Publications

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.  Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE.  Cell. 2016 Aug 25;166(5):1269-1281.e19. doi:10.1016/j.cell.2016.07.049. PubMed PMID: 27565349.

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Frank CL, Manandhar D, Gordân R, Crawford GE.  Epigenetics Chromatin. 2016 Apr 16;9:15. doi: 10.1186/s13072-016-0065-5. eCollection 2016. PubMed PMID: 27087856; PubMed Central PMCID: PMC4833939.

The genetic regulatory signature of type 2 diabetes in human skeletal muscle.  Scott LJ, Erdos MR, Huyghe JR, Welch RP, Beck AT, Wolford BN, Chines PS, Didion JP, Narisu N, Stringham HM, Taylor DL, Jackson AU, Vadlamudi S, Bonnycastle LL, Kinnunen L, Saramies J, Sundvall J, Albanus RD, Kiseleva A, Hensley J, Crawford GE, Jiang H, Wen X, Watanabe RM, Lakka TA, Mohlke KL, Laakso M, Tuomilehto J, Koistinen HA, Boehnke M, Collins FS, Parker SC. Nat Commun. 2016 Jun 29;7:11764. doi: 10.1038/ncomms11764. PubMed PMID: 27353450; PubMed Central PMCID: PMC4931250.

Mapping nucleosome positions using DNase-seq. Zhong J, Luo K, Winter PS, Crawford GE, Iversen ES, Hartemink AJ.  Genome Res. 2016 Mar;26(3):351-64. doi:10.1101/gr.195602.115. Epub 2016 Jan 15. PubMed PMID: 26772197; PubMed Central PMCID: PMC4772017.

Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A. Nucleic Acids Res. 2016 Apr 20;44(7):3082-94. doi: 10.1093/nar/gkv1358. Epub 2015 Dec 15. PubMed PMID: 26673704; PubMed Central PMCID: PMC4838340.

The PsychENCODE project. PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. Nat Neurosci. 2015 Dec;18(12):1707-12. doi:10.1038/nn.4156. Review. PubMed PMID: 26605881; PubMed Central PMCID: PMC4675669.

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.  Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK, Kabadi AM, Reddy TE, Crawford GE, Gersbach CA. Nat Methods. 2015 Dec;12(12):1143-9. doi: 10.1038/nmeth.3630. Epub 2015 Oct 26. PubMed PMID: 26501517; PubMed Central PMCID: PMC4666778.

Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus. Hauser MA, Aboobakar IF, Liu Y, Miura S, Whigham BT, Challa P, Wheeler J, Williams A, Santiago-Turla C, Qin X, Rautenbach RM, Ziskind A, Ramsay M, Uebe S, Song L, Safi A, Vithana EN, Mizoguchi T, Nakano S, Kubota T, Hayashi K, Manabe S, Kazama S, Mori Y, Miyata K, Yoshimura N, Reis A, Crawford GE, Pasutto F, Carmichael TR, Williams SE, Ozaki M, Aung T, Khor CC, Stamer WD, Ashley-Koch AE, Allingham RR. Hum Mol Genet. 2015 Nov 15;24(22):6552-63. doi: 10.1093/hmg/ddv347. Epub 2015 Aug 25. PubMed PMID: 26307087; PubMed Central PMCID: PMC4614704.


Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Fufa TD, Harris ML, Watkins-Chow DE, Levy D, Gorkin DU, Gildea DE, Song L, Safi A, Crawford GE, Sviderskaya EV, Bennett DC, Mccallion AS, Loftus SK, Pavan
WJ.  Hum Mol Genet. 2015 Oct 1;24(19):5433-50. doi: 10.1093/hmg/ddv267. Epub 2015 Jul 23. PubMed PMID: 26206884; PubMed Central PMCID: PMC4572067.

Genome-wide specificity of DNA binding, gene  regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Polstein LR, Perez-Pinera P, Kocak DD, Vockley CM, Bledsoe P, Song L, Safi A, Crawford GE, Reddy TE, Gersbach CA. Genome Res. 2015 Aug;25(8):1158-69. doi: 10.1101/gr.179044.114. Epub 2015 May 29. PubMed PMID: 26025803; PubMed Central PMCID: PMC4510000.

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Frank CL, Liu F, Wijayatunge R, Song L, Biegler MT, Yang MG, Vockley CM, Safi A, Gersbach CA, Crawford GE, West AE.  Nat Neurosci. 2015 May;18(5):647-56. doi: 10.1038/nn.3995. Epub 2015 Apr 6. PubMed PMID: 25849986; PubMed Central PMCID: PMC4414887.

