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Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor.
Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Islam SMA, et al. Among authors: alexandrov bs. Cell Genom. 2022 Nov 9;2(11):None. doi: 10.1016/j.xgen.2022.100179. Cell Genom. 2022. PMID: 36388765 Free PMC article.
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: alexandrov lb. 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: alexandrov bs, alexandrov lb. 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.
The role of structural parameters in DNA cyclization.
Alexandrov LB, Bishop AR, Rasmussen KØ, Alexandrov BS. Alexandrov LB, et al. Among authors: alexandrov bs. BMC Bioinformatics. 2016 Feb 4;17:68. doi: 10.1186/s12859-016-0897-9. BMC Bioinformatics. 2016. PMID: 26846597 Free PMC article.
Nonnegative/Binary matrix factorization with a D-Wave quantum annealer.
O'Malley D, Vesselinov VV, Alexandrov BS, Alexandrov LB. O'Malley D, et al. Among authors: alexandrov bs, alexandrov lb. PLoS One. 2018 Dec 10;13(12):e0206653. doi: 10.1371/journal.pone.0206653. eCollection 2018. PLoS One. 2018. PMID: 30532243 Free PMC article.
The genomic and epigenomic evolutionary history of papillary renal cell carcinomas.
Zhu B, Poeta ML, Costantini M, Zhang T, Shi J, Sentinelli S, Zhao W, Pompeo V, Cardelli M, Alexandrov BS, Otlu B, Hua X, Jones K, Brodie S, Dabrowska ME, Toro JR, Yeager M, Wang M, Hicks B, Alexandrov LB, Brown KM, Wedge DC, Chanock S, Fazio VM, Gallucci M, Landi MT. Zhu B, et al. Among authors: alexandrov bs. Nat Commun. 2020 Jun 18;11(1):3096. doi: 10.1038/s41467-020-16546-5. Nat Commun. 2020. PMID: 32555180 Free PMC article.
37 results