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Items: 1 to 20 of 85

1.

Physical aspects of precision in genetic regulation.

Tamari Z, Barkai N, Fouxon I.

J Biol Phys. 2011 Mar;37(2):213-25. doi: 10.1007/s10867-010-9208-2. Epub 2010 Nov 19.

2.

Diffusion, dimensionality, and noise in transcriptional regulation.

Tkacik G, Bialek W.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 May;79(5 Pt 1):051901. Epub 2009 May 4.

PMID:
19518474
3.

Spatial effects on the speed and reliability of protein-DNA search.

Wunderlich Z, Mirny LA.

Nucleic Acids Res. 2008 Jun;36(11):3570-8. doi: 10.1093/nar/gkn173. Epub 2008 May 3.

4.

Facilitated diffusion framework for transcription factor search with conformational changes.

Cartailler J, Reingruber J.

Phys Biol. 2015 Jul 22;12(4):046012. doi: 10.1088/1478-3975/12/4/046012.

PMID:
26200216
5.

Obstacle bypass in protein motion along DNA by two-dimensional rather than one-dimensional sliding.

Kampmann M.

J Biol Chem. 2004 Sep 10;279(37):38715-20. Epub 2004 Jul 2.

6.

System size reduction in stochastic simulations of the facilitated diffusion mechanism.

Zabet NR.

BMC Syst Biol. 2012 Sep 8;6:121. doi: 10.1186/1752-0509-6-121.

7.

Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites.

Rezania V, Tuszynski J, Hendzel M.

Phys Biol. 2007 Nov 21;4(4):256-67. doi: 10.1088/1478-3975/4/4/003.

PMID:
18185004
8.

Nonspecific transcription factor binding can reduce noise in the expression of downstream proteins.

Soltani M, Bokes P, Fox Z, Singh A.

Phys Biol. 2015 Aug 12;12(5):055002. doi: 10.1088/1478-3975/12/5/055002.

PMID:
26267711
9.

Are DNA transcription factor proteins maxwellian demons?

Hu L, Grosberg AY, Bruinsma R.

Biophys J. 2008 Aug;95(3):1151-6. doi: 10.1529/biophysj.108.129825. Epub 2008 May 2.

10.

The effects of transcription factor competition on gene regulation.

Zabet NR, Adryan B.

Front Genet. 2013 Oct 7;4:197. doi: 10.3389/fgene.2013.00197. eCollection 2013.

11.

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.

Dror I, Rohs R, Mandel-Gutfreund Y.

Bioessays. 2016 Jul;38(7):605-12. doi: 10.1002/bies.201600005. Epub 2016 May 19.

12.

Transcription factor search for a DNA promoter in a three-state model.

Reingruber J, Holcman D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Aug;84(2 Pt 1):020901. Epub 2011 Aug 8.

PMID:
21928941
13.

Sequence-dependent sliding kinetics of p53.

Leith JS, Tafvizi A, Huang F, Uspal WE, Doyle PS, Fersht AR, Mirny LA, van Oijen AM.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16552-7. doi: 10.1073/pnas.1120452109. Epub 2012 Sep 25.

14.

Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression.

Paijmans J, ten Wolde PR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Sep;90(3):032708. Epub 2014 Sep 25.

PMID:
25314474
15.

Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data.

Tabaka M, Burdzy K, HoƂyst R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Aug;92(2):022721. Epub 2015 Aug 28.

PMID:
26382446
16.

Asymmetric DNA-search dynamics by symmetric dimeric proteins.

Khazanov N, Marcovitz A, Levy Y.

Biochemistry. 2013 Aug 13;52(32):5335-44. doi: 10.1021/bi400357m. Epub 2013 Jul 31.

PMID:
23866074
17.

An end to 40 years of mistakes in DNA-protein association kinetics?

Halford SE.

Biochem Soc Trans. 2009 Apr;37(Pt 2):343-8. doi: 10.1042/BST0370343. Review.

PMID:
19290859
18.

Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states.

Bauer M, Metzler R.

Biophys J. 2012 May 16;102(10):2321-30. doi: 10.1016/j.bpj.2012.04.008. Epub 2012 May 15.

19.

Stochastic modeling of gene activation and applications to cell regulation.

Malherbe G, Holcman D.

J Theor Biol. 2011 Feb 21;271(1):51-63. doi: 10.1016/j.jtbi.2010.11.032. Epub 2010 Dec 1.

PMID:
21129382
20.

The influence of transcription factor competition on the relationship between occupancy and affinity.

Zabet NR, Foy R, Adryan B.

PLoS One. 2013 Sep 27;8(9):e73714. doi: 10.1371/journal.pone.0073714. eCollection 2013.

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