Project 2.3: 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
An B, Guo J, Liu Y. "Hypothesis testing for band size detection of high-dimensional banded precision matrices." Biometrika.;101(2):477-483. PubMed
Appell ML, Berg J, Duley J, Evans WE, Kennedy MA, Lennard L, Marinaki T, McLeod HL, Relling MV, Schaeffeler E, Schwab M, Weinshilboum R, Yeoh AEJ, McDonagh EM, Hebert JM, Klein TE, Coulthard SA. "Nomenclature for alleles of the thiopurine methyltransferase gene." Pharmacogenet Genomics.;23(4):242-8. 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
Bhattacharya A, García-Closas M, Olshan AF, Perou CM, Troester MA, Love MI. "A framework for transcriptome-wide association studies in breast cancer in diverse study populations." Genome Biol.;21(1):42. PubMed
Bondell HD, Reich BJ. "Consistent high-dimensional Bayesian variable selection via penalized credible regions." J Am Stat Assoc.;107(500):1610-1624. 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
Cao H, Kosorok MR. "Simultaneous critical values for t-tests in very high dimensions." Bernoulli (Andover).;17(1):347-394. PubMed
Cao H, Sun W, Kosorok MR. "The optimal power puzzle: Scrutiny of the monotone likelihood ratio assumption in multiple testing." Biometrika.;100(2):495-502. 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, Ren Z, Zhao H, Zhou H. "Asymptotically normal and efficient estimation of covariate-adjusted Gaussian graphical model." J Am Stat Assoc.;111(513):394-406. PubMed
Chen G, Sullivan PF, Kosorok MR. "Biclustering with heterogeneous variance." Proc Natl Acad Sci U S A.;110(30):12253-8. 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 G, Liu Y, Shen D, Kosorok MR. "Composite large margin classifiers with latent subclasses for heterogeneous biomedical data." Stat Anal Data Min.;9(2):75-88. PubMed
Chen TH, Sun W, Fine JP. "Designing penalty functions in high dimensional problems: The role of tuning parameters." Electron J Stat.;10(2):2312-2328. PubMed
Chen J, Zhang C, Kosorok MR, Liu Y. "Double sparsity kernel learning with automatic variable selection and data extraction." Stat Interface.;11(3):401-420. 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
Chen M, Gao C, Zhao H. "Posterior contraction rates of the phylogenetic Indian buffet processes." Bayesian Anal.;11(2):477-497. PubMed
Chen TH, Sun W. "Prediction of cancer drug sensitivity using high-dimensional omic features." Biostatistics.;18(1):1-14. PubMed
Chen L, Lin DY, Zeng D. "Predictive accuracy of covariates for event times." Biometrika.;99(3):615-630. PubMed
Cobran EK, Chen RC, Overman R, Meyer AM, Kuo TM, O'Brien J, Stürmer T, Sheets NC, Goldin GH, Penn DC, Godley PA, Carpenter WR. "Racial differences in diffusion of intensity-modulated radiation therapy for localized prostate cancer." Am J Mens Health.;10(5):399-407. 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
Dasgupta S, Goldberg Y, Kosorok MR. "Feature elimination in kernel machines in moderately high dimensions." Ann Stat.;47(1):497-526. PubMed
Davenport CA, Maity A, Sullivan PF, Tzeng JY. "A powerful test for SNP effects on multivariate binary outcomes using kernel machine regression." Stat Biosci.;10(1):117-138. PubMed
Diao G, Zeng D, Yang S. "Efficient semiparametric estimation of short-term and long-term hazard ratios with right-censored data." Biometrics.;69(4):840-9. PubMed
Fu S, Zhang S, Liu Y. "Adaptively weighted large margin angle-based classifiers." J Multivar Anal.;166:282-299. 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
Gao F, Zeng D, Lin DY. "Semiparametric regression analysis of interval-censored data with informative dropout." Biometrics.;74(4):1213-1222. PubMed
