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Predator Dormancy is a Stable Adaptive Strategy due to Parrondo's Paradox.

Tan ZX, Koh JM, Koonin EV, Cheong KH.

Adv Sci (Weinh). 2019 Dec 12;7(3):1901559. doi: 10.1002/advs.201901559. eCollection 2020 Feb.


A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes.

Subramaniam K, Behringer DC, Bojko J, Yutin N, Clark AS, Bateman KS, van Aerle R, Bass D, Kerr RC, Koonin EV, Stentiford GD, Waltzek TB.

mBio. 2020 Jan 14;11(1). pii: e02938-19. doi: 10.1128/mBio.02938-19.


Phages build anti-defence barriers.

Koonin EV, Krupovic M.

Nat Microbiol. 2020 Jan;5(1):8-9. doi: 10.1038/s41564-019-0635-y. No abstract available.


Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV.

Nat Rev Microbiol. 2020 Feb;18(2):67-83. doi: 10.1038/s41579-019-0299-x. Epub 2019 Dec 19. Review.


Crossing fitness valleys via double substitutions within codons.

Belinky F, Sela I, Rogozin IB, Koonin EV.

BMC Biol. 2019 Dec 16;17(1):105. doi: 10.1186/s12915-019-0727-4.


Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.

Iranzo J, Wolf YI, Koonin EV, Sela I.

Nat Commun. 2019 Nov 26;10(1):5376. doi: 10.1038/s41467-019-13429-2.


Virus-borne mini-CRISPR arrays are involved in interviral conflicts.

Medvedeva S, Liu Y, Koonin EV, Severinov K, Prangishvili D, Krupovic M.

Nat Commun. 2019 Nov 15;10(1):5204. doi: 10.1038/s41467-019-13205-2.


Reply to Hedrick and Klitz: High haplotype discovery rate in the HLA locus.

Louzoun Y, Lobkovsky AE, Levi L, Wolf YI, Maiers M, Gragert L, Alter I, Koonin EV.

Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23388-23389. doi: 10.1073/pnas.1916124116. Epub 2019 Oct 29. No abstract available.


Key role of recombination in evolutionary processes with migration between two habitats.

Saakian DB, Koonin EV, Cheong KH.

Phys Rev E. 2019 Sep;100(3-1):030401. doi: 10.1103/PhysRevE.100.030401.


A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk.

Auslander N, Wolf YI, Shabalina SA, Koonin EV.

Version 2. F1000Res. 2019 Jul 2 [revised 2019 Jan 1];8:1000. doi: 10.12688/f1000research.19590.2. eCollection 2019.


Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire.

Koonin EV, Makarova KS, Wolf YI, Krupovic M.

Nat Rev Genet. 2020 Feb;21(2):119-131. doi: 10.1038/s41576-019-0172-9. Epub 2019 Oct 14. Review.


On the feasibility of saltational evolution.

Katsnelson MI, Wolf YI, Koonin EV.

Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21068-21075. doi: 10.1073/pnas.1909031116. Epub 2019 Sep 30.


Systematic prediction of functionally linked genes in bacterial and archaeal genomes.

Shmakov SA, Faure G, Makarova KS, Wolf YI, Severinov KV, Koonin EV.

Nat Protoc. 2019 Oct;14(10):3013-3031. doi: 10.1038/s41596-019-0211-1. Epub 2019 Sep 13.


Translational coupling via termination-reinitiation in archaea and bacteria.

Huber M, Faure G, Laass S, Kolbe E, Seitz K, Wehrheim C, Wolf YI, Koonin EV, Soppa J.

Nat Commun. 2019 Sep 5;10(1):4006. doi: 10.1038/s41467-019-11999-9.


Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues.

Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, Faltas BM, Rubin MA, Geiger T, Koonin EV, Demichelis F, Horn D.

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16987-16996. doi: 10.1073/pnas.1908790116. Epub 2019 Aug 6.


Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids.

Kazlauskas D, Varsani A, Koonin EV, Krupovic M.

Nat Commun. 2019 Jul 31;10(1):3425. doi: 10.1038/s41467-019-11433-0.


Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea.

Shimosaka T, Makarova KS, Koonin EV, Atomi H.

mBio. 2019 Jul 23;10(4). pii: e01146-19. doi: 10.1128/mBio.01146-19.


Origin of programmed cell death from antiviral defense?

Koonin EV, Krupovic M.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16167-16169. doi: 10.1073/pnas.1910303116. Epub 2019 Jul 9. No abstract available.


Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.

Puigbò P, Wolf YI, Koonin EV.

Methods Mol Biol. 2019;1910:241-269. doi: 10.1007/978-1-4939-9074-0_8.


Multiplicative fitness, rapid haplotype discovery, and fitness decay explain evolution of human MHC.

Lobkovsky AE, Levi L, Wolf YI, Maiers M, Gragert L, Alter I, Louzoun Y, Koonin EV.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14098-14104. doi: 10.1073/pnas.1714436116. Epub 2019 Jun 21.


RNA-guided DNA insertion with CRISPR-associated transposases.

Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F.

Science. 2019 Jul 5;365(6448):48-53. doi: 10.1126/science.aax9181. Epub 2019 Jun 6.


CRISPR-Cas in mobile genetic elements: counter-defence and beyond.

Faure G, Shmakov SA, Yan WX, Cheng DR, Scott DA, Peters JE, Makarova KS, Koonin EV.

Nat Rev Microbiol. 2019 Aug;17(8):513-525. doi: 10.1038/s41579-019-0204-7.


Origin of viruses: primordial replicators recruiting capsids from hosts.

Krupovic M, Dolja VV, Koonin EV.

Nat Rev Microbiol. 2019 Jul;17(7):449-458. doi: 10.1038/s41579-019-0205-6. Review.


Corrigendum: Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages.

Stough JMA, Yutin N, Chaban YV, Moniruzzaman M, Gann ER, Pound HL, Steffen MM, Black JN, Koonin EV, Wilhelm SW, Short SM.

Front Microbiol. 2019 Apr 24;10:907. doi: 10.3389/fmicb.2019.00907. eCollection 2019.


Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts.

Makarova KS, Wolf YI, Karamycheva S, Zhang D, Aravind L, Koonin EV.

mBio. 2019 May 7;10(3). pii: e00715-19. doi: 10.1128/mBio.00715-19.


Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages.

Stough JMA, Yutin N, Chaban YV, Moniruzzaman M, Gann ER, Pound HL, Steffen MM, Black JN, Koonin EV, Wilhelm SW, Short SM.

Front Microbiol. 2019 Apr 5;10:703. doi: 10.3389/fmicb.2019.00703. eCollection 2019. Erratum in: Front Microbiol. 2019 Apr 24;10:907.


Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

Makarova KS, Wolf YI, Koonin EV.

CRISPR J. 2018 Oct;1(5):325-336. doi: 10.1089/crispr.2018.0033. Review.


In silico learning of tumor evolution through mutational time series.

Auslander N, Wolf YI, Koonin EV.

Proc Natl Acad Sci U S A. 2019 May 7;116(19):9501-9510. doi: 10.1073/pnas.1901695116. Epub 2019 Apr 23.


Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array.

Makarova KS, Karamycheva S, Shah SA, Vestergaard G, Garrett RA, Koonin EV.

FEMS Microbiol Lett. 2019 Apr 1;366(7). pii: fnz079. doi: 10.1093/femsle/fnz079.


Reply to Holmes and Duchêne, "Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?": Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless.

Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV.

mBio. 2019 Apr 16;10(2). pii: e00542-19. doi: 10.1128/mBio.00542-19. No abstract available.


Allele fixation probability in a Moran model with fluctuating fitness landscapes.

Saakian DB, Yakushkina T, Koonin EV.

Phys Rev E. 2019 Feb;99(2-1):022407. doi: 10.1103/PhysRevE.99.022407.


CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology.

Koonin EV.

Biol Philos. 2019;34(1):9. doi: 10.1007/s10539-018-9658-7. Epub 2019 Jan 19.


