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Xiaole Shirley Liu, PhD


Researcher


Researcher

  • Director, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute
  • Professor of Biostatistics and Computational Biology, Harvard T.H. Chan School of Public Health

Contact Information

  • Office Phone Number(617) 632-2472
  • Fax(617) 632-2444

Bio

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:

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

Location

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

Carey CD, Gusenleitner D, Lipschitz M, Roemer MGM, Stack EC, Gjini E, Hu X, Redd R, Freeman GJ, Neuberg D, Hodi FS, Liu XS, Shipp MA, Rodig SJ. Topological analysis reveals a PD-L1-associated microenvironmental niche for Reed-Sternberg cells in Hodgkin lymphoma. Blood. 2017 11 30; 130(22):2420-2430.
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Fei T, Chen Y, Xiao T, Li W, Cato L, Zhang P, Cotter MB, Bowden M, Lis RT, Zhao SG, Wu Q, Feng FY, Loda M, He HH, Liu XS, Brown M. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proc Natl Acad Sci U S A. 2017 Jun 27; 114(26):E5207-E5215.
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Liu Y, Chen S, Wang S, Soares F, Fischer M, Meng F, Du Z, Lin C, Meyer C, DeCaprio JA, Brown M, Liu XS, He HH. Transcriptional landscape of the human cell cycle. Proc Natl Acad Sci U S A. 2017 Mar 28; 114(13):3473-3478.
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Liu XS, Mardis ER. Applications of Immunogenomics to Cancer. Cell. 2017 Feb 09; 168(4):600-612.
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Gao W, Li W, Xiao T, Liu XS, Kaelin WG. Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL-/- clear cell renal carcinoma. Proc Natl Acad Sci U S A. 2017 Jan 31; 114(5):1027-1032.
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Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol. 2016 Dec; 34(12):1279-1286.
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Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. 2017 Jan 04; 45(D1):D658-D662.
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Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics. 2016 Oct 03; 17(1):404.
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Li B, Severson E, Pignon JC, Zhao H, Li T, Novak J, Jiang P, Shen H, Aster JC, Rodig S, Signoretti S, Liu JS, Liu XS. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biol. 2016 Aug 22; 17(1):174.
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Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li X, Xu K, He HH, Brown M, Meyer CA, Liu XS. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Res. 2016 Oct; 26(10):1417-1429.
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Zang C, Luyten A, Chen J, Liu XS, Shivdasani RA. NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes. Sci Rep. 2016 Jul 26; 6:30255.
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Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics. 2016 Nov 01; 32(21):3336-3338.
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Li B, Li T, Pignon JC, Wang B, Wang J, Shukla SA, Dou R, Chen Q, Hodi FS, Choueiri TK, Wu C, Hacohen N, Signoretti S, Liu JS, Liu XS. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat Genet. 2016 07; 48(7):725-32.
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Cejas P, Li L, O'Neill NK, Duarte M, Rao P, Bowden M, Zhou CW, Mendiola M, Burgos E, Feliu J, Moreno-Rubio J, Guadalajara H, Moreno V, García-Olmo D, Bellmunt J, Mullane S, Hirsch M, Sweeney CJ, Richardson A, Liu XS, Brown M, Shivdasani RA, Long HW. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nat Med. 2016 06; 22(6):685-91.
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Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XS. High-dimensional genomic data bias correction and data integration using MANCIE. Nat Commun. 2016 Apr 13; 7:11305.
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Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nat Commun. 2016 Mar 15; 7:10982.
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Liu Y, Fei T, Zheng X, Brown M, Zhang P, Liu XS, Wang H. An Integrative Pharmacogenomic Approach Identifies Two-drug Combination Therapies for Personalized Cancer Medicine. Sci Rep. 2016 Feb 26; 6:22120.
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Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, Janiszewska M, Huh SJ, Liang Y, Ryan J, Doherty E, Mohammed H, Guo H, Stover DG, Ekram MB, Brown J, D'Santos C, Krop IE, Dillon D, McKeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Wu SY, Chiang CM, Anders L, Young RA, Winer E, Letai A, Barry WT, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak K. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016 Jan 21; 529(7586):413-417.
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Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biol. 2015 Dec 16; 16:281.
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Xu H, Xu K, He HH, Zang C, Chen CH, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu XS. Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression. Mol Cancer Res. 2016 Feb; 14(2):163-172.
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Jiang P, Wang H, Li W, Zang C, Li B, Wong YJ, Meyer C, Liu JS, Aster JC, Liu XS. Network analysis of gene essentiality in functional genomics experiments. Genome Biol. 2015 Oct 30; 16:239.
