Xia X, Lemieux M, Li W, Carroll JS, Brown M, Liu X, Kung AL.
Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostatis.
Proc Natl Acad Sci USA. 2009;106(11):4260-5.
[Abstract]
[Full Paper]
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns
and expressed exons by H3K36me3. Nat Genet. 2009;41(3):376-81.
[Abstract]
[Full Paper]
Shin H, Liu T, Manrai AK, Liu XS. CEAS: Cis-regulatory element annotation system. Bioinformatics 2009;25(19):2605-6.
[Abstract]
[Full Paper]
Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes, DR, Liu XS,
Brown M. Coactivator function defines the active estrogen
receptor alpha cistrome. Moll Cell Biol. 2009;29(12):3413-23.
[Abstract]
[Full Paper]
Eeckhoute J, Lupein 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;19(3)372-80.
[Abstract]
[Full Paper]
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 small RNA transcriptomes in maize.
Plant Cell. 2009;21(4):1053-69.
[Abstract]
[Full Paper]
Wang Q, Li W, Zhang Y, Yuan X, et al., Kantoff PW, Liu XS*,
Brown M*. Androgen receptor regulates a distinct transcription program in androgen-independent
prostate cancer. Cell. 2009;138(2):245-56.
*Joint corresponding authors.
[Abstract]
[Full Paper]
Zhang Y, Moqtaderi Z, Rattner B, Zhenhai Zhang Z, Euskirchen G, Snyder M, Kadonaga JT, Pugh BF, Liu XS,
Struhl K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo: evidence
against a nucleosome code. Nat Struct Mol Biol. 2009;16(8):847-52.
[Abstract]
[Full Paper]
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 MAPK. Mol Endocrinol. 2009. Epub ahead of print.
Boros J, Donaldson IJ, O'Donnel A, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks AD. Elucidation of the Elk-1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res. 2009 Sep 17. Epub ahead of print.
Johnson WE, Liu JS, Liu XS. Doubly-stochastic continuous hidden Markov approach for applications on genome tiling arrays. Annals of Applied Statistics. In press.
Ji H*,Liu XS. Use hierarchical models to improve the analysis of omics data. Nat Biotech. Conditionally accepted.
Li W, Liu XS, Struhl K, Wade JT. Distinguishing function from noise: identification of functional protein-DNA interactions from genome-wide binding profiles. Submitted.
Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Liu XS, Struhl K. A transcriptional signature and common gene networks link cancer with metabolic syndrome and auto-immune diseases. Submitted
Wittner B, Wolfer A, Lupien M, Meyer CA, Lightcap E, Liu XS, Shioda T, Brugge J, Brown M, Ramaswamy S. Coordinate regulation of twelve poor-outcome cancer signatures by c-MYC. Submitted
Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Marson A, Frampton GM, Cole MF, Odom D, Geng Y, Young RA, Liu XS, Gygi SP, Sicinski P. Analyses of cyclin D1 Interactome and cistrome in mouse development and in cancer using a "genetic-preteomic" approach. Submitted.
He HH, Meyer CA, Shin H, Bailey S, Wei G, Wang Q, Zhang Y,Xu K, Ni M, Lupien M, Mieczkowski P, Leib JD, Zhao K, Brown M*,Liu XS. Nucleosome dynamics defines transcriptional enhancers. Submitted.
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. Submitted
Vastenhouw N, Zhang Y, Wood I, Imam F, Regev A, Liu XS*, Rinn J*, Schier A*. A distinct chromatin signature underlies zygotic genome activation and embryonic pluripotency. Submitted.
Cao Q, Meyer CA, Li C, Liu XS. CaSNP: a database for interrogating genomic copy number alteration of cancer from SNP array data. Submitted.
Lupien M, Meyer CA, Eeckhoute J, Cook J, Bailey ST, Carroll JS, Rhodes DR, Liu XS*. Growth factor- specific ERa activation underlies breast cancer endocrine resistance. Submitted.
Lefterova M, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D,
Zhuo D, Stoeckert CJ, Liu XS, Lazar MA. PPARgamma and C/EBP factors orchestrate
adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 2008; 22:2941-2952.
[Abstract]
[Full Paper]
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. *Joint first authors.
