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Items: 1 to 20 of 93

1.

motifStack for the analysis of transcription factor binding site evolution.

Ou J, Wolfe SA, Brodsky MH, Zhu LJ.

Nat Methods. 2018 Jan 3;15(1):8-9. doi: 10.1038/nmeth.4555. No abstract available.

PMID:
29298290
2.

The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?

Lis M, Walther D.

BMC Genomics. 2016 Mar 3;17:185. doi: 10.1186/s12864-016-2549-x. Erratum in: BMC Genomics. 2016;17(1):310.

3.

Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

Müller-Molina AJ, Schöler HR, Araúzo-Bravo MJ.

PLoS One. 2012;7(11):e49086. doi: 10.1371/journal.pone.0049086. Epub 2012 Nov 28.

4.

TRES: comparative promoter sequence analysis.

Katti MV, Sakharkar MK, Ranjekar PK, Gupta VS.

Bioinformatics. 2000 Aug;16(8):739-40.

PMID:
11099260
5.

Sf-PHB2, a new transcription factor, drives WSSV Ie1 gene expression via a 12-bp DNA element.

Ma G, Yu L, Wang Q, Liu W, Cui Y, Kwang J.

Virol J. 2012 Sep 17;9:206. doi: 10.1186/1743-422X-9-206.

6.
7.

Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences.

Zambelli F, Pesole G, Pavesi G.

Curr Protoc Bioinformatics. 2014 Sep 8;47:2.11.1-31. doi: 10.1002/0471250953.bi0211s47.

PMID:
25199791
8.

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.

Vandenbon A, Kumagai Y, Teraguchi S, Amada KM, Akira S, Standley DM.

BMC Bioinformatics. 2013 Jan 21;14:26. doi: 10.1186/1471-2105-14-26.

9.

Discovery of sequence motifs related to coexpression of genes using evolutionary computation.

Fogel GB, Weekes DG, Varga G, Dow ER, Harlow HB, Onyia JE, Su C.

Nucleic Acids Res. 2004 Jul 20;32(13):3826-35. Print 2004.

10.

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.

Corcoran DL, Feingold E, Benos PV.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

11.

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

Mitra S, Biswas A, Narlikar L.

PLoS Comput Biol. 2018 Apr 23;14(4):e1006090. doi: 10.1371/journal.pcbi.1006090. eCollection 2018 Apr.

12.

CONREAL web server: identification and visualization of conserved transcription factor binding sites.

Berezikov E, Guryev V, Cuppen E.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W447-50.

13.
14.

Mapping DNA sequence to transcription factor binding energy in vivo.

Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R.

PLoS Comput Biol. 2019 Feb 4;15(2):e1006226. doi: 10.1371/journal.pcbi.1006226. eCollection 2019 Feb.

15.

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W247-52. doi: 10.1093/nar/gkp464. Epub 2009 May 31.

16.

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

Erb I, van Nimwegen E.

PLoS One. 2011;6(9):e24279. doi: 10.1371/journal.pone.0024279. Epub 2011 Sep 9.

17.

TFBScluster: a resource for the characterization of transcriptional regulatory networks.

Donaldson IJ, Chapman M, Göttgens B.

Bioinformatics. 2005 Jul 1;21(13):3058-9. Epub 2005 Apr 26.

PMID:
15855248
18.

Identification of functional SNPs in the 5-prime flanking sequences of human genes.

Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engström PG, Lenhard B, Wasserman WW, Wahlestedt C.

BMC Genomics. 2005 Feb 17;6:18.

19.

Transcription factor binding sites are highly enriched within microRNA precursor sequences.

Piriyapongsa J, Jordan IK, Conley AB, Ronan T, Smalheiser NR.

Biol Direct. 2011 Dec 2;6:61. doi: 10.1186/1745-6150-6-61.

20.

DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.

Quach B, Furey TS.

Bioinformatics. 2017 Apr 1;33(7):956-963. doi: 10.1093/bioinformatics/btw740.

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