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Items: 1 to 20 of 101

1.

Linking DNA-binding proteins to their recognition sequences by using protein microarrays.

Ho SW, Jona G, Chen CT, Johnston M, Snyder M.

Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9940-5. Epub 2006 Jun 19.

2.

High-resolution DNA-binding specificity analysis of yeast transcription factors.

Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML.

Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21.

3.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML.

Genome Biol. 2011 Dec 21;12(12):R125. doi: 10.1186/gb-2011-12-12-r125.

4.

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML.

Nat Genet. 2004 Dec;36(12):1331-9. Epub 2004 Nov 14.

5.

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
6.

Accuracy and reproducibility of protein-DNA microarray technology.

Field S, Udalova I, Ragoussis J.

Adv Biochem Eng Biotechnol. 2007;104:87-110. Review.

PMID:
17290820
7.

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.

8.

Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.

Afek A, Lukatsky DB.

Biophys J. 2013 Oct 1;105(7):1653-60. doi: 10.1016/j.bpj.2013.08.033.

10.

In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae.

Beinoraviciūte-Kellner R, Lipps G, Krauss G.

FEBS Lett. 2005 Aug 15;579(20):4535-40.

11.

The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.

Gong W, He K, Covington M, Dinesh-Kumar SP, Snyder M, Harmer SL, Zhu YX, Deng XW.

Mol Plant. 2008 Jan;1(1):27-41. doi: 10.1093/mp/ssm009. Epub 2007 Oct 23.

12.

Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.

Afek A, Cohen H, Barber-Zucker S, Gordân R, Lukatsky DB.

PLoS Comput Biol. 2015 Aug 18;11(8):e1004429. doi: 10.1371/journal.pcbi.1004429. eCollection 2015 Aug 18.

13.

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

Mintseris J, Eisen MB.

BMC Bioinformatics. 2006 Oct 3;7:429.

14.

A common DNA-binding site for SZF1 and the BRCA1-associated zinc finger protein, ZBRK1.

Peng H, Zheng L, Lee WH, Rux JJ, Rauscher FJ 3rd.

Cancer Res. 2002 Jul 1;62(13):3773-81.

15.

Protein binding microarrays for the characterization of DNA-protein interactions.

Bulyk ML.

Adv Biochem Eng Biotechnol. 2007;104:65-85. Review.

16.
17.

ChIP-chip to analyze the binding of replication proteins to chromatin using oligonucleotide DNA microarrays.

Viggiani CJ, Aparicio JG, Aparicio OM.

Methods Mol Biol. 2009;521:255-78. doi: 10.1007/978-1-60327-815-7_14.

PMID:
19563111
18.

A transdimensional Bayesian model for pattern recognition in DNA sequences.

Li SM, Wakefield J, Self S.

Biostatistics. 2008 Oct;9(4):668-85. doi: 10.1093/biostatistics/kxm058. Epub 2008 Mar 18.

PMID:
18349034
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