[Full Paper]
Gottardo R, Li W, Johnson WE, Liu XS. A flexible and powerful
Bayesian hierarchical model for ChIP-chip experiments.
Biometrics.2008; 64(2):468-78.
[Abstract]
[Full Paper]
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. 2008; 18(3):393-403.
[Abstract]
[Full Paper]
Li W, Carroll JS, Brown M, Liu XS. xMAN: extreme
Mapping of OligoNucleotides. BIOCOMP '07 (acceptance rate
27%). BMC Genomics 9 2008; (Suppl 1):S20.
[Abstract]
[Full Paper]
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;132(6):958-70.
[Abstract]
[Full Paper]
Song J, Liu X, Liu XS, He X. A high-resolution map of nucelosome positioning on a fission yeast centromere. Genome Res. 2008, 18(7):1064-72.
[Full Paper]
Zhang Y*, Liu T*, Meyer CA, Eeckhoute J, Johnson DS, Myers RM,
Brown M, Li W, Liu XS. Model-based Analysis of ChIP-seq
(MACS). Genome Biology 2008, 9(9) R137. *Joint first authors.
[Abstract]
[Full Paper]
Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T.,
Hattori N, Ohgane J, Tanaka S, Liu XS, Shiota K. DNA
methaylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter
regions demonstrating tissue-specific gene expression. Genome Res 2008. Epub ahead of print.
[Abstract]
[Full Paper]
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.
[Abstract]
[Full Paper]
Ozsolak F, Poling L, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X,
Song JS, Fisher DE. Chromatin structure analyses identify miRNA promoters. Genes Development
2008; 22(22):3172-83.
[Abstract]
[Full Paper]
O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser R, Wong KK, Li
W, KcKenna K, Liu X, Neuberg D, Silverman L, DeAngelo D,
Kutok J, Rothstein R, DePinho R, Chin L, Lee C, Look AT.
Tandem duplication as a novel mechanism of MYB activation in
human T-ALL. J Exp Med (2007) 204(13):3059-66.
[Abstract]
[Full Paper]
He H, Wang J, Liu T, Liu X, Li T, Wang Y, Qian Z, Zheng H, Zhu
X, Wu T, Shi B, Deng W, Zhou W, Skogerbo G, Chen R. Mapping
the C. elegans noncoding transcriptome with a whole genome
tiling microarray. Genome Res. 14 (2007) 1471-1477.
[Abstract]
[Full Paper]
Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS,
Chen R, Liu XS. Model based analysis for 2-color arrays (MA2C).
Genome Biol. 8(8) R178.
[Abstract]
[Full Paper]
Liu XS. Getting started in tiling arrays analysis. PLoS Comput
Biol. 3(10):1842-4. (2007).
[Full Paper]
Wang Q, Li W, Liu XS, Carroll JS, Janne OA, Keeton EK,
Chinnaiyan AM, Pienta KJ and Brown M. A hierarchical network of
transcription factors governs androgen receptor dependent
prostate cancer growth. Mol. Cell 27(3):380-92 (2007).
[Abstract]
[Full Paper]
Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK,
Velmurugan S, Chen R, Washburn MP, Liu XS, DeCaprio JA.
Evolutionally conserved multi-subunit RBL2/p130 and E2F4
protein complex represses human cell cycle-dependent genes in
quiescence. Mol Cell 26 (2007) 539-51.
[Abstract]
[Full Paper]
Song J, Maghsoudi K, Li W, Fox A, Quackenbush J and Liu XS.
Microarray Blob-Defect Removal Improves Array Analysis.
Bioinformatics 23 (2007) 966-971.
[Abstract]
[Full Paper]
F. Ozsolak*, J.S. Song*, X.S. Liu#, D.E. Fisher#.
High-throughput mapping of the chromatin structure of human
promoters. Nat. Biotech. 25 (2007) 244-248.
*Joint first authors; #Joint corresponding authors.
[Abstract]
[Full Paper]
Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J,
Brodsky AS,KeetonEK, 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. 38 (2006) 1289-1297.
*Joint corresponding authors.
[Abstract]
[Full Paper]
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. USA 103 (2006) 12457-12462.
*Joint first authors.
[Abstract]
[Full Paper]
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. 281 (2006)
26216-26224.
