Xaohui Xie, PhDXaohui Xie, Ph.D.

Computational Biology, Bioinformatics, Genomics, Neural Computation, and Machine Learning – …

Recent Publications

    • Daily K, Rigor P, Christley S, Xie X, Baldi P. (2010) Data structures and compression algorithms for high-throughput sequencing technologies.BMC Bioinformatics. 11:514.
    • Wang Y, Christley S, Mjolsness E, Xie X. (2010) Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent.BMC Syst Biol. 4:99.
    • Potkin SG, Macciardi F, Guffanti G, Fallon JH, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X. (2010) Identifying gene regulatory networks in schizophrenia. Neuroimage. 53(3):839-47. Epub 2010 Jun 22.
    • Chong HK, Infante AM, Seo YK, Jeon TI, Zhang Y, Edwards PA, Xie X, Osborne TF.(2010) Genome-wide interrogation of hepatic FXR reveals an asymmetric IR-1 motif and synergy with LRH-1. Nucleic Acids Res38(18):6007-17. Epub 2010 May 18.
    • Xie X. (2010) The Site-Frequency Spectrum of Linked Sites. Bull Math Biol [Epub ahead of print]
    • Christley S, Nie Q, Xie X.(2009) Incorporating existing network information into gene network inference. PLoS One. 4(8):e6799.
    • Seo YK, Chong HK, Infante AM, Im SS, Xie X, Osborne TF. (2009) Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif. Proc Natl Acad Sci U S A. 106(33):13765-9. Epub 2009 Aug 4.
    • Xie X, Rigor P, Baldi P. (2009) MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics. 25(2):167-74. Epub 2008 Nov 18.


  • Christley S, Lu Y, Li C, Xie X. (2009) Human genomes as email attachments. Bioinformatics. 25(2):274-5. Epub 2008 Nov 7.
  • Sabeti, Varilly, Fry, Lohmueller, Hostetter, Sotsapos, Xie, Byrne, et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-918 (2007)
  • Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci USA 104:7145-7150 (2007)
  • Xie X, Kamal M, and Lander ES. A family of conserved noncoding elements derived from an ancient transposable element. Proc Natl Acad Sci USA 103:11659-11664 (2006)
  • Kamal M, Xie X, and Lander ES. A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci USA 103:2740-2745 (2006)
  • Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al. A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells. Cell 125:315-26 (2006)

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