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Results: 1 to 20 of 133

1.

A force-based, parallel assay for the quantification of protein-DNA interactions.

Limmer K, Pippig DA, Aschenbrenner D, Gaub HE.

PLoS One. 2014 Feb 27;9(2):e89626. doi: 10.1371/journal.pone.0089626. eCollection 2014.

PMID:
24586920
[PubMed - in process]
Free PMC Article
2.

Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data.

Zeigler RD, Cohen BA.

Nucleic Acids Res. 2014 Feb;42(4):2224-34. doi: 10.1093/nar/gkt1230. Epub 2013 Nov 27.

PMID:
24288374
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Protein-DNA binding: complexities and multi-protein codes.

Siggers T, Gordân R.

Nucleic Acids Res. 2014 Feb;42(4):2099-111. doi: 10.1093/nar/gkt1112. Epub 2013 Nov 16. Review.

PMID:
24243859
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Predicting tissue specific transcription factor binding sites.

Zhong S, He X, Bar-Joseph Z.

BMC Genomics. 2013 Nov 15;14:796. doi: 10.1186/1471-2164-14-796.

PMID:
24238150
[PubMed - in process]
Free PMC Article
5.

An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example.

Gu G, Wang T, Yang Y, Xu X, Wang J.

PLoS One. 2013 Oct 10;8(10):e76109. doi: 10.1371/journal.pone.0076109. eCollection 2013.

PMID:
24130762
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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. Epub 2013 Oct 3.

PMID:
24097433
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The next generation of transcription factor binding site prediction.

Mathelier A, Wasserman WW.

PLoS Comput Biol. 2013;9(9):e1003214. doi: 10.1371/journal.pcbi.1003214. Epub 2013 Sep 5.

PMID:
24039567
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Navigating the transcriptional roadmap regulating plant secondary cell wall deposition.

Hussey SG, Mizrachi E, Creux NM, Myburg AA.

Front Plant Sci. 2013 Aug 29;4:325. doi: 10.3389/fpls.2013.00325. Review.

PMID:
24009617
[PubMed]
Free PMC Article
9.

Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome.

Morozov VY, Ioshikhes IP.

PLoS One. 2013 Aug 6;8(8):e68712. doi: 10.1371/journal.pone.0068712. Print 2013.

PMID:
23936309
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence.

Platt JM, Ryvkin P, Wanat JJ, Donahue G, Ricketts MD, Barrett SP, Waters HJ, Song S, Chavez A, Abdallah KO, Master SR, Wang LS, Johnson FB.

Genes Dev. 2013 Jun 15;27(12):1406-20. doi: 10.1101/gad.218776.113. Epub 2013 Jun 11.

PMID:
23756653
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

STAT1:DNA sequence-dependent binding modulation by phosphorylation, protein:protein interactions and small-molecule inhibition.

Bonham AJ, Wenta N, Osslund LM, Prussin AJ 2nd, Vinkemeier U, Reich NO.

Nucleic Acids Res. 2013 Jan;41(2):754-63. doi: 10.1093/nar/gks1085. Epub 2012 Nov 24.

PMID:
23180800
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A multi-parametric flow cytometric assay to analyze DNA-protein interactions.

Arbab M, Mahony S, Cho H, Chick JM, Rolfe PA, van Hoff JP, Morris VW, Gygi SP, Maas RL, Gifford DK, Sherwood RI.

Nucleic Acids Res. 2013 Jan;41(2):e38. doi: 10.1093/nar/gks1034. Epub 2012 Nov 11.

PMID:
23143268
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

TATA binding proteins can recognize nontraditional DNA sequences.

Ahn S, Huang CL, Ozkumur E, Zhang X, Chinnala J, Yalcin A, Bandyopadhyay S, Russek S, Unlü MS, DeLisi C, Irani RJ.

Biophys J. 2012 Oct 3;103(7):1510-7. doi: 10.1016/j.bpj.2012.08.030. Epub 2012 Oct 2.

PMID:
23062343
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.

PMID:
22955618
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.

Dümcke S, Seizl M, Etzold S, Pirkl N, Martin DE, Cramer P, Tresch A.

Nucleic Acids Res. 2012 Oct;40(18):8883-92. doi: 10.1093/nar/gks695. Epub 2012 Jul 25.

PMID:
22844089
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions.

Nakaki R, Kang J, Tateno M.

Nucleic Acids Res. 2012 Oct;40(18):8835-48. doi: 10.1093/nar/gks642. Epub 2012 Jul 13.

PMID:
22798493
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.

Gabdoulline R, Eckweiler D, Kel A, Stegmaier P.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W180-5. doi: 10.1093/nar/gks551. Epub 2012 Jun 11.

PMID:
22693215
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Improved models for transcription factor binding site identification using nonindependent interactions.

Zhao Y, Ruan S, Pandey M, Stormo GD.

Genetics. 2012 Jul;191(3):781-90. doi: 10.1534/genetics.112.138685. Epub 2012 Apr 13.

PMID:
22505627
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.

Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD.

Nature. 2012 Apr 11;484(7393):251-5. doi: 10.1038/nature10985.

PMID:
22498630
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Thermodynamic state ensemble models of cis-regulation.

Sherman MS, Cohen BA.

PLoS Comput Biol. 2012;8(3):e1002407. doi: 10.1371/journal.pcbi.1002407. Epub 2012 Mar 29.

PMID:
22479169
[PubMed - indexed for MEDLINE]
Free PMC Article

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