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Results: 1 to 20 of 163

1.

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
2.

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
3.

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
4.

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
5.

Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition.

Harrison MM, Li XY, Kaplan T, Botchan MR, Eisen MB.

PLoS Genet. 2011 Oct;7(10):e1002266. doi: 10.1371/journal.pgen.1002266. Epub 2011 Oct 20.

PMID:
22028662
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Temporal coordination of gene networks by Zelda in the early Drosophila embryo.

Nien CY, Liang HL, Butcher S, Sun Y, Fu S, Gocha T, Kirov N, Manak JR, Rushlow C.

PLoS Genet. 2011 Oct;7(10):e1002339. doi: 10.1371/journal.pgen.1002339. Epub 2011 Oct 20.

PMID:
22028675
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

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
9.

Computational identification of Ftz/Ftz-F1 downstream target genes.

Bowler T, Kosman D, Licht JD, Pick L.

Dev Biol. 2006 Nov 1;299(1):78-90. Epub 2006 Jul 12.

PMID:
16996052
[PubMed - indexed for MEDLINE]
Free Article
10.

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
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.

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila.

Liang HL, Nien CY, Liu HY, Metzstein MM, Kirov N, Rushlow C.

Nature. 2008 Nov 20;456(7220):400-3. doi: 10.1038/nature07388. Epub 2008 Oct 19.

PMID:
18931655
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Hairless is a cofactor for Runt-dependent transcriptional regulation.

Walrad PB, Hang S, Gergen JP.

Mol Biol Cell. 2011 Apr 15;22(8):1364-74. doi: 10.1091/mbc.E10-06-0483. Epub 2011 Feb 16.

PMID:
21325629
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.

Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20768-73. doi: 10.1073/pnas.1210415109. Epub 2012 Nov 26.

PMID:
23184988
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

Ludwig MZ, Patel NH, Kreitman M.

Development. 1998 Mar;125(5):949-58.

PMID:
9449677
[PubMed - indexed for MEDLINE]
Free Article
17.

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness.

Ludwig MZ, Manu, Kittler R, White KP, Kreitman M.

PLoS Genet. 2011 Nov;7(11):e1002364. doi: 10.1371/journal.pgen.1002364. Epub 2011 Nov 10.

PMID:
22102826
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo.

Papatsenko D, Levine M.

Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4966-71. Epub 2005 Mar 28.

PMID:
15795372
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62.

PMID:
11805330
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila.

Ho MC, Johnsen H, Goetz SE, Schiller BJ, Bae E, Tran DA, Shur AS, Allen JM, Rau C, Bender W, Fisher WW, Celniker SE, Drewell RA.

PLoS Genet. 2009 Nov;5(11):e1000709. doi: 10.1371/journal.pgen.1000709. Epub 2009 Nov 6.

PMID:
19893611
[PubMed - indexed for MEDLINE]
Free PMC Article

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