Berger MF - Search Results

1

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. Berger MF, et al. Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024. Cell. 2008. PMID: 18585359 Free PMC article.

2

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. Mukherjee S, et al. Among authors: berger mf. Nat Genet. 2004 Dec;36(12):1331-9. doi: 10.1038/ng1473. Epub 2004 Nov 14. Nat Genet. 2004. PMID: 15543148 Free PMC article.

3

Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins.

Berger MF, Bulyk ML. Berger MF, et al. Methods Mol Biol. 2006;338:245-60. doi: 10.1385/1-59745-097-9:245. Methods Mol Biol. 2006. PMID: 16888363 Free PMC article.

4

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. Berger MF, et al. Nat Biotechnol. 2006 Nov;24(11):1429-35. doi: 10.1038/nbt1246. Epub 2006 Sep 24. Nat Biotechnol. 2006. PMID: 16998473 Free PMC article.

5

Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.

Hu Y, Rolfs A, Bhullar B, Murthy TV, Zhu C, Berger MF, Camargo AA, Kelley F, McCarron S, Jepson D, Richardson A, Raphael J, Moreira D, Taycher E, Zuo D, Mohr S, Kane MF, Williamson J, Simpson A, Bulyk ML, Harlow E, Marsischky G, Kolodner RD, LaBaer J. Hu Y, et al. Among authors: berger mf. Genome Res. 2007 Apr;17(4):536-43. doi: 10.1101/gr.6037607. Epub 2007 Feb 23. Genome Res. 2007. PMID: 17322287 Free PMC article.

6

Inferring condition-specific transcription factor function from DNA binding and gene expression data.

McCord RP, Berger MF, Philippakis AA, Bulyk ML. McCord RP, et al. Among authors: berger mf. Mol Syst Biol. 2007;3:100. doi: 10.1038/msb4100140. Epub 2007 Apr 17. Mol Syst Biol. 2007. PMID: 17437025 Free PMC article.

7

Microarray analyses of newborn mouse ovaries lacking Nobox.

Choi Y, Qin Y, Berger MF, Ballow DJ, Bulyk ML, Rajkovic A. Choi Y, et al. Among authors: berger mf. Biol Reprod. 2007 Aug;77(2):312-9. doi: 10.1095/biolreprod.107.060459. Epub 2007 May 9. Biol Reprod. 2007. PMID: 17494914

8

Design of compact, universal DNA microarrays for protein binding microarray experiments.

Philippakis AA, Qureshi AM, Berger MF, Bulyk ML. Philippakis AA, et al. Among authors: berger mf. J Comput Biol. 2008 Sep;15(7):655-65. doi: 10.1089/cmb.2007.0114. J Comput Biol. 2008. PMID: 18651798 Free PMC article.

9

The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters.

Pompeani AJ, Irgon JJ, Berger MF, Bulyk ML, Wingreen NS, Bassler BL. Pompeani AJ, et al. Among authors: berger mf. Mol Microbiol. 2008 Oct;70(1):76-88. doi: 10.1111/j.1365-2958.2008.06389.x. Epub 2008 Aug 4. Mol Microbiol. 2008. PMID: 18681939 Free PMC article.

10

Predicting the binding preference of transcription factors to individual DNA k-mers.

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR. Alleyne TM, et al. Among authors: berger mf. Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16. Bioinformatics. 2009. PMID: 19088121 Free PMC article.

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