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Reference Year Description PMID #Motifs in DB
V Foat BC, Tepper RG, Bussemaker HJ. TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Res. 2008 Jan;36(Database issue):D125-31. Epub 2007 Oct 18. 2008 ChIP-chip 17947326 445
V Reddy TE, DeLisi C, Shakhnovich BE. Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10. 2006 ChIP-chip 17500587 261
V Zhao Y, Granas D, Stormo GD. Inferring binding energies from selected binding sites. PLoS Comput Biol. 2009 Dec;5(12):e1000590. Epub 2009 Dec 4. 2009 PBM 19997485 132
V MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics. 2006 Mar 7;7:113. 2006 ChIP-chip 16522208 125
V 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. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell. 2008 Dec 26;32(6):878-87. 2008 PBM 19111667 114
V Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25;298(5594):799-804. 2002 ChIP-chip 12399584 100
V 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. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009 Apr;19(4):556-66. Epub 2009 Jan 21. 2009 PBM 19158363 89
V Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol. 2010 Sep;28(9):970-5. Epub 2010 Aug 29. 2010 MITOMI 20802496 84
V Pachkov M, Erb I, Molina N, van Nimwegen E. SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res. 2007 Jan;35(Database issue):D127-31. Epub 2006 Nov 27. 2007 ChIP-chip, conservation, combination of existing motifs 17130146 81
V Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73. Epub 2007 Apr 16. 2007 ChIP-chip, structural prior 17438293 79
V Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature. 2004 Sep 2;431(7004):99-104. 2004 ChIP-chip 15343339 65
V Gordan R, Murphy K, McCord RP, Zhu C, Vedenko A, Bulyk ML. Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol. 2011 Dec 21;12(12):R125. 2011 PBM 22189060 42
V Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003 May 15;423(6937):241-54. 2003 Conservation 12748633 41
V Chen X, Guo L, Fan Z, Jiang T. W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data. Bioinformatics. 2008 May 1;24(9):1121-8. Epub 2008 Mar 5. 2008 ChIP-chip 18325926 33
V Zhu J, Zhang MQ. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics. 1999 Jul-Aug;15(7-8):607-11. 1999 alignments of various mapped sites 10487868 20

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