Warning: The NCBI web site requires JavaScript to function. more...
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools.
Huang W, Nevins JR, Ohler U.
Genome Biol. 2007;8(10):R225.
Related citations
Incorporating evolution of transcription factor binding sites into annotated alignments.
Bais AS, Grossmann S, Vingron M.
J Biosci. 2007 Aug;32(5):841-50.
CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing.
Ray P, Shringarpure S, Kolar M, Xing EP.
PLoS Comput Biol. 2008 Jun 6;4(6):e1000090.
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 of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.
Dermitzakis ET, Clark AG.
Mol Biol Evol. 2002 Jul;19(7):1114-21.
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.
Evaluating phylogenetic footprinting for human-rodent comparisons.
Sauer T, Shelest E, Wingender E.
Bioinformatics. 2006 Feb 15;22(4):430-7. Epub 2005 Dec 6.
A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.
Stepanova M, Tiazhelova T, Skoblov M, Baranova A.
Bioinformatics. 2005 May 1;21(9):1789-96. Epub 2005 Feb 4.
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.
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.
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.
Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP.
Bioinformatics. 2006 Sep 15;22(18):2210-6. Epub 2006 Jun 29.
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.
Large-scale turnover of functional transcription factor binding sites in Drosophila.
Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.
PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.
Mahony S, Corcoran DL, Feingold E, Benos PV.
Genome Biol. 2007;8(5):R84.
Dcode.org anthology of comparative genomic tools.
Loots GG, Ovcharenko I.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression.
Murakami K, Kojima T, Sakaki Y.
BMC Genomics. 2004 Feb 23;5(1):16.
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.
Polavarapu N, Mariño-Ramírez L, Landsman D, McDonald JF, Jordan IK.
BMC Genomics. 2008 May 17;9:226.
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.
Berezikov E, Guryev V, Plasterk RH, Cuppen E.
Genome Res. 2004 Jan;14(1):170-8. Epub 2003 Dec 12.
Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter.
Liu GE, Weirauch MT, Van Tassell CP, Li RW, Sonstegard TS, Matukumalli LK, Connor EE, Hanson RW, Yang J.
Genomics Proteomics Bioinformatics. 2008 Dec;6(3-4):129-43.
BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences.
Meng H, Banerjee A, Zhou L.
BMC Bioinformatics. 2006 Jun 7;7:287.
Filter your results:
Your browsing activity is empty.
Activity recording is turned off.
Turn recording back on