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Items: 23


Unsupervised Machine Learning for Analysis of Phase Separation in Ternary Lipid Mixture.

Löpez CA, Vesselinov VV, Gnanakaran S, Alexandrov BS.

J Chem Theory Comput. 2019 Oct 7. doi: 10.1021/acs.jctc.9b00074. [Epub ahead of print]


Nonnegative/Binary matrix factorization with a D-Wave quantum annealer.

O'Malley D, Vesselinov VV, Alexandrov BS, Alexandrov LB.

PLoS One. 2018 Dec 10;13(12):e0206653. doi: 10.1371/journal.pone.0206653. eCollection 2018.


Nonnegative tensor factorization for contaminant source identification.

Vesselinov VV, Alexandrov BS, O'Malley D.

J Contam Hydrol. 2019 Jan;220:66-97. doi: 10.1016/j.jconhyd.2018.11.010. Epub 2018 Dec 4.


Nonnegative Matrix Factorization for identification of unknown number of sources emitting delayed signals.

Iliev FL, Stanev VG, Vesselinov VV, Alexandrov BS.

PLoS One. 2018 Mar 8;13(3):e0193974. doi: 10.1371/journal.pone.0193974. eCollection 2018.


Contaminant source identification using semi-supervised machine learning.

Vesselinov VV, Alexandrov BS, O'Malley D.

J Contam Hydrol. 2018 May;212:134-142. doi: 10.1016/j.jconhyd.2017.11.002. Epub 2017 Nov 8.


Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization.

Alexandrov LB, Rasmussen KØ, Bishop AR, Alexandrov BS.

Sci Rep. 2017 Aug 29;7(1):9731. doi: 10.1038/s41598-017-09537-y.


Dynamical Model of Drug Accumulation in Bacteria: Sensitivity Analysis and Experimentally Testable Predictions.

Vesselinova N, Alexandrov BS, Wall ME.

PLoS One. 2016 Nov 8;11(11):e0165899. doi: 10.1371/journal.pone.0165899. eCollection 2016.


The role of structural parameters in DNA cyclization.

Alexandrov LB, Bishop AR, Rasmussen KØ, Alexandrov BS.

BMC Bioinformatics. 2016 Feb 4;17:68. doi: 10.1186/s12859-016-0897-9.


A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder.

Duan J, Shi J, Fiorentino A, Leites C, Chen X, Moy W, Chen J, Alexandrov BS, Usheva A, He D, Freda J, O'Brien NL; Molecular Genetics of Schizophrenia collaboration; Genomic Psychiatric Cohort consortium, McQuillin A, Sanders AR, Gershon ES, DeLisi LE, Bishop AR, Gurling HM, Pato MT, Levinson DF, Kendler KS, Pato CN, Gejman PV.

Am J Hum Genet. 2014 Dec 4;95(6):744-53. doi: 10.1016/j.ajhg.2014.11.001. Epub 2014 Nov 26.


Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells.

Alexandrov BS, Phipps ML, Alexandrov LB, Booshehri LG, Erat A, Zabolotny J, Mielke CH, Chen HT, Rodriguez G, Rasmussen KØ, Martinez JS, Bishop AR, Usheva A.

Sci Rep. 2013;3:1184. doi: 10.1038/srep01184. Epub 2013 Jan 31.


Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing.

Alexandrov BS, Stanev VG, Bishop AR, Rasmussen KØ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Dec;86(6 Pt 1):061913. Epub 2012 Dec 26.


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.

PLoS Comput Biol. 2013;9(1):e1002881. doi: 10.1371/journal.pcbi.1002881. Epub 2013 Jan 17.


DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells.

Alexandrov BS, Fukuyo Y, Lange M, Horikoshi N, Gelev V, Rasmussen KØ, Bishop AR, Usheva A.

Nucleic Acids Res. 2012 Nov 1;40(20):10116-23. doi: 10.1093/nar/gks758. Epub 2012 Aug 16.


Non-thermal effects of terahertz radiation on gene expression in mouse stem cells.

Alexandrov BS, Rasmussen KØ, Bishop AR, Usheva A, Alexandrov LB, Chong S, Dagon Y, Booshehri LG, Mielke CH, Phipps ML, Martinez JS, Chen HT, Rodriguez G.

Biomed Opt Express. 2011 Sep 1;2(9):2679-89. doi: 10.1364/BOE.2.002679. Epub 2011 Aug 23.


DNA dynamics is likely to be a factor in the genomic nucleotide repeats expansions related to diseases.

Alexandrov BS, Valtchinov VI, Alexandrov LB, Gelev V, Dagon Y, Bock J, Kohane IS, Rasmussen KØ, Bishop AR, Usheva A.

PLoS One. 2011;6(5):e19800. doi: 10.1371/journal.pone.0019800. Epub 2011 May 20. Erratum in: PLoS One. 2011;6(6). doi:10.1371/annotation/f68e9b71-cae1-4f9c-9308-a444d3ea753d.


Feigenbaum cascade of discrete breathers in a model of DNA.

Maniadis P, Alexandrov BS, Bishop AR, Rasmussen KØ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jan;83(1 Pt 1):011904. Epub 2011 Jan 11.


Mammalian stem cells reprogramming in response to terahertz radiation.

Bock J, Fukuyo Y, Kang S, Phipps ML, Alexandrov LB, Rasmussen KØ, Bishop AR, Rosen ED, Martinez JS, Chen HT, Rodriguez G, Alexandrov BS, Usheva A.

PLoS One. 2010 Dec 31;5(12):e15806. doi: 10.1371/journal.pone.0015806.


DNA Breathing Dynamics in the Presence of a Terahertz Field.

Alexandrov BS, Gelev V, Bishop AR, Usheva A, Rasmussen KO.

Phys Lett A. 2010 Feb 22;374(10):1214.


DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation.

Alexandrov BS, Gelev V, Yoo SW, Alexandrov LB, Fukuyo Y, Bishop AR, Rasmussen KØ, Usheva A.

Nucleic Acids Res. 2010 Apr;38(6):1790-5. doi: 10.1093/nar/gkp1084. Epub 2009 Dec 17.


Toward a detailed description of the thermally induced dynamics of the core promoter.

Alexandrov BS, Gelev V, Yoo SW, Bishop AR, Rasmussen KØ, Usheva A.

PLoS Comput Biol. 2009 Mar;5(3):e1000313. doi: 10.1371/journal.pcbi.1000313. Epub 2009 Mar 13.


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.

Nucleic Acids Res. 2009 Apr;37(7):2405-10. doi: 10.1093/nar/gkp016. Epub 2009 Mar 5.


Bubble statistics and dynamics in double-stranded DNA.

Alexandrov BS, Wille LT, Rasmussen KØ, Bishop AR, Blagoev KB.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Nov;74(5 Pt 1):050901. Epub 2006 Nov 1.


Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition.

Blagoev KB, Alexandrov BS, Goodwin EH, Bishop AR.

DNA Repair (Amst). 2006 Jul 13;5(7):863-7. Epub 2006 Jun 13.


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