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Results: 1 to 20 of 21

1.

Identification of a Functional In Vivo p53 Response Element in the Coding Sequence of the Xeroderma Pigmentosum Group C Gene.

Hastak K, Adimoolam S, Trinklein ND, Myers RM, Ford JM.

Genes Cancer. 2012 Feb;3(2):131-40. doi: 10.1177/1947601912456288.

PMID:
23050045
[PubMed]
Free PMC Article
2.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

PMID:
22955616
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Functional analysis of transcription factor binding sites in human promoters.

Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z.

Genome Biol. 2012 Sep 26;13(9):R50. doi: 10.1186/gb-2012-13-9-r50.

PMID:
22951020
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.

Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, Ramirez J, Liu W, Lin YS, Moloney C, Aldred SF, Trinklein ND, Schuetz E, Nickerson DA, Thummel KE, Rieder MJ, Rettie AE, Ratain MJ, Cox NJ, Brown CD.

PLoS Genet. 2011 May;7(5):e1002078. doi: 10.1371/journal.pgen.1002078. Epub 2011 May 26.

PMID:
21637794
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium.

PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.

PMID:
21526222
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122.

Boutz DR, Collins PJ, Suresh U, Lu M, Ramírez CM, Fernández-Hernando C, Huang Y, Abreu Rde S, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein ND, Marcotte EM, Penalva LO.

J Biol Chem. 2011 May 20;286(20):18066-78. doi: 10.1074/jbc.M110.196451. Epub 2011 Mar 14.

PMID:
21402708
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Sequence features that drive human promoter function and tissue specificity.

Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM.

Genome Res. 2010 Jul;20(7):890-8. doi: 10.1101/gr.100370.109. Epub 2010 May 25.

PMID:
20501695
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

Hartzell DD, Trinklein ND, Mendez J, Murphy N, Aldred SF, Wood K, Urh M.

BMC Genomics. 2009 Oct 27;10:497. doi: 10.1186/1471-2164-10-497.

PMID:
19860899
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

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.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

PMID:
18258921
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The ets-related transcription factor GABP directs bidirectional transcription.

Collins PJ, Kobayashi Y, Nguyen L, Trinklein ND, Myers RM.

PLoS Genet. 2007 Nov;3(11):e208.

PMID:
18020712
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
17571346
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Transcription factor binding and modified histones in human bidirectional promoters.

Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z.

Genome Res. 2007 Jun;17(6):818-27.

PMID:
17568000
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.

Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z.

Genome Res. 2007 Jun;17(6):720-31.

PMID:
17567992
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Serum response factor binding sites differ in three human cell types.

Cooper SJ, Trinklein ND, Nguyen L, Myers RM.

Genome Res. 2007 Feb;17(2):136-44. Epub 2007 Jan 2.

PMID:
17200232
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.

Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM.

Genome Res. 2006 Jan;16(1):1-10. Epub 2005 Dec 12.

PMID:
16344566
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Direct isolation and identification of promoters in the human genome.

Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM, Ren B.

Genome Res. 2005 Jun;15(6):830-9. Epub 2005 May 17.

PMID:
15899964
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Transcriptional regulation and binding of heat shock factor 1 and heat shock factor 2 to 32 human heat shock genes during thermal stress and differentiation.

Trinklein ND, Chen WC, Kingston RE, Myers RM.

Cell Stress Chaperones. 2004 Mar;9(1):21-8.

PMID:
15270074
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Diverse and specific gene expression responses to stresses in cultured human cells.

Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D.

Mol Biol Cell. 2004 May;15(5):2361-74. Epub 2004 Mar 5.

PMID:
15004229
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An abundance of bidirectional promoters in the human genome.

Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM.

Genome Res. 2004 Jan;14(1):62-6.

PMID:
14707170
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response.

Trinklein ND, Murray JI, Hartman SJ, Botstein D, Myers RM.

Mol Biol Cell. 2004 Mar;15(3):1254-61. Epub 2003 Dec 10.

PMID:
14668476
[PubMed - indexed for MEDLINE]
Free PMC Article

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