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Items: 1 to 20 of 97

1.

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee.

Pizzollo J, Nielsen WJ, Shibata Y, Safi A, Crawford GE, Wray GA, Babbitt CC.

Genome Biol Evol. 2018 Mar 1;10(3):826-839. doi: 10.1093/gbe/evy041.

2.

Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal.

Mateo JL, van den Berg DLC, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B.

Genome Res. 2017 Dec;27(12):2129. doi: 10.1101/gr.231845.117. No abstract available.

3.

Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice.

Chappell GA, Israel JW, Simon JM, Pott S, Safi A, Eklund K, Sexton KG, Bodnar W, Lieb JD, Crawford GE, Rusyn I, Furey TS.

Environ Health Perspect. 2017 Oct 16;125(10):107006. doi: 10.1289/EHP1937.

4.

Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.

Manandhar D, Song L, Kabadi A, Kwon JB, Edsall LE, Ehrlich M, Tsumagari K, Gersbach CA, Crawford GE, Gordân R.

Nucleic Acids Res. 2017 Nov 16;45(20):11684-11699. doi: 10.1093/nar/gkx773.

5.

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.

Davison JM, Lickwar CR, Song L, Breton G, Crawford GE, Rawls JF.

Genome Res. 2017 Jul;27(7):1195-1206. doi: 10.1101/gr.220111.116. Epub 2017 Apr 6.

6.

CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.

Klann TS, Black JB, Chellappan M, Safi A, Song L, Hilton IB, Crawford GE, Reddy TE, Gersbach CA.

Nat Biotechnol. 2017 Jun;35(6):561-568. doi: 10.1038/nbt.3853. Epub 2017 Apr 3.

7.

Genome-wide identification of regulatory elements in Sertoli cells.

Maatouk DM, Natarajan A, Shibata Y, Song L, Crawford GE, Ohler U, Capel B.

Development. 2017 Feb 15;144(4):720-730. doi: 10.1242/dev.142554. Epub 2017 Jan 13.

8.

Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation.

Gopinath C, Law WD, Rodríguez-Molina JF, Prasad AB, Song L, Crawford GE, Mullikin JC, Svaren J, Antonellis A.

BMC Genomics. 2016 Nov 7;17(1):887.

9.

Corrigendum: 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, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B.

Genome Res. 2016 Nov;26(11):1626. No abstract available.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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. No abstract available.

16.

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.

17.

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.

18.

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.

19.

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.

20.

Correction: 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. 2015 Apr 28;11(4):e1005177. doi: 10.1371/journal.pgen.1005177. eCollection 2015 Apr.

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