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Items: 1 to 20 of 105

2.
3.

Using Weeder for the discovery of conserved transcription factor binding sites.

Pavesi G, Pesole G.

Curr Protoc Bioinformatics. 2006 Oct;Chapter 2:Unit 2.11. doi: 10.1002/0471250953.bi0211s15.

PMID:
18428764
4.

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

BMC Bioinformatics. 2009 Jul 7;10:208. doi: 10.1186/1471-2105-10-208.

5.

Conformational model for binding site recognition by the E.coli MetJ transcription factor.

Liu R, Blackwell TW, States DJ.

Bioinformatics. 2001 Jul;17(7):622-33.

6.

Conformational and physicochemical DNA features specific for transcription factor binding sites.

Ponomarenko JV, Ponomarenko MP, Frolov AS, Vorobyev DG, Overton GC, Kolchanov NA.

Bioinformatics. 1999 Jul-Aug;15(7-8):654-68.

7.

Sequence features of DNA binding sites reveal structural class of associated transcription factor.

Narlikar L, Hartemink AJ.

Bioinformatics. 2006 Jan 15;22(2):157-63. Epub 2005 Nov 2.

8.

A novel ensemble learning method for de novo computational identification of DNA binding sites.

Chakravarty A, Carlson JM, Khetani RS, Gross RH.

BMC Bioinformatics. 2007 Jul 12;8:249.

9.

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D91-4.

10.

CTF: a CRF-based transcription factor binding sites finding system.

He Y, Zhang Y, Zheng G, Wei C.

BMC Genomics. 2012;13 Suppl 8:S18. doi: 10.1186/1471-2164-13-S8-S18. Epub 2012 Dec 17.

11.

Regulatory motif finding by logic regression.

Keles S, van der Laan MJ, Vulpe C.

Bioinformatics. 2004 Nov 1;20(16):2799-811. Epub 2004 May 27.

12.

Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

Reddy TE, DeLisi C, Shakhnovich BE.

PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10.

13.
14.

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.

Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D95-7.

15.

Using TESS to predict transcription factor binding sites in DNA sequence.

Schug J.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 2:Unit 2.6. doi: 10.1002/0471250953.bi0206s21.

PMID:
18428685
16.

A subspace method for the detection of transcription factor binding sites.

Pairó E, Maynou J, Marco S, Perera A.

Bioinformatics. 2012 May 15;28(10):1328-35. doi: 10.1093/bioinformatics/bts147. Epub 2012 Mar 29.

17.

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

Bauer AL, Hlavacek WS, Unkefer PJ, Mu F.

PLoS Comput Biol. 2010 Nov 18;6(11):e1001007. doi: 10.1371/journal.pcbi.1001007.

18.

Position specific variation in the rate of evolution in transcription factor binding sites.

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB.

BMC Evol Biol. 2003 Aug 28;3:19. Epub 2003 Aug 28.

19.

Finding optimal degenerate patterns in DNA sequences.

Shinozaki D, Akutsu T, Maruyama O.

Bioinformatics. 2003 Oct;19 Suppl 2:ii206-14.

20.

A structural-based strategy for recognition of transcription factor binding sites.

Xu B, Schones DE, Wang Y, Liang H, Li G.

PLoS One. 2013;8(1):e52460. doi: 10.1371/journal.pone.0052460. Epub 2013 Jan 8. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/0312e1be-336d-430a-aa90-101bbb44f8db.

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