matthew, and Joseph G. Ibrahim. design_biomAR: Bayes adaptive randomization for the probit model (SAS).., 2016.
Walter, Vonn, Andrew B. Nobel, and Fred A. Wright. DiNAMIC: Discovering copy number aberrations manifested in cancer (R).., 2011.
Tsiatis, Anastasios A., Marie Davidian, Weihua Cao, and Shannon T. Holloway. doublyRobust: Doubly robust estimation for monotonely coarsened data in longitudinal studies with dropout and/or incomplete data (R).. 2nd ed., 2013.
Line, Danyu, Donglin Zeng, and Shannon T. Holloway. DOVE: Durability of Vaccine Efficacy. v1.2 ed., 2021.
Liu, Ying, Yuanjia Wang, and Donglin Zeng. DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R). 1.3 ed., 2018.
Holloway, Shannon, and Hunyong Cho. dtrSurv: Dynamic Treatment Regimes for Survival Analysis (R). 1.1 ed., 2020.
Holloway, Shannon T., Eric B. Laber, Kristin A. Linn, Baqun Zhang, Marie Davidian, and Anastasios A. Tsiatis. DynTxRegime: A comprehensive package for analysis of dynamic treatment regimes (R).. v3.1 ed., 2017.
Lin, Jiaxing, Alexander Sibley, Ivo D. Shterev, and Kouros Owzar. fastJT: Efficient Jonckheere-Terpstra Test Statistics for Robust Machine Learning and Genome-Wide Association Studies (R). 1.0.4 ed., 2017.
Marceau, Rachel, Wenbin Lu, Michèle M. Sale, Bradford B. Worrall, Stephen R. Williams, Fang-Chi Hsu, Jung-Ying Tzeng, and Shannon T. Holloway. FastKM: A fast multiple-kernel method based on a low-rank approximation (R).. 1.0 ed., 2015.
Jiang, Yu, Yujun Han, Slavé Petrovski, Kouros Owzar, David B. Goldstein, and Andrew S. Allen. fitDNM: Test of de novo enrichment that incorporates functional information (R).. 1.0 ed., 2015.
Psioda, Matthew, and Joseph G. Ibrahim. fitRE: Bayesian superiority design for gamma frailty recurrent events model (SAS).., 2016.
Ibrahim, Joseph G., Hongtu Zhu, Ramon I. Garcia, and Ruixin Guo. Fixed and random effects selection in mixed effects toolkit (R).., 2011.
Ibrahim, Joseph G., Ming-Hui Chen, Amy H Xia, and Thomas Liu. Fixed: Bayesian meta-experimental design (SAS).., 2012.
Lewis, Paul O.. Galax (C++)., 2016.
Pang, Herbert. geneSelRSF: Gene selection using iterative recursive feature elimination (R).. 1.0 ed., 2012.
Ha, Min Jin, and Shannon T. Holloway. GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R).. 1.0 ed., 2016.
Diao, Guoqing. GHREG: Semiparametric general hazards rate model for right-censored data (C).., 2013.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R)., 2017.
Lin, Jiaxing, Alexander Sibley, Tracy Truong, Kouros Owzar, and Zhiguo Li. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed., 2018.
He, Qianchuan, and Dan-Yu Lin. GWASelect: A variable selection method for genomewide association studies (C++).., 2011.
Bondell, Howard D., Jung-Ying Tzeng, Megan L. Koehler, and Shannon T. Holloway. Haplo.CasGLM: Haplotype specific simultaneous factor selection and collapsing levels in GLM (R).. 3rd ed., 2013.
Cao, Hongyuan, Michael R. Kosorok, and Shannon T. Holloway. highTtest: Simultaneous critical values for t-tests in very high dimensions (R).. 1.0 ed., 2014.
Chen, Guanhua, and Michael R. Kosorok. HSSVD: Biclustering with heterogeneous variance (R).., 2013.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. ICGOR: Fit Generalized Odds Rate Hazards Model with Interval Censored Data (R). 2.0 ed., 2017.
Holloway, Shannon T., Qingning Zhou, Jianwen Cai, and Haibo Zhou. ICODS: Data Analysis for ODS and Case-Cohort Designs with Interval-Censoring (R). 1.0 ed., 2019.
Bunn, Paul, Donglin Zeng, and Dan-Yu Lin. IntCens: Nonparametric maximum likelihood estimation for a broad class of semiparametric regression models with general interval-censored data (R).., 2016.
Lin, Jiaxing, Yuan Wu, Xiaofei F. Wang, and Kouros Owzar. intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R). 0.1.1 ed., 2018.
Linn, Kristin A., Eric B. Laber, and Leonard A. Stefanski. iqLearn: Interactive Q-learning (R).., 2013.
Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. 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.
Cornea, Emil, Liddy M. Chen, Bahjat Qaqish, Haitao Chu, and Joseph G. Ibrahim. JMDesign: Statistical design for joint models of longitudinal and survival data (R).. v1.1 ed., 2012.
Zhang, Danjie, Ming-Hui Chen, and Joseph G. Ibrahim. JMfit - For fitting joint models for longitudinal and survival data (SAS)., 2014.
Lin, Jiaxing, Alexander Sibley, Ivo D. Shterev, and Kouros Owzar. jtGWAS: Efficient Jonckheere-Terpstra test statistics (R).. 1.0 ed., 2016.
Lin, Jiaxing, Alexander Sibley, Trach Truong, Nancy Cox, Eileen Dolan, Yu Jiang, Janice M. McCarthy, Andrew S. Allen, Kouros Owzar, and Zhiguo Li. lclGWAS: Efficient estimation of discrete-time multivariate frailty model using exact likelihood function for grouped survival data (R).., 2016.
Boos, Dennis D., and Shannon T. Holloway. logi: Logistic regression using forward selection (R).. 2.0 ed., 2013.
Ibrahim, Joseph G., and Stuart Lipsitz. Macros for missing data (SAS).., 2014.