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Results: 1 to 20 of 185

1.

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. doi: 10.1101/gr.131201.111. Epub 2012 Feb 2.

PMID:
22300769
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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. doi: 10.1101/gr.127597.111. Epub 2011 Nov 16.

PMID:
22090374
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Sequence and chromatin determinants of cell-type-specific transcription factor binding.

Arvey A, Agius P, Noble WS, Leslie C.

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.

PMID:
22955984
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
22537144
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Genome-wide nucleosome mapping of Plasmodium falciparum reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes.

Westenberger SJ, Cui L, Dharia N, Winzeler E, Cui L.

BMC Genomics. 2009 Dec 16;10:610. doi: 10.1186/1471-2164-10-610.

PMID:
20015349
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.

Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E.

Nucleic Acids Res. 2012 Jan;40(1):148-58. doi: 10.1093/nar/gkr720. Epub 2011 Sep 13.

PMID:
21914722
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Variation in transcription factor binding among humans.

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M.

Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621. Epub 2010 Mar 18.

PMID:
20299548
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

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

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

PMID:
22863112
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.

Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112.

PMID:
22955990
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

He A, Kong SW, Ma Q, Pu WT.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5632-7. doi: 10.1073/pnas.1016959108. Epub 2011 Mar 17.

PMID:
21415370
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines.

Nie Y, Liu H, Sun X.

PLoS One. 2013;8(3):e60002. doi: 10.1371/journal.pone.0060002. Epub 2013 Mar 19.

PMID:
23527292
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

PMID:
19956545
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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. doi: 10.1126/science.1184655. Epub 2010 Mar 18.

PMID:
20299549
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Targeted screening of cis-regulatory variation in human haplotypes.

Verlaan DJ, Ge B, Grundberg E, Hoberman R, Lam KC, Koka V, Dias J, Gurd S, Martin NW, Mallmin H, Nilsson O, Harmsen E, Dewar K, Kwan T, Pastinen T.

Genome Res. 2009 Jan;19(1):118-27. doi: 10.1101/gr.084798.108. Epub 2008 Oct 29.

PMID:
18971308
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Analysis of sequence variation underlying tissue-specific transcription factor binding and gene expression.

Lower KM, De Gobbi M, Hughes JR, Derry CJ, Ayyub H, Sloane-Stanley JA, Vernimmen D, Garrick D, Gibbons RJ, Higgs DR.

Hum Mutat. 2013 Aug;34(8):1140-8. doi: 10.1002/humu.22343. Epub 2013 Jun 18.

PMID:
23616472
[PubMed - indexed for MEDLINE]
16.

Identification of genetic variants that affect histone modifications in human cells.

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK.

Science. 2013 Nov 8;342(6159):747-9. doi: 10.1126/science.1242429. Epub 2013 Oct 17.

PMID:
24136359
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

An equilibrium partitioning model connecting gene expression and cis-motif content.

Mellor J, DeLisi C.

Bioinformatics. 2006 Jul 15;22(14):e368-74.

PMID:
16873495
[PubMed - indexed for MEDLINE]
Free Article
18.

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.

Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL.

Mol Cell Biol. 2007 Jul;27(14):5090-104. Epub 2007 May 21.

PMID:
17515612
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

HaploChIP: an in vivo assay.

Charles Knight J.

Methods Mol Biol. 2005;311:49-60.

PMID:
16100399
[PubMed - indexed for MEDLINE]
20.

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649.

PMID:
20098497
[PubMed - indexed for MEDLINE]
Free PMC Article

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