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Zhang J, Wang C, Chen X, Takada M, Fan C, Zheng X, Wen H, Liu Y, Wang C, Pestell RG, Aird KM, Kaelin WG, Liu XS, Zhang Q. EglN2 associates with the NRF1-PGC1a complex and controls mitochondrial function in breast cancer. EMBO J. 2015 Dec 02; 34(23):2953-70.
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Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, Yi W, Zhou S, Chen T, Lu C, Atadja P, Liu XS, Li E, Zhang Y, Shou J. SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells. Genome Res. 2015 Sep; 25(9):1325-35.
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Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS. Sequence determinants of improved CRISPR sgRNA design. Genome Res. 2015 Aug; 25(8):1147-57.
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Jiang P, Freedman ML, Liu JS, Liu XS. Inference of transcriptional regulation in cancers. Proc Natl Acad Sci U S A. 2015 Jun 23; 112(25):7731-6.
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Wang H, Zang C, Liu XS, Aster JC. The role of Notch receptors in transcriptional regulation. J Cell Physiol. 2015 May; 230(5):982-8.
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Cai C, He HH, Gao S, Chen S, Yu Z, Gao Y, Chen S, Chen MW, Zhang J, Ahmed M, Wang Y, Metzger E, Schüle R, Liu XS, Brown M, Balk SP. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity. Cell Rep. 2014 Dec 11; 9(5):1618-27.
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Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, Bernstein BE, Blacklow SC, Liu XS, Aster JC, Pear WS. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proc Natl Acad Sci U S A. 2014 Nov 18; 111(46):E4946-53.
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Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014 Nov; 15(11):709-21.
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Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52.
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Luyten A, Zang C, Liu XS, Shivdasani RA. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells. Genes Dev. 2014 Aug 15; 28(16):1827-39.
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Stoeck A, Lejnine S, Truong A, Pan L, Wang H, Zang C, Yuan J, Ware C, MacLean J, Garrett-Engele PW, Kluk M, Laskey J, Haines BB, Moskaluk C, Zawel L, Fawell S, Gilliland G, Zhang T, Kremer BE, Knoechel B, Bernstein BE, Pear WS, Liu XS, Aster JC, Sathyanarayanan S. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov. 2014 Oct; 4(10):1154-67.
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Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, Zhang P, Zhang Y, Liu XS. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 2014 Aug 07; 15(8):419.
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Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K. JARID1B is a luminal lineage-driving oncogene in breast cancer. Cancer Cell. 2014 Jun 16; 25(6):762-77.
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Hsieh CL, Fei T, Chen Y, Li T, Gao Y, Wang X, Sun T, Sweeney CJ, Lee GS, Chen S, Balk SP, Liu XS, Brown M, Kantoff PW. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci U S A. 2014 May 20; 111(20):7319-24.
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Chen X, Iliopoulos D, Zhang Q, Tang Q, Greenblatt MB, Hatziapostolou M, Lim E, Tam WL, Ni M, Chen Y, Mai J, Shen H, Hu DZ, Adoro S, Hu B, Song M, Tan C, Landis MD, Ferrari M, Shin SJ, Brown M, Chang JC, Liu XS, Glimcher LH. XBP1 promotes triple-negative breast cancer by controlling the HIF1a pathway. Nature. 2014 Apr 03; 508(7494):103-107.
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Wee S, Dhanak D, Li H, Armstrong SA, Copeland RA, Sims R, Baylin SB, Liu XS, Schweizer L. Targeting epigenetic regulators for cancer therapy. Ann N Y Acad Sci. 2014 Feb; 1309:30-6.
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Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014; 15(12):554.
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Wang H, Zang C, Taing L, Arnett KL, Wong YJ, Pear WS, Blacklow SC, Liu XS, Aster JC. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proc Natl Acad Sci U S A. 2014 Jan 14; 111(2):705-10.
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Sulahian R, Casey F, Shen J, Qian ZR, Shin H, Ogino S, Weir BA, Vazquez F, Liu XS, Hahn WC, Bass AJ, Chan V, Shivdasani RA. An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer. Oncogene. 2014 Dec 04; 33(49):5637-48.
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He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods. 2014 Jan; 11(1):73-78.
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Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 2014 Feb; 24(2):260-6.
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Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013 Dec; 8(12):2502-15.
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Wang H, Meyer CA, Fei T, Wang G, Zhang F, Liu XS. A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer. BMC Genomics. 2013 Oct 04; 14:680.
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Tam WL, Lu H, Buikhuisen J, Soh BS, Lim E, Reinhardt F, Wu ZJ, Krall JA, Bierie B, Guo W, Chen X, Liu XS, Brown M, Lim B, Weinberg RA. Protein kinase C a is a central signaling node and therapeutic target for breast cancer stem cells. Cancer Cell. 2013 Sep 09; 24(3):347-64.
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Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda Z, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell Stem Cell. 2013 Jul 03; 13(1):117-30.
