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Items: 31

1.

An oestrogen-receptor-alpha-bound human chromatin interactome.

Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y.

Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497.

2.

Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries.

Vega VB, Cheung E, Palanisamy N, Sung WK.

PLoS One. 2009;4(4):e5241. doi: 10.1371/journal.pone.0005241. Epub 2009 Apr 15.

3.

Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge.

Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND.

Ann N Y Acad Sci. 2009 Mar;1158:215-23. doi: 10.1111/j.1749-6632.2008.03759.x.

PMID:
19348643
4.

De-novo identification of PPARgamma/RXR binding sites and direct targets during adipogenesis.

Hamza MS, Pott S, Vega VB, Thomsen JS, Kandhadayar GS, Ng PW, Chiu KP, Pettersson S, Wei CL, Ruan Y, Liu ET.

PLoS One. 2009;4(3):e4907. doi: 10.1371/journal.pone.0004907. Epub 2009 Mar 20.

5.

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb.

Feng B, Jiang J, Kraus P, Ng JH, Heng JC, Chan YS, Yaw LP, Zhang W, Loh YH, Han J, Vega VB, Cacheux-Rataboul V, Lim B, Lufkin T, Ng HH.

Nat Cell Biol. 2009 Feb;11(2):197-203. doi: 10.1038/ncb1827. Epub 2009 Jan 11.

PMID:
19136965
6.

Transcriptional regulatory networks in embryonic stem cells.

Chen X, Vega VB, Ng HH.

Cold Spring Harb Symp Quant Biol. 2008;73:203-9. doi: 10.1101/sqb.2008.73.026. Epub 2008 Nov 6. Review.

PMID:
19022762
7.

Evolution of the mammalian transcription factor binding repertoire via transposable elements.

Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, Liu ET.

Genome Res. 2008 Nov;18(11):1752-62. doi: 10.1101/gr.080663.108. Epub 2008 Aug 5.

8.

Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

Lam SH, Mathavan S, Tong Y, Li H, Karuturi RK, Wu Y, Vega VB, Liu ET, Gong Z.

PLoS Genet. 2008 Jul 11;4(7):e1000121. doi: 10.1371/journal.pgen.1000121.

9.

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH.

Cell. 2008 Jun 13;133(6):1106-17. doi: 10.1016/j.cell.2008.04.043.

10.

Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation.

Lim CA, Yao F, Wong JJ, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J, Shahab A, Zhao XD, Hibberd M, Wei CL, Lim B, Ng HH, Ruan Y, Chin KC.

Mol Cell. 2007 Aug 17;27(4):622-35.

11.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

12.

Whole-genome cartography of estrogen receptor alpha binding sites.

Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET.

PLoS Genet. 2007 Jun;3(6):e87. Epub 2007 Apr 17.

13.

Inhibitory effects of estrogen receptor beta on specific hormone-responsive gene expression and association with disease outcome in primary breast cancer.

Lin CY, Ström A, Li Kong S, Kietz S, Thomsen JS, Tee JB, Vega VB, Miller LD, Smeds J, Bergh J, Gustafsson JA, Liu ET.

Breast Cancer Res. 2007;9(2):R25.

14.

Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites.

Vega VB, Lin CY, Lai KS, Kong SL, Xie M, Su X, Teh HF, Thomsen JS, Yeo AL, Sung WK, Bourque G, Liu ET.

Genome Biol. 2006;7(9):R82.

15.

cis-regulatory region analysis using BEARR.

Vega VB.

Methods Mol Biol. 2006;338:119-27.

PMID:
16888354
16.

Gene expression preferentially regulated by tamoxifen in breast cancer cells and correlations with clinical outcome.

Frasor J, Chang EC, Komm B, Lin CY, Vega VB, Liu ET, Miller LD, Smeds J, Bergh J, Katzenellenbogen BS.

Cancer Res. 2006 Jul 15;66(14):7334-40.

17.

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.

Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH.

Nat Genet. 2006 Apr;38(4):431-40. Epub 2006 Mar 5.

PMID:
16518401
18.

