A Consistent Information Criterion for Support Vector Machines in Diverging Model Spaces. Zhang, Xiang, Yichao Wu, Lan Wang, and Runze Li. "A Consistent Information Criterion for Support Vector Machines in Diverging Model Spaces." J Mach Learn Res 17, no. 16 (2016): 1-26. Read more about A Consistent Information Criterion for Support Vector Machines in Diverging Model Spaces.PubMed
A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101. R Baldwin, Michael, Kouros Owzar, Hitoshi Zembutsu, Aparna Chhibber, Michiaki Kubo, Chen Jiang, Dorothy Watson, Rachel J. Eclov, Joel Mefford, Howard L. McLeod et al. "A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res 18, no. 18 (2012): 5099-109. Read more about A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101.PubMed
Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time. Little, Paul, Dan-Yu Lin, and Wei Sun. "Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37. Read more about Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time.PubMed
Biclustering via sparse clustering. Helgeson, Erika S., Qian Liu, Guanhua Chen, Michael R. Kosorok, and Eric Bair. "Biclustering via sparse clustering." Biometrics 76, no. 1 (2020): 348-358. Read more about Biclustering via sparse clustering.PubMed
CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS. Chen, Mengjie, Haifan Lin, and Hongyu Zhao. "CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS." Ann Appl Stat 10, no. 1 (2016): 506-526. Read more about CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS.PubMed
Efficient estimation of grouped survival models. Li, Zhiguo, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew Allen, and Kouros Owzar. "Efficient estimation of grouped survival models." BMC Bioinformatics 20, no. 1 (2019): 269. Read more about Efficient estimation of grouped survival models.PubMed
Efficient Estimation of Semiparametric Transformation Models for the Cumulative Incidence of Competing Risks. Mao, Lu, and D Y. Lin. "Efficient Estimation of Semiparametric Transformation Models for the Cumulative Incidence of Competing Risks." J R Stat Soc Series B Stat Methodol 79, no. 2 (2017): 573-587. Read more about Efficient Estimation of Semiparametric Transformation Models for the Cumulative Incidence of Competing Risks.PubMed
Efficient Semiparametric Inference Under Two-Phase Sampling, With Applications to Genetic Association Studies. Tao, Ran, Donglin Zeng, and Dan-Yu Lin. "Efficient Semiparametric Inference Under Two-Phase Sampling, With Applications to Genetic Association Studies." J Am Stat Assoc 112, no. 520 (2017): 1468-1476. Read more about Efficient Semiparametric Inference Under Two-Phase Sampling, With Applications to Genetic Association Studies.PubMed
Estimating individualized treatment rules for ordinal treatments. Chen, Jingxiang, Haoda Fu, Xuanyao He, Michael R. Kosorok, and Yufeng Liu. "Estimating individualized treatment rules for ordinal treatments." Biometrics 74, no. 3 (2018): 924-933. Read more about Estimating individualized treatment rules for ordinal treatments.PubMed
Exploiting expression patterns across multiple tissues to map expression quantitative trait loci. Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257. Read more about Exploiting expression patterns across multiple tissues to map expression quantitative trait loci.PubMed
False discovery rate control for high dimensional networks of quantile associations conditioning on covariates. Xie, Jichun, and Ruosha Li. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates." J R Stat Soc Series B Stat Methodol 80, no. 5 (2018): 1015-1034. Read more about False discovery rate control for high dimensional networks of quantile associations conditioning on covariates.PubMed
Fast Bayesian Variable Screenings for Binary Response Regressions with Small Sample Size. Chang, S-M, J-Y Tzeng, and R-B Chen. "Fast Bayesian Variable Screenings for Binary Response Regressions with Small Sample Size." J Stat Comput Simul 87, no. 14 (2017): 2708-2723. Read more about Fast Bayesian Variable Screenings for Binary Response Regressions with Small Sample Size.PubMed
fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies. Lin, Jiaxing, Alexander Sibley, Ivo Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan, and Kouros Owzar. "fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies." BMC Bioinformatics 20, no. 1 (2019): 333. Read more about fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies.PubMed
Fitting Cox Models with Doubly Censored Data Using Spline-Based Sieve Marginal Likelihood. Li, Zhiguo, and Kouros Owzar. "Fitting Cox Models with Doubly Censored Data Using Spline-Based Sieve Marginal Likelihood." Scand Stat Theory Appl 43, no. 2 (2016): 476-486. Read more about Fitting Cox Models with Doubly Censored Data Using Spline-Based Sieve Marginal Likelihood.PubMed
Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos. Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88. Read more about Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos.PubMed
Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics. Yazdani, Azam, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael R. Kosorok, Gita Dangol, and Ahmad Samiei. "Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics." BMC Genomics 20, no. 1 (2019): 395. Read more about Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics.PubMed
GHREG: Semiparametric general hazards rate model for right-censored data (C). Diao, Guoqing. GHREG: Semiparametric general hazards rate model for right-censored data (C).., 2013. Read more about GHREG: Semiparametric general hazards rate model for right-censored data (C).
groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R) 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. Read more about groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R)
Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules. Butler, Emily L., Eric B. Laber, Sonia M. Davis, and Michael R. Kosorok. "Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics 74, no. 1 (2018): 18-26. Read more about Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules.PubMed
Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks. Xue, Hongqi, Shuang Wu, Yichao Wu, Juan C. Ramirez Idarraga, and Hulin Wu. "Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks." Stat Med 37, no. 17 (2018): 2630-2644. Read more about Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks.PubMed
Inference on phenotype-specific effects of genes using multivariate kernel machine regression. Maity, Arnab, Jing Zhao, Patrick F. Sullivan, and Jung-Ying Tzeng. "Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet Epidemiol 42, no. 1 (2018): 64-79. Read more about Inference on phenotype-specific effects of genes using multivariate kernel machine regression.PubMed
intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R) 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. Read more about intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R)
Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population. Liu, Jianyu, Wei Sun, and Yufeng Liu. "Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics 75, no. 1 (2019): 36-47. Read more about Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population.PubMed
LOCAL INDEPENDENCE FEATURE SCREENING FOR NONPARAMETRIC AND SEMIPARAMETRIC MODELS BY MARGINAL EMPIRICAL LIKELIHOOD. Chang, Jinyuan, Cheng Yong Tang, and Yichao Wu. "LOCAL INDEPENDENCE FEATURE SCREENING FOR NONPARAMETRIC AND SEMIPARAMETRIC MODELS BY MARGINAL EMPIRICAL LIKELIHOOD." Ann Stat 44, no. 2 (2016): 515-539. Read more about LOCAL INDEPENDENCE FEATURE SCREENING FOR NONPARAMETRIC AND SEMIPARAMETRIC MODELS BY MARGINAL EMPIRICAL LIKELIHOOD.PubMed
Mapping eQTL by leveraging multiple tissues and DNA methylation. Acharya, Chaitanya R., Kouros Owzar, and Andrew S. Allen. "Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC Bioinformatics 18, no. 1 (2017): 455. Read more about Mapping eQTL by leveraging multiple tissues and DNA methylation.PubMed
Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data. Zeng, Donglin, Fei Gao, and D Y. Lin. "Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data." Biometrika 104, no. 3 (2017): 505-525. Read more about Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data.PubMed
Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration. Chen, Tianle, Donglin Zeng, and Yuanjia Wang. "Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration." Biometrics 71, no. 4 (2015): 918-28. Read more about Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration.PubMed
On Quantile Regression in Reproducing Kernel Hilbert Spaces with Data Sparsity Constraint. Zhang, Chong, Yufeng Liu, and Yichao Wu. "On Quantile Regression in Reproducing Kernel Hilbert Spaces with Data Sparsity Constraint." J Mach Learn Res 17, no. 40 (2016): 1-45. Read more about On Quantile Regression in Reproducing Kernel Hilbert Spaces with Data Sparsity Constraint.PubMed
On the substructure controls in rare variant analysis: Principal components or variance components? Luo, Yiwen, Arnab Maity, Michael C. Wu, Chris Smith, Qing Duan, Yun Li, and Jung-Ying Tzeng. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287. Read more about On the substructure controls in rare variant analysis: Principal components or variance components?PubMed
OTRselect: Variable selection for optimal treatment decision (R). 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. Read more about OTRselect: Variable selection for optimal treatment decision (R).
Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression. Chen, Huaihou, Donglin Zeng, and Yuanjia Wang. "Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression." Biometrics 73, no. 4 (2017): 1343-1354. Read more about Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression.PubMed
Precision Medicine. Kosorok, Michael R., and Eric B. Laber. "Precision Medicine." Annu Rev Stat Appl 6 (2019): 263-286. Read more about Precision Medicine.PubMed
PreMeta: a tool to facilitate meta-analysis of rare-variant associations. Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Zhouwen Liu, and Dan-Yu Lin. "PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160. Read more about PreMeta: a tool to facilitate meta-analysis of rare-variant associations.PubMed
Principal Components Adjusted Variable Screening. Liu, Zhongkai, Rui Song, Donglin Zeng, and Jiajia Zhang. "Principal Components Adjusted Variable Screening." Comput Stat Data Anal 110 (2017): 134-144. Read more about Principal Components Adjusted Variable Screening.PubMed
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. Zhao, Jingkang, Dongshunyi Li, Jungkyun Seo, Andrew S. Allen, and Raluca Gordân. "Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding." Res Comput Mol Biol 10229 (2017): 336-352. Read more about Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.PubMed
Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data. Pang, Herbert, Inyoung Kim, and Hongyu Zhao. "Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data." Stat Biosci 7, no. 2 (2015): 167-186. Read more about Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data.PubMed
