Warning: The NCBI web site requires JavaScript to function. more...
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB.
Genome Biol. 2004;5(12):R98. Epub 2004 Nov 30.
Related citations
Identification of functional transcription factor binding sites using closely related Saccharomyces species.
Doniger SW, Huh J, Fay JC.
Genome Res. 2005 May;15(5):701-9. Epub 2005 Apr 18.
PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.
Siddharthan R, Siggia ED, van Nimwegen E.
PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.
Incorporating evolution of transcription factor binding sites into annotated alignments.
Bais AS, Grossmann S, Vingron M.
J Biosci. 2007 Aug;32(5):841-50.
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
He X, Ling X, Sinha S.
PLoS Comput Biol. 2009 Mar;5(3):e1000299. Epub 2009 Mar 13.
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.
Raijman D, Shamir R, Tanay A.
PLoS Comput Biol. 2008 Jan;4(1):e7.
Position specific variation in the rate of evolution in transcription factor binding sites.
Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB.
BMC Evol Biol. 2003 Aug 28;3:19. Epub 2003 Aug 28.
Conservation and evolution of cis-regulatory systems in ascomycete fungi.
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB.
PLoS Biol. 2004 Dec;2(12):e398. Epub 2004 Nov 9.
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.
Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.
Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.
Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.
Lusk RW, Eisen MB.
Pac Symp Biocomput. 2008:489-500.
Yeast general transcription factor GFI: sequence requirements for binding to DNA and evolutionary conservation.
Dorsman JC, van Heeswijk WC, Grivell LA.
Nucleic Acids Res. 1990 May 11;18(9):2769-76.
Functional conservation of Rel binding sites in drosophilid genomes.
Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA.
Genome Res. 2007 Sep;17(9):1327-35.
Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer.
Eisermann K, Tandon S, Bazarov A, Brett A, Fraizer G, Piontkivska H.
BMC Genomics. 2008 Jul 16;9:337.
The design of transcription-factor binding sites is affected by combinatorial regulation.
Bilu Y, Barkai N.
Genome Biol. 2005;6(12):R103. Epub 2005 Dec 2.
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.
Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.
BMC Bioinformatics. 2008 Nov 26;9:495.
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.
Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB.
Genome Biol. 2003;4(7):R43. Epub 2003 Jun 26.
Precise physical models of protein-DNA interaction from high-throughput data.
Kinney JB, Tkacik G, Callan CG Jr.
Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):501-6. Epub 2006 Dec 29.
Context specific transcription factor prediction.
Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP.
Ann Biomed Eng. 2007 Jun;35(6):1053-67. Epub 2007 Mar 22.
Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.
Pollard DA, Moses AM, Iyer VN, Eisen MB.
BMC Bioinformatics. 2006 Aug 14;7:376.
An evolutionary approach for identifying potential transcription factor binding sites: the renin gene as an example.
Mrowka R, Steinhage K, Patzak A, Persson PB.
Am J Physiol Regul Integr Comp Physiol. 2003 Apr;284(4):R1147-50.
Filter your results:
Your browsing activity is empty.
Activity recording is turned off.
Turn recording back on