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Improved Protein Decoy Selection via Non-Negative Matrix Factorization.
Akhter N, Kabir KL, Chennupati G, Vangara R, Alexandrov BS, Djidjev H, Shehu A. Akhter N, et al. Among authors: alexandrov bs. IEEE/ACM Trans Comput Biol Bioinform. 2022 May-Jun;19(3):1670-1682. doi: 10.1109/TCBB.2020.3049088. Epub 2022 Jun 3. IEEE/ACM Trans Comput Biol Bioinform. 2022. PMID: 33400654
Quantum annealing algorithms for Boolean tensor networks.
Pelofske E, Hahn G, O'Malley D, Djidjev HN, Alexandrov BS. Pelofske E, et al. Among authors: alexandrov bs. Sci Rep. 2022 May 20;12(1):8539. doi: 10.1038/s41598-022-12611-9. Sci Rep. 2022. PMID: 35595786 Free PMC article.
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.
Examining DNA Breathing with pyDNA-EPBD.
Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov BS. Kabir A, et al. Among authors: alexandrov bs. bioRxiv [Preprint]. 2023 Sep 12:2023.09.09.557010. doi: 10.1101/2023.09.09.557010. bioRxiv. 2023. PMID: 37745370 Free PMC article. Updated. Preprint.
Examining DNA breathing with pyDNA-EPBD.
Kabir A, Bhattarai M, Rasmussen KØ, Shehu A, Usheva A, Bishop AR, Alexandrov B. Kabir A, et al. Bioinformatics. 2023 Nov 1;39(11):btad699. doi: 10.1093/bioinformatics/btad699. Bioinformatics. 2023. PMID: 37991847 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.
40 results