[Abstract]
[Full Paper]
Zhang Y, Liu XS, Liu Q, Wei L.Genome-wide in silico
Identification and Analysis of cis Natural Antisense Transcripts
(cis-NATs) in Ten Species. Nucleic Acids Res. 34 (2006)
3465-3475.
[Abstract]
[Full Paper]
Swinburn 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. 16 (2006)
912-921.
[Abstract]
[Full Paper]
Ji X*, Li W*, Song J, Wei L, Liu XS. CEAS: cis-regulatory
element annotation system. Nucleic Acids Res. 34 (2006)
W551-554 *Joint first authors.
[Abstract]
[Full Paper]
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 108
(2006) 986-992.
[Abstract]
[Full Paper]
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, 114:1-15. [Abstract] [Full Paper]
Brodsky AS, Meyer CA, Hall G, Swinburne IA, Keenan BJ, Liu XS,
Fox EA, Silver PA. Genomic mapping of RNA polymerase II
reveals sites of co-transcriptional regulation in human cells.
Genome Biology. 2005, 6(8):R64.
[Abstract]
[Full Paper]
Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, 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, 122(1):33-43.
[Abstract]
[Full Paper]
Liu XS. Gibbs sampling and bioinformatics. Encyclopedia of
Genetics, Genomics, Proteomics and Bioinformatics. John Wiley
& Sons, Ltd, UK, 2005.ISBN: 0-470-84974-6.
[Publication]
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. ISMB2005. Bioinformatics
2005, 21 Suppl.1:i274-i282.
[Abstract]
[Full Paper]
Hong P, Liu XS, Zhou Q, Lu X, Liu JS, Wong WH. A boosting approach for motif modeling using ChIP-chip data. Bioinformatics 2005, 21(11):2636-43. [Abstract] [Full Paper]
Ben-Yehuda S, Jujita M, Liu XS, Gorbatyuk B, Skoko D, Yan J,
Eichenberger P, Rudner DZ, Marko JF, Liu JS, 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.
[Abstract]
[Full Paper]
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.
[Abstract]
[Full Paper]
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, 32(Web Server
Issue):W204-W207.
[Abstract]
[Full Paper]
Liu Y*, Liu XS*, Wei L, Altman RB, Batzoglou S. Eukaryotic
regulatory element conservation analysis and identification
using comparative genomics. Genome Res. 2004, 14(3):451-8.
*Joint first authors.
[Abstract]
[Full Paper]
Jensen ST, Liu XS, Zhou Q, Liu JS. Computational discovery of
gene regulatory binding motifs: a Bayesian perspective.
Statistical Science 2004, 19(1): 188-204.
[Full Paper]
Conlon EM*, Liu XS*, Lieb JD, Liu JS. Integrating regulatory
motif discovery and genome-wide expression analysis. Proc. Natl.
Acad. Sci. USA 2003, 100(6):3339-44.
*Joint first authors.
[Abstract]
[Full Paper]
Liu XS*, Brutlag DL, Liu JS. An algorithm for finding protein-DNA
binding sites with applications to chromatin
immunoprecipitation microarray experiments. Nat. Biotech.
2002, 20(8):835-9. *Liu X added middle name Shirley.
[Abstract]
[Full Paper]
Liu JS, Gupta M, Liu X, Mayerhofere L, Lawrence CE. Statistical
models for biological sequence motif discovery. Case Studies in
Bayesian Statistics, IV, 2002, Springer-Verlag, New York.
[Full Paper]
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, 28(4):327-34.
[Abstract]
[Full Paper]
Liu X, Brutlag DL, Liu JS. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Proc. Pac. Symp. Biocomput. 2001:127-38. [Abstract] [Full Paper]
Dugan JM, Berrios DC, Liu X, Kim DK, Kaizer H, Fagan LM.
Automation and integration of components for generalized
semantic markup of electronic medical texts. Proc. AMIA Symp.
1999:736-40.
[Full Paper]
Fischer P, Liu X, Lizotte-Waniewski M, Kamal IH, Ramzy RM,
Williams SA. Development of a quantitative, competitive
polymerase chain reaction-enzyme-linked immunosorbent assay
for the detection of Wuchereria bancrofti DNA. XParasitol Res.
1999,85(3):176-83.
[Full Paper]
Liu X, Altman RB. Updating a bibliography using the related articles function within PubMed. Proc. AMIA Symp. 1998:750-4.