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YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.
de Boer CG, Hughes TR. de Boer CG, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D169-79. doi: 10.1093/nar/gkr993. Epub 2011 Nov 18. Nucleic Acids Res. 2012. PMID: 22102575 Free PMC article.
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays.
Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR. Lam KN, et al. Nucleic Acids Res. 2011 Jun;39(11):4680-90. doi: 10.1093/nar/gkq1303. Epub 2011 Feb 14. Nucleic Acids Res. 2011. PMID: 21321018 Free PMC article.
A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.
Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B. Ding P, et al. PLoS Pathog. 2015 Jun 11;11(6):e1004967. doi: 10.1371/journal.ppat.1004967. eCollection 2015 Jun. PLoS Pathog. 2015. PMID: 26068099 Free PMC article.
Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.
Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA. Sullivan AM, et al. Cell Rep. 2014 Sep 25;8(6):2015-2030. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15. Cell Rep. 2014. PMID: 25220462
CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo.
Mann IK, Chatterjee R, Zhao J, He X, Weirauch MT, Hughes TR, Vinson C. Mann IK, et al. Genome Res. 2013 Jun;23(6):988-97. doi: 10.1101/gr.146654.112. Epub 2013 Apr 16. Genome Res. 2013. PMID: 23590861 Free PMC article.
Similarity regression predicts evolution of transcription factor sequence specificity.
Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR. Lambert SA, et al. Among authors: hughes tr. Nat Genet. 2019 Jun;51(6):981-989. doi: 10.1038/s41588-019-0411-1. Epub 2019 May 27. Nat Genet. 2019. PMID: 31133749
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