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Items: 1 to 20 of 92

1.

Detection of functional DNA motifs via statistical over-representation.

Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z.

Nucleic Acids Res. 2004 Feb 26;32(4):1372-81. Print 2004.

2.
3.

Flanking sequences modulate the cell specificity of M-CAT elements.

Larkin SB, Farrance IK, Ordahl CP.

Mol Cell Biol. 1996 Jul;16(7):3742-55.

4.

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.

Down TA, Hubbard TJ.

Nucleic Acids Res. 2005 Mar 10;33(5):1445-53. Print 2005.

5.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

6.

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.

7.

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.

8.

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Corà D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M.

BMC Bioinformatics. 2005 May 2;6:110.

9.

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.

Johansson O, Alkema W, Wasserman WW, Lagergren J.

Bioinformatics. 2003;19 Suppl 1:i169-76.

PMID:
12855453
10.

DNA motif representation with nucleotide dependency.

Chin F, Leung HC.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):110-9. doi: 10.1109/TCBB.2007.70220.

PMID:
18245880
11.

Finding motifs from all sequences with and without binding sites.

Leung HC, Chin FY.

Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.

PMID:
16870937
12.

Regulatory motif discovery using a population clustering evolutionary algorithm.

Lones MA, Tyrrell AM.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):403-14.

PMID:
17666760
14.

Nucleotide variation of regulatory motifs may lead to distinct expression patterns.

Segal L, Lapidot M, Solan Z, Ruppin E, Pilpel Y, Horn D.

Bioinformatics. 2007 Jul 1;23(13):i440-9.

PMID:
17646329
15.

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models.

Maaskola J, Rajewsky N.

Nucleic Acids Res. 2014 Dec 1;42(21):12995-3011. doi: 10.1093/nar/gku1083. Epub 2014 Nov 11.

16.

High sequence turnover in the regulatory regions of the developmental gene hunchback in insects.

Hancock JM, Shaw PJ, Bonneton F, Dover GA.

Mol Biol Evol. 1999 Feb;16(2):253-65.

PMID:
10028291
17.

MotifViz: an analysis and visualization tool for motif discovery.

Fu Y, Frith MC, Haverty PM, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W420-3.

18.

Finding motifs in the twilight zone.

Keich U, Pevzner PA.

Bioinformatics. 2002 Oct;18(10):1374-81.

PMID:
12376382
19.

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.

20.

Cluster-Buster: Finding dense clusters of motifs in DNA sequences.

Frith MC, Li MC, Weng Z.

Nucleic Acids Res. 2003 Jul 1;31(13):3666-8.

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