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Results: 1 to 20 of 41

1.

A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors.

Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ.

Cell. 2009 Jul 23;138(2):314-27. doi: 10.1016/j.cell.2009.04.058.

PMID:
19632181
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.

PMID:
19443739
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19158363
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.

PMID:
19111667
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The DNA-encoded nucleosome organization of a eukaryotic genome.

Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E.

Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17.

PMID:
19092803
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
18585359
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Saccharomyces cerevisiae SFP1: at the crossroads of central metabolism and ribosome biogenesis.

Cipollina C, van den Brink J, Daran-Lapujade P, Pronk JT, Porro D, de Winde JH.

Microbiology. 2008 Jun;154(Pt 6):1686-99. doi: 10.1099/mic.0.2008/017392-0.

PMID:
18524923
[PubMed - indexed for MEDLINE]
Free Article
8.

Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.

Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR.

PLoS Biol. 2008 Mar 18;6(3):e65. doi: 10.1371/journal.pbio.0060065.

PMID:
18351804
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A high-resolution atlas of nucleosome occupancy in yeast.

Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C.

Nat Genet. 2007 Oct;39(10):1235-44. Epub 2007 Sep 16.

PMID:
17873876
[PubMed - indexed for MEDLINE]
10.

Genome-wide mapping of in vivo protein-DNA interactions.

Johnson DS, Mortazavi A, Myers RM, Wold B.

Science. 2007 Jun 8;316(5830):1497-502. Epub 2007 May 31.

PMID:
17540862
[PubMed - indexed for MEDLINE]
Free Article
11.

Potential interface between ribosomal protein production and pre-rRNA processing.

Rudra D, Mallick J, Zhao Y, Warner JR.

Mol Cell Biol. 2007 Jul;27(13):4815-24. Epub 2007 Apr 23.

PMID:
17452446
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Predicting transcription factor affinities to DNA from a biophysical model.

Roider HG, Kanhere A, Manke T, Vingron M.

Bioinformatics. 2007 Jan 15;23(2):134-41. Epub 2006 Nov 10.

PMID:
17098775
[PubMed - indexed for MEDLINE]
Free Article
13.

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD.

Genome Res. 2006 Dec;16(12):1517-28. Epub 2006 Oct 19.

PMID:
17053089
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
16998473
[PubMed - indexed for MEDLINE]
15.

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

Foat BC, Morozov AV, Bussemaker HJ.

Bioinformatics. 2006 Jul 15;22(14):e141-9.

PMID:
16873464
[PubMed - indexed for MEDLINE]
Free Article
16.

Extensive low-affinity transcriptional interactions in the yeast genome.

Tanay A.

Genome Res. 2006 Aug;16(8):962-72. Epub 2006 Jun 29.

PMID:
16809671
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Fine-structure analysis of ribosomal protein gene transcription.

Zhao Y, McIntosh KB, Rudra D, Schawalder S, Shore D, Warner JR.

Mol Cell Biol. 2006 Jul;26(13):4853-62.

PMID:
16782874
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Regulation of mating and filamentation genes by two distinct Ste12 complexes in Saccharomyces cerevisiae.

Chou S, Lane S, Liu H.

Mol Cell Biol. 2006 Jul;26(13):4794-805.

PMID:
16782869
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E.

BMC Bioinformatics. 2006 Mar 7;7:113.

PMID:
16522208
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A global map of p53 transcription-factor binding sites in the human genome.

Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y.

Cell. 2006 Jan 13;124(1):207-19.

PMID:
16413492
[PubMed - indexed for MEDLINE]
Free Article

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