Software Developed

  • EM-DeCODER (haplotype phasing using EM algorithm).
  • HAPLOTYPER (haplotype phasing using Partition-Ligation and Gibbs Sampler).
  • PL-EM (haplotype phasing using Partition-Ligation and EM algorithm).
  • BMC (putative binding motif clustering using Gibbs Sampler).
  • FESTA (tagSNP selection based on pairwise LD) With Shyam Gopalakrishnan.
  • tripleM (PL-EM for phasing trios).
  • CRC (model-based clustering algorithm for gene expression microarray data).
  • OperonHMM (a hidden Markov model for predicting operon structure using only sequence data). Codeveloped with Dr. Nick Bergman.
  • CRCView (point-and-click web server for clustering, visualizing and interpreting microarray gene expression data). Co-developed with Zuoshuang Xiang and Yongqun He.
  • BEST (query large scale microarray compendium datasets using model-based Bayesian approach with variable selection). Developed by Ming Hu.
  • HPeak (A hidden Markov model-based algorithm for calling ChIP-enriched peaks using ChIP-seq data).
  • ChIP-meta (hierarchical hidden Markov model-based algorithm for inferring ChIP-enriched regions using both ChIP-seq and ChIP-chip data). Developed by Hyung Won Choi.
  • HMS (a hybrid Monte Carlo-based de nono motif discovery tool designed specifically for analyzing ChIP-Seq data). Developed by Ming Hu.
  • POME (Poisson mixed-effects model for quantification expression in RNA-Seq data). Developed by Ming Hu in collaboration with Michael Yu Zhu.
  • GPUmotif (de novo motif finding and motif scan using GPU). Developed by Pooya Zandevakili.
  • Methylphet (predict TF binding in vivo from base-level methylome profiling data). Developed by Tianlei Xu, Ben Li and Meng Zhao.
  • RefEditor (customize reference genome using individual’s known mutation profile). Developed by Shuai Yuan.
  • IPBT (detect differentially expressed genes with informative prior obtained from historical data). Developed by Ben Li.
  • traseR (to perform trait associated SNP enrichment analysis). Developed by Li Chen.
  • DIVAN (provide disease-specific annotation on nonocoding variants using epigenomcis profiles). Developed by Li Chen.