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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. 2013 Jul; 20(7):908-13.
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Ni M, Chen Y, Fei T, Li D, Lim E, Liu XS, Brown M. Amplitude modulation of androgen signaling by c-MYC. Genes Dev. 2013 Apr 01; 27(7):734-48.
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Sun H, Qin B, Liu T, Wang Q, Liu J, Wang J, Lin X, Yang Y, Taing L, Rao PK, Brown M, Zhang Y, Long HW, Liu XS. CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinformatics. 2013 May 15; 29(10):1352-4.
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Cai C, Wang H, He HH, Chen S, He L, Ma F, Mucci L, Wang Q, Fiore C, Sowalsky AG, Loda M, Liu XS, Brown M, Balk SP, Yuan X. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer. J Clin Invest. 2013 Mar; 123(3):1109-22.
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Xu K, Wu ZJ, 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 C, Vessella RL, Montironi R, Magi-Galluzzi C, Kantoff PW, Balk SP, Liu XS, Brown M. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science. 2012 Dec 14; 338(6113):1465-9.
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Verzi MP, Shin H, San Roman AK, Liu XS, Shivdasani RA. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Mol Cell Biol. 2013 Jan; 33(2):281-92.
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Bailey ST, Shin H, Westerling T, Liu XS, Brown M. Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):18060-5.
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Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012 Sep; 7(9):1728-40.
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Meyer CA, Tang Q, Liu XS. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol. 2012 Oct; 26(10):1651-9.
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Chen S, Ma J, Wu F, Xiong LJ, Ma H, Xu W, Lv R, Li X, Villen J, Gygi SP, Liu XS, Shi Y. The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes Dev. 2012 Jun 15; 26(12):1364-75.
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He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 2012 Jun; 22(6):1015-25.
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Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res. 2012 Aug; 40(14):6414-23.
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Cai C, He HH, Chen S, Coleman I, Wang H, Fang Z, Chen S, Nelson PS, Liu XS, Brown M, Balk SP. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell. 2011 Oct 18; 20(4):457-71.
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Tang Q, Chen Y, Meyer C, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS. A comprehensive view of nuclear receptor cancer cistromes. Cancer Res. 2011 Nov 15; 71(22):6940-7.
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Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, 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. 2011 Aug 22; 12(8):R83.
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Ni M, Chen Y, Lim E, Wimberly H, Bailey ST, Imai Y, Rimm DL, Liu XS, Brown M. Targeting androgen receptor in estrogen receptor-negative breast cancer. Cancer Cell. 2011 Jul 12; 20(1):119-31.
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Marotta LL, Almendro V, Marusyk A, Shipitsin M, Schemme J, Walker SR, Bloushtain-Qimron N, Kim JJ, Choudhury SA, Maruyama R, Wu Z, Gönen M, Mulvey LA, Bessarabova MO, Huh SJ, Silver SJ, Kim SY, Park SY, Lee HE, Anderson KS, Richardson AL, Nikolskaya T, Nikolsky Y, Liu XS, Root DE, Hahn WC, Frank DA, Polyak K. The JAK2/STAT3 signaling pathway is required for growth of CD44?CD24? stem cell-like breast cancer cells in human tumors. J Clin Invest. 2011 Jul; 121(7):2723-35.
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Meyer CA, He HH, Brown M, Liu XS. BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics. 2011 Jul 01; 27(13):1867-8.
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Maruyama R, Choudhury S, Kowalczyk A, Bessarabova M, Beresford-Smith B, Conway T, Kaspi A, Wu Z, Nikolskaya T, Merino VF, Lo PK, Liu XS, Nikolsky Y, Sukumar S, Haviv I, Polyak K. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium. PLoS Genet. 2011 Apr; 7(4):e1001369.
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Verzi MP, Shin H, Ho LL, Liu XS, Shivdasani RA. Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Mol Cell Biol. 2011 May; 31(10):2026-39.
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Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol. 2011; 12(2):R11.
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Maruyama R, Shipitsin M, Choudhury S, Wu Z, Protopopov A, Yao J, Lo PK, Bessarabova M, Ishkin A, Nikolsky Y, Liu XS, Sukumar S, Polyak K. Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2820-4.
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Verzi MP, Shin H, He HH, Sulahian R, Meyer CA, Montgomery RK, Fleet JC, Brown M, Liu XS, Shivdasani RA. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell. 2010 Nov 16; 19(5):713-26.
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Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 2010 Dec; 20(12):1730-9.
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Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 2011 Jan; 39(Database issue):D968-74.
