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Items: 1 to 20 of 158

1.

Systematic identification of conserved motif modules in the human genome.

Cai X, Hou L, Su N, Hu H, Deng M, Li X.

BMC Genomics. 2010 Oct 14;11:567. doi: 10.1186/1471-2164-11-567.

2.

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.

3.

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC.

Genome Res. 2006 Dec;16(12):1480-92. Epub 2006 Oct 12.

4.

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.

5.

An integrated approach to identifying cis-regulatory modules in the human genome.

Won KJ, Agarwal S, Shen L, Shoemaker R, Ren B, Wang W.

PLoS One. 2009;4(5):e5501. doi: 10.1371/journal.pone.0005501. Epub 2009 May 12.

7.

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.

Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M, Lander ES.

Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7145-50. Epub 2007 Apr 18.

8.

Selective constraints in experimentally defined primate regulatory regions.

Gaffney DJ, Blekhman R, Majewski J.

PLoS Genet. 2008 Aug 15;4(8):e1000157. doi: 10.1371/journal.pgen.1000157.

9.

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.

BMC Genomics. 2014 Jun 13;15:472. doi: 10.1186/1471-2164-15-472.

10.

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

Drawid A, Gupta N, Nagaraj VH, GĂ©linas C, Sengupta AM.

BMC Bioinformatics. 2009 Jul 7;10:208. doi: 10.1186/1471-2105-10-208.

11.

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. doi: 10.1186/1471-2105-9-495.

12.

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1.

Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ.

Genome Res. 2006 Dec;16(12):1585-95. Epub 2006 Oct 19.

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15.

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.

Nucleic Acids Res. 2010 Jun;38(11):e126. doi: 10.1093/nar/gkq217. Epub 2010 Apr 7.

16.

Computational identification of combinatorial regulation and transcription factor binding sites.

Ryu T, Kim Y, Kim DW, Lee D.

Biotechnol Bioeng. 2007 Aug 15;97(6):1594-602.

PMID:
17252601
17.

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.

18.

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.

19.

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. doi: 10.1186/1471-2164-9-337.

20.

A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.

Hatanaka Y, Nagasaki M, Yamaguchi R, Obayashi T, Numata K, Fujita A, Shimamura T, Tamada Y, Imoto S, Kinoshita K, Nakai K, Miyano S.

Genome Inform. 2008;20:212-21.

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