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Results: 1 to 20 of 663

1.

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. doi: 10.1186/1471-2164-9-226.

PMID:
18485226
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.

Conley AB, Jordan IK.

Methods Mol Biol. 2010;674:225-40. doi: 10.1007/978-1-60761-854-6_14.

PMID:
20827595
[PubMed - indexed for MEDLINE]
3.

A c-Myc regulatory subnetwork from human transposable element sequences.

Wang J, Bowen NJ, Mariño-Ramírez L, Jordan IK.

Mol Biosyst. 2009 Dec;5(12):1831-9. doi: 10.1039/B908494k. Epub 2009 Jul 21.

PMID:
19763338
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identification of transcription factor binding sites in the human genome sequence.

Levy S, Hannenhalli S.

Mamm Genome. 2002 Sep;13(9):510-4.

PMID:
12370781
[PubMed - indexed for MEDLINE]
5.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

PMID:
17914226
[PubMed - indexed for MEDLINE]
Free Article
6.

Evolution of the mammalian transcription factor binding repertoire via transposable elements.

Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, Liu ET.

Genome Res. 2008 Nov;18(11):1752-62. doi: 10.1101/gr.080663.108. Epub 2008 Aug 5.

PMID:
18682548
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
12946282
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Transposable element derived DNaseI-hypersensitive sites in the human genome.

Mariño-Ramírez L, Jordan IK.

Biol Direct. 2006 Jul 20;1:20.

PMID:
16857058
[PubMed]
Free PMC Article
9.

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
10.

Origin and evolution of human microRNAs from transposable elements.

Piriyapongsa J, Mariño-Ramírez L, Jordan IK.

Genetics. 2007 Jun;176(2):1323-37. Epub 2007 Apr 15.

PMID:
17435244
[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.

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.

PMID:
15699025
[PubMed - indexed for MEDLINE]
Free Article
13.

Evaluating the protein coding potential of exonized transposable element sequences.

Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK.

Biol Direct. 2007 Nov 26;2:31.

PMID:
18036258
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Origin of a substantial fraction of human regulatory sequences from transposable elements.

Jordan IK, Rogozin IB, Glazko GV, Koonin EV.

Trends Genet. 2003 Feb;19(2):68-72. Review.

PMID:
12547512
[PubMed - indexed for MEDLINE]
16.

Database of repetitive elements in complete genomes and data mining using transcription factor binding sites.

Horng JT, Lin FM, Lin JH, Huang HD, Liu BJ.

IEEE Trans Inf Technol Biomed. 2003 Jun;7(2):93-100.

PMID:
12834164
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
12082130
[PubMed - indexed for MEDLINE]
Free Article
18.

Widespread occurrence of power-law distributions in inter-repeat distances shaped by genome dynamics.

Klimopoulos A, Sellis D, Almirantis Y.

Gene. 2012 May 10;499(1):88-98. doi: 10.1016/j.gene.2012.02.005. Epub 2012 Feb 18.

PMID:
22370293
[PubMed - indexed for MEDLINE]
19.

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.

PMID:
17506886
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Repetitive DNA elements, nucleosome binding and human gene expression.

Huda A, Mariño-Ramírez L, Landsman D, Jordan IK.

Gene. 2009 May 1;436(1-2):12-22. doi: 10.1016/j.gene.2009.01.013. Epub 2009 Feb 5.

PMID:
19393174
[PubMed - indexed for MEDLINE]
Free PMC Article

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