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A nonlinear dynamic model of DNA with a sequence-dependent stacking term.
Alexandrov BS, Gelev V, Monisova Y, Alexandrov LB, Bishop AR, Rasmussen KØ, Usheva A. Alexandrov BS, et al. Among authors: bishop ar. Nucleic Acids Res. 2009 Apr;37(7):2405-10. doi: 10.1093/nar/gkp016. Epub 2009 Mar 5. Nucleic Acids Res. 2009. PMID: 19264801 Free PMC article.
Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.
Nowak-Lovato K, Alexandrov LB, Banisadr A, Bauer AL, Bishop AR, Usheva A, Mu F, Hong-Geller E, Rasmussen KØ, Hlavacek WS, Alexandrov BS. Nowak-Lovato K, et al. Among authors: bishop ar. PLoS Comput Biol. 2013;9(1):e1002881. doi: 10.1371/journal.pcbi.1002881. Epub 2013 Jan 17. PLoS Comput Biol. 2013. PMID: 23341768 Free PMC article.
Healing length and bubble formation in DNA.
Rapti Z, Smerzi A, Rasmussen KO, Bishop AR, Choi CH, Usheva A. Rapti Z, et al. Among authors: bishop ar. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 May;73(5 Pt 1):051902. doi: 10.1103/PhysRevE.73.051902. Epub 2006 May 4. Phys Rev E Stat Nonlin Soft Matter Phys. 2006. PMID: 16802962
Bubble statistics and dynamics in double-stranded DNA.
Alexandrov BS, Wille LT, Rasmussen KØ, Bishop AR, Blagoev KB. Alexandrov BS, et al. Among authors: bishop ar. Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Nov;74(5 Pt 1):050901. doi: 10.1103/PhysRevE.74.050901. Epub 2006 Nov 1. Phys Rev E Stat Nonlin Soft Matter Phys. 2006. PMID: 17279870
Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing.
Alexandrov BS, Stanev VG, Bishop AR, Rasmussen KØ. Alexandrov BS, et al. Among authors: bishop ar. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Dec;86(6 Pt 1):061913. doi: 10.1103/PhysRevE.86.061913. Epub 2012 Dec 26. Phys Rev E Stat Nonlin Soft Matter Phys. 2012. PMID: 23367981
Profiling the thermodynamic softness of adenoviral promoters.
Choi CH, Rapti Z, Gelev V, Hacker MR, Alexandrov B, Park EJ, Park JS, Horikoshi N, Smerzi A, Rasmussen KØ, Bishop AR, Usheva A. Choi CH, et al. Among authors: bishop ar. Biophys J. 2008 Jul;95(2):597-608. doi: 10.1529/biophysj.107.123471. Epub 2008 Apr 4. Biophys J. 2008. PMID: 18390611 Free PMC article.
Nonlinearity in DNA and its relation to specific functions.
Alexandrov B, Rasmussen KØ, Bishop AR. Alexandrov B, et al. Among authors: bishop ar. J Biol Phys. 2009 Feb;35(1):31-41. doi: 10.1007/s10867-009-9125-4. Epub 2009 Feb 25. J Biol Phys. 2009. PMID: 19669567 Free PMC article.
282 results