Publications

Web Article
George, Stephen L.. Sorting the wheat from the chaff: How do we know which cancer therapies really work? . Huffington Post, 2013.
Laber, Eric B., E Rose, Marie Davidian, and Anastasios A. Tsiatis. Q-Learning. In Wiley StatsRef: Statistics Reference Online. Wiley, 2018.
Davidian, Marie, Anastasios A. Tsiatis, and Eric B. Laber. Optimal dynamic treatment regimes In Wiley Statsref. Optimal dynamic treatment regimes., 2016.
Chen, G, Michael R. Kosorok, and X Zhou. Nonconvex Optimization. In Wiley StatsRef: Statistics Reference Online., 2018.
Wang, Xiaofei, Jianwen Cai, and Stephen L. George. Enriched biomarker-driven clinical trials. In Wiley StatsRef: Statistics Reference Online. Wiley, 2019.
Software
Chen, Yong, Chuan Hong, Haitao Chu, and Yulun Liu. xmeta: A Toolbox for Multivariate Meta-Analysis (R)., 2017.
Tao, Ran. TwoPhaseReg: Regression Analysis Under General Two-Phase Sampling (R)., 2018.
Song, Guochen. TRECASE_MLE: eQTL mapping based on total read count and allele-specific expression in RNA-Seq data with maximum-likelihood estimation (C/C++).., 2015.
Hung, Hung, Yu-Ting Lin, Penweng Chen, Chen-Chien Wang, Su-Yun Huang, and Jung-Ying Tzeng. TensorGxG: A sparse and low-rank screening based on the combination of a low-rank interaction model and the Lasso screening (Matlab).., 2015.
Hu, Yi-Juan, and Dan-Yu Lin. tagIMPUTE: Tag-based imputation.. 1.0 ed., 2010.
Chen, Mengjie. SynthEx: Tools for CNA detection and tumor heterogeneity profiling (R)., 2017.
Jung, Sin-Ho, and Stanley S Young. survSNP: Power and sample size calculations for SNP association studies with censored time-to-event outcomes (R).., 2012.
Cao, Hongyuan, Mathew M. Churpek, Donglin Zeng, Jason P. Fine, and Shannon T. Holloway. SurvLong: Analysis of proportional hazards model with sparse longitudinal covariates (R).. 1.0 ed., 2015.
Lin, Dan-Yu, R Tao, W Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. SUGEN: Genetic Association Analysis Under Complex Survey Sampling (C++)., 2014.
Fan, Aiilin, and Shannon T. Holloway. subdetect: Detect subgroup with an enhanced treatment effect (R).. 1.1 ed., 2016.
Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar. SNPpy: Database management for SNP data from genome wide association studies.., 2011.
Vock, David M., Marie Davidian, and Anastasios A. Tsiatis. SNP_NLMM: Implement a flexible random effects density for generalized linear and nonlinear mixed models (SAS).., 2014.
Hu, Yi-Juan, Dan-Yu Lin, and Donglin Zeng. SNPMStat v4.0 : Statistical analysis of SNP-disease association with missing genotype data.., 2011.
Yi, Chanhee, Alexander Sibley, and Kouros Owzar. snplist: Tools to create gene sets (R).. 0.12 ed., 2013.
Stefanski, Leonard A., Yichao Wu, and Kyle White. skda: Sparse (multicategory) kernel discriminant analysis (R).. 0.1 ed., 2013.
Ivanova, Anastasia, and A Deal. Simon’s like design with relaxed futility stopping (Web)., 2017.
Kimes, Patrick. sigclust2: Statistical Significance for Hierarchical Clustering (R). 1.2.4 ed., 2016.
Hu, Yi-Juan, Yun Li, Paul L. Auer, and Dan-Yu Lin. SEQGWAS: Integrative analysis of sequencing and GWAS data (C/C++).. 1.0 ed., 2015.
Lin, Dan-Yu, Donglin Zeng, and Zheng-Zheng Tang. SCORE-SeqTDS: Score tests for sequencing studies with trait-dependent sampling (C).. 3.0 ed., 2013.
Lin, Dan-Yu, and Zheng-Zheng Tang. SCORE-Seq: Score tests for detecting disease associations with rare variants in sequencing studies (C).. 5.0 ed., 2013.
Jung, Sin-Ho, and Shein-Chung Chow. Sample size calculation for comparing survival curves under general hypotheses testing (Fortran).., 2012.
Liu, Yang, Wei Sun, and Qianchuan He. SAME: Somatic mutation Association test with Measurement Errors (R)., 2018.
