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Results: 1 to 20 of 124

1.

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. doi: 10.1101/gr.085449.108. Epub 2009 Jan 13.

PMID:
19141595
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.

Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A.

Genome Biol. 2006;7(8):R78. Epub 2006 Aug 17.

PMID:
16916456
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

High sensitivity TSS prediction: estimates of locations where TSS cannot occur.

Schaefer U, Kodzius R, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bajic VB.

PLoS One. 2010 Nov 15;5(11):e13934. doi: 10.1371/journal.pone.0013934.

PMID:
21085627
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.

Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U.

Genome Biol. 2009;10(7):R73. doi: 10.1186/gb-2009-10-7-r73. Epub 2009 Jul 9.

PMID:
19589141
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.

Lin Z, Wu WS, Liang H, Woo Y, Li WH.

BMC Genomics. 2010 Oct 19;11:581. doi: 10.1186/1471-2164-11-581.

PMID:
20958978
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Characterization of transcription from TATA-less promoters: identification of a new core promoter element XCPE2 and analysis of factor requirements.

Anish R, Hossain MB, Jacobson RH, Takada S.

PLoS One. 2009;4(4):e5103. doi: 10.1371/journal.pone.0005103. Epub 2009 Apr 1.

PMID:
19337366
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site.

Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E.

PLoS One. 2007 Aug 29;2(8):e807.

PMID:
17726537
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box.

Forget D, Robert F, Grondin G, Burton ZF, Greenblatt J, Coulombe B.

Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7150-5.

PMID:
9207059
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.

Lee TY, Chang WC, Hsu JB, Chang TH, Shien DM.

BMC Genomics. 2012;13 Suppl 1:S3. doi: 10.1186/1471-2164-13-S1-S3. Epub 2012 Jan 17.

PMID:
22369687
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation.

Wang G, Wang Y, Shen C, Huang YW, Huang K, Huang TH, Nephew KP, Li L, Liu Y.

PLoS One. 2010 Nov 2;5(11):e13798. doi: 10.1371/journal.pone.0013798.

PMID:
21072189
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A code for transcription initiation in mammalian genomes.

Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A.

Genome Res. 2008 Jan;18(1):1-12. Epub 2007 Nov 21.

PMID:
18032727
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis.

Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, Obokata J.

Plant J. 2009 Oct;60(2):350-62. doi: 10.1111/j.1365-313X.2009.03958.x. Epub 2009 Jun 29.

PMID:
19563441
[PubMed - indexed for MEDLINE]
13.

Functional binding of the "TATA" box binding component of transcription factor TFIID to the -30 region of TATA-less promoters.

Wiley SR, Kraus RJ, Mertz JE.

Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5814-8.

PMID:
1321424
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

GC-compositional strand bias around transcription start sites in plants and fungi.

Fujimori S, Washio T, Tomita M.

BMC Genomics. 2005 Feb 28;6:26.

PMID:
15733327
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

MicroRNA transcription start site prediction with multi-objective feature selection.

Bhattacharyya M, Feuerbach L, Bhadra T, Lengauer T, Bandyopadhyay S.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(1):Article 6. doi: 10.2202/1544-6115.1743.

PMID:
22499686
[PubMed - indexed for MEDLINE]
16.

Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation.

Tummala P, Mali RS, Guzman E, Zhang X, Mitton KP.

Mol Vis. 2010 Feb 17;16:252-71.

PMID:
20161818
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements.

Park D, Morris AR, Battenhouse A, Iyer VR.

Nucleic Acids Res. 2014 Apr;42(6):3736-49. doi: 10.1093/nar/gkt1366. Epub 2014 Jan 10.

PMID:
24413663
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Regulation of gene expression via the core promoter and the basal transcriptional machinery.

Juven-Gershon T, Kadonaga JT.

Dev Biol. 2010 Mar 15;339(2):225-9. doi: 10.1016/j.ydbio.2009.08.009. Epub 2009 Aug 13. Review.

PMID:
19682982
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures.

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M.

Plant Cell. 2014 Jul 17. pii: tpc.114.125617. [Epub ahead of print]

PMID:
25035402
[PubMed - as supplied by publisher]
20.

ARTS: accurate recognition of transcription starts in human.

Sonnenburg S, Zien A, R├Ątsch G.

Bioinformatics. 2006 Jul 15;22(14):e472-80.

PMID:
16873509
[PubMed - indexed for MEDLINE]
Free Article

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