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Results: 1 to 20 of 26

1.

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.

Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR.

Nat Biotechnol. 2014 Jan;32(1):71-5. doi: 10.1038/nbt.2778. Epub 2013 Dec 15.

PMID:
24336318
[PubMed - in process]
Free PMC Article
2.

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.

Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA.

Cell. 2013 Aug 15;154(4):888-903. doi: 10.1016/j.cell.2013.07.020.

PMID:
23953118
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Genome-scale mapping of DNase I hypersensitivity.

John S, Sabo PJ, Canfield TK, Lee K, Vong S, Weaver M, Wang H, Vierstra J, Reynolds AP, Thurman RE, Stamatoyannopoulos JA.

Curr Protoc Mol Biol. 2013 Jul;Chapter 27:Unit 21.27. doi: 10.1002/0471142727.mb2127s103.

PMID:
23821440
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
23482648
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22955981
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Widespread plasticity in CTCF occupancy linked to DNA methylation.

Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA.

Genome Res. 2012 Sep;22(9):1680-8. doi: 10.1101/gr.136101.111.

PMID:
22955980
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22955828
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22955618
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22955617
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418.

PMID:
22889292
[PubMed - as supplied by publisher]
Free PMC Article
11.

BEDOPS: high-performance genomic feature operations.

Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA.

Bioinformatics. 2012 Jul 15;28(14):1919-20. doi: 10.1093/bioinformatics/bts277. Epub 2012 May 9.

PMID:
22576172
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding.

Biddie SC, John S, Sabo PJ, Thurman RE, Johnson TA, Schiltz RL, Miranda TB, Sung MH, Trump S, Lightman SL, Vinson C, Stamatoyannopoulos JA, Hager GL.

Mol Cell. 2011 Jul 8;43(1):145-55. doi: 10.1016/j.molcel.2011.06.016.

PMID:
21726817
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

DNA methylation status predicts cell type-specific enhancer activity.

Wiench M, John S, Baek S, Johnson TA, Sung MH, Escobar T, Simmons CA, Pearce KH, Biddie SC, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, Hager GL.

EMBO J. 2011 Jun 24;30(15):3028-39. doi: 10.1038/emboj.2011.210.

PMID:
21701563
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA.

Genome Biol. 2011;12(5):R43. doi: 10.1186/gb-2011-12-5-r43. Epub 2011 May 11.

PMID:
21569360
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements.

Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL.

Genome Res. 2011 May;21(5):697-706. doi: 10.1101/gr.111153.110. Epub 2011 Apr 6.

PMID:
21471403
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA.

Nat Genet. 2011 Mar;43(3):264-8. doi: 10.1038/ng.759. Epub 2011 Jan 23.

PMID:
21258342
[PubMed - indexed for MEDLINE]
17.

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ.

Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22.

PMID:
21179089
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA.

Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. doi: 10.1073/pnas.0912402107. Epub 2009 Dec 4.

PMID:
19966280
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.

Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA.

Nat Methods. 2009 Apr;6(4):283-9. doi: 10.1038/nmeth.1313. Epub 2009 Mar 22.

PMID:
19305407
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Human mutation rate associated with DNA replication timing.

Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR.

Nat Genet. 2009 Apr;41(4):393-5. doi: 10.1038/ng.363. Epub 2009 Mar 15.

PMID:
19287383
[PubMed - indexed for MEDLINE]
Free PMC Article

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