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  • BayClone (Aug. 2014)

         A Bayesian Feature Allocation Model for Inference of Tumor Subclones Using Next-Generation Sequencing Data PrePrint    R program  

  • CompGenome Website (Feb. 2014)

        We have put together a selected and newly developed BIG-DATA tools and a refined Phase I trial design on a comprehensive website. Computation and Genomics  

  • TCGA-Assembler (Setp. 2013)

        Zhu Y, Qiu P, Ji Y. TCGA-Assembler: An Open-Source Pipeline for TCGA Data Downloading, Assembling, and Processing. Submitted. Software  

  • High-dimensional Data Analysis

  • 1. BM-MAP

       Ji Y*, Xu, Y, Zhang, Q, Tsui, K-W, Yuan, Y, Liang, S, Liang, H*. BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data. Biometrics. (2011) In Press. Manuscript   Software

  • 2. BM-DE (no replicates)

        Lee JH, Mueller P*, Liang S, Cai G, Ji Y*. On Differential Gene Expression Using RNA-Seq Data. Cancer Informatics (2011), in press. Manuscript   Software in R with examples (with a Manual )

  • 3. BM-DE2 (with replicates and improved models)

        Lee JH, Ji Y , Liang S, Cai G, Mueller P . Bayesian Hierarchical Model for Differential Gene Expression Using RNA-Seq Data. Submitted. Manuscript   Software in R with examples

  • 4. BM-BC

        Ji Y, Quintana F, Jara A, Liu P, Lu Y, Liang S,. BABC -- Bayesian base calling for Solexa sequence data. Submitted.   R package BMBC

  • 5. HM-Net

        Mitra R, Mueller, P*, Liang, S, Yue, L, Ji Y*. A Bayesian Graphical Model for ChIP-Seq Data on Histone Modifications. Submitted. R package

  • Bayesian Adaptive Design

  • 1. mTPI doseing finding

        Ji Y et al. (2010; 2013 -- with Sue-Jane Wang). Manuscript Software (is now fully web-based)  

  • 2. SEARS

         Pan H, Xie F, Liu P, Xia J, Ji Y*, SEARS: A Seamless Dose Escalation/Expansion with Adaptive Randomization Scheme Submitted. Manuscript   R Code   Trial Movie