Publications

2019
Neupane S, Fučíková K, Lewis LA, Kuo L, Chen M-H, Lewis PO. "Assessing Combinability of Phylogenomic Data using Bayes Factors." Syst. Biol.. 2019.
Williams LA, Hoadley KA, Nichols HB, et al. "Differences in race, molecular and tumor characteristics among women diagnosed with invasive ductal and lobular breast carcinomas." Cancer Causes Control. 2019;30(1):31-39.
Yimit A, Adebali O, Sancar A, Jiang Y. "Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs." Nat Commun. 2019;10(1):309.
Dasgupta S, Goldberg Y, Kosorok MR. "FEATURE ELIMINATION IN KERNEL MACHINES IN MODERATELY HIGH DIMENSIONS." Ann Stat. 2019;47(1):497-526.
Lachos VH, Matos LA, Castro LM, Chen M-H. "Flexible longitudinal linear mixed models for multiple censored responses data." Stat Med. 2019;38(6):1074-1102.
Wong KYau, Fan C, Tanioka M, et al. "I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms." Genome Biol.. 2019;20(1):52.
West RMarceau, Lu W, Rotroff DM, et al. "Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput. Biol.. 2019;15(2):e1006722.
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. 2019;2(1).
Jung S-H, Chi SAh, Ahn HJoo. "K-Sample comparisons using propensity analysis." Biom J. 2019.
Maitra P, Amorim LDAF, Cai J. "Multiplicative rates model for recurrent events in case-cohort studies." Lifetime Data Anal. 2019.
Xiao W, Zhang HH, Lu W. "Robust regression for optimal individualized treatment rules." Stat Med. 2019.
Zhou Q, Cai J, Zhou H. "Semiparametric inference for a two-stage outcome-dependent sampling design with interval-censored failure time data." Lifetime Data Anal. 2019.
Lin D-Y. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet. Epidemiol.. 2019.
Yang Y, Hu J, Selby CP, et al. "Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice." J. Biol. Chem.. 2019;294(1):210-217.
Brownstein NC, Cai J. "Tests of trend between disease outcomes and ordinal covariates discretized from underlying continuous variables: simulation studies and applications to NHANES 2007-2008." BMC Med Res Methodol. 2019;19(1):2.
2018
Fu S, Zhang S, Liu Y. "Adaptively weighted large-margin angle-based classifiers." J Multivar Anal. 2018;166:282-299.
Wang T. AEBSD: Sample size of AEBSD and Comparison with BSD (R).; 2018.
Burbank AJ, Todoric K, Steele P, et al. "Age and African-American race impact the validity and reliability of the asthma control test in persistent asthmatics." Respir. Res.. 2018;19(1):152.
Kim S, Zeng D, Cai J. "Analysis of multiple survival events in generalized case-cohort designs." Biometrics. 2018;74(4):1250-1260.
Zhu A, Ibrahim JG, Love MI. apeglm: Approximate posterior estimation for GLM coefficients (R).; 2018.
Wu J, DE Castro M, Schifano ED, Chen M-H. "Assessing covariate effects using Jeffreys-type prior in the Cox model in the presence of a monotone partial likelihood." J Stat Theory Pract. 2018;12(1):23-41.
Zhao J, Yu G, Liu Y. "ASSESSING ROBUSTNESS OF CLASSIFICATION USING ANGULAR BREAKDOWN POINT." Ann Stat. 2018;46(6B):3362-3389.
Liu Y, He Q, Sun W. "Association analysis using somatic mutations." PLoS Genet.. 2018;14(11):e1007746.
Sun W, Bunn P, Jin C, et al. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res.. 2018;46(6):3009-3018.
Liu Y, Wang Y, Kosorok MR, Zhao Y, Zeng D. "Augmented outcome-weighted learning for estimating optimal dynamic treatment regimens." Stat Med. 2018;37(26):3776-3788.
Wang T, Wang X, Zhou H, Cai J, George SL. "Auxiliary variable-enriched biomarker-stratified design." Stat Med. 2018;37(30):4610-4635.