Gao F, Zeng D, Couper D, Lin DY. "Semiparametric regression analysis of multiple right- and interval-censored events." J Am Stat Assoc.;114(527):1232-1240. PubMed
Ghosh A, Wright FA, Zou F. "Unified analysis of secondary traits in case-control association studies." J Am Stat Assoc.;108(502). PubMed
Gong S, Zhang K, Liu Y. "Efficient test-based variable selection for high-dimensional linear models." J Multivar Anal.;166:17-31. PubMed
Han X, Li Y, Huang J, Zhang Y, Holford T, Lan Q, Rothman N, Zheng T, Kosorok MR, Ma S. "Identification of predictive pathways for non-hodgkin lymphoma prognosis." Cancer Inform.;9:281-92. PubMed
Hao B, Sun WWei, Liu Y, Cheng G. "Simultaneous clustering and estimation of heterogeneous graphical models." J Mach Learn Res.;18. PubMed
He Q, Avery CL, Lin DY. "A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol.;37(8):759-67. PubMed
He Q, Lin DY. "A variable selection method for genome-wide association studies." Bioinformatics.;27(1):1-8. PubMed
He Q, Zhang HHelen, Avery CL, Lin DY. "Sparse meta-analysis with high-dimensional data." Biostatistics.;17(2):205-20. PubMed
Helgeson ES, Liu Q, Chen G, Kosorok MR, Bair E. "Biclustering via sparse clustering." Biometrics.;76(1):348-358. PubMed
Hidalgo SJTeran, Wu MC, Engel SM, Kosorok MR. "Goodness-of-fit test for nonparametric regression models: Smoothing spline ANOVA models as example." Comput Stat Data Anal.;122:135-155. PubMed
Hu YJ, Lin DY, Zeng D. "A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics.;11(4):583-98. PubMed
Hu YJ, Lin DY. "Analysis of untyped SNPs: Maximum likelihood and imputation methods." Genet Epidemiol.;34(8):803-15. PubMed
Hu YJ, Li Y, Auer PL, Lin DY. "Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations." Proc Natl Acad Sci U S A.;112(4):1019-24. PubMed
Hu J, Tzeng JY. "Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics.;30(11):1501-7. PubMed
Hu YJ, Berndt SI, Gustafsson S, Ganna A, Hirschhorn J, North KE, Ingelsson E, Lin DY. "Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet.;93(2):236-48. PubMed
Hu YJ, Sun W, Tzeng JY, Perou CM. "Proper use of allele-specific expression improves statistical power for cis-eQTL mapping with RNA-Seq data." J Am Stat Assoc.;110(511):962-974. PubMed
Huang H, Liu Y, Marron JS. "Bidirectional discrimination with application to data visualization." Biometrika.;99(4):851-864. PubMed
Huang H, Liu Y, Yuan M, Marron JS. "Statistical significance of clustering using soft thresholding." J Comput Graph Stat.;24(4):975-993. PubMed
Hung H, Lin YT, Chen P, Wang CC, Huang SY, Tzeng JY. "Detection of gene-gene interactions using multistage sparse and low-rank regression." Biometrics.;72(1):85-94. PubMed
Isogai Y, Wu Z, Love MI, Ahn MHoYoung, Bambah-Mukku D, Hua V, Farrell K, Dulac C. "Multisensory logic of infant-directed aggression by males. " Cell.;175(7):1827-1841.e17. PubMed
Jeng J, Rhyne J, Zhang T, Tzeng JY. "Effective SNP ranking improves the performance of eQTL mapping." Genet Epidemiol.;44(6):611-619. PubMed
Jeng J, Zhang T, Tzeng JY. "Efficient signal inclusion with genomic applications" J Am Stat Assoc.;114(528):1787-1799. PubMed
Jeng XJessie, Daye ZJohn, Lu W, Tzeng JY. "Rare variants association analysis in large-scale sequencing studies at the single locus level." PLoS Comput Biol.;12(6):e1004993. PubMed
Jensen BC, McLeod HL. "Pharmacogenomics as a risk mitigation strategy for chemotherapeutic cardiotoxicity." Pharmacogenomics.;14(2):205-13. PubMed
Jiang Y, Wang R, Urrutia E, Anastopoulos IN, Nathanson KL, Zhang NR. "CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing." Genome Biol.;19(1):202. PubMed
Jiang Y, Han Y, Petrovski S, Owzar K, Goldstein DB, Allen AS. "Incorporating functional information in tests of excess De Novo mutational load." Am J Hum Genet.;97(2):272-83. PubMed
