*: Co-first authors

Coming Soon

  • Xu Y, Müller P, Berry D. and et. al., A Population-Finding Design with Covariate-Dependent Random Partitions.
  • Xu Y, Müller P, and Thall P, Bayesian Subgroup-Based Adaptive Designs in Sequential, Multiple Assignment, Randomized Biomarker Trials (SMART).


  • Xu Y, Müller P, and Telesca D, Bayesian Inference for Latent Biologic Structure with Determinantal Point Processes (DPP).
  • Xu Y, Thall P, Müller P, and Mehran R, A Bayesian Nonparametric Utility-Based Design for Comparing Treatments to Resolve Air Leaks After Lung Surgery.
  • Xu Y and Ji Y.
    A Latent Gaussian Process Model with Application to Monitoring Clinical Trials. Manuscript Software


  • Xu Y, Müller P, Wahed A and Thall P.
    Bayesian Nonparametric Estimation for Dynamic Treatment Regimes with Sequential Transition Times. Manuscript Software Supplement
  • Journal of the American Statistical Association. In press
    (Winner of the 2015 David P. Byar Young Investigator Travel Award Sponsored by ASA Biometrics Section)
  • 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. Manuscript Software
  • Journal of the National Cancer Institute. Accepted
  • Xu Y, Müller P, Yuan Y, Gulukota K and Ji Y.
    MAD Bayes for Tumor Heterogeneity Feature Allocation with Exponential Family Sampling. Manuscript Software
  • Journal of the American Statistical Association. In Press
  • Xu Y, Trippa L, Müller P and Ji Y.
    Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trial. Manuscript
  • Statistics in Biosciences. In Press
    (1st Place Winner of the 2014 JSM Biopharmaceutical Section Student Paper)
  • Yuan Y, Van Allen EM, Omberg L, Wagle N, Sokolov A, Xu Y, and et al.
    Assessing the Clinical Utility of Cancer Genomic and Proteomic Data across Tumor Types.
    Nature Biotechnology. 2014, 32: 644-652
  • Han L, Yuan Y, Zheng S, Yang Y, Li J, Edgerton M, Diao L, Xu Y, Verhaak R and Liang H.
    The Pan-Cancer Analysis of Pseudogene Expression Reveals Biologically and Clinically Relevant Tumor Subtypes.
    Nature Communications. 2014, 5: 3963
  • Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, NCI DREAM Community (including Xu Y), Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, Collins JJ, Gallahan CD, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.
    The Challenge of Drug Sensitivity Prediction: an Assessment of Methods through Collaborative Competition.
    Nature Biotechnology. In press
  • Xu Y, Zheng X, Yuan Y, Estecio M, Issa J-P, Ji Y and Liang S.
    BM-SNP: A Bayesian Model for SNP Calling using High Throughput Sequencing Data. Supplement
    IEEE/ACM transactions on computational biology and bioinformatics. In Press
  • Mitra R, Müller P, Liang S, Xu Y and Ji Y
    Towards the Discovery of the Histone Code - A Bayesian Graphical Model for Histone Modifications.
    Circulation: Cardiovascular Genetics, 2013; 6: 419-426.
  • Xu Y, Lee J, Yuan Y, Mitra R, Liang S, Müller P and Ji Y.
    Nonparametric Bayesian Bi-Clustering for ChIP-Seq Count Data.
    Bayesian Analysis, 2013, 8(2): 1-22.
  • 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, 2011 Dec; 67(4): 1215-24.
  • (Winner of the 2011 ENAR Distinguished Student Paper Award)
  • Xu Y, Zheng X, Yuan Y, Estecio M, Issa J-P, Ji Y and Liang S
    A Bayesian Model for SNP Discovery Based on Next-Generation Sequencing Data.
    2012 IEEE Workshop on Genomic Signal Processing and Statisticss.
  • Yuan Y, Xu Y, Xu J and Liang H
    Predicting the lethal phenotype of the knockout mouse by integrating genomic data.
    Bioinformatics, 2012 May 1; 28(9): 1246-52.
  • Xu Y, Zhang J, Yuan Y, Mitra R, Müller P and Ji Y
    A Bayesian Graphical Model for Integrative Analysis of TCGA Data.
    2012 IEEE Workshop on Genomic Signal Processing and Statisticss.
  • 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.
  • Trindade A.A. and Xu Y.
    Quantile Versions of Holt-Winters Forecasting Algorithms.
    Journal of Statistics: Advances in Theory and Applications, 2011, 5(1): 15-35.

Book Chapter

  • Xu Y, Zhu Y and Ji Y, Graphical models for integrating omics data. In: Integrating omics data: statistical and computational methods. Editors: George C. Tseng, Xianghong Jasmine Zhou and Debashis Ghosh. This book is under copyediting and production in Cambridge University Press; expected in early 2015.
  • Xu Y, Ji Y and Müller P, Biomarker-Driven Adaptive Design. In: Nonparametric Bayesian Methods in Biostatistics and Bioinformatics. Editors: Mitra R and Müller P. Springer-Verlag, to appear.