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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. Maurano MT, et al. Among authors: lee k. Science. 2012 Sep 7;337(6099):1190-5. doi: 10.1126/science.1222794. Epub 2012 Sep 5. Science. 2012. PMID: 22955828 Free PMC article.
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. Thurman RE, et al. Among authors: lee bk, lee k. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. Nature. 2012. PMID: 22955617 Free PMC article.
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. Neph S, et al. Among authors: lee k. Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212. Nature. 2012. PMID: 22955618 Free PMC article.
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. John S, et al. Among authors: lee k. Curr Protoc Mol Biol. 2013 Jul;Chapter 27:Unit 21.27. doi: 10.1002/0471142727.mb2127s103. Curr Protoc Mol Biol. 2013. PMID: 23821440 Free PMC article.
Conservation of trans-acting circuitry during mammalian regulatory evolution.
Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA. Stergachis AB, et al. Among authors: lee k. Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972. Nature. 2014. PMID: 25409825 Free PMC article.
Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium; Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Cheng Y, et al. Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985. Nature. 2014. PMID: 25409826 Free PMC article.
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. Vierstra J, et al. Among authors: lee k. Science. 2014 Nov 21;346(6212):1007-12. doi: 10.1126/science.1246426. Science. 2014. PMID: 25411453 Free PMC article.
Role of DNA Methylation in Modulating Transcription Factor Occupancy.
Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA. Maurano MT, et al. Among authors: lee k. Cell Rep. 2015 Aug 18;12(7):1184-95. doi: 10.1016/j.celrep.2015.07.024. Epub 2015 Aug 6. Cell Rep. 2015. PMID: 26257180 Free article.
Index and biological spectrum of human DNase I hypersensitive sites.
Meuleman W, Muratov A, Rynes E, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Teodosiadis A, Reynolds A, Haugen E, Nelson J, Johnson A, Frerker M, Buckley M, Sandstrom R, Vierstra J, Kaul R, Stamatoyannopoulos J. Meuleman W, et al. Among authors: lee k. Nature. 2020 Aug;584(7820):244-251. doi: 10.1038/s41586-020-2559-3. Epub 2020 Jul 29. Nature. 2020. PMID: 32728217 Free PMC article.
Global reference mapping of human transcription factor footprints.
Vierstra J, Lazar J, Sandstrom R, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Haugen E, Rynes E, Reynolds A, Nelson J, Johnson A, Frerker M, Buckley M, Kaul R, Meuleman W, Stamatoyannopoulos JA. Vierstra J, et al. Among authors: lee k. Nature. 2020 Jul;583(7818):729-736. doi: 10.1038/s41586-020-2528-x. Epub 2020 Jul 29. Nature. 2020. PMID: 32728250 Free PMC article.
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