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Xiaole Shirley Liu, PhD


  • 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.
  • 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.
  • Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG.Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development.Cell. 2012 Dec 7;151(6):1200-13.
  • 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.
  • 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.
  • Feng J, Liu T, Qin B, Zhang Y, Liu XS.Identifying ChIP-seq enrichment using MACS.Nat Protoc. 2012 Sep;7(9):1728-40.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.Breast Cancer Special Feature: Altered antisense-to-sense transcript ratios in breast cancer.Proc Natl Acad Sci U S A. 2010 Nov 22.
  • 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.
  • 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.
  • 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 1;24(19):2219-27.
  • Liu XR, Zheng XF, Ji SZ, Lv YH, Zheng DY, Xia ZF, Zhang WD.Metabolomic analysis of thermally injured and/or septic rats.Burns. 2010 Nov;36(7):992-8.
  • Zhou L, Li X, Chen X, Li Z, Liu X, Zhou S, Zhong Q, Yi T, Wei Y, Zhao X, Qian Z.In vivo antitumor and antimetastatic activities of camptothecin encapsulated with N-trimethyl chitosan in a preclinical mouse model of liver cancer.Cancer Lett. 2010 Nov 1;297(1):56-64.
  • Han C, Liu J, Liu X, Li M.Angiotensin II induces C-reactive protein expression through ERK1/2 and JNK signaling in human aortic endothelial cells.Atherosclerosis. 2010 Sep;212(1):206-12.
  • 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.
  • Liu XE, Dewaele S, Vanhooren V, Fan YD, Wang L, Van Huysse J, Zhuang H, Contreras R, Libert C, Chen CC.Alteration of N-glycome in diethylnitrosamine-induced hepatocellular carcinoma mice: a non-invasive monitoring tool for liver cancer.Liver Int. 2010 Sep;30(8):1221-8.
  • Shao D, Liu Y, Liu X, Zhu L, Cui Y, Cui A, Qiao A, Kong X, Liu Y, Chen Q, Gupta N, Fang F, Chang Y.PGC-1beta-Regulated mitochondrial biogenesis and function in myotubes is mediated by NRF-1 and ERRalpha.Mitochondrion. 2010 Aug;10(5):516-27.
  • Liu X, Jiang Y, Russell JE.A potential regulatory role for mRNA secondary structures within the prothrombin 3'UTR.Thromb Res. 2010 Aug;126(2):130-6.
  • Leng SX, Tian X, Liu X, Lazarus G, Bellantoni M, Greenough W, Fried LP, Shen T, Durso SC.An International Model for Geriatrics Program Development in China: The Johns Hopkins-Peking Union Medical College Experience.J Am Geriatr Soc. 2010 Jul;58(7):1376-81.
  • Zhang YJ, Zhang S, Liu XZ, Wen HA, Wang M.A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains.Lett Appl Microbiol. 2010 Jul;51(1):114-8.
  • Zhang Y, Zhao H, Yu GY, Liu XD, Shen JH, Lee WH, Zhang Y.Structure-function relationship of king cobra cathelicidin.Peptides. 2010 Aug;31(8):1488-93.
  • Sun C, Liu X, Zhang H, Guo W, Cai Z, Chen H, Zhang K, Zhu D, Wang Y.Functional polymorphism of hOGG1 gene is associated with type 2 diabetes mellitus in Chinese population.Mol Cell Endocrinol. 2010 Aug 30;325(1-2):128-34.
  • Liu X, Wu Z, Zhou F, Li D, Chen H.Poly(vinylpyrrolidone-b-styrene) block copolymers tethered surfaces for protein adsorption and cell adhesion regulation.Colloids And Surfaces. B, Biointerfaces. 2010 Sep 1;79(2):452-9.
  • Zhang T, Liu X, Li Q, Wang J, Jia W, Sun X.Exacerbation of ischemia-induced amyloid-beta generation by diabetes is associated with autophagy activation in mice brain.Neurosci Lett. 2010 Aug 2;479(3):215-20.
  • Chapman S, Liu X, Meyers C, Schlegel R, McBride AA.Human keratinocytes are efficiently immortalized by a Rho kinase inhibitor.J Clin Invest. 2010 Jul 1;120(7):2619-26.