Yi, Chanhee, Alexander Sibley, and Kouros Owzar. RSNPset: Genome-wide SNP set analysis on the basis of efficient scores (R).. v0.2 ed., 2014.
Zhu, Ruoqing, and Michael R. Kosorok. RLT: Reinforcement learning trees (R).. 2.0 ed., 2015.
Zhang, Chong, Yufeng Liu, and Shannon T. Holloway. RAMSVM: Reinforced angle-based multicategory support vector machines (R).. 2.0 ed., 2016.
Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Z Liu, and Dan-Yu Lin. PreMeta: Facilitates the Exchange of Information Between Software Packages for Meta-Analysis (C++)., 2017.
Gao, Fei, Donglin Zeng, and Joseph G. Ibrahim. Power calculations and confidence intervals in phase II design with over enrollment (SAS/R).., 2014.
Jung, Sin-Ho, and Stanley S Young. Power and sample size calculation for microarray studies (Fortran).., 2012.
West, Rachel Marceau, and Shannon T. Holloway. POINT: Protein Structure Guided Local Test (R). 1.0 ed., 2019.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. PICAFT: Semiparametric Estimation of the Accelerated Failure Time Model With Partly Interval-Censored Data (R)., 2017.
Zhu, Hongtu, Joseph G. Ibrahim, and Hyunsoon Cho. Perturbation and scaled Cook's distance (C++/Matlab).., 2012.
Shterev, Ivo D., Sin-Ho Jung, Stephen L. George, and Kouros Owzar. permGPU: Using graphics processing units in RNA microarray association studies (CUDA).., 2011.
Lin, Lifeng, Jing Zhang, and Haitao Chu. pcnetmeta: Methods for patient-centered network meta-analysis (R).. 1.2 ed., 2014.
Lu, Wenbin, Hao Helen Zhang, Donglin Zeng, Yuan Geng, and Shannon T. Holloway. OTRselect: Variable selection for optimal treatment decision (R).. 1.0 ed. CRAN Repository, 2016.
Wang, Xiaofei, Junling Ma, Stephen L. George, and Haibo Zhou. odsroc: Nonparametric estimation of AUC and partial AUC under test-result-dependent sampling (R).., 2012.
Psioda, Matthew, and Joseph G. Ibrahim. normDesignPP: Bayesian sample size for non-inferiority randomized trials with normal data with power prior (SAS).., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. normDesign: Bayesian sample size for non-inferiority randomized trials with normal data (SAS).., 2016.
Psioda, Matthew, and Joseph G. Ibrahim. NormalMean_BSS: Calculates the Bayesian sample size based on ACC, ALC, and WOC for normal model (SAS).., 2016.
Tao, Ran, Donglin Zeng, Nora Franceschini, Kari E. North, Eric Boerwinkle, and Dan-Yu Lin. MultiTDS: Analysis of Sequence Data Under Multivariate Trait-Dependent Sampling (C++)., 2015.
Psioda, Matthew, and Joseph G. Ibrahim. MultiARMSBinary: Simulates Bayes adaptive randomization of multiple arms in a beta-binomial simulation (SAS).., 2016.
He, Qianchuan, and Dan-Yu Lin. MOST: Multivariate outcome score test (C).. 1.0 ed., 2013.
Holloway, Shannon T.. modelObj: A model object framework for regression analysis (R).. 1.0 ed., 2015.
Luo, Sheng, Yong Chen, Xiao Su, and Haitao Chu. mmeta: Multivariate meta-analysis (R).. 2.2 ed., 2014.
Zhou, Yi-Hui. mcc: Moment corrected correlation an approximation to exact association testing of two vectors (R).. 1.0 ed., 2014.
Tang, Zheng-Zheng, and Dan-Yu Lin. MASS: Meta-analysis of sequencing studies (C).. 5.0 ed., 2013.
Urrutia, Eugene, Hao Chen, Zilu Zhou, Nancy R. Zhang, and Yuchao Jiang. MARATHON: Integrates Multiple Related Statistical Software for Copy Number Profiling and Downstream Analyses (R)., 2018.
Ibrahim, Joseph G., and Stuart Lipsitz. Macros for missing data (SAS).., 2014.
Boos, Dennis D., and Shannon T. Holloway. logi: Logistic regression using forward selection (R).. 2.0 ed., 2013.
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.
Lin, Jiaxing, Alexander Sibley, Ivo D. Shterev, and Kouros Owzar. jtGWAS: Efficient Jonckheere-Terpstra test statistics (R).. 1.0 ed., 2016.
