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Items: 1 to 20 of 132

1.

A reexamination of information theory-based methods for DNA-binding site identification.

Erill I, O'Neill MC.

BMC Bioinformatics. 2009 Feb 11;10:57. doi: 10.1186/1471-2105-10-57.

2.

Comparative analysis of methods for representing and searching for transcription factor binding sites.

Osada R, Zaslavsky E, Singh M.

Bioinformatics. 2004 Dec 12;20(18):3516-25. Epub 2004 Aug 5.

PMID:
15297295
3.

Transcription factor site dependencies in human, mouse and rat genomes.

Tomovic A, Stadler M, Oakeley EJ.

BMC Bioinformatics. 2009 Oct 16;10:339. doi: 10.1186/1471-2105-10-339.

4.

Identifying target sites for cooperatively binding factors.

GuhaThakurta D, Stormo GD.

Bioinformatics. 2001 Jul;17(7):608-21.

PMID:
11448879
5.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

6.

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

Liu Z, Mao F, Guo JT, Yan B, Wang P, Qu Y, Xu Y.

Nucleic Acids Res. 2005 Jan 26;33(2):546-58. Print 2005.

7.

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs.

Garcia-Alcalde F, Blanco A, Shepherd AJ.

BMC Bioinformatics. 2010 Nov 8;11:551. doi: 10.1186/1471-2105-11-551.

8.

Eukaryotic transcription factor binding sites--modeling and integrative search methods.

Hannenhalli S.

Bioinformatics. 2008 Jun 1;24(11):1325-31. doi: 10.1093/bioinformatics/btn198. Epub 2008 Apr 21. Review.

PMID:
18426806
9.

Bioinformatic principles underlying the information content of transcription factor binding sites.

Kim JT, Martinetz T, Polani D.

J Theor Biol. 2003 Feb 21;220(4):529-44.

PMID:
12623284
10.
11.

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158.

12.

An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization.

Qian Z, Lu L, Liu X, Cai YD, Li Y.

Bioinformatics. 2007 Sep 15;23(18):2449-54. Epub 2007 Jul 10.

PMID:
17623704
13.

New scoring schema for finding motifs in DNA Sequences.

Zare-Mirakabad F, Ahrabian H, Sadeghi M, Nowzari-Dalini A, Goliaei B.

BMC Bioinformatics. 2009 Mar 20;10:93. doi: 10.1186/1471-2105-10-93.

14.

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes.

Bohlin J, Skjerve E, Ussery DW.

BMC Genomics. 2008 Feb 28;9:104. doi: 10.1186/1471-2164-9-104.

15.

Exploring conservation of transcription factor binding sites with CONREAL.

Berezikov E, Guryev V, Cuppen E.

Methods Mol Biol. 2007;395:437-48.

PMID:
17993690
16.

FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral.

Garcia F, Lopez FJ, Cano C, Blanco A.

BMC Bioinformatics. 2009 Jul 20;10:224. doi: 10.1186/1471-2105-10-224.

17.

Identifying promoter features of co-regulated genes with similar network motifs.

Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1. doi: 10.1186/1471-2105-10-S4-S1.

18.

Recovering motifs from biased genomes: application of signal correction.

Hasan S, Schreiber M.

Nucleic Acids Res. 2006;34(18):5124-32. Epub 2006 Sep 20.

19.

Evolution of transcription factor DNA binding sites.

Kotelnikova EA, Makeev VJ, Gelfand MS.

Gene. 2005 Mar 14;347(2):255-63. Epub 2005 Feb 17.

PMID:
15725380
20.

Information content of individual genetic sequences.

Schneider TD.

J Theor Biol. 1997 Dec 21;189(4):427-41.

PMID:
9446751

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