Reinforced Angle-based Multicategory Support Vector Machines. Zhang, Chong, Yufeng Liu, Junhui Wang, and Hongtu Zhu. "Reinforced Angle-based Multicategory Support Vector Machines." J Comput Graph Stat 25, no. 3 (2016): 806-825. Read more about Reinforced Angle-based Multicategory Support Vector Machines.PubMed
Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine". Kong, Dehan, Arnab Maity, Fang-Chi Hsu, and Jung-Ying Tzeng. "Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"." Biometrics 74, no. 2 (2018): 767-768. Read more about Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine".PubMed
Residual Weighted Learning for Estimating Individualized Treatment Rules. Zhou, Xin, Nicole Mayer-Hamblett, Umer Khan, and Michael R. Kosorok. "Residual Weighted Learning for Estimating Individualized Treatment Rules." J Am Stat Assoc 112, no. 517 (2017): 169-187. Read more about Residual Weighted Learning for Estimating Individualized Treatment Rules.PubMed
Semiparametric estimation of the accelerated failure time model with partly interval-censored data. Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric estimation of the accelerated failure time model with partly interval-censored data." Biometrics 73, no. 4 (2017): 1161-1168. Read more about Semiparametric estimation of the accelerated failure time model with partly interval-censored data.PubMed
Semiparametric regression analysis of interval-censored competing risks data. Mao, Lu, Dan-Yu Lin, and Donglin Zeng. "Semiparametric regression analysis of interval-censored competing risks data." Biometrics 73, no. 3 (2017): 857-865. Read more about Semiparametric regression analysis of interval-censored competing risks data.PubMed
Semiparametric Single-Index Model for Estimating Optimal Individualized Treatment Strategy. Song, Rui, Shikai Luo, Donglin Zeng, Hao Helen Zhang, Wenbin Lu, and Zhiguo Li. "Semiparametric Single-Index Model for Estimating Optimal Individualized Treatment Strategy." Electron J Stat 11, no. 1 (2017): 364-384. Read more about Semiparametric Single-Index Model for Estimating Optimal Individualized Treatment Strategy.PubMed
Sequential multiple assignment randomization trials with enrichment design. Liu, Ying, Yuanjia Wang, and Donglin Zeng. "Sequential multiple assignment randomization trials with enrichment design." Biometrics 73, no. 2 (2017): 378-390. Read more about Sequential multiple assignment randomization trials with enrichment design.PubMed
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Phanstiel, Douglas H., Kevin Van Bortle, Damek Spacek, Gaelen T. Hess, Muhammad Saad Shamim, Ido Machol, Michael I. Love, Erez Lieberman Aiden, Michael C. Bassik, and Michael P. Snyder. "Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development." Mol Cell 67, no. 6 (2017): 1037-1048.e6. Read more about Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.PubMed
Statistical significance for hierarchical clustering. Kimes, Patrick K., Yufeng Liu, David Neil Hayes, and James Stephen Marron. "Statistical significance for hierarchical clustering." Biometrics 73, no. 3 (2017): 811-821. Read more about Statistical significance for hierarchical clustering.PubMed
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. Silva, Grace O., Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou, and Mengjie Chen. "SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol 18, no. 1 (2017): 66. Read more about SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.PubMed
TensorGxG: A sparse and low-rank screening based on the combination of a low-rank interaction model and the Lasso screening (Matlab). 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. Read more about TensorGxG: A sparse and low-rank screening based on the combination of a low-rank interaction model and the Lasso screening (Matlab).
TRECASE_MLE: eQTL mapping based on total read count and allele-specific expression in RNA-Seq data with maximum-likelihood estimation (C/C++). 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. Read more about TRECASE_MLE: eQTL mapping based on total read count and allele-specific expression in RNA-Seq data with maximum-likelihood estimation (C/C++).
Tree based weighted learning for estimating individualized treatment rules with censored data. Cui, Yifan, Ruoqing Zhu, and Michael Kosorok. "Tree based weighted learning for estimating individualized treatment rules with censored data." Electron J Stat 11, no. 2 (2017): 3927-3953. Read more about Tree based weighted learning for estimating individualized treatment rules with censored data.PubMed
Utility-based Weighted Multicategory Robust Support Vector Machines. Liu, Yufeng, Yichao Wu, and Qinying He. "Utility-based Weighted Multicategory Robust Support Vector Machines." Stat Interface 3, no. 4 (2010): 465-476. Read more about Utility-based Weighted Multicategory Robust Support Vector Machines.PubMed
Variable Selection for Support Vector Machines in Moderately High Dimensions. Zhang, Xiang, Yichao Wu, Lan Wang, and Runze Li. "Variable Selection for Support Vector Machines in Moderately High Dimensions." J R Stat Soc Series B Stat Methodol 78, no. 1 (2016): 53-76. Read more about Variable Selection for Support Vector Machines in Moderately High Dimensions.PubMed
Weighted NPMLE for the Subdistribution of a Competing Risk. Bellach, Anna, Michael R. Kosorok, Ludger Rüschendorf, and Jason P. Fine. "Weighted NPMLE for the Subdistribution of a Competing Risk." J Am Stat Assoc 114, no. 525 (2019): 259-270. Read more about Weighted NPMLE for the Subdistribution of a Competing Risk.PubMed
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135. Read more about Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.PubMed