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Items: 1 to 20 of 114

1.

Recognition models to predict DNA-binding specificities of homeodomain proteins.

Christensen RG, Enuameh MS, Noyes MB, Brodsky MH, Wolfe SA, Stormo GD.

Bioinformatics. 2012 Jun 15;28(12):i84-9. doi: 10.1093/bioinformatics/bts202.

2.

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.

Liu J, Stormo GD.

Bioinformatics. 2008 Sep 1;24(17):1850-7. doi: 10.1093/bioinformatics/btn331.

3.

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA.

Genome Res. 2013 Jun;23(6):928-40. doi: 10.1101/gr.151472.112.

4.

An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.

Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD.

Nucleic Acids Res. 2014 Apr;42(8):4800-12. doi: 10.1093/nar/gku132.

5.

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.

6.

ZiF-Predict: a web tool for predicting DNA-binding specificity in C2H2 zinc finger proteins.

Molparia B, Goyal K, Sarkar A, Kumar S, Sundar D.

Genomics Proteomics Bioinformatics. 2010 Jun;8(2):122-6. doi: 10.1016/S1672-0229(10)60013-7.

7.

Prediction of DNA-binding residues from protein sequence information using random forests.

Wang L, Yang MQ, Yang JY.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S1. doi: 10.1186/1471-2164-10-S1-S1.

8.
9.

Predicting DNA recognition by Cys2His2 zinc finger proteins.

Persikov AV, Osada R, Singh M.

Bioinformatics. 2009 Jan 1;25(1):22-9. doi: 10.1093/bioinformatics/btn580.

10.

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins.

Persikov AV, Singh M.

Nucleic Acids Res. 2014 Jan;42(1):97-108. doi: 10.1093/nar/gkt890.

11.

Combination of a zinc finger and homeodomain required for protein-interaction.

Smith GE, Darling DS.

Mol Biol Rep. 2003 Dec;30(4):199-206.

12.

PSSM-based prediction of DNA binding sites in proteins.

Ahmad S, Sarai A.

BMC Bioinformatics. 2005 Feb 19;6:33.

13.

Predicting DNA-binding specificities of eukaryotic transcription factors.

Schröder A, Eichner J, Supper J, Eichner J, Wanke D, Henneges C, Zell A.

PLoS One. 2010 Nov 30;5(11):e13876. doi: 10.1371/journal.pone.0013876.

14.

Predicting RNA-binding sites of proteins using support vector machines and evolutionary information.

Cheng CW, Su EC, Hwang JK, Sung TY, Hsu WL.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S6. doi: 10.1186/1471-2105-9-S12-S6.

15.

Covariation between homeodomain transcription factors and the shape of their DNA binding sites.

Dror I, Zhou T, Mandel-Gutfreund Y, Rohs R.

Nucleic Acids Res. 2014 Jan;42(1):430-41. doi: 10.1093/nar/gkt862.

16.

Deconvolving the recognition of DNA shape from sequence.

Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS.

Cell. 2015 Apr 9;161(2):307-18. doi: 10.1016/j.cell.2015.02.008.

17.

Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.

Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA.

Cell. 2008 Jun 27;133(7):1277-89. doi: 10.1016/j.cell.2008.05.023.

18.

Sequence-based prediction of DNA-binding residues in proteins with conservation and correlation information.

Ma X, Guo J, Liu HD, Xie JM, Sun X.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1766-75.

PMID:
22868682
19.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

20.

ZIFIBI: Prediction of DNA binding sites for zinc finger proteins.

Cho SY, Chung M, Park M, Park S, Lee YS.

Biochem Biophys Res Commun. 2008 May 9;369(3):845-8. doi: 10.1016/j.bbrc.2008.02.106.

PMID:
18325330

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