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G+C content dominates intrinsic nucleosome occupancy.
Tillo D, Hughes TR. Tillo D, et al. Among authors: hughes tr. BMC Bioinformatics. 2009 Dec 22;10:442. doi: 10.1186/1471-2105-10-442. BMC Bioinformatics. 2009. PMID: 20028554 Free PMC article.
FunSpec: a web-based cluster interpreter for yeast.
Robinson MD, Grigull J, Mohammad N, Hughes TR. Robinson MD, et al. Among authors: hughes tr. BMC Bioinformatics. 2002 Nov 13;3:35. doi: 10.1186/1471-2105-3-35. Epub 2002 Nov 13. BMC Bioinformatics. 2002. PMID: 12431279 Free PMC article.
A high-resolution atlas of nucleosome occupancy in yeast.
Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. Lee W, et al. Among authors: hughes tr. Nat Genet. 2007 Oct;39(10):1235-44. doi: 10.1038/ng2117. Epub 2007 Sep 16. Nat Genet. 2007. PMID: 17873876
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: hughes tr. Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16. Bioinformatics. 2009. PMID: 19088121 Free PMC article.
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. Kaplan N, et al. Among authors: hughes tr. Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17. Nature. 2009. PMID: 19092803 Free PMC article.
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. Badis G, et al. Among authors: hughes tr. Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020. Mol Cell. 2008. PMID: 19111667 Free PMC article.
High nucleosome occupancy is encoded at human regulatory sequences.
Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR. Tillo D, et al. Among authors: hughes tr. PLoS One. 2010 Feb 9;5(2):e9129. doi: 10.1371/journal.pone.0009129. PLoS One. 2010. PMID: 20161746 Free PMC article.
274 results