Research Department

Biostatistics and Computational Biology

Area of Research

Biography

X. Shirley Liu graduated summa cum laude from Smith College and received her PhD from Stanford University. Her research focuses on computational models of transcription and epigenetic regulation by integrating data from genome-wide ChIP-chip / Seq, gene expression microarray / sequencing, genomic sequence and nucleosome occupancy. She has developed a number of widely used transcription factor motif finding and ChIP-chip/Seq analysis algorithms, and has collaborated widely with pioneers in ChIP technology, transcription and epigenetic regulation.

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

We develop computation and statistical algorithms to analyze high throughput genomics data, especially ChIP-seq data. We integrate gene expression, transcription factor binding, epigenetic status, and sequence motif analysis to understand global gene regulation. We are especially interested in studying the transcription and epigenetic regulation in cancers, aging, metabolic and immune diseases, and stem cells.

Select Publications

• Lieb JD, Liu X, Botstein D, Brown PO (2001). Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 28(4):327-34.
• 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(8):835-9. @Xiaole Liu added middle name Shirley.
• 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(6):3339-44.
• 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(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* (2006). Genome wide analysis of estrogen receptor binding sites. Nat Genet. 38:1289-97.
• Ozsolak F, Song JS, Liu XS*, Fisher DE* (2007). 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* (2008). 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 (2008). 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 (2008). FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription. Cell. 132(6):958-70.
• Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J (2009). Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet. 41(3):376-81.
• Wang X, Elling A, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize. Plant Cell. 21(4):1053-69.
• 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*. (2009) 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. Accepted, Nat.
• 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. Accepted, Nat Genet.
• Liu Y#, Liu XS#, Wei L, Altman RB, Batzoglou (2004). Conservation of eukaryotic regulatory elements and their identification using comparative genomics. Genome Res. 14(3):451-8.
• Zhang Y, Moqtaderi Z, Rattner B, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K (2009). Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 16(8):847-52.

Investigators

• Meyer, Clifford A.

Trainees

• Shin, Hyunjin (Gene), PhD
• Liu, Tao, PhD
• Wu, Zhenhua (Jeremy), PhD
• Wang, Xiangfeng (Bryan), PhD
• He, Housheng (Hansen), PhD
• Chen, Yiwen, PhD
• Pape, Utz, PhD