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Items 1 - 20 of 86
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1:

PhyloScan: identification of transcription factor binding sites using cross-species evidence.

Carmack CS, McCue LA, Newberg LA, Lawrence CE.

Algorithms Mol Biol. 2007 Jan 23;2:1.

PMID: 17244358 [PubMed]

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]

3:

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

McCue LA, Thompson W, Carmack CS, Lawrence CE.

Genome Res. 2002 Oct;12(10):1523-32.

PMID: 12368244 [PubMed - indexed for MEDLINE]

4:

Extracting transcription factor binding sites from unaligned gene sequences with statistical models.

Lu CC, Yuan WH, Chen TM.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S7.

PMID: 19091030 [PubMed - in process]

5:

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.

PMID: 19036135 [PubMed - in process]

6:

A model of evolution with constant selective pressure for regulatory DNA sites.

Enikeeva FN, Kotelnikova EA, Gelfand MS, Makeev VJ.

BMC Evol Biol. 2007 Jul 27;7:125.

PMID: 17662135 [PubMed - indexed for MEDLINE]

7:

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]

8:

Context specific transcription factor prediction.

Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP.

Ann Biomed Eng. 2007 Jun;35(6):1053-67. Epub 2007 Mar 22.

PMID: 17377845 [PubMed - indexed for MEDLINE]

9:

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.

Pavesi G, Zambelli F, Pesole G.

BMC Bioinformatics. 2007 Feb 7;8:46.

PMID: 17286865 [PubMed - indexed for MEDLINE]

10:

Improved benchmarks for computational motif discovery.

Sandve GK, Abul O, Walseng V, Drabløs F.

BMC Bioinformatics. 2007 Jun 8;8:193.

PMID: 17559676 [PubMed - indexed for MEDLINE]

11:

SwissRegulon: a database of genome-wide annotations of regulatory sites.

Pachkov M, Erb I, Molina N, van Nimwegen E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D127-31. Epub 2006 Nov 27.

PMID: 17130146 [PubMed - indexed for MEDLINE]

12:

A new approach to the assessment of the quality of predictions of transcription factor binding sites.

Nowakowski S, Tiuryn J.

J Biomed Inform. 2007 Apr;40(2):139-49. Epub 2006 Jul 21.

PMID: 16949346 [PubMed - indexed for MEDLINE]

13:

A novel ensemble learning method for de novo computational identification of DNA binding sites.

Chakravarty A, Carlson JM, Khetani RS, Gross RH.

BMC Bioinformatics. 2007 Jul 12;8:249.

PMID: 17626633 [PubMed - indexed for MEDLINE]

14:

Position dependencies in transcription factor binding sites.

Tomovic A, Oakeley EJ.

Bioinformatics. 2007 Apr 15;23(8):933-41. Epub 2007 Feb 18.

PMID: 17308339 [PubMed - indexed for MEDLINE]

15:

Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites.

Vega VB, Lin CY, Lai KS, Kong SL, Xie M, Su X, Teh HF, Thomsen JS, Yeo AL, Sung WK, Bourque G, Liu ET.

Genome Biol. 2006;7(9):R82.

PMID: 16961928 [PubMed - indexed for MEDLINE]

16:

Inference of miRNA targets using evolutionary conservation and pathway analysis.

Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M.

BMC Bioinformatics. 2007 Mar 1;8:69. Erratum in: BMC Bioinformatics. 2007 Jul 12;8(1):248.

PMID: 17331257 [PubMed - indexed for MEDLINE]

17:

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

Zadissa A, McEwan JC, Brown CM.

BMC Genomics. 2007 Aug 3;8:265.

PMID: 17683551 [PubMed - indexed for MEDLINE]

18:

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.

PMID: 17559640 [PubMed - indexed for MEDLINE]

19:

Prediction of transcription factor binding sites using ChIP-chip and phylogenetic footprinting data.

Friberg MT.

J Bioinform Comput Biol. 2007 Feb;5(1):105-16.

PMID: 17477493 [PubMed - indexed for MEDLINE]

20:

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.

Chen X, Hughes TR, Morris Q.

Bioinformatics. 2007 Jul 1;23(13):i72-9.

PMID: 17646348 [PubMed - indexed for MEDLINE]

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