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Items: 1 to 50 of 850

1.

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 Jun 6. pii: eaax9181. doi: 10.1126/science.aax9181. [Epub ahead of print]

PMID:
31171706
2.

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 Jun 5. doi: 10.1038/s41579-019-0204-7. [Epub ahead of print]

PMID:
31165781
3.

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.

PMID:
31142823
4.

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.

5.
6.

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.

7.

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.

8.

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

Makarova KS, Wolf YI, Koonin EV.

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

PMID:
31021272
9.

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.

10.

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.

PMID:
30993331
11.

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.

12.

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.

PMID:
30934266
13.

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.

14.

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.

15.

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.

16.

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.

PMID:
30804545
17.

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.

PMID:
30787460
18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

PMID:
30635076
23.

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.

24.

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.

PMID:
30556814
25.

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.

26.

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.

PMID:
30523077
27.

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.

28.

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.

PMID:
30451355
29.

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.

30.

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.

PMID:
30344094
31.

Anti-CRISPRs on the march.

Koonin EV, Makarova KS.

Science. 2018 Oct 12;362(6411):156-157. doi: 10.1126/science.aav2440. No abstract available.

PMID:
30309933
32.

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons.

Kozlenkov A, Li J, Apontes P, Hurd YL, Byne WM, Koonin EV, Wegner M, Mukamel EA, Dracheva S.

Sci Adv. 2018 Sep 26;4(9):eaau6190. doi: 10.1126/sciadv.aau6190. eCollection 2018 Sep.

33.

Open questions: CRISPR biology.

Koonin EV.

BMC Biol. 2018 Sep 24;16(1):95. doi: 10.1186/s12915-018-0565-9.

34.

Environmental microbiology and metagenomics: the Brave New World is here, what's next?

Koonin EV.

Environ Microbiol. 2018 Dec;20(12):4210-4212. doi: 10.1111/1462-2920.14403. Epub 2018 Oct 15. No abstract available.

PMID:
30198178
35.

CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity.

Faure G, Makarova KS, Koonin EV.

J Mol Biol. 2019 Jan 4;431(1):3-20. doi: 10.1016/j.jmb.2018.08.030. Epub 2018 Sep 5. Review.

36.

Physical foundations of biological complexity.

Wolf YI, Katsnelson MI, Koonin EV.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8678-E8687. doi: 10.1073/pnas.1807890115. Epub 2018 Aug 27.

37.

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems.

Faure G, Shmakov SA, Makarova KS, Wolf YI, Crawley AB, Barrangou R, Koonin EV.

RNA Biol. 2019 Apr;16(4):435-448. doi: 10.1080/15476286.2018.1493331. Epub 2018 Aug 14.

38.

The depths of virus exaptation.

Koonin EV, Krupovic M.

Curr Opin Virol. 2018 Aug;31:1-8. doi: 10.1016/j.coviro.2018.07.011. Epub 2018 Jul 30. Review.

PMID:
30071360
39.

Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X.

Nat Microbiol. 2018 Sep;3(9):1076. doi: 10.1038/s41564-018-0184-9.

PMID:
29934592
40.

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics.

Pushkarev A, Inoue K, Larom S, Flores-Uribe J, Singh M, Konno M, Tomida S, Ito S, Nakamura R, Tsunoda SP, Philosof A, Sharon I, Yutin N, Koonin EV, Kandori H, Béjà O.

Nature. 2018 Jun;558(7711):595-599. doi: 10.1038/s41586-018-0225-9. Epub 2018 Jun 20.

PMID:
29925949
41.

Purifying and positive selection in the evolution of stop codons.

Belinky F, Babenko VN, Rogozin IB, Koonin EV.

Sci Rep. 2018 Jun 18;8(1):9260. doi: 10.1038/s41598-018-27570-3.

42.

Cancer-mutation network and the number and specificity of driver mutations.

Iranzo J, Martincorena I, Koonin EV.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E6010-E6019. doi: 10.1073/pnas.1803155115. Epub 2018 Jun 12.

43.

Hunting for Treasure Chests in Microbial Defense Islands.

Koonin EV.

Mol Cell. 2018 Jun 7;70(5):761-762. doi: 10.1016/j.molcel.2018.05.025. Epub 2018 Jun 7.

44.

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis.

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

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):E5307-E5316. doi: 10.1073/pnas.1803440115. Epub 2018 May 21.

45.

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov.

