Xiaole Shirley Liu

Xiaole Shirley Liu

Professor of Statistics
Professor of Biostatistics and Computational Biology, Harvard T.H. Chan School of Public Health
Xiaole   Shirley Liu

Research Interests

  • Statistical modeling of transcription regulation
  • ChIP-chip analysis on genome tiling microarrays
  • Nucleosome occupancy, and genome-wide epigenetics
  • Transcription factor binding location and motif finding
  • Transcript mapping and copy number change detection on genome tiling microarrays


  • Ph.D. in Biomedical Informatics, Stanford University, 2002.
  • Ph.D. minor in Computer Science, Stanford University, 2002.
  • B.A. in Biochemistry, Smith College, 1997.
  • B.A. in Computer Science, Smith College, 1997.


  • 2006-present, Editorial Board, Genomics, Elsevier.
  • 2005-present, Program Committee, Annual International conference on Intelligent Systems for Molecular Biology
  • 2005-present, Steering Committee, International Bioinformatics Workshop
  • 2008-present, Associate Professor of Biostatistics, Dana-Farber Cancer Institute, Harvard School of Public Health
  • 2003-2007, Assistant Professor of Biostatistics, Dana-Farber Cancer Institute, Harvard School of Public Health
  • 2002-2003, Research Fellow, Dana-Farber Cancer Institute

Sample Publications

  • Carroll JS, Meyer CA, Song J, Li W, Brodsky AS, Hall G, Geistlinger TR, Eeckhoute J, Wang QB, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS*, Brown M* (2006). Genome Wide Analysis of Estrogen Receptor Binding Sites. In press, Nat Gen. *Co-corresponding authors.
  • Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS (2006). MAT: Model-based Analysis of Tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 103: 12457-12462.
  • Ji X, Li W, Song J, Wei L, Liu XS (2006). CEAS: Cis-Elements Annotation Systems. In press, Nucleic Acids Res.
  • Carroll JS, Liu XS, Brodsky AS, Li W, Szary AJ, Meyer CA, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M (2005). Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 122(1):33-43
  • Li W, Meyer CA, Liu XS (2005). A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (ISMB2005). 21 Suppl 1:i274-i282.
  • Liu Y*, Liu XS*, Wei L, Altman RB, Batzoglou (2004). Conservation of eukaryotic regulatory elements and their identification using comparative genomics. Genome Res. 14:451-8. *Joint first authors.
  • Conlon EM*, Liu XS*, Lieb JD, Liu JS (2003). Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A. 100:3339-44. *Joint first authors.
  • Liu XS*, Brutlag DL, Liu JS (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat Biotechnol. 20:835-9. *Xiaole Liu added middle name Shirley.
  • Lieb JD, Liu X, Botstein D, Brown PO (2001). Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Gen. 28:327-34.
  • Liu X, Brutlag DL, Liu JS (2001). BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Proc Pac Symp Biocomput. 127-38.

Personal Website

Lab Website


Contact Information

p: (617) 632-2472