Project 1.4: Publications




 

Aims       Publications       Software       Investigators

Acharya CR, McCarthy JM, Owzar K, Allen AS. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics.;17:257. PubMed
Acharya CR, Owzar K, Allen AS. "Mapping eQTL by leveraging multiple tissues and DNA methylation." BMC Bioinformatics.;18(1):455. PubMed
Baldwin M, Owzar K, Zembutsu H, Chhibber A, Kubo M, Jiang C, Watson D, Eclov RJ, Mefford J, McLeod HL, Friedman PN, Hudis CA, Winer EP, Jorgenson EM, Witte JS, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL. "A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res.;18(18):5099-109. PubMed
Bellach A, Kosorok MR, Rüschendorf L, Fine JP. "Weighted NPMLE for the subdistribution of a competing risk." J Am Stat Assoc.;114(525):259-270. PubMed
Butler EL, Laber EB, Davis SM, Kosorok MR. "Incorporating patient preferences into estimation of optimal individualized treatment rules." Biometrics.;74(1):18-26. PubMed
Chang SM, Tzeng JY, Chen RB. "Fast Bayesian variable screenings for binary response regressions with small sample size." J Stat Comput Simul.;87(14):2708-2723. PubMed
Chang J, Tang CYong, Wu Y. "Local independence feature screening for nonparametric and semiparametric models by marginal empirical likelihood." Ann Stat.;44(2):515-539. PubMed
Chen M, Lin H, Zhao H. "Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains." Ann Appl Stat.;10(1):506-526. PubMed
Chen J, Fu H, He X, Kosorok MR, Liu Y. "Estimating individualized treatment rules for ordinal treatments." Biometrics.;74(3):924-933. PubMed
Chen T, Zeng D, Wang Y. "Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration." Biometrics.;71(4):918-28. PubMed
Chen H, Zeng D, Wang Y. "Penalized nonlinear mixed effects model to identify biomarkers that predict disease progression." Biometrics.;73(4):1343-1354. PubMed
Cui Y, Zhu R, Kosorok M. "Tree based weighted learning for estimating individualized treatment rules with censored data." Electron J Stat.;11(2):3927-3953. PubMed
Gao F, Zeng D, Lin DY. "Semiparametric estimation of the accelerated failure time model with partly interval-censored data." Biometrics.;73(4):1161-1168. PubMed
Helgeson ES, Liu Q, Chen G, Kosorok MR, Bair E. "Biclustering via sparse clustering." Biometrics.;76(1):348-358. PubMed
Jusakul A, Cutcutache I, Yong CHan, Lim JQuan, Huang MNi, Padmanabhan N, Nellore V, Kongpetch S, Ng AWei Tian, Ng LMoy, Choo SPin, Myint SSwe, Thanan R, Nagarajan S, Lim WKhong, Ng CChuan Youn, Boot A, Liu M, Ong CKiat, Rajasegaran V, Lie S, Lim ASoon Tiong, Lim THui, Tan J, Loh JLiang, McPherson JR, Khuntikeo N, Bhudhisawasdi V, Yongvanit P, Wongkham S, Totoki Y, Nakamura H, Arai Y, Yamasaki S, Chow PKahHoe, Chung AYaw Fui, Ooi LLucien Pen, Lim KHon, Dima S, Duda DG, Popescu I, Broet P, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho ALopes, Vettore ALuiz, Rhee H, Park YNyun, Alexandrov LB, Gordân R, Rozen SG, Shibata T, Pairojkul C, Teh BTean, Tan P. "Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma." Cancer Discov.;7(10):1116-1135. PubMed
Kimes PK, Liu Y, Hayes DNeil, Marron JStephen. "Statistical significance of hierarchical clustering." Biometrics.;73(3):811-821. PubMed
Kong D, Maity A, Hsu FC, Tzeng JY. "Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"." Biometrics.;74(2):767-768. PubMed
Kosorok MR, Laber EB. "Precision medicine." Annu Rev Stat Appl.;6:263-286. PubMed
Li Z, Lin J, Sibley AB, Truong T, Chua KC, Jiang Y, McCarthy J, Kroetz DL, Allen A, Owzar K. "Efficient estimation of grouped survival models." BMC Bioinformatics.;20(1):269. PubMed
Li Z, Owzar K. "Fitting Cox models with doubly censored data using spline-based sieve marginal likelihood." Scand Stat Theory Appl.;43(2):476-486. PubMed
Lin J, Sibley A, Shterev I, Nixon A, Innocenti F, Chan C, Owzar K. "fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies." BMC Bioinformatics.;20(1):333. PubMed
