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Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells.

Rhie SK, Hazelett DJ, Coetzee SG, Yan C, Noushmehr H, Coetzee GA.

BMC Genomics. 2014 May 2;15:331. doi: 10.1186/1471-2164-15-331.


Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.


A novel method to predict regulatory regions based on histone mark landscapes in macrophages.

Nagy G, Dániel B, Jónás D, Nagy L, Barta E.

Immunobiology. 2013 Nov;218(11):1416-27. doi: 10.1016/j.imbio.2013.07.006. Epub 2013 Jul 26.


Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq).

Bianco S, Rodrigue S, Murphy BD, Gévry N.

Methods Mol Biol. 2015;1334:261-72. doi: 10.1007/978-1-4939-2877-4_17.


Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells.

Hong CP, Choe MK, Roh TY.

Genomics Inform. 2012 Sep;10(3):145-52. doi: 10.5808/GI.2012.10.3.145. Epub 2012 Sep 28.


Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.


Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.

Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111.


Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.

Rhie SK, Guo Y, Tak YG, Yao L, Shen H, Coetzee GA, Laird PW, Farnham PJ.

Epigenetics Chromatin. 2016 Nov 9;9:50. eCollection 2016.


Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

Kwon SY, Grisan V, Jang B, Herbert J, Badenhorst P.

PLoS Genet. 2016 Apr 5;12(4):e1005969. doi: 10.1371/journal.pgen.1005969. eCollection 2016 Apr.


Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions.

Kim SG, Theera-Ampornpunt N, Fang CH, Harwani M, Grama A, Chaterji S.

BMC Syst Biol. 2016 Aug 1;10 Suppl 2:54. doi: 10.1186/s12918-016-0302-3.


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.


Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions.

Yaragatti M, Basilico C, Dailey L.

Genome Res. 2008 Jun;18(6):930-8. doi: 10.1101/gr.073460.107. Epub 2008 Apr 25.


Nucleosome Organization in Human Embryonic Stem Cells.

Yazdi PG, Pedersen BA, Taylor JF, Khattab OS, Chen YH, Chen Y, Jacobsen SE, Wang PH.

PLoS One. 2015 Aug 25;10(8):e0136314. doi: 10.1371/journal.pone.0136314. eCollection 2015.


Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci.

Paul DS, Albers CA, Rendon A, Voss K, Stephens J; HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P.

Genome Res. 2013 Jul;23(7):1130-41. doi: 10.1101/gr.155127.113. Epub 2013 Apr 9.


Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells.

Andreu-Vieyra C, Lai J, Berman BP, Frenkel B, Jia L, Jones PA, Coetzee GA.

Mol Cell Biol. 2011 Dec;31(23):4648-62. doi: 10.1128/MCB.05934-11. Epub 2011 Oct 3.


Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer.

Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA.

Genome Res. 2014 Sep;24(9):1421-32. doi: 10.1101/gr.163485.113. Epub 2014 Jun 10.


Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

Giresi PG, Lieb JD.

Methods. 2009 Jul;48(3):233-9. doi: 10.1016/j.ymeth.2009.03.003. Epub 2009 Mar 18.


The histone variant H2A.Z is an important regulator of enhancer activity.

Brunelle M, Nordell Markovits A, Rodrigue S, Lupien M, Jacques PÉ, Gévry N.

Nucleic Acids Res. 2015 Nov 16;43(20):9742-56. doi: 10.1093/nar/gkv825. Epub 2015 Aug 28.


Nucleosome repositioning during differentiation of a human myeloid leukemia cell line.

Teif VB, Mallm JP, Sharma T, Mark Welch DB, Rippe K, Eils R, Langowski J, Olins AL, Olins DE.

Nucleus. 2017 Mar 4;8(2):188-204. doi: 10.1080/19491034.2017.1295201.


Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3.

Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K.

Genome Biol. 2013;14(10):R121. Erratum in: Genome Biol. 2016;17:21.

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