Jung SH, Young S. "Power and sample size calculation for microarray studies." J Biopharm Stat.;22(1):30-42. 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
Kang C, Zhu H, Wright FA, Zou F, Kosorok MR. "The interactive decision committee for chemical toxicity analysis." J Stat Res.;46(2):157-186. PubMed
Kimes PK, Liu Y, Hayes DNeil, Marron JStephen. "Statistical significance of hierarchical clustering." Biometrics.;73(3):811-821. PubMed
Koehler ML, Bondell HD, Tzeng JY. "Evaluating haplotype effects in case-control studies via penalized-likelihood approaches: Prospective or retrospective analysis?" Genet Epidemiol.;34(8):892-911. PubMed
Kong D, Giovanello KS, Wang Y, Lin W, Lee E, Fan Y, Doraiswamy M, Zhu H. "Predicting Alzheimer's disease using combined imaging-whole genome SNP data." J Alzheimers Dis.;46(3):695-702. 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
Kong D, Maity A, Hsu FC, Tzeng JY. "Testing and estimation in marker-set association study using semiparametric quantile regression kernel machine." Biometrics.;72(2):364-71. PubMed
Kosorok MR, Laber EB. "Precision medicine." Annu Rev Stat Appl.;6:263-286. PubMed
Krens SD, McLeod HL, Hertz DL. "Pharmacogenetics, enzyme probes and therapeutic drug monitoring as potential tools for individualizing taxane therapy." Pharmacogenomics.;14(5):555-74. PubMed
Lee MH, Tzeng JY, Huang SY, Hsiao CKate. "Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies." BMC Genet.;12:48. PubMed
Lee W, Liu Y. "Joint estimation of multiple precision matrices with common structures." J Mach Learn Res.;16:1035-1062. PubMed
Li W, Chen MH, Wangy X, Dey DK. "Bayesian design of non-inferiority clinical trials via the Bayes factor." Stat Biosci.;10(2):439-459. 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 DY, Tang ZZ. "A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet.;89(3):354-67. PubMed
Lin DY. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol.;43(4):365-372. PubMed
Lin J, Gresham J, Wang T, Kim SYoung, Alvarez J, Damrauer JS, Floyd S, Granek J, Allen A, Chan C, Xie J, Owzar K. "bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics.;34(20):3581-3583. PubMed
Lin DY. "Discussion of the Paper by R. L. Prentice and Y. Huang - Optimal Designs and Efficient Inference for Biomarker Studies." Stat Theory Relat Fields.;2(1):21-22. 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
Lin DY, Zeng D. "Meta-analysis of genome-wide association studies: No efficiency gain in using individual participant data." Genet Epidemiol.;34(1):60-6. PubMed
Lin DY, Zeng D. "On the relative efficiency of using summary statistics versus individual-level data in meta-analysis." Biometrika.;97(2):321-332. PubMed
Lin DY, Zeng D, Tang ZZ. "Quantitative trait analysis in sequencing studies under trait-dependent sampling." Proc Natl Acad Sci U S A.;110(30):12247-52. 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 Y, He Q, Sun W. "Association analysis using somatic mutations." PLoS Genet.;14(11):e1007746. PubMed
Liu Y, Zhang HHelen, Wu Y. "Hard or soft classification? Large-margin unified machines." J Am Stat Assoc.;106(493):166-177. 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, Wu Y, He Q. "Utility-based weighted multicategory robust support vector machines." Stat Interface.;3(4):465-476. PubMed
Love MI, Soneson C, Patro R. "Swimming downstream: Statistical analysis of differential transcript usage following Salmon quantification." F1000Res.;7:952. PubMed
Love MI, Soneson C, Hickey PF, Johnson LK, Pierce T, Shepherd L, Morgan M, Patro R. "Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol.;16(2):e1007664. PubMed
