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Items: 1 to 20 of 25

1.

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

Annala M, Laurila K, Lähdesmäki H, Nykter M.

PLoS One. 2011;6(5):e20059. doi: 10.1371/journal.pone.0020059. Epub 2011 May 26.

2.

The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.

3.

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10. doi: 10.1093/nar/gkp950. Epub 2009 Nov 11.

4.

PROSITE, a protein domain database for functional characterization and annotation.

Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N.

Nucleic Acids Res. 2010 Jan;38(Database issue):D161-6. doi: 10.1093/nar/gkp885. Epub 2009 Oct 25.

5.

The Universal Protein Resource (UniProt) in 2010.

UniProt Consortium.

Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. doi: 10.1093/nar/gkp846. Epub 2009 Oct 20.

6.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538. Review.

PMID:
19274049
7.

Predicting the binding preference of transcription factors to individual DNA k-mers.

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR.

Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16.

8.

SMART 6: recent updates and new developments.

Letunic I, Doerks T, Bork P.

Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. doi: 10.1093/nar/gkn808. Epub 2008 Oct 31.

9.

InterPro: the integrative protein signature database.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

10.

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Newburger DE, Bulyk ML.

Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82. doi: 10.1093/nar/gkn660. Epub 2008 Oct 8.

11.

Probabilistic inference of transcription factor binding from multiple data sources.

Lähdesmäki H, Rust AG, Shmulevich I.

PLoS One. 2008 Mar 26;3(3):e1820. doi: 10.1371/journal.pone.0001820.

12.
13.

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML.

Nat Biotechnol. 2006 Nov;24(11):1429-35. Epub 2006 Sep 24.

14.

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

Foat BC, Morozov AV, Bussemaker HJ.

Bioinformatics. 2006 Jul 15;22(14):e141-9.

PMID:
16873464
15.

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.

Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10.

16.

WebLogo: a sequence logo generator.

Crooks GE, Hon G, Chandonia JM, Brenner SE.

Genome Res. 2004 Jun;14(6):1188-90.

17.

Applied bioinformatics for the identification of regulatory elements.

Wasserman WW, Sandelin A.

Nat Rev Genet. 2004 Apr;5(4):276-87. Review. No abstract available.

PMID:
15131651
18.

INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling.

Thijs G, Moreau Y, De Smet F, Mathys J, Lescot M, Rombauts S, Rouze P, De Moor B, Marchal K.

Bioinformatics. 2002 Feb;18(2):331-2.

PMID:
11847086
19.

Identifying regulatory networks by combinatorial analysis of promoter elements.

Pilpel Y, Sudarsanam P, Church GM.

Nat Genet. 2001 Oct;29(2):153-9.

PMID:
11547334
20.

The TRANSFAC system on gene expression regulation.

Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Prüss M, Schacherer F, Thiele S, Urbach S.

Nucleic Acids Res. 2001 Jan 1;29(1):281-3.

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