Origins and evolution of CRISPR-Cas systems.

Koonin EV, Makarova KS.

Philos Trans R Soc Lond B Biol Sci. 2019 May 13;374(1772):20180087. doi: 10.1098/rstb.2018.0087.


Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism.

Bäckström D, Yutin N, Jørgensen SL, Dharamshi J, Homa F, Zaremba-Niedwiedzka K, Spang A, Wolf YI, Koonin EV, Ettema TJG.

mBio. 2019 Mar 5;10(2). pii: e02497-18. doi: 10.1128/mBio.02497-18.


Reply to 'Evolutionary placement of Methanonatronarchaeia'.

Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciorda S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM, Koonin EV.

Nat Microbiol. 2019 Apr;4(4):560-561. doi: 10.1038/s41564-019-0358-0. No abstract available.


Classify viruses - the gain is worth the pain.

Kuhn JH, Wolf YI, Krupovic M, Zhang YZ, Maes P, Dolja VV, Koonin EV.

Nature. 2019 Feb;566(7744):318-320. doi: 10.1038/d41586-019-00599-8. No abstract available.


Integrated mobile genetic elements in Thaumarchaeota.

Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV.

Environ Microbiol. 2019 Jun;21(6):2056-2078. doi: 10.1111/1462-2920.14564. Epub 2019 Mar 18.


Grammar of protein domain architectures.

Yu L, Tanwar DK, Penha EDS, Wolf YI, Koonin EV, Basu MK.

Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3636-3645. doi: 10.1073/pnas.1814684116. Epub 2019 Feb 7.


Towards functional characterization of archaeal genomic dark matter.

Makarova KS, Wolf YI, Koonin EV.

Biochem Soc Trans. 2019 Feb 28;47(1):389-398. doi: 10.1042/BST20180560. Epub 2019 Feb 1. Review.


Engineering of CRISPR-Cas12b for human genome editing.

Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F.

Nat Commun. 2019 Jan 22;10(1):212. doi: 10.1038/s41467-018-08224-4.


Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism.

Koonin EV, Yutin N.

Adv Virus Res. 2019;103:167-202. doi: 10.1016/bs.aivir.2018.09.002. Epub 2018 Nov 10. Review.


Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve.

Berezovskaya F, Karev GP, Katsnelson MI, Wolf YI, Koonin EV.

Biol Direct. 2018 Dec 14;13(1):27. doi: 10.1186/s13062-018-0230-9.


Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.


Multiple evolutionary origins of giant viruses.

Koonin EV, Yutin N.

F1000Res. 2018 Nov 22;7. pii: F1000 Faculty Rev-1840. doi: 10.12688/f1000research.16248.1. eCollection 2018. Review.


Functionally diverse type V CRISPR-Cas systems.

Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV, Cheng DR, Scott DA.

Science. 2019 Jan 4;363(6422):88-91. doi: 10.1126/science.aav7271. Epub 2018 Dec 6.


Origins and Evolution of the Global RNA Virome.

Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV.

mBio. 2018 Nov 27;9(6). pii: e02329-18. doi: 10.1128/mBio.02329-18.


New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures.

Liu Y, Brandt D, Ishino S, Ishino Y, Koonin EV, Kalinowski J, Krupovic M, Prangishvili D.

Environ Microbiol. 2019 Jun;21(6):2002-2014. doi: 10.1111/1462-2920.14479. Epub 2019 Jan 8.


Criticality in tumor evolution and clinical outcome.

Persi E, Wolf YI, Leiserson MDM, Koonin EV, Ruppin E.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11101-E11110. doi: 10.1073/pnas.1807256115. Epub 2018 Nov 7.


A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition.

Mohr G, Silas S, Stamos JL, Makarova KS, Markham LM, Yao J, Lucas-Elío P, Sanchez-Amat A, Fire AZ, Koonin EV, Lambowitz AM.

Mol Cell. 2018 Nov 15;72(4):700-714.e8. doi: 10.1016/j.molcel.2018.09.013. Epub 2018 Oct 18.

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