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Protein structural motifs in prediction and design.
Mackenzie CO, Grigoryan G. Mackenzie CO, et al. Curr Opin Struct Biol. 2017 Jun;44:161-167. doi: 10.1016/j.sbi.2017.03.012. Epub 2017 Apr 28. Curr Opin Struct Biol. 2017. PMID: 28460216 Free PMC article. Review.
Tertiary alphabet for the observable protein structural universe.
Mackenzie CO, Zhou J, Grigoryan G. Mackenzie CO, et al. Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7438-E7447. doi: 10.1073/pnas.1607178113. Epub 2016 Nov 3. Proc Natl Acad Sci U S A. 2016. PMID: 27810958 Free PMC article.
Large-scale design and refinement of stable proteins using sequence-only models.
Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, Zaitzeff A, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewart LJ, Baker D, Klavins E. Singer JM, et al. Among authors: mackenzie co. PLoS One. 2022 Mar 14;17(3):e0265020. doi: 10.1371/journal.pone.0265020. eCollection 2022. PLoS One. 2022. PMID: 35286324 Free PMC article.
OrbId: Origin-based identification of microRNA targets.
Filshtein TJ, Mackenzie CO, Dale MD, Dela-Cruz PS, Ernst DM, Frankenberger EA, He C, Heath KL, Jones AS, Jones DK, King ER, Maher MB, Mitchell TJ, Morgan RR, Sirobhushanam S, Halkyard SD, Tiwari KB, Rubin DA, Borchert GM, Larson ED. Filshtein TJ, et al. Among authors: mackenzie co. Mob Genet Elements. 2012 Jul 1;2(4):184-192. doi: 10.4161/mge.21617. Mob Genet Elements. 2012. PMID: 23087843 Free PMC article.