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, Gersbach CA.  Nat Biotechnol. 2015 May;33(5):510-7. doi:10.1038/nbt.3199. Epub 2015 Apr 6. PubMed PMID: 25849900; PubMed Central PMCID:PMC4430400.

 Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Raposo AA, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DL, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, Guillemot F, Castro DS. Cell Rep. 2015 Mar 4. pii: S2211-1247(15)00171-0. doi: 10.1016/j.celrep.2015.02.025. [Epub ahead of print] PubMed PMID: 25753420.

Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation. 15: Su D, Wang X, Campbell MR, Song L, Safi A, Crawford GE, Bell DA.PLoS Genet. 2015 Jan 8;11(1):e1004885. doi: 10.1371/journal.pgen.1004885. eCollection 2015 Jan. PubMed PMID: 25569532; PubMed Central PMCID: PMC4287438.

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I,  Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E.  PLoS Genet. 2014 Nov 20;10(11):e1004798. doi: 10.1371/journal.pgen.1004798. eCollection 2014 Nov. Erratum in: PLoS Genet. 2015  Apr;11(4):e1005177. PubMed PMID: 25411781; PubMed Central PMCID: PMC4238955.

Genome accessibility is widely preserved and locally modulated during mitosis. Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B,  Crawford GE, Sung MH, Hardison RC, Blobel GA. Genome Res. 2015. Feb;25(2):213-25. doi: 10.1101/gr.180646.114. Epub 2014 Nov 4. PubMed PMID:25373146; PubMed Central PMCID: PMC4315295.

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Yardımcı GG, Frank CL, Crawford GE, Ohler U.  Nucleic Acids Res. 2014 Oct 29;42(19):11865-78. doi: 10.1093/nar/gku810. Epub 2014 Oct 7. PubMed PMID: 25294828; PubMed Central PMCID: PMC4231734.


Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.  Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Genome Res. 2015 Jan;25(1):41-56. doi: 10.1101/gr.173435.114. Epub 2014 Oct 7. PubMed PMID: 25294244; PubMed Central PMCID: PMC4317172.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.  Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA,  Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC. Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. PubMed PMID: 25275169; PubMed Central PMCID: PMC4143047.

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.  Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. PLoS One. 2014 Sep 8;9(9):e107156. doi: 10.1371/journal.pone.0107156. eCollection 2014. PubMed PMID: 25198066; PubMed Central PMCID: PMC4157845.

Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.  Browne JA, Yang R, Song L, Crawford GE, Leir SH, Harris A. Mol Hum Reprod. 2014 Dec;20(12):1198-207. doi: 10.1093/molehr/gau075. Epub 2014 Sep 1. PubMed PMID: 25180270; PubMed Central PMCID: PMC4235575.

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Genome Res. 2014 Sep;24(9):1504-16. doi: 10.1101/gr.165845.113. Epub 2014 Jun 24. PubMed PMID: 24963153; PubMed Central PMCID: PMC4158762.

Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency.  Factor DC, Corradin O, Zentner GE, Saiakhova A, Song L, Chenoweth JG, McKay
RD, Crawford GE, Scacheri PC, Tesar PJ. Cell Stem Cell. 2014 Jun 5;14(6):854-63. doi: 10.1016/j.stem.2014.05.005. PubMed PMID: 24905169; PubMed Central PMCID: PMC4149284.

Defining functional DNA elements in the human genome. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA,  Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Proc Natl 

Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review. PubMed PMID: 24753594; PubMed Central PMCID: PMC4035993.

Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine. Terragni J, Zhang G, Sun Z, Pradhan S, Song L, Crawford GE, Lacey M, Ehrlich M. Epigenetics. 2014 Jun;9(6):842-50. doi:10.4161/epi.28597. Epub 2014 Mar 26. Abstract

Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription. Balasubramani A, Winstead CJ, Turner H, Janowski KM, Harbour SN, Shibata Y, Crawford GE, Hatton RD, Weaver CT. PLoS Genet. 2014 Jan;10(1):e1003969. doi:10.1371/journal.pgen.1003969. Epub 2014 Jan 9. Abstract

Distinct properties of cell-type-specific and shared transcription factor binding sites. Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Mol Cell. 2013 Oct 10; 52(1): 25-36. Abstract

A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Bischof JM, Gillen AE, Song L, Gosalia N, London D, Furey TS, Crawford GE, Harris A, Biol Reprod. 2013 Sept. 4. Abstract

DNA methylation and differentiation: HOX genes in muscle cells. Tsumagari K, Baribault C, Terragni J, Chandra S, Renshaw C, Sun Z, Song L, Crawford GE, PRadhan S, Lacey M, Ehrlich M, Epigenetics Chromatin. 2013; 6(1): 25. Abstract

RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA, Nat Methods. 2013 Oct; 10(10): 973-6. Abstract

