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Results: 1 to 20 of 135

1.

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.

Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD.

Genome Biol. 2011;12(4):R34. doi: 10.1186/gb-2011-12-4-r34. Epub 2011 Apr 7.

PMID:
21473766
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.

Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB.

PLoS Genet. 2011 Feb 3;7(2):e1001290. doi: 10.1371/journal.pgen.1001290.

PMID:
21304941
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.

MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV, Knowles DW, Stapleton M, Bickel P, Biggin MD, Eisen MB.

Genome Biol. 2009;10(7):R80. doi: 10.1186/gb-2009-10-7-r80. Epub 2009 Jul 23.

PMID:
19627575
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo.

Satija R, Bradley RK.

Genome Res. 2012 Apr;22(4):656-65. doi: 10.1101/gr.130682.111. Epub 2012 Jan 13.

PMID:
22247430
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Accurate prediction of inducible transcription factor binding intensities in vivo.

Guertin MJ, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2012;8(3):e1002610. doi: 10.1371/journal.pgen.1002610. Epub 2012 Mar 29.

PMID:
22479205
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA.

Genome Biol. 2011;12(5):R43. doi: 10.1186/gb-2011-12-5-r43. Epub 2011 May 11.

PMID:
21569360
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.

Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S.

PLoS Genet. 2013;9(8):e1003571. doi: 10.1371/journal.pgen.1003571. Epub 2013 Aug 1.

PMID:
23935523
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.

Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12027-32. Epub 2006 Jul 31.

PMID:
16880385
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.

Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21330-5. doi: 10.1073/pnas.1209589110. Epub 2012 Dec 10.

PMID:
23236164
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE.

Genome Biol. 2004;5(9):R61. Epub 2004 Aug 20.

PMID:
15345045
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Quantitative models of the mechanisms that control genome-wide patterns of animal transcription factor binding.

Kaplan T, Biggin MD.

Methods Cell Biol. 2012;110:263-83. doi: 10.1016/B978-0-12-388403-9.00011-4.

PMID:
22482953
[PubMed - indexed for MEDLINE]
14.

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
15.

High-resolution mapping of transcription factor binding sites on native chromatin.

Kasinathan S, Orsi GA, Zentner GE, Ahmad K, Henikoff S.

Nat Methods. 2014 Feb;11(2):203-9. doi: 10.1038/nmeth.2766. Epub 2013 Dec 15.

PMID:
24336359
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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
17.

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.

PLoS Biol. 2008 Feb;6(2):e27. doi: 10.1371/journal.pbio.0060027.

PMID:
18271625
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Genome-wide analysis of the binding of the Hox protein Ultrabithorax and the Hox cofactor Homothorax in Drosophila.

Choo SW, White R, Russell S.

PLoS One. 2011 Apr 5;6(4):e14778. doi: 10.1371/journal.pone.0014778.

PMID:
21483667
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genome-wide in vivo cross-linking of sequence-specific transcription factors.

Li XY, Biggin MD.

Methods Mol Biol. 2012;809:3-26. doi: 10.1007/978-1-61779-376-9_1.

PMID:
22113265
[PubMed - indexed for MEDLINE]
20.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

PMID:
22456606
[PubMed - indexed for MEDLINE]
Free PMC Article

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