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Items: 1 to 20 of 96

1.

Precise physical models of protein-DNA interaction from high-throughput data.

Kinney JB, Tkacik G, Callan CG Jr.

Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):501-6. Epub 2006 Dec 29.

2.

Ab initio prediction of transcription factor binding sites.

Liu LA, Bader JS.

Pac Symp Biocomput. 2007:484-95.

3.

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.

Le DD, Shimko TC, Aditham AK, Keys AM, Longwell SA, Orenstein Y, Fordyce PM.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3702-E3711. doi: 10.1073/pnas.1715888115. Epub 2018 Mar 27.

4.

Thermodynamics and specificity of the Mbp1-DNA interaction.

Deleeuw L, Tchernatynskaia AV, Lane AN.

Biochemistry. 2008 Jun 17;47(24):6378-85. doi: 10.1021/bi702339q. Epub 2008 May 21.

PMID:
18491920
5.

Biophysical fitness landscapes for transcription factor binding sites.

Haldane A, Manhart M, Morozov AV.

PLoS Comput Biol. 2014 Jul 10;10(7):e1003683. doi: 10.1371/journal.pcbi.1003683. eCollection 2014 Jul.

6.

Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site.

Cranz S, Berger C, Baici A, Jelesarov I, Bosshard HR.

Biochemistry. 2004 Jan 27;43(3):718-27.

PMID:
14730976
7.

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.

8.

Physical constraints and functional characteristics of transcription factor-DNA interaction.

Gerland U, Moroz JD, Hwa T.

Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12015-20. Epub 2002 Sep 6.

9.

Protein binding microarrays for the characterization of DNA-protein interactions.

Bulyk ML.

Adv Biochem Eng Biotechnol. 2007;104:65-85. Review.

10.

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

Ozonov EA, van Nimwegen E.

PLoS Comput Biol. 2013;9(8):e1003181. doi: 10.1371/journal.pcbi.1003181. Epub 2013 Aug 22.

11.

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.

Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB.

Genome Biol. 2004;5(12):R98. Epub 2004 Nov 30.

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Facilitated dissociation of transcription factors from single DNA binding sites.

Kamar RI, Banigan EJ, Erbas A, Giuntoli RD, Olvera de la Cruz M, Johnson RC, Marko JF.

Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):E3251-E3257. doi: 10.1073/pnas.1701884114. Epub 2017 Mar 31.

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Genome-wide inference of transcription factor-DNA binding specificity in cell regeneration using a combination strategy.

Wang X, Zhang A, Ren W, Chen C, Dong J.

Chem Biol Drug Des. 2012 Nov;80(5):734-44. doi: 10.1111/cbdd.12013. Epub 2012 Sep 10.

PMID:
22863142
19.

Stability selection for regression-based models of transcription factor-DNA binding specificity.

Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gordân R.

Bioinformatics. 2013 Jul 1;29(13):i117-25. doi: 10.1093/bioinformatics/btt221.

20.

Identifying cooperative transcription factors in yeast using multiple data sources.

Lai FJ, Jhu MH, Chiu CC, Huang YM, Wu WS.

BMC Syst Biol. 2014;8 Suppl 5:S2. doi: 10.1186/1752-0509-8-S5-S2. Epub 2014 Dec 12.

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