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Xiaole Shirley Liu, PhD

Publications

  • 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.
    24937458
  • Sun T, Wang X, He HH, Sweeney CJ, Liu SX, Brown M, Balk S, Lee GS, Kantoff PW.MiR-221 promotes the development of androgen independence in prostate cancer cells via downregulation of HECTD2 and RAB1A.Oncogene. 2014 May 22(21):2790-800.
    23770851
  • 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(20):7319-24.
    24778216
  • 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 HIF1α pathway.Nature. 2014 Apr 3;508(7494):103-7.
    24670641
  • Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, Deluca DS, Brooks AN, Wang S, Que J, Rustgi AK, Wong KK, Ligon KL, Liu XS, Marto JA, Meyerson M, Bass AJ.SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.J Clin Invest. 2014 Apr 1;124(4):1636-45.
    24590290
  • 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.
    24571255
  • 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.
    24285721
  • 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.
    24374627
  • 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):73-8.
    24317252
  • Wang Q, Huang J, Sun H, Liu J, Wang J, Wang Q, Qin Q, Mei S, Zhao C, Yang X, Liu XS, Zhang Y.CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.Nucleic Acids Res. 2014 Jan;42(Database issue):D450-8.
    24253304
  • Catic A, Suh CY, Hill CT, Daheron L, Henkel T, Orford KW, Dombkowski DM, Liu T, Liu XS, Scadden DT.Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation.Cell. 2013 Dec 5;155(6):1380-95.
    24315104
  • 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.
    24263090
  • 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 α is a central signaling node and therapeutic target for breast cancer stem cells.Cancer Cell. 2013 Sep 9;24(3):347-64.
    24029232
  • 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 3;13(1):117-30.
    23770079
  • 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.
    23728290
  • 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 Apr 17.
    23508969
  • 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 1;27(7):734-48.
    23530127
  • Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S.Chromatin marks identify critical cell types for fine mapping complex trait variants.Nat Genet. 2013 Feb;45(2):124-30.
    23263488
  • 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.
    23239736
  • 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. 2012 Nov 5.
    23129810
  • 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.
    23077249
  • 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. Review.
    22930692
  • Feng J, Liu T, Qin B, Zhang Y, Liu XS.Identifying ChIP-seq enrichment using MACS.Nat Protoc. 2012 Sep;7(9):1728-40.
    22936215
  • Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.Systematic evaluation of factors influencing ChIP-seq fidelity.Nat Methods. 2012 Jun;9(6):609-14.
    22522655
  • 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.
    22495509
  • Fu K, Tang Q, Feng J, Liu XS, Zhang Y.DiNuP: a systematic approach to identify regions of differential nucleosome positioning.Bioinformatics. 2012 Aug 1;28(15):1965-71.
    22668788
  • 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.
    22713873
  • 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.
    22508765
  • Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS.CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.Bioinformatics. 2012 May 15;28(10):1411-2.
    22495751
  • 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.
    21859476
  • 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.
    21741601
  • Meyer CA, He HH, Brown M, Liu XS.BINOCh: binding inference from nucleosome occupancy changes.Bioinformatics. 2011 Jul 1;27(13):1867-8.
    21551136
  • 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 Mar 14.
    21402776
  • Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, Liu XS, Lazar MA.A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism.Science. 2011 Mar 11;331(6022):1315-9.
    21393543
  • 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 Feb 1;12(2):R11.
    21284836
  • 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.
    20972221
  • Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS, An J, Lamperti ED, Koh KP, Ganetzky R, Liu XS, Aravind L, Agarwal S, Maciejewski JP, Rao A.Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2.Nature. 2010 Dec 9;468(7325):839-43.
    21057493
  • 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.
    21045080
  • 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.
    21074721
  • Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu XS, Struhl K.Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation.Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17945-50.
    20921369
  • 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.
    20696899
  • Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Tsichlis PN, Shirley Liu X, Struhl K.A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.Cancer Cell. 2010 Apr 13;17(4):348-61.
    20385360
  • 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.
    20208536
  • Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.Nat Struct Mol Biol. 2009 Aug;16(8):847-52.
    19620965
  • 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.
    19632176
  • Liu XS, Meyer CA.ChIP-Chip: algorithms for calling binding sites.Methods Mol Biol. 2009;556:165-75.
    19488878
  • 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.
