Xie Jun Purdue Bayesian and HMM model for Motif analysis

Hidden Markov model and Bayesian method of identifying cis-regulatory modules in promoter sequences

Current Research Interests

• Statistical approaches for identifying protein motifs with the secondary characteristics of hydrophobicity and polarity
  
  
• Protein Multiple Alignment Incorporating Primary and Secondary Structure Information
  • "Protein Multiple Alignment Incorporating Primary and Secondary Structure Information", Nak-Kyeong Kim and Jun Xie, 2006, Journal of Computational Biology Vol 13 No 10 (Preprint)
  
  
• Hidden Markov model and Bayesian method of identifying cis-regulatory modules in promoter sequences
  • "Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model", Jing Wu and Jun Xie, Journal of Computational Biology (Preprint)
  
  
• Integrative analysis of sequences, gene expression microarray, and ChIP-chip binding data for transcriptional regulation and network
  
  
• Iterated dynamic programming for identifying protein motifs in multiple sequences
  
  
• Analysis of survival data with censoring
  • "Adjusted Kaplan-Meier Estimator and Log-rank Test with Inverse Probability of Treatment Weighting for Survival Data", Jun Xie
    and Chaofeng Liu, 2005, Statistics in Medicine, Vol. 24, No. 20.(Preprint)
    • Selected Publications:
    • "dPattern: Transcription Factor Binding Site (TFBS) Discovery in Human Genome using a Discriminative Pattern Analysis", Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie and Sun Kim, Bioinformatics, doi:10.1093/bioinformatics/btm288.
      
      
    • "Weighted Nonparametric Maximum Likelihood Estimate of a Mixing Distribution in Nonrandomized Clinical Trials", Chaofeng Liu, Jun Xie, and Ying Zhang, Statistics in Medicine, in press.
      
      
    • "Computation-Based Discovery of Cis-Regulatory Modules by Hidden Markov Model", Jing Wu and Jun Xie, Journal of Computational Biology, 2007, Vol 14, No 6, in press.
      
      
    • "Influence of NuMA on higher order chromatin structure in human mammary epithelium", Patricia C. Abad, Jason Lewis, I. Saira Mian, Sunil Badve, Jun Xie, and Sophie A. Lelièvre, Molecular Biology of the Cell, Vol. 18, 348-361.
      
      
    • "Nonparametric Empirical Bayes Method for Comparison of Treatment Effects with Application to Stress Urinary Incontinence Data", Chaofeng Liu, Wei Shen, and Jun Xie, Pharmaceutical Statistics, Online DOI: 10.1002/pst.264.
      
      
    • "Protein Multiple Alignment Incorporating Primary and Secondary Structure Information", Nak-Kyeong Kim and Jun Xie, Journal of Computational Biology 2006, Vol 13, No. 10, 1735-1748.
      
      
    • "Context Dependent Models for Discovery of Transcription Factor Binding Sites", Chuancai Wang, Jun Xie and Bruce A. Craig, 2005, Statistical Methodology, Vol 3, 55-68.
      
      
    • "Bayesian Models and Markov Chain Monte Carlo Methods for Protein Motifs with the Secondary Characteristics", Jun Xie and Nak-Kyeong Kim, 2005, Journal of Computational Biology, Vol. 12, No. 7, 950-968.
      
      
    • "Adjusted Kaplan-Meier Estimator and Log-rank Test with Inverse Probability of Treatment Weighting for Survival Data", Jun Xie and Chaofeng Liu, 2005, Statistics in Medicine, Vol. 24, No. 20, 3089-3011.
      
      
    • "A Bayesian Insertion/Deletion Algorithm for Distant Protein Motif Searching via Entropy Filtering", Jun Xie, Ker-Chau Li, and Minou Bina, 2004, JASA, Vol. 99, No. 466, 409-420.
      
      
    • "Covariance Structure Models for Gene Expression Data", Jun Xie and Peter M. Bentler, 2003, Structural Equation Modeling , Vol. 10, No.4, 566-582.
      
      
    • "Reversible algorithm of simulating multivariate densities with multi-hump", Guanglu Gong, Minping Qian and Jun Xie, 2001 Science in China Series A, Vol. 44, No. 3, 357-364.
      
      
    • "Corrections to Test Statistics in Principal Hessian Directions", Peter M. Bentler and Jun Xie, 2000, Statistics & Probability Letters, 47, 381-389.
      
      
    • "The Reduction Method, the Loop Erased Exit Path, and the Meta-Stability of the Biased Majority Vote Processes", Olivier. Catoni, Dayue Chen and Jun Xie, 2000, Stochastic Processes and Their Applications, Vol.86, No.2, 231-261.