Bioinformatics

• Zodiac

  • 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
  Journal of the National Cancer Institute. Under Review

• Cancer-specific Network Download

  • Xu Y, Zhu Y, Müller P, Mitra R and Ji Y.
    Charactering Cancer-Specific Networks by Integrating TCGA Data.
  Cancer Informatics. Under Review

• BM-Map

  • 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. Manuscript
  • 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 Download

  • Xu Y, Müller P, Yuan Y, Gulukota K and Ji Y, MAD Bayes for Tumor Heterogeneity Feature Allocation with Non-Normal Sampling. Manuscript

Clinical Trial

• SUBA

  • Xu Y, Trippa L, Müller P and Ji Y, Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trial. Statistics in Biosciences. Manuscript. We are currently developing a user-friendly interface. Code is available upon request.