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Phylogenetic footprinting
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21	Open Access et al. Chiang 2003 Volume Add to Reading List Source URL: web.mit.edu Language: English - Date: 2003-11-18 18:59:57 Molecular biology DNA Genomics Phylogenetic footprinting Enhancer Ridge Transcription factor Gene expression profiling Gene Biology Gene expression Genetics
22	letters to nature breaks induced at ectopic transcription units 21 activated by demethylation. The data presented here show that Dnmt3L is required for heritable silencing of retrotransposons in male germ cells. Temporar Add to Reading List Source URL: web.mit.edu Language: English - Date: 2004-10-01 16:35:11 Molecular biology Molecular genetics Transcription factors Promoter Phylogenetic footprinting DNA methylation Ridge DNA binding site Regulation of gene expression Biology Gene expression DNA
23	Comparative promoter region analysis powered by CORG. Christoph Dieterich∗1 , Steffen Grossmann1 , Andrea Tanzer2,3 , Stefan R¨opcke1 , Peter F. Arndt1 , Peter F. Stadler2,3 and Martin Vingron1 1 2 3 Add to Reading List Source URL: lips.informatik.uni-leipzig.de Language: English - Date: 2009-09-10 09:47:25 Bioinformatics DNA RNA Promoter Phylogenetic footprinting Noncoding DNA Gene Conserved sequence Regulatory sequence Biology Genetics Gene expression
24	Guan et al. BMC Genomics 2011, 12:466 http://www.biomedcentral.com[removed] RESEARCH ARTICLE Open Access Add to Reading List Source URL: www.ncbi.nlm.nih.gov Language: English Gene expression Transcription factors Molecular biology Nucleosome Chip-sequencing FACT Chromatin Histone Phylogenetic footprinting Biology Genetics Epigenetics
25	Published online 11 December[removed]Nucleic Acids Research, 2011, Vol. 39, No. 7 e42 doi:[removed]nar/gkq948 A new framework for identifying cis-regulatory Add to Reading List Source URL: bioenergycenter.org Language: English - Date: 2011-08-26 15:16:46 DNA Molecular biology Computational phylogenetics Sequence motif Phylogenetic footprinting Consensus sequence DNA binding site Operon Promoter Biology Bioinformatics Gene expression
26	Bioinformatics Advance Access published July 10, 2013 Original Papers An integrated toolkit for accurate prediction and analysis of cis regulatory motifs at a genome scale Add to Reading List Source URL: bioenergycenter.org Language: English - Date: 2013-07-30 12:32:40 Sequence motif DNA binding site Phylogenetic footprinting Biology Bioinformatics Biochemistry
27	Guan et al. BMC Genomics 2011, 12:466 http://www.biomedcentral.com[removed] RESEARCH ARTICLE Open Access Add to Reading List Source URL: dunham.gs.washington.edu Language: English - Date: 2011-11-08 19:17:49 Gene expression Transcription factors Molecular biology Nucleosome Chip-sequencing FACT Chromatin Histone Phylogenetic footprinting Biology Genetics Epigenetics
28	Gaussian Processes and Gene Regulation Multiple Transcription Factors, Networks and Model Organisms[removed]Background and Motivation. Gaussian Processes (Rasmussen and Williams, 2005) can provide a convenient framework Add to Reading List Source URL: www.stats.ox.ac.uk Language: English - Date: 2013-08-26 08:49:50 Molecular biology Genetics Transcription factors Gene regulatory network Gene Bioinformatics Gaussian process Phylogenetic footprinting Bayesian network Biology Gene expression Networks
29	Footprinting with additional knowledge Add to Reading List Source URL: www.stats.ox.ac.uk Language: English - Date: 2013-08-26 08:49:54 Molecular genetics DNA Transcription factors Phylogenetic footprinting Chip-sequencing Nucleosome Cis-regulatory module DNA binding site Chromatin Biology Gene expression Molecular biology
30	Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila Alan M. Moses1, Daniel A. Pollard1, David A. Nix2, Venky N. Iyer3, Xiao-Yong Li2, Mark D. Biggin2, Michael B. Eisen1,2,3,4* 1 Graduate G Add to Reading List Source URL: rana.lbl.gov Language: English - Date: 2009-08-09 15:41:46 DNA Proteins Transcription factors RNA Phylogenetic footprinting DNA binding site Promoter Enhancer Protein domain Biology Biochemistry Gene expression

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