R package doct (short for “Decisions Optimized in
- Hua W+ , Mei H, Zohar S, Giral M and Xu Y# , “Personalized Dynamic Treatment Regimes in Continuous Time: A Bayesian Joint Model for Optimizing Clinical Decisions with Timing.”
Bayesian Nonparametric Approach for Semi-competing Risks
- Xu Y# , Scharfstein D, Müller P, and Daniels M, “A Bayesian Nonparametric Approach for Evaluating the Causal Effect of Treatment in Randomized Trials with Semi-Competing Risks.”
Biostatistics, 2020, kxaa008.
Bayesian Basket Trial Design
- Xu Y, Müller P, Tsimberidou A, and Berry D, “A Nonparametric Bayesian Basket Trial Design”.
Biometrical Journal, 2019; 61(5): 1160-1174.
R package DDPGPSurv
- Xu Y# , Thall P, Hua W+ , and Andersson B, “Bayesian Nonparametric Survival Regression for Optimizing Precision Dosing of Intravenous Busulfan in Allogeneic Stem Cell Transplantation.”
Journal of the Royal Statistical Society: Series C, 2019; 68(3): 809-828
- Zhu Y* , Xu Y* , Helseth D* , Gulukota K, Yang S, Pesce L, Mitra R, Müller P, Sengupta S, Guo W, Silverstein J, Foster I, Parsad N, White K and Ji Y, “Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.”
JNCI: Journal of the National Cancer Institute 107.8 (2015)
- Ji Y, Xu Y, Zhang Q, Tsui K-W, Yuan Y, Liang S and Liang H, “BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data”.
Biometrics 67.4 (2011): 1215-1224.
(Winner of the 2011 ENAR Distinguished Student Paper Award)
- Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y and Liang H, “BM-Map: an efficient software package for accurately allocating multireads of RNA-seq data”.
BMC Genomics, 2012, 13(Suppl 8): S9.
MAD-Bayes for Tumor Heterogeneity
- Xu Y, Müller P, Yuan Y, Gulukota K and Ji Y, “MAD Bayes for Tumor Heterogeneity Feature Allocation with Exponential Family Sampling.”
Journal of the American Statistical Association 110.510 (2015): 503-514