  • Liu X, Karnell JL, Yin B, Zhang R, Zhang J, Li P, Choi Y, Maltzman JS, Pear WS, Bassing CH, Turka LA.Distinct roles for PTEN in prevention of T cell lymphoma and autoimmunity in mice.J Clin Invest. 2010 Jul 1;120(7):2497-507.
  • Liu X, Zhou B, Lin R, Jia L, Deng P, Fan K, Wang G, Wang L, Zhang J.Extraction and antioxidant activities of intracellular polysaccharide from Pleurotus sp. mycelium.Int. J. Biol. Macromol. 2010 Aug 1;47(2):116-9.
  • Liu XH, Liu HF, Shen X, Song BA, Bhadury PS, Zhu HL, Liu JX, Qi XB.Synthesis and molecular docking studies of novel 2-chloro-pyridine derivatives containing flavone moieties as potential antitumor agents.Bioorg Med Chem Lett. 2010 Jul 15;20(14):4163-7.
  • Juran BD, Atkinson EJ, Larson JJ, Schlicht EM, Liu X, Jenny Heathcote E, Hirschfield GM, Siminovitch KA, Lazaridis KN.Carriage of a tumor necrosis factor polymorphism amplifies the cytotoxic T-lymphocyte antigen 4 attributed risk of primary biliary cirrhosis: Evidence for a gene-gene interaction.Hepatology. 2010 Mar 15;52(1):223-229.
  • Xu Y, Yao LH, Chen AJ, Guo JQ, Liu XY, Bo H, Liu LQ, Shu YL, Zhang ZQ.[Construction, expression and immunogenicity analysis of a fusion protein containing M2e of influenza A virus fused to a modified Pseudomonas aeruginosa exotoxin A].Bing Du Xue Bao. 2010 May;26(3):189-94.
  • Rao Q, Liu XH, Zhou HB, Ma HH, Lu ZF, Zhou XJ.Expression analysis of Wnt-5a in renal epithelial neoplasms: distinguishing renal oncocytoma from a wide spectrum of renal cell carcinomas.Tumori.;96(2):304-9.
  • Chen FY, Wang HM, Yang SH, Wu JM, Gao YD, Liu X, Yang HJ, Wang CF, Zhong JF, Wang LQ, He HB.[ShRNA against NSP4 gene inhibits the proliferation of bovine rotavirus in vitro].Bing Du Xue Bao. 2010 May;26(3):244-8.
  • Chen YP, Ning B, Liu N, Feng Y, Liu Z, Liu X, Gao ZX.A rapid and sensitive fluoroimmunoassay based on quantum dot for the detection of chlorpyrifos residue in drinking water.J Environ Sci Health B. 2010;45(6):508-15.
  • Han J, Cao Z, Liu X, Zhang W, Zhang S.[Effect of early pregnancy electromagnetic field exposure on embryo growth ceasing].Wei Sheng Yan Jiu. 2010 May;39(3):349-52.
  • Xie X, Hu J, Liu X, Qin H, Percival-Smith A, Rao Y, Li SS.NIP/DuoxA is essential for Drosophila embryonic development and regulates oxidative stress response.Int. J. Biol. Sci. 2010;6(3):252-67.
  • Liu P, Sun J, Zhao J, Liu X, Gu X, Li J, Xiao T, Xu LX.Microvascular imaging using synchrotron radiation.J Synchrotron Radiat. 2010 Jul;17(Pt 4):517-21.
  • Han H, Zeng X, Yin S, Yang R, Liu X, Zhou D.[Development and evaluation of whole-genome DNA microarray of Vibrio parahaemolyticus].Wei Sheng Wu Xue Bao. 2010 Apr 4;50(4):548-53.
  • Wang Y, Chen S, Liu W, Qiu X, Dong L, Peng D, Liu X.[Induction of potent immune responses by recombinant fowlpox virus with deleted ORF73 or ORF214].Wei Sheng Wu Xue Bao. 2010 Apr 4;50(4):512-6.
  • Pei G, Dai H, Ren B, Liu X, Zhang L.[Exploiting bioactive Enediynes from marine microbe based on activity and gene screening].Wei Sheng Wu Xue Bao. 2010 Apr 4;50(4):472-7.
