• Researcher Profile

    Xiaole Shirley Liu, PhD

     
    Xiaole Shirley Liu, PhD
     
    Director, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute

    Professor of Biostatistics and Computational Biology, Harvard School of Public Health

    Office phone: 617-632-2472
    Fax: 617-632-2444
    Email: xsliu@jimmy.harvard.edu
    Website: Liu Lab Website

    Preferred contact method: email
     
     

    Research Department

    Biostatistics and Computational Biology

    Area of Research

    Computational Cancer Epigenetics


    Dana-Farber Cancer Institute
    450 Brookline Avenue
    CLSB 11022
    Boston, MA 02215

    Biography

    Dr. X. Shirley Liu graduated summa cum laude from Smith College double majoring in Biochemistry and Computer Science in 1997, and received PhD in Biomedical Informatics and PhD minor in Computer Science from Stanford University in 2002. She is now Professor at the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Harvard School of Public Health. She is the Director of the Center of Functional Cancer Epigenetics at Dana-Farber Cancer Institute, and an associate member of the Broad Institute. Her research focuses on computational cancer epigenetics, and developing algorithms for big cancer data integration and mining. 

    Recent Awards

    • Sloan Research Fellowship, 2008
    • Department of Defense Prostate Cancer Research Program New Investigator Award, 2006
    • Claudia Adams Barr Award for Innovative Basic Cancer Research, 2005

    Research

    Computational Cancer Epigenetics

    Through genome-wide transcription factor binding, chromatin dynamics, and gene expression profiles, we try to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance. 

    Select Publications

    • Liu XS, Brutlag DL, Liu JS. An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat Biotechnol. 20(8):835-9. 
    • Conlon EM#, Liu XS#, Lieb JD, Liu JS. Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A. 100(6):3339-44.
    • Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. MAT: Model-based Analysis of Tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 103(33): 12457-12462.
    • 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*. Genome wide analysis of estrogen receptor binding sites. Nat Genet. 38:1289-97.
    • Ozsolak F, Song JS, Liu XS*, Fisher DE*. Global chromatin structure mapping of human promoters. Nat Biotechnol. 25:244-8.
    • Johnson DS, Li W, et al., Struhl K*, Myers RM*, Lieb JD*, Liu XS*. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18(3):393-403.
    • Zhang Y#, Liu T#, Meyer CA, Eeckhoute J, Johnson DS, Bernstein B, Nusbaum C, Myers RM, Brown M, Li W*, Liu XS*. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9(9):R137.
    • Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription. Cell. 132(6):958-70.
    • Wang Q, Li W, Zhang Y, Yuan X, Beroukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK, Jnne OA, Balk SP, Mehra R, Chinnaiyan AM, Rubin MA, True L, Giorentino M, Fiore C, Loda M, Kantoff PW, Liu XS*, Brown M*. Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer. Cell. 138(2):245-56.
    • Vastenhouw N, Zhang Y, Woods I, Imam F, Regev A, Liu XS*, Rinn J*, Schier A*. Chromatin signature of embryonic pluripotency is established during zygotic genome activation in zebrafish. Nature. 464(7290):922-6. 
    • He HH#, Meyer C#, Shin H, Bailey S, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M*, Liu XS*. Nucleosome dynamics defines transcriptional enhancers. Nat Genet. 42(4):343-7. 
    • Wu ZJ#, Meyer CA#, Choudhury S, Shipitsin M, Bessarabova M, Nikolsky Y, Sukumar S, Schwartzman A, Liu JS, Polyak K*, Liu XS*. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 20(12):1730-9.
    • Feng D#, Liu T#, Sun Z, Bugge A, Mullican SE, Liu XS, Lazar MA. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science. 331(6022):1315-9.
    • Liu T#, Ortiz JA#, Taing L, Meyer CA, Lee B, Zhang Y, Shin HG, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M*, Turpaz Y*, Liu XS*. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 12(8):R83.
    • He HH#, Meyer CA#, Chen MW, Jordan C, Brown M*, Liu XS*. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 22(6):1015-25.
    • Xu K#, Wu ZJ#, Anna C. Groner AC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, Xu H, Cato L, Thornton JE, Gregory RI, Morrissey M, Vessella RL, Montironi R, Magi-Galluzzi C, Kantoff PW, Balk SP, Liu XS*, Brown M*. EZH2 Oncogenic activity in castration resistant prostate cancer is polycomb-independent. Science. 338(6113):1465-9.
    • Du Z#, Fei T#, Verhaak RG, Su Z, Zhang Y, Brown M*, Chen Y*, Liu XS*. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol. 20(7):908-13.

    Investigators

    • Meyer, Clifford A.

    Trainees

    • Chen, Yiwen, PhD
    • Chongzhi, Zang, Ph.D.
    • Han, Xu, Ph.D.
    • Teng, Fei, Ph.D.
    • Wei, Li, Ph.D.
    • Graham, McVicker, Ph.D.
    • Tengfei, Xiao, Ph.D.
    • Peng, Jiang, Ph.D.
    • Chen-Hao, Chen, M.D.