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Lupien M, Meyer CA, Bailey ST, Eeckhoute J, Cook J, Westerling T, Zhang X, Carroll JS, Rhodes DR, Liu XS, Brown M. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev. 2010 Oct 01; 24(19):2219-27.
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Verzi MP, Hatzis P, Sulahian R, Philips J, Schuijers J, Shin H, Freed E, Lynch JP, Dang DT, Brown M, Clevers H, Liu XS, Shivdasani RA. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proc Natl Acad Sci U S A. 2010 Aug 24; 107(34):15157-62.
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Ahmadiyeh N, Pomerantz MM, Grisanzio C, Herman P, Jia L, Almendro V, He HH, Brown M, Liu XS, Davis M, Caswell JL, Beckwith CA, Hills A, Macconaill L, Coetzee GA, Regan MM, Freedman ML. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A. 2010 May 25; 107(21):9742-6.
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Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, Liu XS, Rinn J, Schier AF. Chromatin signature of embryonic pluripotency is established during genome activation. Nature. 2010 Apr 08; 464(7290):922-6.
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He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS. Nucleosome dynamics define transcriptional enhancers. Nat Genet. 2010 Apr; 42(4):343-7.
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Wolfer A, Wittner BS, Irimia D, Flavin RJ, Lupien M, Gunawardane RN, Meyer CA, Lightcap ES, Tamayo P, Mesirov JP, Liu XS, Shioda T, Toner M, Loda M, Brown M, Brugge JS, Ramaswamy S. MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703.
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Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 2010 Jan 21; 463(7279):374-8.
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Boros J, Donaldson IJ, O'Donnell A, Odrowaz ZA, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks AD. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res. 2009 Nov; 19(11):1963-73.
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Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, Chen Z, Beroukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK, Jänne OA, Balk SP, Mehra R, Han B, Chinnaiyan AM, Rubin MA, True L, Fiorentino M, Fiore C, Loda M, Kantoff PW, Liu XS, Brown M. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009 Jul 23; 138(2):245-56.
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Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown M. Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol. 2009 Jun; 29(12):3413-23.
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Xia X, Lemieux ME, Li W, Carroll JS, Brown M, Liu XS, Kung AL. Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4260-5.
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Eeckhoute J, Lupien M, Meyer CA, Verzi MP, Shivdasani RA, Liu XS, Brown M. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 2009 Mar; 19(3):372-80.
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Liu XS, Meyer CA. ChIP-Chip: algorithms for calling binding sites. Methods Mol Biol. 2009; 556:165-75.
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Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137.
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Holmes KA, Song JS, Liu XS, Brown M, Carroll JS. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Res. 2008 Sep 15; 68(18):7380-5.
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Agoulnik IU, Bingman WE, Nakka M, Li W, Wang Q, Liu XS, Brown M, Weigel NL. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase. Mol Endocrinol. 2008 Nov; 22(11):2420-32.
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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. 2008 Mar 21; 132(6):958-70.
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Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403.
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Li W, Carroll JS, Brown M, Liu xS. xMAN: extreme MApping of OligoNucleotides. BMC Genomics. 2008; 9 Suppl 1:S20.
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Liu XS. Getting started in tiling microarray analysis. PLoS Comput Biol. 2007 Oct; 3(10):1842-4.
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Wang Q, Li W, Liu XS, Carroll JS, Jänne OA, Keeton EK, Chinnaiyan AM, Pienta KJ, Brown M. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell. 2007 Aug 03; 27(3):380-92.
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Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97.
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Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12457-62.
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Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky AS. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 2006 Jul; 16(7):912-21.
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Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005 Jul 15; 122(1):33-43.
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Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 2005; 6(8):R64.
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Li W, Meyer CA, Liu XS. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics. 2005 Jun; 21 Suppl 1:i274-82.
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Ben-Yehuda S, Fujita M, Liu XS, Gorbatyuk B, Skoko D, Yan J, Marko JF, Liu JS, Eichenberger P, Rudner DZ, Losick R. Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA. Mol Cell. 2005 Mar 18; 17(6):773-82.
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