  • Jiang XJ, Liu XJ, Huang F, Jiang HY, Cao WX, Zhu Y.[Comparison of spatial interpolation methods for daily meteorological elements].Ying Yong Sheng Tai Xue Bao. 2010 Mar;21(3):624-30.
  • DI XH, Chen RL, Liu XL, Tian C, Guo YN.[Effects of PTK787 on Cell Proliferation and Expression of fak mRNA in K562.].Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2010 Jun;18(3):597-600.
  • Lu Y, Liu M, Shi S, Jiang H, Yang L, Liu X, Zhang Q, Pan F.Effects of stress in early life on immune functions in rats with asthma and the effects of music therapy.J Asthma. 2010 Jun;47(5):526-31.
  • Wang MF, Yang LH, Yang XL, Zhang RJ, Hou LH, Liu XE.[Correlation of inflammatory marker and coagulation factors with deep vein thrombosis.].Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2010 Jun;18(3):753-6.
  • Wang Y, Liu XR, Tan YF, Yin XC.[Effects of CXCR4 silence induced by RNA interference on cell cycle distribution and apoptosis of jurkat cells.].Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2010 Jun;18(3):625-8.
  • Liu JQ, Yang LH, Chen XH, Tan YH, Liu XE, Chen JF, Chang LX, Gao Y.[Significance of B Cell Activating Factor of TNF Family Promoter Polymorphisms in Patients with Immune Thrombocytopenic Purpura.].Zhongguo Shi Yan Xue Ye Xue Za Zhi. 2010 Jun;18(3):690-3.
  • Liu L, Zeng F, Zeng X, Xue Q, Nie S, Kang C, Wu J, Kang Q, Wang X, Liu X, Li T, Chen J, Li Q, Xu R, Yang X, Kang H, Jiang F, Li Z, Wang X, Zhang L, Long Y.Revaluation of clopidogrel: let the data speak for themselves.J. Huazhong Univ. Sci. Technol. Med. Sci. 2010 Jun;30(3):299-306.
  • He Y, Jiang Y, Li YJ, Liu XH, Zhang L, Liu LJ, Shi H, Li HN, Ma YC, Jin XM.19-peptide, a fragment of tumstatin, inhibits the growth of poorly differentiated gastric carcinoma cells in vitro and in vivo.J Gastroenterol Hepatol. 2010 May;25(5):935-41.
  • Yuan CY, Liu XY, Meng G, Zhao L.[Theoretical study on radial resonance coupling of cylindrical photoacoustic cells].Guang Pu Xue Yu Guang Pu Fen Xi. 2010 Apr;30(4):879-82.
  • Liu X, Wang J, Dai K.[Research advance of treatment of peripheral nerve injury with neuromuscular electric stimulation].Zhongguo Xiu Fu Chong Jian Wai Ke Za Zhi. 2010 May;24(5):622-7.
  • Trawicki M, Liu XC, Tassone C, Thometz J, Lyon R.Improvements in three-dimensional back contour after spinal fusion for idiopathic scoliosis.Stud Health Technol Inform. 2010;158:19-23.
  • Liu XY, Chen SL, Zhang WX.[Clinical study of strengthening pi and nourishing shen therapy combined with Western medicine on patients with glucocorticoid resistant myasthenia gravis].Zhongguo Zhong Xi Yi Jie He Za Zhi. 2010 Mar;30(3):271-4.
  • Cao D, Ren M, Liu X, Jin C, Meng Z, Qiu G.[Molecular and prenatal diagnosis of a pedigree with spinocerebellar ataxia.].Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2010 Jun;27(3):320-3.
  • Liu X, Xu Y, Cui D, Jiang S, Qian Y, Yu S, Jiang K.[Association of cyclic adenosine monophosphate response element-binding protein gene and major depressive disorder.].Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2010 Jun;27(3):263-6.
  • Zhang LF, Liu XQ, Zuo LY, Li TS, Deng GH, Wang AX.Longitudinal observation of an interferon gamma-released assay (T-SPOT.TB) for Mycobacterium tuberculosis infection in AIDS patients on highly active antiretroviral therapy.Chin Med J (Engl). 2010 May;123(9):1117-21.
