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Results: 1 to 20 of 101

1.

A motif-independent metric for DNA sequence specificity.

Pinello L, Lo Bosco G, Hanlon B, Yuan GC.

BMC Bioinformatics. 2011 Oct 21;12:408. doi: 10.1186/1471-2105-12-408.

PMID:
22017798
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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
3.

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
4.

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.

PMID:
12101404
[PubMed - indexed for MEDLINE]
5.

Prediction of TF target sites based on atomistic models of protein-DNA complexes.

Angarica VE, Pérez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B.

BMC Bioinformatics. 2008 Oct 16;9:436. doi: 10.1186/1471-2105-9-436.

PMID:
18922190
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Identification of context-dependent motifs by contrasting ChIP binding data.

Mason MJ, Plath K, Zhou Q.

Bioinformatics. 2010 Nov 15;26(22):2826-32. doi: 10.1093/bioinformatics/btq546. Epub 2010 Sep 23.

PMID:
20870645
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A feature-based approach to modeling protein-DNA interactions.

Sharon E, Lubliner S, Segal E.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000154. doi: 10.1371/journal.pcbi.1000154.

PMID:
18725950
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data.

Narlikar L.

Nucleic Acids Res. 2013 Jan 7;41(1):21-32. doi: 10.1093/nar/gks950. Epub 2012 Oct 22.

PMID:
23093591
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites.

Roulet E, Bucher P, Schneider R, Wingender E, Dusserre Y, Werner T, Mermod N.

J Mol Biol. 2000 Apr 7;297(4):833-48.

PMID:
10736221
[PubMed - indexed for MEDLINE]
10.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

PMID:
23181585
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.

Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB.

PLoS Genet. 2011 Feb 3;7(2):e1001290. doi: 10.1371/journal.pgen.1001290.

PMID:
21304941
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Genomic footprinting and sequencing of human beta-globin locus. Tissue specificity and cell line artifact.

Reddy PM, Stamatoyannopoulos G, Papayannopoulou T, Shen CK.

J Biol Chem. 1994 Mar 18;269(11):8287-95.

PMID:
8132552
[PubMed - indexed for MEDLINE]
Free Article
13.

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P.

Nat Biotechnol. 2002 Aug;20(8):831-5. Epub 2002 Jul 8.

PMID:
12101405
[PubMed - indexed for MEDLINE]
14.

Genome-wide mapping of in vivo protein-DNA interactions.

Johnson DS, Mortazavi A, Myers RM, Wold B.

Science. 2007 Jun 8;316(5830):1497-502. Epub 2007 May 31.

PMID:
17540862
[PubMed - indexed for MEDLINE]
Free Article
15.

Metamotifs--a generative model for building families of nucleotide position weight matrices.

Piipari M, Down TA, Hubbard TJ.

BMC Bioinformatics. 2010 Jun 25;11:348. doi: 10.1186/1471-2105-11-348.

PMID:
20579334
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

PiDNA: Predicting protein-DNA interactions with structural models.

Lin CK, Chen CY.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W523-30. doi: 10.1093/nar/gkt388. Epub 2013 May 22.

PMID:
23703214
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Better estimation of protein-DNA interaction parameters improve prediction of functional sites.

Nagaraj VH, O'Flanagan RA, Sengupta AM.

BMC Biotechnol. 2008 Dec 23;8:94. doi: 10.1186/1472-6750-8-94.

PMID:
19105805
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

PMID:
19652015
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

PMID:
20838582
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
15673715
[PubMed - indexed for MEDLINE]
Free PMC Article

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