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Transcription Factors Expressed in Mouse Cochlear Inner and Outer Hair Cells.

Li Y, Liu H, Barta CL, Judge PD, Zhao L, Zhang WJ, Gong S, Beisel KW, He DZ.

PLoS One. 2016 Mar 14;11(3):e0151291. doi: 10.1371/journal.pone.0151291. eCollection 2016.


Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity.

Raj P, Rai E, Song R, Khan S, Wakeland BE, Viswanathan K, Arana C, Liang C, Zhang B, Dozmorov I, Carr-Johnson F, Mitrovic M, Wiley GB, Kelly JA, Lauwerys BR, Olsen NJ, Cotsapas C, Garcia CK, Wise CA, Harley JB, Nath SK, James JA, Jacob CO, Tsao BP, Pasare C, Karp DR, Li QZ, Gaffney PM, Wakeland EK.

Elife. 2016 Feb 15;5. pii: e12089. doi: 10.7554/eLife.12089.


Functional transcription factor target discovery via compendia of binding and expression profiles.

Banks CJ, Joshi A, Michoel T.

Sci Rep. 2016 Feb 9;6:20649. doi: 10.1038/srep20649.


Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors.

Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P.

Epigenetics Chromatin. 2015 Dec 14;8:55. doi: 10.1186/s13072-015-0043-3. eCollection 2015.


Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation.

González AJ, Setty M, Leslie CS.

Nat Genet. 2015 Nov;47(11):1249-59. doi: 10.1038/ng.3402. Epub 2015 Sep 21.


Chromatin Dynamics in the Regulation of CFTR Expression.

Gosalia N, Harris A.

Genes (Basel). 2015 Jul 13;6(3):543-58. doi: 10.3390/genes6030543. Review.


groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data.

Chae M, Danko CG, Kraus WL.

BMC Bioinformatics. 2015 Jul 16;16:222. doi: 10.1186/s12859-015-0656-3.


Functional validation of a constitutive autonomous silencer element.

Qi H, Liu M, Emery DW, Stamatoyannopoulos G.

PLoS One. 2015 Apr 24;10(4):e0124588. doi: 10.1371/journal.pone.0124588. eCollection 2015.


Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo.

Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG.

BMC Genomics. 2014 Dec 15;15:1104. doi: 10.1186/1471-2164-15-1104.


Comparative FAIRE-seq analysis reveals distinguishing features of the chromatin structure of ground state- and primed-pluripotent cells.

Murtha M, Strino F, Tokcaer-Keskin Z, Sumru Bayin N, Shalabi D, Xi X, Kluger Y, Dailey L.

Stem Cells. 2015 Feb;33(2):378-91. doi: 10.1002/stem.1871.


Deletions of chromosomal regulatory boundaries are associated with congenital disease.

Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN.

Genome Biol. 2014 Sep 4;15(9):423. doi: 10.1186/s13059-014-0423-1.


Comparative studies of gene regulatory mechanisms.

Pai AA, Gilad Y.

Curr Opin Genet Dev. 2014 Dec;29:68-74. doi: 10.1016/j.gde.2014.08.010. Epub 2014 Sep 16. Review.


Identification of logic relationships between genes and subtypes of non-small cell lung cancer.

Su Y, Pan L.

PLoS One. 2014 Apr 17;9(4):e94644. doi: 10.1371/journal.pone.0094644. eCollection 2014.


Epigenetics decouples mutational from environmental robustness. Did it also facilitate multicellularity?

Gombar S, MacCarthy T, Bergman A.

PLoS Comput Biol. 2014 Mar 6;10(3):e1003450. doi: 10.1371/journal.pcbi.1003450. eCollection 2014 Mar.


Identifying and mapping cell-type-specific chromatin programming of gene expression.

Marstrand TT, Storey JD.

Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):E645-54. doi: 10.1073/pnas.1312523111. Epub 2014 Jan 27.


Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions.

Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, Hager GL.

Nat Struct Mol Biol. 2014 Jan;21(1):73-81. doi: 10.1038/nsmb.2718. Epub 2013 Dec 8.


Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression.

Jeong KW, Andreu-Vieyra C, You JS, Jones PA, Stallcup MR.

Nucleic Acids Res. 2014 Feb;42(4):2245-56. doi: 10.1093/nar/gkt1236. Epub 2013 Nov 27.


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.


Identification and characterization of enhancer-blocking insulators to reduce retroviral vector genotoxicity.

Groth AC, Liu M, Wang H, Lovelett E, Emery DW.

PLoS One. 2013 Oct 3;8(10):e76528. doi: 10.1371/journal.pone.0076528. eCollection 2013.


Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9.

Harth-Hertle ML, Scholz BA, Erhard F, Glaser LV, Dölken L, Zimmer R, Kempkes B.

PLoS Pathog. 2013 Sep;9(9):e1003638. doi: 10.1371/journal.ppat.1003638. Epub 2013 Sep 19.

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