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Results: 1 to 20 of 119

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.

PMID:
20946653
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
16477324
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19434238
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
17038566
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
18704158
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
16756683
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.

Jenjaroenpun P, Kuznetsov VA.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S9. doi: 10.1186/1471-2164-10-S3-S9.

PMID:
19958507
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

PMID:
19956545
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.

Hu J, Hu H, Li X.

Nucleic Acids Res. 2008 Aug;36(13):4488-97. doi: 10.1093/nar/gkn407. Epub 2008 Jul 7.

PMID:
18606616
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.

Marinescu VD, Kohane IS, Riva A.

BMC Bioinformatics. 2005 Mar 30;6:79.

PMID:
15799782
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Enrichment of regulatory signals in conserved non-coding genomic sequence.

Levy S, Hannenhalli S, Workman C.

Bioinformatics. 2001 Oct;17(10):871-7.

PMID:
11673231
[PubMed - indexed for MEDLINE]
Free Article
12.

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.

PMID:
17442748
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

PMID:
20158869
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.

Sharan R, Ovcharenko I, Ben-Hur A, Karp RM.

Bioinformatics. 2003;19 Suppl 1:i283-91.

PMID:
12855471
[PubMed - indexed for MEDLINE]
Free Article
15.

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.

Oh YM, Kim JK, Choi S, Yoo JY.

Nucleic Acids Res. 2012 Mar;40(5):e38. doi: 10.1093/nar/gkr1252. Epub 2011 Dec 19.

PMID:
22187154
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Computation-based discovery of cis-regulatory modules by hidden Markov model.

Wu J, Xie J.

J Comput Biol. 2008 Apr;15(3):279-90. doi: 10.1089/cmb.2008.0024.

PMID:
18333759
[PubMed - indexed for MEDLINE]
17.

SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.

Ding J, Hu H, Li X.

Nucleic Acids Res. 2014 Mar;42(5):e35. doi: 10.1093/nar/gkt1288. Epub 2013 Dec 9.

PMID:
24322294
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
[PubMed - indexed for MEDLINE]
19.

Discovering motifs in ranked lists of DNA sequences.

Eden E, Lipson D, Yogev S, Yakhini Z.

PLoS Comput Biol. 2007 Mar 23;3(3):e39.

PMID:
17381235
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Flexibility of transcription factor target site position in conserved cis-regulatory modules.

Cameron RA, Davidson EH.

Dev Biol. 2009 Dec 1;336(1):122-35. doi: 10.1016/j.ydbio.2009.09.018. Epub 2009 Sep 18.

PMID:
19766623
[PubMed - indexed for MEDLINE]
Free Article

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