Publications

Software
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.
Tang, Zheng-Zheng, and Dan-Yu Lin. MASS: Meta-analysis of sequencing studies (C).. 5.0 ed., 2013.
Zhou, Yi-Hui. mcc: Moment corrected correlation an approximation to exact association testing of two vectors (R).. 1.0 ed., 2014.
Luo, Sheng, Yong Chen, Xiao Su, and Haitao Chu. mmeta: Multivariate meta-analysis (R).. 2.2 ed., 2014.
Holloway, Shannon T.. modelObj: A model object framework for regression analysis (R).. 1.0 ed., 2015.
He, Qianchuan, and Dan-Yu Lin. MOST: Multivariate outcome score test (C).. 1.0 ed., 2013.
Psioda, Matthew, and Joseph G. Ibrahim. MultiARMSBinary: Simulates Bayes adaptive randomization of multiple arms in a beta-binomial simulation (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. NormalMean_BSS: Calculates the Bayesian sample size based on ACC, ALC, and WOC for normal model (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. normDesignPP: Bayesian sample size for non-inferiority randomized trials with normal data with power prior (SAS).., 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.
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.
Lin, Lifeng, Jing Zhang, and Haitao Chu. pcnetmeta: Methods for patient-centered network meta-analysis (R).. 1.2 ed., 2014.
Shterev, Ivo D., Sin-Ho Jung, Stephen L. George, and Kouros Owzar. permGPU: Using graphics processing units in RNA microarray association studies (CUDA).., 2011.
Zhu, Hongtu, Joseph G. Ibrahim, and Hyunsoon Cho. Perturbation and scaled Cook's distance (C++/Matlab).., 2012.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. PICAFT: Semiparametric Estimation of the Accelerated Failure Time Model With Partly Interval-Censored Data (R)., 2017.
West, Rachel Marceau, and Shannon T. Holloway. POINT: Protein Structure Guided Local Test (R). 1.0 ed., 2019.
Jung, Sin-Ho, and Stanley S Young. Power and sample size calculation for microarray studies (Fortran).., 2012.
Gao, Fei, Donglin Zeng, and Joseph G. Ibrahim. Power calculations and confidence intervals in phase II design with over enrollment (SAS/R).., 2014.
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.
Zhang, Chong, Yufeng Liu, and Shannon T. Holloway. RAMSVM: Reinforced angle-based multicategory support vector machines (R).. 2.0 ed., 2016.
Zhu, Ruoqing, and Michael R. Kosorok. RLT: Reinforcement learning trees (R).. 2.0 ed., 2015.
Yi, Chanhee, Alexander Sibley, and Kouros Owzar. RSNPset: Genome-wide SNP set analysis on the basis of efficient scores (R).. v0.2 ed., 2014.
Liu, Yang, Wei Sun, and Qianchuan He. SAME: Somatic mutation Association test with Measurement Errors (R)., 2018.
Jung, Sin-Ho, and Shein-Chung Chow. Sample size calculation for comparing survival curves under general hypotheses testing (Fortran).., 2012.
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.
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.
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.
Kimes, Patrick. sigclust2: Statistical Significance for Hierarchical Clustering (R). 1.2.4 ed., 2016.
Ivanova, Anastasia, and A Deal. Simon’s like design with relaxed futility stopping (Web)., 2017.
Stefanski, Leonard A., Yichao Wu, and Kyle White. skda: Sparse (multicategory) kernel discriminant analysis (R).. 0.1 ed., 2013.
Yi, Chanhee, Alexander Sibley, and Kouros Owzar. snplist: Tools to create gene sets (R).. 0.12 ed., 2013.
Hu, Yi-Juan, Dan-Yu Lin, and Donglin Zeng. SNPMStat v4.0 : Statistical analysis of SNP-disease association with missing genotype data.., 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.
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.
Fan, Aiilin, and Shannon T. Holloway. subdetect: Detect subgroup with an enhanced treatment effect (R).. 1.1 ed., 2016.
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.
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.
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.
Chen, Mengjie. SynthEx: Tools for CNA detection and tumor heterogeneity profiling (R)., 2017.
Hu, Yi-Juan, and Dan-Yu Lin. tagIMPUTE: Tag-based imputation.. 1.0 ed., 2010.
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.
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.
Tao, Ran. TwoPhaseReg: Regression Analysis Under General Two-Phase Sampling (R)., 2018.
Chen, Yong, Chuan Hong, Haitao Chu, and Yulun Liu. xmeta: A Toolbox for Multivariate Meta-Analysis (R)., 2017.
Web Article
Wang, Xiaofei, Jianwen Cai, and Stephen L. George. Enriched biomarker-driven clinical trials. In Wiley StatsRef: Statistics Reference Online. Wiley, 2019.
Chen, G, Michael R. Kosorok, and X Zhou. Nonconvex Optimization. In Wiley StatsRef: Statistics Reference Online., 2018.
Davidian, Marie, Anastasios A. Tsiatis, and Eric B. Laber. Optimal dynamic treatment regimes In Wiley Statsref. Optimal dynamic treatment regimes., 2016.
Laber, Eric B., E Rose, Marie Davidian, and Anastasios A. Tsiatis. Q-Learning. In Wiley StatsRef: Statistics Reference Online. Wiley, 2018.
George, Stephen L.. Sorting the wheat from the chaff: How do we know which cancer therapies really work? . Huffington Post, 2013.

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