Eggleston BS, Wilson D, McNeil B, Ibrahim JG, Catellier D. BayesCTDesign: Two Arm Bayesian Clinical Trial Design with and Without Historical Control Data (R).; 2018.
Psioda M, Ibrahim JG. "Bayesian clinical trial design using historical data that inform the treatment effect." Biostatistics. 2018.
Psioda MA, Ibrahim JG. "Bayesian design of a survival trial with a cured fraction using historical data." Stat Med. 2018;37(26):3814-3831.
Li W, Chen M-H, Wangy X, Dey DK. "Bayesian Design of Non-Inferiority Clinical Trials via the Bayes Factor." Stat Biosci. 2018;10(2):439-459.
Li H, Chen M-H, Ibrahim JG, et al. "Bayesian inference for network meta-regression using multivariate random effects with applications to cholesterol lowering drugs." Biostatistics. 2018.
Wu J, Ibrahim JG, Chen M-H, Schifano ED, Fisher JD. "Bayesian Modeling and Inference for Nonignorably Missing Longitudinal Binary Response Data with Applications to HIV Prevention Trials." Stat Sin. 2018;28:1929-1963.
Ibrahim JG, Kim S, Chen M-H, Shah AK, Lin J. "Bayesian multivariate skew meta-regression models for individual patient data." Stat Methods Med Res. 2018:962280218801147.
Lin J, Gresham J, Wang T, et al. "bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics. 2018;34(20):3581-3583.
Diao G, Dong J, Zeng D, Ke C, Rong A, Ibrahim JG. "Biomarker threshold adaptive designs for survival endpoints." J Biopharm Stat. 2018;28(6):1038-1054.
Diao G, Dong J, Zeng D, Ibrahim JG. BTAD : Biomarker Threshold Adaptive Designs for Survival Endpoints (C++).; 2018.
Wei S, Kosorok MR. "The Change-Plane Cox Model." Biometrika. 2018;105(4):891-903.
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.. 2018;19(1):202.
Jiang Y, Zhang NR. CODEX2: Full-spectrum copy number variation detection by high-throughput DNA sequencing. (R).; 2018.
Zhou J, Zhang J, Lu W. "Computationally Efficient Estimation for the Generalized Odds Rate Mixture Cure Model with Interval-Censored Data." J Comput Graph Stat. 2018;27(1):48-58.
Liang S, Lu W, Song R. "Deep advantage learning for optimal dynamic treatment regime." Stat Theory Relat Fields. 2018;2(1):80-88.
Potthoff RF. "Differential losses to follow-up that are outcome-dependent can vitiate a clinical trial: Simulation results." J Biopharm Stat. 2018;28(4):633-644.
Lawson MT, Cho H, Choudhury A, et al. "Discussion of Laber et al. "Optimal treatment allocations in space and time for on-line control of an emerging infectious disease"." J R Stat Soc Ser C Appl Stat. 2018;67(4):779-780.
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. 2018;2(1):21-22.
Chen J, Zhang C, Kosorok MR, Liu Y. "Double Sparsity Kernel Learning with Automatic Variable Selection and Data Extraction." Stat Interface. 2018;11(3):401-420.
Liu Y, Wang Y, Zeng D. DTRlearn: Learning Algorithms for Dynamic Treatment Regimes (R). 1.3 ed.; 2018.
Wong KYau, Zeng D, Lin DY. "Efficient Estimation for Semiparametric Structural Equation Models With Censored Data." J Am Stat Assoc. 2018;113(522):893-905.
Gong S, Zhang K, Liu Y. "Efficient test-based variable selection for high-dimensional linear models." J Multivar Anal. 2018;166:17-31.
Wang X, Zhou J, Wang T, George SL. "On Enrichment Strategies for Biomarker Stratified Clinical Trials." J Biopharm Stat. 2018;28(2):292-308.
Chen J, Fu H, He X, Kosorok MR, Liu Y. "Estimating individualized treatment rules for ordinal treatments." Biometrics. 2018;74(3):924-933.
Gao F, Zeng D, Wei H, Wang X, Ibrahim JG. "Estimating Treatment Effects for Recurrent Events in the Presence of Rescue Medications: An Application to the Immune Thrombocytopenia Study." Stat Biosci. 2018;10(2):473-489.
