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Items: 1 to 20 of 600

1.

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.

PMID:
12101404
2.

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.

Tsai HK, Chou MY, Shih CH, Huang GT, Chang TH, Li WH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W221-6. Epub 2007 May 30.

3.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

4.
5.

Design of a combinatorial DNA microarray for protein-DNA interaction studies.

Mintseris J, Eisen MB.

BMC Bioinformatics. 2006 Oct 3;7:429.

6.

Extracting transcription factor binding sites from unaligned gene sequences with statistical models.

Lu CC, Yuan WH, Chen TM.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S7. doi: 10.1186/1471-2105-9-S12-S7.

7.

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.

J Mol Biol. 2001 May 25;309(1):99-120.

PMID:
11491305
8.

Systematic identification of cell cycle regulated transcription factors from microarray time series data.

Cheng C, Li LM.

BMC Genomics. 2008 Mar 3;9:116. doi: 10.1186/1471-2164-9-116.

9.
10.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

11.

In vivo protein-protein and protein-DNA crosslinking for genomewide binding microarray.

Kurdistani SK, Grunstein M.

Methods. 2003 Sep;31(1):90-5.

PMID:
12893178
12.

Combining frequency and positional information to predict transcription factor binding sites.

Kiełbasa SM, Korbel JO, Beule D, Schuchhardt J, Herzel H.

Bioinformatics. 2001 Nov;17(11):1019-26.

13.

Transcription factor binding element detection using functional clustering of mutant expression data.

Chen G, Hata N, Zhang MQ.

Nucleic Acids Res. 2004 Apr 28;32(8):2362-71. Print 2004.

14.
15.

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae.

Yarragudi A, Parfrey LW, Morse RH.

Nucleic Acids Res. 2007;35(1):193-202. Epub 2006 Dec 7.

16.

Identifying target sites for cooperatively binding factors.

GuhaThakurta D, Stormo GD.

Bioinformatics. 2001 Jul;17(7):608-21.

17.

Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data.

Seifert M, Keilwagen J, Strickert M, Grosse I.

Bioinformatics. 2009 Aug 15;25(16):2118-25. doi: 10.1093/bioinformatics/btp276. Epub 2009 Apr 28.

18.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
19.

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID:
16900145
20.

Mining ChIP-chip data for transcription factor and cofactor binding sites.

Smith AD, Sumazin P, Das D, Zhang MQ.

Bioinformatics. 2005 Jun;21 Suppl 1:i403-12.

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