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Items: 1 to 20 of 88

1.

Assessing computational tools for the discovery of transcription factor binding sites.

Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z.

Nat Biotechnol. 2005 Jan;23(1):137-44.

PMID:
15637633
2.

Scoring functions for transcription factor binding site prediction.

Friberg M, von Rohr P, Gonnet G.

BMC Bioinformatics. 2005 Apr 4;6:84.

3.

An improved Gibbs sampling method for motif discovery via sequence weighting.

Chen X, Jiang T.

Comput Syst Bioinformatics Conf. 2006:239-47.

4.

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.

Linhart C, Halperin Y, Shamir R.

Genome Res. 2008 Jul;18(7):1180-9. doi: 10.1101/gr.076117.108. Epub 2008 Apr 14.

5.
6.

A statistical analysis of the TRANSFAC database.

Fogel GB, Weekes DG, Varga G, Dow ER, Craven AM, Harlow HB, Su EW, Onyia JE, Su C.

Biosystems. 2005 Aug;81(2):137-54.

PMID:
15941617
7.

A summary of computational resources for protein phosphorylation.

Xue Y, Gao X, Cao J, Liu Z, Jin C, Wen L, Yao X, Ren J.

Curr Protein Pept Sci. 2010 Sep;11(6):485-96. Review.

PMID:
20491621
8.

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.

Rajewsky N, Vergassola M, Gaul U, Siggia ED.

BMC Bioinformatics. 2002 Oct 24;3:30. Epub 2002 Oct 24.

9.

An overview of the computational analyses and discovery of transcription factor binding sites.

Ladunga I.

Methods Mol Biol. 2010;674:1-22. doi: 10.1007/978-1-60761-854-6_1. Review.

PMID:
20827582
10.

Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome.

Khan MA, Soto-Jimenez LM, Howe T, Streit A, Sosinsky A, Stern CD.

Genesis. 2013 May;51(5):311-24. doi: 10.1002/dvg.22375. Epub 2013 Mar 30. Review.

11.

CoMoDis: composite motif discovery in mammalian genomes.

Donaldson IJ, Göttgens B.

Nucleic Acids Res. 2007;35(1):e1. Epub 2006 Nov 27.

13.

Assessing computational tools for the discovery of small RNA genes in bacteria.

Lu X, Goodrich-Blair H, Tjaden B.

RNA. 2011 Sep;17(9):1635-47. doi: 10.1261/rna.2689811. Epub 2011 Jul 18.

14.

The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites.

Harb OS, Roos DS.

Methods Mol Biol. 2015;1201:1-18. doi: 10.1007/978-1-4939-1438-8_1.

PMID:
25388105
15.

G =  MAT: linking transcription factor expression and DNA binding data.

Tretyakov K, Laur S, Vilo J.

PLoS One. 2011 Jan 31;6(1):e14559. doi: 10.1371/journal.pone.0014559.

16.

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.

J Mol Biol. 2001 May 25;309(1):99-120.

PMID:
11491305
17.

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.

Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D443-7. doi: 10.1093/nar/gkp910. Epub 2009 Nov 1.

18.

Computational prediction of protein-protein interactions.

Ehrenberger T, Cantley LC, Yaffe MB.

Methods Mol Biol. 2015;1278:57-75. doi: 10.1007/978-1-4939-2425-7_4.

19.

In silico prediction of transcriptional factor-binding sites.

Oshchepkov DY, Levitsky VG.

Methods Mol Biol. 2011;760:251-67. doi: 10.1007/978-1-61779-176-5_16.

PMID:
21780002
20.

A classification-based framework for predicting and analyzing gene regulatory response.

Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C.

BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S5.

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