Kang S, Lu W, Zhang J. "ON ESTIMATION OF THE OPTIMAL TREATMENT REGIME WITH THE ADDITIVE HAZARDS MODEL." Stat Sin. 2018;28(3):1539-1560.
Sibley A, Li Z, Jiang Y, et al. "Facilitating the Calculation of the Efficient Score Using Symbolic Computing." Am Stat. 2018;72(2):199-205.
Kong D, Ibrahim JG, Lee E, Zhu H. "FLCRM: Functional linear cox regression model." Biometrics. 2018;74(1):109-117.
Li T, Xie F, Feng X, Ibrahim JG, Zhu H. "Functional Linear Regression Models for Nonignorable Missing Scalar Responses." Stat Sin. 2018;28(4):1867-1886.
Mathur R, Rotroff D, Ma J, Shojaie A, Motsinger-Reif A. "Gene set analysis methods: a systematic comparison." BioData Min. 2018;11:8.
Innocenti F, Jiang C, Sibley AB, et al. "Genetic variation determines VEGF-A plasma levels in cancer patients." Sci Rep. 2018;8(1):16332.
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. 2018;122:135-155.
Lin J, Sibley A, Truong T, Owzar K, Li Z. groupedSurv: Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function (R). 1.0.0 ed.; 2018.
Zhu A, Ibrahim JG, Love MI. "Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences." Bioinformatics. 2018.
Shi C, Fan A, Song R, Lu W. "HIGH-DIMENSIONAL A-LEARNING FOR OPTIMAL DYNAMIC TREATMENT REGIMES." Ann Stat. 2018;46(3):925-957.
X Jeng J, Lu W, Peng H. "High-Dimensional Inference for Personalized Treatment Decision." Electron J Stat. 2018;12(1):2074-2089.
Laber EB, Wu F, Munera C, Lipkovich I, Colucci S, Ripa S. "Identifying optimal dosage regimes under safety constraints: An application to long term opioid treatment of chronic pain." Stat Med. 2018;37(9):1407-1418.
Butler EL, Laber EB, Davis SM, Kosorok MR. "Incorporating Patient Preferences into Estimation of Optimal Individualized Treatment Rules." Biometrics. 2018;74(1):18-26.
Maity A, Zhao J, Sullivan PF, Tzeng J-Y. "Inference on phenotype-specific effects of genes using multivariate kernel machine regression." Genet. Epidemiol.. 2018;42(1):64-79.
Lin J, Wu Y, Wang XF, Owzar K. intcensROC: Fast Spline Function Based Constrained Maximum Likelihood Estimator for AUC Estimation of Interval Censored Survival Data (R). 0.1.1 ed.; 2018.
Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. "Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics. 2018;34(12):2126-2128.
Pietryk EW, Clement K, Elnagheeb M, et al. "Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme." Reprod. Toxicol.. 2018;78:9-19.
Zhang Y, Laber EB, Davidian M, Tsiatis AA. "Interpretable Dynamic Treatment Regimes." J Am Stat Assoc. 2018;113(524):1541-1549.
Choi J, Zeng D, Olshan AF, Cai J. "Joint modeling of survival time and longitudinal outcomes with flexible random effects." Lifetime Data Anal. 2018;24(1):126-152.
Hibbard JC, Friedstat JS, Thomas SM, Edkins RE, C Hultman S, Kosorok MR. "LIBERTI: A SMART study in plastic surgery." Clin Trials. 2018;15(3):286-293.
Urrutia E, Chen H, Zhou Z, Zhang NR, Jiang Y. MARATHON: Integrates Multiple Related Statistical Software for Copy Number Profiling and Downstream Analyses (R).; 2018.
Shi C, Lu W, Song R. "A Massive Data Framework for M-Estimators with Cubic-Rate." J Am Stat Assoc. 2018;113(524):1698-1709.
Shi C, Song R, Lu W, Fu B. "Maximin Projection Learning for Optimal Treatment Decision with Heterogeneous Individualized Treatment Effects." J R Stat Soc Series B Stat Methodol. 2018;80(4):681-702.
