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Items: 1 to 20 of 101

1.

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.

3.

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

Bulyk ML.

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

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6.

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.

7.

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.

8.

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.

Orenstein Y, Shamir R.

Nucleic Acids Res. 2014 Apr;42(8):e63. doi: 10.1093/nar/gku117. Epub 2014 Feb 5.

9.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

10.

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.

11.

ARS binding factor 1 binds adjacent to RAP1 at the UASs of the yeast glycolytic genes PGK and PYK1.

Chambers A, Stanway C, Tsang JS, Henry Y, Kingsman AJ, Kingsman SM.

Nucleic Acids Res. 1990 Sep 25;18(18):5393-9.

12.

DNA binding site analysis of Burkholderia thailandensis response regulators.

Nowak-Lovato KL, Hickmott AJ, Maity TS, Bulyk ML, Dunbar J, Hong-Geller E.

J Microbiol Methods. 2012 Jul;90(1):46-52. doi: 10.1016/j.mimet.2012.03.019. Epub 2012 Apr 13.

PMID:
22521922
13.

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites.

Jaeger SA, Chan ET, Berger MF, Stottmann R, Hughes TR, Bulyk ML.

Genomics. 2010 Apr;95(4):185-95. doi: 10.1016/j.ygeno.2010.01.002. Epub 2010 Jan 15.

14.

Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors.

Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R.

Plant J. 2011 May;66(4):700-11. doi: 10.1111/j.1365-313X.2011.04519.x. Epub 2011 Mar 9.

15.

Quantitative modeling of transcription factor binding specificities using DNA shape.

Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4654-9. doi: 10.1073/pnas.1422023112. Epub 2015 Mar 9.

16.

Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene.

Gailus-Durner V, Xie J, Chintamaneni C, Vershon AK.

Mol Cell Biol. 1996 Jun;16(6):2777-86.

18.

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

Schlecht U, Erb I, Demougin P, Robine N, Borde V, van Nimwegen E, Nicolas A, Primig M.

Mol Biol Cell. 2008 May;19(5):2193-207. doi: 10.1091/mbc.E07-12-1242. Epub 2008 Feb 27.

19.

Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays.

Bonham AJ, Neumann T, Tirrell M, Reich NO.

Nucleic Acids Res. 2009 Jul;37(13):e94. doi: 10.1093/nar/gkp424. Epub 2009 May 31.

20.

Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?

Venkataram S, Fay JC.

Genome Biol Evol. 2010;2:851-8. doi: 10.1093/gbe/evq066. Epub 2010 Nov 10.

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