Lu W, Zhang HHelen, Zeng D. "Variable selection for optimal treatment decision." Stat Methods Med Res.;22(5):493-504. 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
Ma S, Kosorok MR, Huang J, Dai Y. "Incorporating higher-order representative features improves prediction in network-based cancer prognosis analysis." BMC Med Genomics.;4:5. 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
Maity A, Sullivan PF, Tzeng JY. "Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol.;36(7):686-95. 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
Mao L, Lin DY. "Semiparametric regression for the weighted composite endpoint of recurrent and terminal events." Biostatistics.;17(2):390-403. PubMed
Marceau R, Lu W, Holloway S, Sale MM, Worrall BB, Williams SR, Hsu FC, Tzeng JY. "A fast multiple-kernel method with applications to detect gene-environment interaction." Genet Epidemiol.;39(6):456-68. PubMed
Martinez K, Maity A, Yolken RH, Sullivan PF, Tzeng JY. "Robust kernel association testing (RobKAT)." Genet Epidemiol.;44(3):272-282. PubMed
Mathur R, Rotroff D, Ma J, Shojaie A, Motsinger-Reif A. "Gene set analysis methods: A systematic comparison." BioData Min.;11:8. PubMed
McCabe SD, Lin DY, Love MI. "Consistency and overfitting of multi-omics methods on experimental data." Brief Bioinform.;21(4):1277-1284. PubMed
McLeod HL. "Cancer pharmacogenomics: early promise, but concerted effort needed." Science.;339(6127):1563-6. PubMed
Mitha F, Herodotou H, Borisov N, Jiang C, Yoder J, Owzar K. "SNPpy--database management for SNP data from genome wide association studies." PLoS One.;6(10):e24982. PubMed
Nadkarni NV, Zhao Y, Kosorok MR. "Inverse regression estimation for censored data." J Am Stat Assoc.;106(493):178-190. PubMed
Naqa IEl, Kosorok MR, Jin J, Mierzwa M, Haken RKTen. "Prospects and challenges for clinical decision support in the era of big data." JCO Clin Cancer Inform.;2. PubMed
Neely ML, Bondell HD, Tzeng JY. "A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies." Biometrics.;71(2):529-37. PubMed
Owzar K, Li Z, Cox N, Jung SH. "Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol.;36(6):538-48. PubMed
Owzar K, Barry WT, Jung SH. "Statistical considerations for analysis of microarray experiments." Clin Transl Sci.;4(6):466-77. PubMed
Pang H, Ebisu K, Watanabe E, Sue LY, Tong T. "Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis." Hum Genomics.;5(1):5-16. PubMed
Pang H, Tong T, Ng M. "Block-diagonal discriminant analysis and its bias-corrected rules." Stat Appl Genet Mol Biol.;12(3):347-59. PubMed
Pang H, George SL, Hui K, Tong T. "Gene selection using iterative feature elimination random forests for survival outcomes." IEEE/ACM Trans Comput Biol Bioinform.;9(5):1422-31. PubMed
Pang H, Hauser M, Minvielle S. "Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet.;19(6):704-9. 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
Pang H, Jung SH. "Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes." Genet Epidemiol.;37(3):276-82. 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
Pietryk EW, Clement K, Elnagheeb M, Kuster R, Kilpatrick K, Love MI, Ideraabdullah FY. "Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod Toxicol.;78:9-19. PubMed
Pongpanich M, Neely ML, Tzeng JY. "On the aggregation of multimarker information for marker-set and sequencing data analysis: Genotype collapsing vs. similarity collapsing." Front Genet.;2:110. PubMed
Reich BJ, Bondell HD. "A spatial dirichlet process mixture model for clustering population genetics data." Biometrics.;67(2):381-90. PubMed
Ren Z, Davidian M, George SL, Goldberg RM, Wright FA, Tsiatis AA, Kosorok MR. "Research methods for clinical trials in personalized medicine: A systematic review..