Yang S, Tsiatis AA, Blazing M. "Modeling survival distribution as a function of time to treatment discontinuation: A dynamic treatment regime approach." Biometrics. 2018;74(3):900-909.
Isogai Y, Wu Z, Love MI, et al. "Multisensory Logic of Infant-Directed Aggression by Males." Cell. 2018;175(7):1827-1841.e17.
Wang Y-B, Chen M-H, Kuo L, Lewis PO. "A New Monte Carlo Method for Estimating Marginal Likelihoods." Bayesian Anal. 2018;13(2):311-333.
Chen G, Kosorok MR, Zhou X. Nonconvex Optimization..; 2018.
Van den Berge K, Perraudeau F, Soneson C, et al. "Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications." Genome Biol.. 2018;19(1):24.
Wang C, Chen M-H, Wu J, Yan J, Zhang Y, Schifano E. "Online updating method with new variables for big data streams." Can J Stat. 2018;46(1):123-146.
Laber EB, Meyer NJ, Reich BJ, Pacifici K, Collazo JA, Drake JM. "Optimal treatment allocations in space and time for on-line control of an emerging infectious disease." J R Stat Soc Ser C Appl Stat. 2018;67(4):743-770.
Hager R, Tsiatis AA, Davidian M. "Optimal two-stage dynamic treatment regimes from a classification perspective with censored survival data." Biometrics. 2018;74(4):1180-1192.
Zhou Q, Cai J, Zhou H. "Outcome-dependent sampling with interval-censored failure time data." Biometrics. 2018;74(1):58-67.
Chung Y, Ivanova A, Hudgens MG, Fine JP. "Partial likelihood estimation of isotonic proportional hazards models." Biometrika. 2018;105(1):133-148.
Jung S-H. "Phase II cancer clinical trials for biomarker-guided treatments." J Biopharm Stat. 2018;28(2):256-263.
West RMarceau, Holloway ST. POINT: Protein Structure Guided Local Test. 1.0 ed.; 2018.
Davenport CA, Maity A, Sullivan PF, Tzeng J-Y. "A Powerful Test for SNP Effects on Multivariate Binary Outcomes using Kernel Machine Regression." Stat Biosci. 2018;10(1):117-138.
Psioda MA, Soukup M, Ibrahim JG. "A practical Bayesian adaptive design incorporating data from historical controls." Stat Med. 2018;37(27):4054-4070.
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. 2018;2.
Laber EB, Rose E, Davidian M, Tsiatis AA. Q-Learning.. Wiley; 2018.
Wang L, Zhou Y, Song R, Sherwood B. "Quantile-Optimal Treatment Regimes." J Am Stat Assoc. 2018;113(523):1243-1254.
Wang C, Tzeng J-Y, Wu P-Z, Preisig M, Hsiao CKate. "Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics. 2018;209(1):105-113.
Pan Y, Cai J, Kim S, Zhou H. "Regression analysis for secondary response variable in a case-cohort study." Biometrics. 2018;74(3):1014-1022.
Ni A, Cai J. "A regularized variable selection procedure in additive hazards model with stratified case-cohort design." Lifetime Data Anal. 2018;24(3):443-463.
Kong D, Maity A, Hsu F-C, Tzeng J-Y. "Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine"." Biometrics. 2018;74(2):767-768.
Chen X, Cai J. "Reweighted estimators for additive hazard model with censoring indicators missing at random." Lifetime Data Anal. 2018;24(2):224-249.
Zhang C, Pham M, Fu S, Liu Y. "Robust Multicategory Support Vector Machines using Difference Convex Algorithm." Math Program. 2018;169(1):277-305.
Yang Y, Huh R, Culpepper HW, Lin Y, Love MI, Li Y. "SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data." Bioinformatics. 2018.
Liu Y, Sun W, He Q. SAME: Somatic mutation Association test with Measurement Errors (R).; 2018.
Li Z, Wang X, Wu Y, Owzar K. "Sample size calculation for studies with grouped survival data." Stat Med. 2018;37(27):3904-3917.

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