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Results: 1 to 20 of 98

1.

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N.

Genome Biol. 2013 Jul 18;14(7):R72. doi: 10.1186/gb-2013-14-7-r72.

PMID:
23867016
[PubMed - in process]
Free PMC Article
2.

Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers.

Orenstein Y, Shamir R.

Bioinformatics. 2013 Jul 1;29(13):i71-9. doi: 10.1093/bioinformatics/btt230.

PMID:
23813011
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes.

Chatterjee S, Bourque G, Lufkin T.

BMC Dev Biol. 2011 Oct 20;11:63. doi: 10.1186/1471-213X-11-63.

PMID:
22011226
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Synthetic design of strong promoters.

Schlabach MR, Hu JK, Li M, Elledge SJ.

Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2538-43. doi: 10.1073/pnas.0914803107. Epub 2010 Jan 21.

PMID:
20133776
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.

BMC Bioinformatics. 2012 Jul 18;13:170. doi: 10.1186/1471-2105-13-170.

PMID:
22808927
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.

Rastegar S, Hess I, Dickmeis T, Nicod JC, Ertzer R, Hadzhiev Y, Thies WG, Scherer G, Strähle U.

Dev Biol. 2008 Jun 15;318(2):366-77. doi: 10.1016/j.ydbio.2008.03.034. Epub 2008 Apr 4.

PMID:
18455719
[PubMed - indexed for MEDLINE]
Free Article
7.

Structural analysis and characterization of tissue and hormonal responsive expression of the avian bone sialoprotein (BSP) gene.

Yang R, Gerstenfeld LC.

J Cell Biochem. 1997 Jan;64(1):77-93.

PMID:
9015757
[PubMed - indexed for MEDLINE]
8.

Learning "graph-mer" motifs that predict gene expression trajectories in development.

Li X, Panea C, Wiggins CH, Reinke V, Leslie C.

PLoS Comput Biol. 2010 Apr 29;6(4):e1000761. doi: 10.1371/journal.pcbi.1000761.

PMID:
20454681
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.

Jenjaroenpun P, Kuznetsov VA.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S9. doi: 10.1186/1471-2164-10-S3-S9.

PMID:
19958507
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control.

Burzynski GM, Reed X, Taher L, Stine ZE, Matsui T, Ovcharenko I, McCallion AS.

Genome Res. 2012 Nov;22(11):2278-89. doi: 10.1101/gr.139717.112. Epub 2012 Jul 3.

PMID:
22759862
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern.

Bagheri-Fam S, Barrionuevo F, Dohrmann U, Günther T, Schüle R, Kemler R, Mallo M, Kanzler B, Scherer G.

Dev Biol. 2006 Mar 15;291(2):382-97. Epub 2006 Feb 3.

PMID:
16458883
[PubMed - indexed for MEDLINE]
Free Article
12.

Two essential regulatory elements in the human interferon gamma promoter confer activation specific expression in T cells.

Penix L, Weaver WM, Pang Y, Young HA, Wilson CB.

J Exp Med. 1993 Nov 1;178(5):1483-96.

PMID:
8228802
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Silencer-delimited transgenesis: NRSE/RE1 sequences promote neural-specific transgene expression in a NRSF/REST-dependent manner.

Xie X, Mathias JR, Smith MA, Walker SL, Teng Y, Distel M, Köster RW, Sirotkin HI, Saxena MT, Mumm JS.

BMC Biol. 2012 Nov 30;10:93. doi: 10.1186/1741-7007-10-93.

PMID:
23198762
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Transcriptional activation of human zeta 2 globin promoter by the alpha globin regulatory element (HS-40): functional role of specific nuclear factor-DNA complexes.

Zhang Q, Reddy PM, Yu CY, Bastiani C, Higgs D, Stamatoyannopoulos G, Papayannopoulou T, Shen CK.

Mol Cell Biol. 1993 Apr;13(4):2298-308.

PMID:
8455611
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N.

Nat Genet. 2013 Sep;45(9):1021-8. doi: 10.1038/ng.2713. Epub 2013 Jul 28.

PMID:
23892608
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord.

Müller F, Chang B, Albert S, Fischer N, Tora L, Strähle U.

Development. 1999 May;126(10):2103-16.

PMID:
10207136
[PubMed - indexed for MEDLINE]
Free Article
17.

The in vivo dissection of direct RFX-target gene promoters in C. elegans reveals a novel cis-regulatory element, the C-box.

Burghoorn J, Piasecki BP, Crona F, Phirke P, Jeppsson KE, Swoboda P.

Dev Biol. 2012 Aug 15;368(2):415-26. doi: 10.1016/j.ydbio.2012.05.033. Epub 2012 Jun 5.

PMID:
22683808
[PubMed - indexed for MEDLINE]
Free Article
18.

Identification and characterization of the promoter for the cytotactin gene.

Jones FS, Crossin KL, Cunningham BA, Edelman GM.

Proc Natl Acad Sci U S A. 1990 Sep;87(17):6497-501.

PMID:
1697683
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Positive and negative cis-acting elements are required for hematopoietic expression of zebrafish GATA-1.

Meng A, Tang H, Yuan B, Ong BA, Long Q, Lin S.

Blood. 1999 Jan 15;93(2):500-8.

PMID:
9885211
[PubMed - indexed for MEDLINE]
Free Article
20.

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