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Items: 1 to 20 of 29

1.
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.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

4.

Predicting expression patterns from regulatory sequence in Drosophila segmentation.

Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U.

Nature. 2008 Jan 31;451(7178):535-40. doi: 10.1038/nature06496. Epub 2008 Jan 2.

PMID:
18172436
5.

Novel repressor of the human FMR1 gene - identification of p56 human (GCC)(n)-binding protein as a Krüppel-like transcription factor ZF5.

Orlov SV, Kuteykin-Teplyakov KB, Ignatovich IA, Dizhe EB, Mirgorodskaya OA, Grishin AV, Guzhova OB, Prokhortchouk EB, Guliy PV, Perevozchikov AP.

FEBS J. 2007 Sep;274(18):4848-62. Epub 2007 Aug 21.

6.
7.

Bcl-6 mediates the germinal center B cell phenotype and lymphomagenesis through transcriptional repression of the DNA-damage sensor ATR.

Ranuncolo SM, Polo JM, Dierov J, Singer M, Kuo T, Greally J, Green R, Carroll M, Melnick A.

Nat Immunol. 2007 Jul;8(7):705-14. Epub 2007 Jun 10.

PMID:
17558410
8.
9.

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML.

Nat Biotechnol. 2006 Nov;24(11):1429-35. Epub 2006 Sep 24.

10.

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.

Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10.

11.

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

Granek JA, Clarke ND.

Genome Biol. 2005;6(10):R87. Epub 2005 Sep 30.

12.

MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules.

Li MZ, Elledge SJ.

Nat Genet. 2005 Mar;37(3):311-9. Epub 2005 Jan 30.

PMID:
15731760
13.

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.

14.

WebLogo: a sequence logo generator.

Crooks GE, Hon G, Chandonia JM, Brenner SE.

Genome Res. 2004 Jun;14(6):1188-90.

15.

Multiple sequence alignment with the Clustal series of programs.

Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD.

Nucleic Acids Res. 2003 Jul 1;31(13):3497-500.

16.

A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays.

Lee ML, Bulyk ML, Whitmore GA, Church GM.

Biometrics. 2002 Dec;58(4):981-8.

PMID:
12495153
17.

Additivity in protein-DNA interactions: how good an approximation is it?

Benos PV, Bulyk ML, Stormo GD.

Nucleic Acids Res. 2002 Oct 15;30(20):4442-51.

18.

Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

Benos PV, Lapedes AS, Stormo GD.

Bioessays. 2002 May;24(5):466-75. Review.

PMID:
12001270
19.

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