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Winnowing sequences from a database search.
Berman P, Zhang Z, Wolf YI, Koonin EV, Miller W. Berman P, et al. J Comput Biol. 2000 Feb-Apr;7(1-2):293-302. doi: 10.1089/10665270050081531. J Comput Biol. 2000. PMID: 10890403
Genome sequence comparison and scenarios for gene rearrangements: a test case.
Hannenhalli S, Chappey C, Koonin EV, Pevzner PA. Hannenhalli S, et al. Genomics. 1995 Nov 20;30(2):299-311. doi: 10.1006/geno.1995.9873. Genomics. 1995. PMID: 8586431
Protein sequence similarity searches using patterns as seeds.
Zhang Z, Schäffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF. Zhang Z, et al. Nucleic Acids Res. 1998 Sep 1;26(17):3986-90. doi: 10.1093/nar/26.17.3986. Nucleic Acids Res. 1998. PMID: 9705509 Free PMC article.
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Schäffer AA, et al. Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. doi: 10.1093/nar/29.14.2994. Nucleic Acids Res. 2001. PMID: 11452024 Free PMC article. Review.
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.
Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV. Shmakov S, et al. Mol Cell. 2015 Nov 5;60(3):385-97. doi: 10.1016/j.molcel.2015.10.008. Epub 2015 Oct 22. Mol Cell. 2015. PMID: 26593719 Free PMC article.
Global Organization and Proposed Megataxonomy of the Virus World.
Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Koonin EV, et al. Microbiol Mol Biol Rev. 2020 Mar 4;84(2):e00061-19. doi: 10.1128/MMBR.00061-19. Print 2020 May 20. Microbiol Mol Biol Rev. 2020. PMID: 32132243 Review.
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