Lin DY, Tao R, Kalsbeek WD, Zeng D, Gonzalez F, Fernández-Rhodes L, Graff M, Koch GG, North KE, Heiss G. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet.;95(6):675-88. PubMed
Little P, Lin DY, Sun W. "Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med.;11(1):37. PubMed
Liu J, Sun W, Liu Y. "Joint skeleton estimation of multiple directed acyclic graphs for heterogeneous population." Biometrics.;75(1):36-47. PubMed
Liu Z, Song R, Zeng D, Zhang J. "Principal components adjusted variable screening." Comput Stat Data Anal.;110:134-144. PubMed
Liu Y, Wang Y, Zeng D. "Sequential multiple assignment randomization trials with enrichment design." Biometrics.;73(2):378-390. PubMed
Liu Y, Wu Y, He Q. "Utility-based weighted multicategory robust support vector machines." Stat Interface.;3(4):465-476. PubMed
Luo Y, Maity A, Wu MC, Smith C, Duan Q, Li Y, Tzeng JY. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol.;42(3):276-287. PubMed
Maity A, Zhao J, Sullivan PF, Tzeng JY. "Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet Epidemiol.;42(1):64-79. PubMed
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.;79(2):573-587. PubMed
Mao L, Lin DY, Zeng D. "Semiparametric regression analysis of interval-censored competing risks data." Biometrics.;73(3):857-865. PubMed
Pang H, Kim I, Zhao H. "Random effects model for multiple pathway analysis with applications to type II diabetes microarray data." Stat Biosci.;7(2):167-186. PubMed
Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MSaad, Machol I, Love MI, Aiden ELieberman, Bassik MC, Snyder MP. "Static and dynamic DNA loops form AP-1-bound activation hubs during macrophage development." Mol Cell.;67(6):1037-1048.e6. PubMed
Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M. "SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling." Genome Biol.;18(1):66. PubMed
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.;11(1):364-384. PubMed
Tang ZZ, Bunn P, Tao R, Liu Z, Lin DY. "PreMeta: A tool to facilitate meta-analysis of rare-variant associations." BMC Genomics.;18(1):160. PubMed
Tao R, Zeng D, Lin DY. "Efficient semiparametric inference under two-phase sampling, with applications to genetic association studies." J Am Stat Assoc.;112(520):1468-1476. PubMed
Xie J, Li R. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates." J R Stat Soc Series B Stat Methodol.;80(5):1015-1034. PubMed
Xue H, Wu S, Wu Y, Idarraga JCRamirez, Wu H. "Independence screening for high dimensional nonlinear additive ODE models with applications to dynamic gene regulatory networks." Stat Med.;37(17):2630-2644. PubMed
Yazdani A, Yazdani A, Elsea SH, Schaid DJ, Kosorok MR, Dangol G, Samiei A. "Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics." BMC Genomics.;20(1):395. PubMed
Zeng D, Gao F, Lin DY. "Maximum likelihood estimation for semiparametric regression models with multivariate interval-censored data." Biometrika.;104(3):505-525. PubMed
Zhang X, Wu Y, Wang L, Li R. "A consistent information criterion for support vector machines in diverging model spaces." J Mach Learn Res.;17(16):1-26. PubMed
Zhang C, Liu Y, Wu Y. "On quantile regression in reproducing kernel Hilbert spaces with data sparsity constraint." J Mach Learn Res.;17(40):1-45. PubMed
Zhang C, Liu Y, Wang J, Zhu H. "Reinforced angle-based multicategory support vector machines." J Comput Graph Stat.;25(3):806-825. PubMed
Zhang X, Wu Y, Wang L, Li R. "Variable selection for support vector machines in moderately high dimensions." J R Stat Soc Series B Stat Methodol.;78(1):53-76. PubMed
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.;10229:336-352. PubMed
Zhou X, Mayer-Hamblett N, Khan U, Kosorok MR. "Residual weighted learning for estimating individualized treatment rules." J Am Stat Assoc.;112(517):169-187. PubMed