  • Chen SM, Jiang CY, Wu JY, Liu B, Chen YJ, Hu CJ, Liu XX.RNA interference-mediated silencing of UBCH10 gene inhibits colorectal cancer cell growth in vitro and in vivo.Clin Exp Pharmacol Physiol. 2010 May;37(5-6):525-9.
  • Huang J, Chen YJ, Bian WH, Yu J, Zhao YW, Liu XY.Unilateral amyloid-beta25-35 injection into the rat amygdala increases the expressions of aberrant tau phosphorylation kinases.Chin Med J (Engl). 2010 May;123(10):1311-4.
  • Liu XY, Xue L, Zheng X, Yan S, Zheng SS.Pancreas transplantation in the mouse.HBPD INT. 2010 Jun;9(3):254-8. Review.
  • Yun TK, Zheng S, Choi SY, Cai SR, Lee YS, Liu XY, Cho KJ, Park KY.Non-organ-specific preventive effect of long-term administration of Korean red ginseng extract on incidence of human cancers.Journal Of Medicinal Food. 2010 Jun;13(3):489-94.
  • Liu Z, Qiao X, Xiao H, Liu X, Wang H, Zheng X.[Construction and identification of different stem shRNA expression vectors].Sheng Wu Gong Cheng Xue Bao. 2010 Mar;26(3):386-92.
  • Liu X, Wang D, Wang SY, Meng XS, Zhang WJ, Ying XX, Kang TG.LC determination and pharmacokinetic study of hyperoside in rat plasma after intravenous administration.Yakugaku Zasshi. 2010 Jun;130(6):873-9.
  • Li N, Yu ZL, Wang L, Zheng YT, Jia JX, Wang Q, Zhu MJ, Liu XL, Xia X, Li WJ.Increased tau phosphorylation and beta amyloid in the hipocampus of mouse pups by early life lead exposure.Acta. Biol. Hung. 2010 Jun;61(2):123-34.
  • Liu X, Crump MJ, Logan GD.Do you know where your fingers have been? Explicit knowledge of the spatial layout of the keyboard in skilled typists.Mem Cognit. 2010 Jun;38(4):474-84.
  • 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.
  • 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.
  • 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.
  • Sheng Q, Liu X, Fleming E, Yuan K, Piao H, Chen J, Moustafa Z, Thomas RK, Greulich H, Schinzel A, Zaghlul S, Batt D, Ettenberg S, Meyerson M, Schoeberl B, Kung AL, Hahn WC, Drapkin R, Livingston DM, Liu JF.An activated ErbB3/NRG1 autocrine loop supports in vivo proliferation in ovarian cancer cells.Cancer Cell. 2010 Mar 16;17(3):298-310.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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, J√§nne 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.
  • Liu XS, Meyer CA.ChIP-Chip: algorithms for calling binding sites.Methods Mol Biol. 2009;556:165-75.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Gottardo R, Li W, Johnson WE, Liu XS.A Flexible and Powerful Bayesian Hierarchical Model for ChIP-Chip Experiments.Biometrics. 2008 Jun;64(2):468-78.
  • Li W, Carroll JS, Brown M, Liu S.xMAN: extreme MApping of OligoNucleotides.BMC Genomics. 2008;9 Suppl 1:S20.
  • 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.
  • O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser RS, Wong KK, Li W, McKenna K, Liu XS, Feng B, Neuberg D, Silverman L, DeAngelo DJ, Kutok JL, Rothstein R, DePinho RA, Chin L, Lee C, Look AT.Alu elements mediate MYB gene tandem duplication in human T-ALL.J Exp Med. 2007 Dec 24;204(13):3059-66.
  • 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.
  • Liu XS.Getting started in tiling microarray analysis.PLoS Comput Biol. 2007 Oct;3(10):1842-4. Review.
  • He H, Wang J, Liu T, Liu XS, Li T, Wang Y, Qian Z, Zheng H, Zhu X, Wu T, Shi B, Deng W, Zhou W, SkogerbÝ G, Chen R.Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.Genome Res. 2007 Oct;17(10):1471-7.
  • 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.
  • Wang Q, Li W, Liu XS, Carroll JS, Jšnne 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 3;27(3):380-92.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.