    19129543
  • Zhang Y, Shin H, Song JS, Lei Y, Liu XS.Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.BMC Genomics. 2008;9:537.
    19014516
  • Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS.Model-based analysis of ChIP-Seq (MACS).Genome Biol. 2008;9(9):R137.
    18798982
  • Song JS, Liu X, Liu XS, He X.A high-resolution map of nucleosome positioning on a fission yeast centromere.Genome Res. 2008 Jul;18(7):1064-72.
    18411404
  • Li W, Carroll JS, Brown M, Liu S.xMAN: extreme MApping of OligoNucleotides.BMC Genomics. 2008;9 Suppl 1:S20.
    18366610
  • 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.
    18358809
  • Stayrook KR, Rogers PM, Savkur RS, Wang Y, Su C, Varga G, Bu X, Wei T, Nagpal S, Liu XS, Burris TP.Regulation of human 3 alpha-hydroxysteroid dehydrogenase (AKR1C4) expression by the liver X receptor alpha.Mol Pharmacol. 2008 Feb;73(2):607-12.
    18024509
  • Liu XS.Getting started in tiling microarray analysis.PLoS Comput Biol. 2007 Oct;3(10):1842-4. Review.
    17967045
  • Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS.Model-based analysis of two-color arrays (MA2C).Genome Biol. 2007;8(8):R178.
    17727723
  • Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK, Velmurugan S, Chen R, Washburn MP, Liu XS, Decaprio JA.Evolutionarily Conserved Multisubunit RBL2/p130 and E2F4 Protein Complex Represses Human Cell Cycle-Dependent Genes in Quiescence.Mol Cell. 2007 May 25;26(4):539-51.
    17531812
  • Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X.Microarray blob-defect removal improves array analysis.Bioinformatics. 2007 Apr 15;23(8):966-71.
    17332024
  • Ozsolak F, Song JS, Liu XS, Fisher DE.High-throughput mapping of the chromatin structure of human promoters.Nat Biotechnol. 2007 Feb;25(2):244-8.
    17220878
  • 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.
    17013392
  • 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.
    16895995
  • Zhang Y, Liu XS, Liu QR, Wei L.Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.Nucleic Acids Res. 2006;34(12):3465-75.
    16849434
  • Ji X, Li W, Song J, Wei L, Liu XS.CEAS: cis-regulatory element annotation system.Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W551-4.
    16845068
  • Nelson EA, Walker SR, Li W, Liu XS, Frank DA.Identification of human STAT5-dependent gene regulatory elements based on interspecies homology.J Biol Chem. 2006 Sep 8;281(36):26216-24.
    16840779
  • Liu XS, Jiang J, Jiao XY, Wu YE, Lin JH.Matrine-induced apoptosis in leukemia U937 cells: involvement of caspases activation and MAPK-independent pathways.Planta Med. 2006 May;72(6):501-6.
    16773533
  • 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.
    16769980
  • Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM.Applying whole-genome studies of epigenetic regulation to study human disease.Cytogenet Genome Res. 2006;114(1):1-15. Review.
    16717444
  • Palomero T, Odom DT, O'neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA, Look AT.Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia.Blood. 2006 Aug 1;108(3):986-92.
    16621969
  • 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.
    16009131
  • 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.
    15961467
  • Hong P, Liu XS, Zhou Q, Lu X, Liu JS, Wong WH.A boosting approach for motif modeling using ChIP-chip data.Bioinformatics. 2005 Jun 1;21(11):2636-43.
    15817698
  • Yildiz FH, Liu XS, Heydorn A, Schoolnik GK.Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant.Mol Microbiol. 2004 Jul;53(2):497-515.
    15228530
  • Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS.A suite of web-based programs to search for transcriptional regulatory motifs.Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W204-7.
    15215381
  • Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S.Eukaryotic regulatory element conservation analysis and identification using comparative genomics.Genome Res. 2004 Mar;14(3):451-8.
    14993210
  • Conlon EM, Liu XS, Lieb JD, Liu JS.Integrating regulatory motif discovery and genome-wide expression analysis.Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3339-44.
    12626739
  • Liu XS, Brutlag DL, Liu JS.An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.Nat Biotechnol. 2002 Aug;20(8):835-9.
    12101404
  • Lieb JD, Liu X, Botstein D, Brown PO.Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.Nat Genet. 2001 Aug;28(4):327-34.
    11455386