PubMed

Determining promoter location based on DNA structure first-principles calculations.

Goñi JR, Pérez A, Torrents D, Orozco M.

Genome Biol. 2007;8(12):R263.PMID: 18072969 [PubMed - indexed for MEDLINE]Related articlesFree article

Triplex-forming oligonucleotide target sequences in the human genome.

Goñi JR, de la Cruz X, Orozco M.

Nucleic Acids Res. 2004 Jan 15;32(1):354-60. Print 2004.PMID: 14726484 [PubMed - indexed for MEDLINE]Related articlesFree article

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles.

Abeel T, Saeys Y, Rouzé P, Van de Peer Y.

Bioinformatics. 2008 Jul 1;24(13):i24-31.PMID: 18586720 [PubMed - indexed for MEDLINE]Related articlesFree article

High-resolution human core-promoter prediction with CoreBoost_HM.

Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ.

Genome Res. 2009 Feb;19(2):266-75. Epub 2008 Nov 7.PMID: 18997002 [PubMed - indexed for MEDLINE]Related articlesFree article

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands.

Srivastava GP, Guo J, Shi H, Xu D.

Bioinformatics. 2008 Sep 1;24(17):1837-42. Epub 2008 Jun 25.PMID: 18579568 [PubMed - indexed for MEDLINE]Related articlesFree article

ContDist: a tool for the analysis of quantitative gene and promoter properties.

Hackenberg M, Lasso G, Matthiesen R.

BMC Bioinformatics. 2009 Jan 7;10:7.PMID: 19128472 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Ward LD, Bussemaker HJ.

Bioinformatics. 2008 Jul 1;24(13):i165-71.PMID: 18586710 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of n-gram based promoter recognition methods and application to whole genome promoter prediction.

Rani TS, Bapi RS.

In Silico Biol. 2009;9(1-2):S1-16.PMID: 19537162 [PubMed - indexed for MEDLINE]Related articles

Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene.

Okabe Y, Yagi Y, Sasai M.

J Chem Phys. 2007 Sep 14;127(10):105107.PMID: 17867786 [PubMed - indexed for MEDLINE]Related articles

The in silico prediction of promoters in bacterial genomes.

Towsey M, Hogan JM, Mathews S, Timms P.

Genome Inform. 2007;19:178-89.PMID: 18546515 [PubMed - indexed for MEDLINE]Related articlesFree article

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. Epub 2009 Jan 13.PMID: 19141595 [PubMed - indexed for MEDLINE]Related articlesFree article

Application of FirstEF to find promoters and first exons in the human genome.

Davuluri RV.

Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.7.PMID: 18428702 [PubMed - indexed for MEDLINE]Related articles

Repair of DNA lesions associated with triplex-forming oligonucleotides.

Chin JY, Glazer PM.

Mol Carcinog. 2009 Apr;48(4):389-99. Review.PMID: 19072762 [PubMed - indexed for MEDLINE]Related articlesFree article

Quantitation of DNA methylation by melt curve analysis.

Smith E, Jones ME, Drew PA.

BMC Cancer. 2009 Apr 24;9:123.PMID: 19393074 [PubMed - indexed for MEDLINE]Related articlesFree article

Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation.

Paramasivam M, Cogoi S, Filichev VV, Bomholt N, Pedersen EB, Xodo LE.

Nucleic Acids Res. 2008 Jun;36(10):3494-507. Epub 2008 May 2.PMID: 18456705 [PubMed - indexed for MEDLINE]Related articlesFree article

COTRASIF: conservation-aided transcription-factor-binding site finder.

Tokovenko B, Golda R, Protas O, Obolenskaya M, El'skaya A.

Nucleic Acids Res. 2009 Apr;37(7):e49. Epub 2009 Mar 5.PMID: 19264796 [PubMed - indexed for MEDLINE]Related articlesFree article

Generic eukaryotic core promoter prediction using structural features of DNA.

Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y.

Genome Res. 2008 Feb;18(2):310-23. Epub 2007 Dec 20.PMID: 18096745 [PubMed - indexed for MEDLINE]Related articlesFree article

Using CorePromoter to find human core promoters.

Zhang MQ.

Curr Protoc Bioinformatics. 2005 Jul;Chapter 2:Unit 2.9.PMID: 18428749 [PubMed - indexed for MEDLINE]Related articles

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

Yang MQ, Elnitski LL.

BMC Genomics. 2008;9 Suppl 1:S2.PMID: 18366609 [PubMed - indexed for MEDLINE]Related articlesFree article

MPDA: microarray pooled DNA analyzer.

Yang HC, Huang MC, Li LH, Lin CH, Yu AL, Diccianni MB, Wu JY, Chen YT, Fann CS.

BMC Bioinformatics. 2008 Apr 15;9:196.PMID: 18412951 [PubMed - indexed for MEDLINE]Related articlesFree article