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Items: 1 to 20 of 115

1.

Systematic localization of common disease-associated variation in regulatory DNA.

Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA.

Science. 2012 Sep 7;337(6099):1190-5. doi: 10.1126/science.1222794. Epub 2012 Sep 5.

2.

The accessible chromatin landscape of the human genome.

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232.

3.

Personal and population genomics of human regulatory variation.

Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM.

Genome Res. 2012 Sep;22(9):1689-97. doi: 10.1101/gr.134890.111.

4.

Regulatory genomic regions active in immune cell types explain a large proportion of the genetic risk of multiple sclerosis.

Elangovan RI, Disanto G, Berlanga-Taylor AJ, Ramagopalan SV, Handunnetthi L.

J Hum Genet. 2014 Apr;59(4):211-5. doi: 10.1038/jhg.2014.3. Epub 2014 Feb 13.

PMID:
24522295
5.

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.

6.

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.

Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA.

Nat Genet. 2015 Dec;47(12):1393-401. doi: 10.1038/ng.3432. Epub 2015 Oct 26. Erratum in: Nat Genet. 2016 Jan;48(1):101.

7.

On the identification of potential regulatory variants within genome wide association candidate SNP sets.

Chen CY, Chang IS, Hsiung CA, Wasserman WW.

BMC Med Genomics. 2014 Jun 11;7:34. doi: 10.1186/1755-8794-7-34.

8.

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.

Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA.

Cell Rep. 2014 Sep 25;8(6):2015-30. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15.

9.

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.

Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal lari R, Lupien M, Markowitz S, Scacheri PC.

Genome Res. 2014 Jan;24(1):1-13. doi: 10.1101/gr.164079.113. Epub 2013 Nov 6.

10.

DNase I sensitivity QTLs are a major determinant of human expression variation.

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808.

11.

Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions.

Benner C, Konovalov S, Mackintosh C, Hutt KR, Stunnenberg R, Garcia-Bassets I.

PLoS Genet. 2013 Nov;9(11):e1003906. doi: 10.1371/journal.pgen.1003906. Epub 2013 Nov 7.

12.

Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.

Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbø G, Zhu X, Chen R.

BMC Genomics. 2009 Feb 25;10:92. doi: 10.1186/1471-2164-10-92.

13.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.

14.

Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.

Wang YM, Zhou P, Wang LY, Li ZH, Zhang YN, Zhang YX.

PLoS One. 2012;7(8):e42414. doi: 10.1371/journal.pone.0042414. Epub 2012 Aug 10.

15.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM.

Genome Res. 2012 May;22(5):860-9. doi: 10.1101/gr.131201.111. Epub 2012 Feb 2.

16.

A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes.

Johnson R, Richter N, Bogu GK, Bhinge A, Teng SW, Choo SH, Andrieux LO, de Benedictis C, Jauch R, Stanton LW.

PLoS Genet. 2012;8(4):e1002624. doi: 10.1371/journal.pgen.1002624. Epub 2012 Apr 5.

17.

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples.

Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka TM, Childs R, Levens D, Zhao K.

Nature. 2015 Dec 3;528(7580):142-6. doi: 10.1038/nature15740.

18.

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.

Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS.

Genome Res. 2013 May;23(5):777-88. doi: 10.1101/gr.152140.112. Epub 2013 Mar 12.

19.

Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.

Paul DS, Albers CA, Rendon A, Voss K, Stephens J; HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P.

Genome Res. 2013 Jul;23(7):1130-41. doi: 10.1101/gr.155127.113. Epub 2013 Apr 9.

20.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA.

Science. 2014 Nov 21;346(6212):1007-12. doi: 10.1126/science.1246426.

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