Sorokin DY, Merkel AY, Abbas B, Makarova KS, Rijpstra WIC, Koenen M, Sinninghe Damsté JS, Galinski EA, Koonin EV, van Loosdrecht MCM.

Int J Syst Evol Microbiol. 2018 Jul;68(7):2199-2208. doi: 10.1099/ijsem.0.002810. Epub 2018 May 29.

PMID:
29781801
46.

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.

Viruses. 2018 May 14;10(5). pii: E256. doi: 10.3390/v10050256.

47.

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

Maes P, Alkhovsky SV, Bào Y, Beer M, Birkhead M, Briese T, Buchmeier MJ, Calisher CH, Charrel RN, Choi IR, Clegg CS, de la Torre JC, Delwart E, DeRisi JL, Di Bello PL, Di Serio F, Digiaro M, Dolja VV, Drosten C, Druciarek TZ, Du J, Ebihara H, Elbeaino T, Gergerich RC, Gillis AN, Gonzalez JJ, Haenni AL, Hepojoki J, Hetzel U, Hồ T, Hóng N, Jain RK, Jansen van Vuren P, Jin Q, Jonson MG, Junglen S, Keller KE, Kemp A, Kipar A, Kondov NO, Koonin EV, Kormelink R, Korzyukov Y, Krupovic M, Lambert AJ, Laney AG, LeBreton M, Lukashevich IS, Marklewitz M, Markotter W, Martelli GP, Martin RR, Mielke-Ehret N, Mühlbach HP, Navarro B, Ng TFF, Nunes MRT, Palacios G, Pawęska JT, Peters CJ, Plyusnin A, Radoshitzky SR, Romanowski V, Salmenperä P, Salvato MS, Sanfaçon H, Sasaya T, Schmaljohn C, Schneider BS, Shirako Y, Siddell S, Sironen TA, Stenglein MD, Storm N, Sudini H, Tesh RB, Tzanetakis IE, Uppala M, Vapalahti O, Vasilakis N, Walker PJ, Wáng G, Wáng L, Wáng Y, Wèi T, Wiley MR, Wolf YI, Wolfe ND, Wú Z, Xú W, Yang L, Yāng Z, Yeh SD, Zhāng YZ, Zhèng Y, Zhou X, Zhū C, Zirkel F, Kuhn JH.

Arch Virol. 2018 Aug;163(8):2295-2310. doi: 10.1007/s00705-018-3843-5. Epub 2018 Apr 21.

PMID:
29680923
48.

Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii.

Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T.

Mol Biol Evol. 2018 Aug 1;35(8):1855-1868. doi: 10.1093/molbev/msy075.

49.

Estimation of universal and taxon-specific parameters of prokaryotic genome evolution.

Sela I, Wolf YI, Koonin EV.

PLoS One. 2018 Apr 13;13(4):e0195571. doi: 10.1371/journal.pone.0195571. eCollection 2018.

50.

Taxonomy of the order Mononegavirales: update 2018.

Amarasinghe GK, Aréchiga Ceballos NG, Banyard AC, Basler CF, Bavari S, Bennett AJ, Blasdell KR, Briese T, Bukreyev A, Caì Y, Calisher CH, Campos Lawson C, Chandran K, Chapman CA, Chiu CY, Choi KS, Collins PL, Dietzgen RG, Dolja VV, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Echevarría JE, Fooks AR, Formenty PBH, Fouchier RAM, Freuling CM, Ghedin E, Goldberg TL, Hewson R, Horie M, Hyndman TH, Jiāng D, Kityo R, Kobinger GP, Kondō H, Koonin EV, Krupovic M, Kurath G, Lamb RA, Lee B, Leroy EM, Maes P, Maisner A, Marston DA, Mor SK, Müller T, Mühlberger E, Ramírez VMN, Netesov SV, Ng TFF, Nowotny N, Palacios G, Patterson JL, Pawęska JT, Payne SL, Prieto K, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Siddell S, Smither SJ, Song Q, Song T, Stenglein MD, Stone DM, Takada A, Tesh RB, Thomazelli LM, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Vázquez-Morón S, Verdugo C, Volchkov VE, Wahl V, Walker PJ, Wang D, Wang LF, Wellehan JFX, Wiley MR, Whitfield AE, Wolf YI, Yè G, Zhāng YZ, Kuhn JH.

Arch Virol. 2018 Aug;163(8):2283-2294. doi: 10.1007/s00705-018-3814-x. Epub 2018 Apr 11.

PMID:
29637429

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