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Winter DR, Song L, Mukherjee S, Furey TS, Crawford GE, Genome Res 2013 Jul; 23(7): 1118-29. Abstract

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Zhang B, Day DS, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT, Genome REs. 2013 June; 23(6): 917-27. Abstract

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. Abstract

Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE, Myers RM, lacey M, Ehrlich M, Epigenetics. 2013 Mar; 8(3): 317-32. Abstract 

Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA, Nat Methods. 2013 Mar; 10(3): 239-42. Abstract

Dynamic DNA methylation across diverse human cell lines and tissues. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, Absher DM, Wold BJ, Myers RM, Genome Res. 2013 Mar; 23(3):555-67. Abstract

Site-specific silencing of regulatory elements as a mechanism of X inactivation. Calabrese JM, Sun W, Song L, Mugford JW, Williams L, Yee D, Starmer J, Mieczkowski P, Crawford GE, Magnuson T, Cell. 2012 Nov 21; 151(5): 951-63. Abstract

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG, Genome Biol. 2012 Oct 3; 13(10):R88. Abstract

Predicting cell-type-specific gene expression from regions of open chromatin. Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U, Genome Res. 2012 Sept; 22(9): 1711-22. Abstract

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 Sept 6; 489(7414):75-82. Abstract

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. Parker SC, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, Crawford GE, Rosenberg SA, Samuels Y, Margulies EH, PLoS Genet. 2012; 8(8):31002871. Abstract

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, Lajoie 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. Abstract

The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM, Mol Cell Biol. 2012 Sep;32(18):3756-67. Abstract

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE, PLoS Genet. 2012 Jun;8(6):e1002789. Abstract

H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Balasubramanian D, Akhtar-Zaidi B, Song L, Bartels CF, Veigl M, Beard L, Myeroff L, Guda K, Lutterbaugh J, Willis J, Crawford GE, Markowitz SD, Scacheri PC, Genome Med. 2012;4(5):47. Abstract

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 16;482(7385):390-4. Abstract

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. Abstract

Dissecting the regulatory architecture of gene expression QTLs. Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK, Genome Biol. 2012;13(1):R7. Abstract

A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function. Bischof JM, Ott CJ, Leir SH, Gosalia N, Song L, London D, Furey TS, Cotton CU, Crawford GE, Harris A, Thorax. 2012 May;67(5):385-91. Abstract

High-resolution mapping of open chromatin in the rice genome. Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J, Genome Res. 2012 Jan;22(1):151-62. Abstract

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR, Genome Res. 2012 Jan;22(1):9-24. Abstract

Gene expression during normal and FSHD myogenesis. Tsumagari K, Chang SC, Lacey M, Baribault C, Chittur SV, Sowden J, Tawil R, Crawford GE, Ehrlich M, BMC Med Genomics. 2011;4:67. Abstract

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC, Genome Res. 2011 Oct;21(10):1659-71. Abstract

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS, Genome Res. 2011 Oct;21(10):1757-67. Abstract

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS, Genome Res. 2011 Mar;21(3):456-64. Abstract

Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, NISC Comparative Sequencing Program, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS, Cell Metab. 2010 Nov 3;12(5):443-55. Abstract

Allele-specific and heritable chromatin signatures in humans. Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR, Hum Mol Genet. 2010 Oct 15;19(R2):R204-9. Abstract

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC, PLoS Genet. 2010 Jul;6(7):e1001023. Abstract

Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli. Balasubramani A, Shibata Y, Crawford GE, Baldwin AS, Hatton RD, Weaver CT, Immunity. 2010 Jul 23;33(1):35-47. Abstract

Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage. Mukasa R, Balasubramani A, Lee YK, Whitley SK, Weaver BT, Shibata Y, Crawford GE, Hatton RD, Weaver CT, Immunity. 2010 May 28;32(5):616-27. Abstract

Heritable individual-specific and allele-specific chromatin signatures in humans. McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E, Science. 2010 Apr 9;328(5975):235-9. Abstract

DNase-seq: a high resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Song L, Crawford GE, Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. Abstract

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus. Ott CJ, Blackledge NP, Kerschner JL, Leir SH, Crawford GE, Cotton CU, Harris A, Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19934-9. Abstract

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2. Xu X, Tsumagari K, Sowden J, Tawil R, Boyle AP, Song L, Furey TS, Crawford GE, Ehrlich M, Nucleic Acids Res. 2009 Dec;37(22):7381-93. Abstract

Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Shibata Y, Crawford GE, Methods Mol Biol. 2009;556:177-90. Abstract

A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. Ott CJ, Suszko M, Blackledge NP, Wright JE, Crawford GE, Harris A, J Cell Mol Med. 2009 Apr;13(4):680-92. Abstract