Genome-wide association study identifies five new schizophrenia loci." Nat Genet.;43(10):969-76. PubMed
Sharma DB, Bondell HD, Zhang HHelen. "Consistent group identification and variable selection in regression with correlated predictors." J Comput Graph Stat.;22(2):319-340. PubMed
Shin S, Fine J, Liu Y. "Adaptive estimation with partially overlapping models." Stat Sin.;26(1):235-253. PubMed
Shin SJun, Wu Y, Zhang HHelen, Liu Y. "Probability-enhanced sufficient dimension reduction for binary classification." Biometrics.;70(3):546-55. PubMed
Shterev ID, Jung SH, George SL, Owzar K. "permGPU: Using graphics processing units in RNA microarray association studies." BMC Bioinformatics.;11:329. PubMed
Sibley A, Li Z, Jiang Y, Li YJ, Chan C, Allen A, Owzar K. "Facilitating the calculation of the efficient score using symbolic computing." Am Stat.;72(2):199-205. 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
Sohn I, Owzar K, Lim J, George SL, Cushman SMackey, Jung SH. "Multiple testing for gene sets from microarray experiments." BMC Bioinformatics.;12:209. PubMed
Sohn I, Owzar K, George SL, Kim S, Jung SH. "Robust test method for time-course microarray experiments." BMC Bioinformatics.;11:391. PubMed
Soneson C, Love MI, Patro R, Hussain S, Malhotra D, Robinson MD. "A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance.;2(1). 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
Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DNeil, Chen M, Lin DY. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res.;46(6):3009-3018. PubMed
Tan HJ, Meyer AM, Kuo TM, Smith AB, Wheeler SB, Carpenter WR, Nielsen ME. "Provider-based research networks and diffusion of surgical technologies among patients with early-stage kidney cancer." Cancer.;121(6):836-43. PubMed
Tang ZZ, Lin DY. "MASS: Meta-analysis of score statistics for sequencing studies." Bioinformatics.;29(14):1803-5. PubMed
Tang ZZ, Lin DY. "Meta-analysis for discovering rare-variant associations: Statistical methods and software programs." Am J Hum Genet.;97(1):35-53. PubMed
Tang ZZ, Lin DY. "Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol.;38(5):389-401. 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, Franceschini N, North KE, Boerwinkle E, Lin DY. "Analysis of sequence data under multivariate trait-dependent sampling." J Am Stat Assoc.;110(510):560-572. 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
Tzeng JY, Magnusson PKE, Sullivan PF, Szatkiewicz JP. "A new method for detecting associations with rare copy-number variants." PLoS Genet.;11(10):e1005403. PubMed
Tzeng JY, Lu W, Hsu FC. "Gene-level pharmacogenetic analysis on survival outcomes using gene-trait similarity regression." Ann Appl Stat.;8(2):1232-1255. PubMed
Tzeng JY, Zhang D, Pongpanich M, Smith C, McCarthy MI, Sale MM, Worrall BB, Hsu FC, Thomas DC, Sullivan PF. "Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression." Am J Hum Genet.;89(2):277-88. PubMed
Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. "Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics.;34(12):2126-2128. PubMed
Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L. "Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol.;19(1):24. PubMed
Walter V, Nobel AB, Wright FA. "DiNAMIC: A method to identify recurrent DNA copy number aberrations in tumors." Bioinformatics.;27(5):678-85. PubMed
Wang WB, Wang W, Sun W, Crowley JJ, Szatkiewicz JP. "Allele-specific copy-number discovery from whole-genome and whole-exome sequencing." Nucleic Acids Res.;43(14):e90. PubMed
Wang X, Epstein MP, Tzeng JY. "Analysis of gene-gene interactions using gene-trait similarity regression." Hum Hered.;78(1):17-26. PubMed
Wang Z, Maity A, Luo Y, Neely ML, Tzeng JY. "Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol.;39(2):122-33. PubMed
Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers S, Krauthammer M. "Global copy number profiling of cancer genomes." Bioinformatics.;32(6):926-8. PubMed
Wang Z, Maity A, Hsiao CKate, Voora D, Kaddurah-Daouk R, Tzeng JY. "Module-based association analysis for omics data with network structure." PLoS One.;10(3):e0122309. PubMed
Wang X, Zhang D, Tzeng JY. "Pathway-guided identification of gene-gene interactions." Ann Hum Genet.;78(6):478-91. PubMed
Wang C, Tzeng JY, Wu PZ, Preisig M, Hsiao CKate. "Reexamining dis/similarity-based tests for rare-variant association with case-control samples." Genetics.;209(1):105-113. PubMed
Wei S, Kosorok MR. "Latent supervised learning." J Am Stat Assoc.;108(503). PubMed
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West RMarceau, Lu W, Rotroff DM, Kuenemann MA, Chang SM, Wu MC, Wagner MJ, Buse JB, Motsinger-Reif AA, Fourches D, Tzeng JY. "Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol.;15(2):e1006722. PubMed
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