A global map of p53 transcription-factor binding sites in the human genome.

Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y.

Cell. 2006 Jan 13;124(1):207-19.

19.

Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression.

Lam SH, Wu YL, Vega VB, Miller LD, Spitsbergen J, Tong Y, Zhan H, Govindarajan KR, Lee S, Mathavan S, Murthy KR, Buhler DR, Liu ET, Gong Z.

Nat Biotechnol. 2006 Jan;24(1):73-5. Epub 2005 Dec 4.

PMID:
16327811
20.

An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival.

Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J.

Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13550-5. Epub 2005 Sep 2. Erratum in: Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17882.

21.

Genome-wide expression profiling; a panel of mouse tissues discloses novel biological functions of liver X receptors in adrenals.

Steffensen KR, Neo SY, Stulnig TM, Vega VB, Rahman SS, Schuster GU, Gustafsson JA, Liu ET.

J Mol Endocrinol. 2004 Dec;33(3):609-22.

PMID:
15591022
22.

A human in vitro model system for investigating genome-wide host responses to SARS coronavirus infection.

Ng LF, Hibberd ML, Ooi EE, Tang KF, Neo SY, Tan J, Murthy KR, Vega VB, Chia JM, Liu ET, Ren EC.

BMC Infect Dis. 2004 Sep 9;4:34.

23.

Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003.

Vega VB, Ruan Y, Liu J, Lee WH, Wei CL, Se-Thoe SY, Tang KF, Zhang T, Kolatkar PR, Ooi EE, Ling AE, Stanton LW, Long PM, Liu ET.

BMC Infect Dis. 2004 Sep 6;4:32.

24.

Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells.

Lin CY, Ström A, Vega VB, Kong SL, Yeo AL, Thomsen JS, Chan WC, Doray B, Bangarusamy DK, Ramasamy A, Vergara LA, Tang S, Chong A, Bajic VB, Miller LD, Gustafsson JA, Liu ET.

Genome Biol. 2004;5(9):R66. Epub 2004 Aug 12.

25.

BEARR: Batch Extraction and Analysis of cis-Regulatory Regions.

Vega VB, Bangarusamy DK, Miller LD, Liu ET, Lin CY.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W257-60.

26.

Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies.

Lee WH, Vega VB.

Bioinformatics. 2004 Nov 1;20(16):2863-4. Epub 2004 May 6.

PMID:
15130927
27.

Laboratory-acquired severe acute respiratory syndrome.

Lim PL, Kurup A, Gopalakrishna G, Chan KP, Wong CW, Ng LC, Se-Thoe SY, Oon L, Bai X, Stanton LW, Ruan Y, Miller LD, Vega VB, James L, Ooi PL, Kai CS, Olsen SJ, Ang B, Leo YS.

N Engl J Med. 2004 Apr 22;350(17):1740-5. No abstract available.

28.

Identification of discriminators of hepatoma by gene expression profiling using a minimal dataset approach.

Neo SY, Leow CK, Vega VB, Long PM, Islam AF, Lai PB, Liu ET, Ren EC.

Hepatology. 2004 Apr;39(4):944-53.

PMID:
15057898
29.

Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays.

Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD.

Genome Res. 2004 Mar;14(3):398-405.

30.

Comment on " 'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature".

Fortunel NO, Otu HH, Ng HH, Chen J, Mu X, Chevassut T, Li X, Joseph M, Bailey C, Hatzfeld JA, Hatzfeld A, Usta F, Vega VB, Long PM, Libermann TA, Lim B.

Science. 2003 Oct 17;302(5644):393; author reply 393. No abstract available.

31.

Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection.

Ruan YJ, Wei CL, Ee AL, Vega VB, Thoreau H, Su ST, Chia JM, Ng P, Chiu KP, Lim L, Zhang T, Peng CK, Lin EO, Lee NM, Yee SL, Ng LF, Chee RE, Stanton LW, Long PM, Liu ET.

Lancet. 2003 May 24;361(9371):1779-85. Erratum in: Lancet. 2003 May 24;361(9371):1832.

PMID:
12781537

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