Zhang, Danjie, Ming-Hui Chen, and Joseph G. Ibrahim. JMfit - For fitting joint models for longitudinal and survival data (SAS)., 2014.
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.
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.
Linn, Kristin A., Eric B. Laber, and Leonard A. Stefanski. iqLearn: Interactive Q-learning (R).., 2013.
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.
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.
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.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. ICGOR: Fit Generalized Odds Rate Hazards Model with Interval Censored Data (R). 2.0 ed., 2017.
Chen, Guanhua, and Michael R. Kosorok. HSSVD: Biclustering with heterogeneous variance (R).., 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.
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.
He, Qianchuan, and Dan-Yu Lin. GWASelect: A variable selection method for genomewide association studies (C++).., 2011.
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.
Zhou, Jie, Jiajia Zhang, and Wenbin Lu. GORCure: Fit Generalized Odds Rate Mixture Cure Model with Interval Censored Data (R)., 2017.
Diao, Guoqing. GHREG: Semiparametric general hazards rate model for right-censored data (C).., 2013.
Ha, Min Jin, and Shannon T. Holloway. GGMridge: Gaussian graphical models using ridge penalty followed by thresholding and reestimation (R).. 1.0 ed., 2016.
Pang, Herbert. geneSelRSF: Gene selection using iterative recursive feature elimination (R).. 1.0 ed., 2012.
Lewis, Paul O.. Galax (C++)., 2016.
Ibrahim, Joseph G., Ming-Hui Chen, Amy H Xia, and Thomas Liu. Fixed: Bayesian meta-experimental design (SAS).., 2012.
Ibrahim, Joseph G., Hongtu Zhu, Ramon I. Garcia, and Ruixin Guo. Fixed and random effects selection in mixed effects toolkit (R).., 2011.
Psioda, Matthew, and Joseph G. Ibrahim. fitRE: Bayesian superiority design for gamma frailty recurrent events model (SAS).., 2016.
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.
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.
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.
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.
Holloway, Shannon, and Hunyong Cho. dtrSurv: Dynamic Treatment Regimes for Survival Analysis (R). 1.1 ed., 2020.
Liu, Ying, Yuanjia Wang, and Donglin Zeng. DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R). 1.3 ed., 2018.
Line, Danyu, Donglin Zeng, and Shannon T. Holloway. DOVE: Durability of Vaccine Efficacy. v1.2 ed., 2021.
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.
Walter, Vonn, Andrew B. Nobel, and Fred A. Wright. DiNAMIC: Discovering copy number aberrations manifested in cancer (R).., 2011.
Psioda, Matthew, and Joseph G. Ibrahim. design_biomAR: Bayes adaptive randomization for the probit model (SAS).., 2016.
Ibrahim, Joseph G., and Matthew Psioda. CureBayes: Bayesian phase 3 design using the cure rate model. (SAS and R)., 2017.
Jung, Sin-Ho. CTD Systems (Java)., 2017.
Li, Meng, Ana-Maria Staicu, and Howard D. Bondell. cSFM: Covariate-adjusted skewed functional model (R).. 1.1 ed., 2014.
Bayar, Mohamed, Anastasia Ivanova, and Gwenael Le Teuff. CRM2DIM: Dual-Agent Bayesian Continual Reassessment Method (SAS). 1.0 ed., 2019.
Cornea, Emil, Bahjat Qaqish, and Joseph G. Ibrahim. CR: Power calculation for weighted log-rank tests in cure rate models (R).., 2012.
Brucker, Amanda, Shannon T. Holloway, and Jung-Ying Tzeng. CONCUR: Kernel-based association test for copy number variation (CNV) aggregate analysis (R)., 2020.
Jiang, Yuchao, and Nancy R. Zhang. CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R)., 2018.
Hu, Yi-Juan, Dan-Yu Lin, Wei Sun, and Donglin Zeng. CNVstat: Statistical association analysis of copy number variants (C).. 1.0 ed., 2012.
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.
Bondell, Howard D., and Shannon T. Holloway. CasANOVA: Simultaneous factor selection and collapsing levels in ANOVA (R).. R 3.0 ed., 2013.
Diao, Guoqing, Jun Dong, Donglin Zeng, and Joseph G. Ibrahim. BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++)., 2018.
Ibrahim, Joseph G., Yeongjin Gwon, and Ming-Hui Chen. BSMED: Bayesian survival meta-experimental design using historical data (SAS).. 1.0 ed., 2015.
Psioda, Matthew, and Joseph G. Ibrahim. BPower: Computes two versions of Bayesian power for normal models (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.

Pages