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Items: 1 to 50 of 833

1.

Integrated Mobile Genetic Elements in Thaumarchaeota.

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

Environ Microbiol. 2019 Feb 17. doi: 10.1111/1462-2920.14564. [Epub ahead of print]

PMID:
30773816
2.

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 7. pii: 201814684. doi: 10.1073/pnas.1814684116. [Epub ahead of print]

3.

Towards functional characterization of archaeal genomic dark matter.

Makarova KS, Wolf YI, Koonin EV.

Biochem Soc Trans. 2019 Feb 1. pii: BST20180560. doi: 10.1042/BST20180560. [Epub ahead of print] Review.

PMID:
30710061
4.

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.

5.

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.

PMID:
30635076
6.

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.

7.

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. 2018 Dec 17. doi: 10.1038/nbt.4306. [Epub ahead of print]

PMID:
30556814
8.

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.

9.

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
10.

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.

11.

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. 2018 Nov 19. doi: 10.1111/1462-2920.14479. [Epub ahead of print]

PMID:
30451355
12.

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.

13.

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
14.

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
15.

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.

16.

Open questions: CRISPR biology.

Koonin EV.

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

17.

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
18.

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.

19.

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.

20.

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. 2018 Aug 14:1-14. doi: 10.1080/15476286.2018.1493331. [Epub ahead of print]

PMID:
30103650
21.

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
22.

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
23.

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
24.

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.

25.

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.

26.

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.

PMID:
29883602
27.

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.

28.

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
29.

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.

30.

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
31.

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.

32.

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.

33.

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
34.

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis.

Yutin N, Bäckström D, Ettema TJG, Krupovic M, Koonin EV.

Virol J. 2018 Apr 10;15(1):67. doi: 10.1186/s12985-018-0974-y.

35.

Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses.

Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski NE, Pappu HR, Pooggin MM, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH.

J Virol. 2018 May 29;92(12). pii: e00515-18. doi: 10.1128/JVI.00515-18. Print 2018 Jun 15. No abstract available.

36.

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein.

Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA.

Mol Cell. 2018 Apr 19;70(2):327-339.e5. doi: 10.1016/j.molcel.2018.02.028. Epub 2018 Mar 15.

PMID:
29551514
37.

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 Apr;3(4):461-469. doi: 10.1038/s41564-018-0120-z. Epub 2018 Mar 5. Erratum in: Nat Microbiol. 2018 Sep;3(9):1076.

PMID:
29507349
38.

Metaviromics: a tectonic shift in understanding virus evolution.

Koonin EV, Dolja VV.

Virus Res. 2018 Feb 15;246:A1-A3. doi: 10.1016/j.virusres.2018.02.001. No abstract available.

PMID:
29433650
39.

Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia".

Ferrer M, Sorokin DY, Wolf YI, Ciordia S, Mena MC, Bargiela R, Koonin EV, Makarova KS.

Genes (Basel). 2018 Jan 23;9(2). pii: E28. doi: 10.3390/genes9020028.

40.

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

Galperin MY, Makarova KS, Wolf YI, Koonin EV.

J Bacteriol. 2018 Mar 12;200(7). pii: e00681-17. doi: 10.1128/JB.00681-17. Print 2018 Apr 1.

41.

Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.

Makarova KS, Galperin MY, Koonin EV.

MBio. 2017 Dec 5;8(6). pii: e01959-17. doi: 10.1128/mBio.01959-17.

42.

Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.

Koonin EV, Wolf YI, Katsnelson MI.

Biol Direct. 2017 Dec 4;12(1):31. doi: 10.1186/s13062-017-0202-5.

43.

Phylogenomics of Cas4 family nucleases.

Hudaiberdiev S, Shmakov S, Wolf YI, Terns MP, Makarova KS, Koonin EV.

BMC Evol Biol. 2017 Nov 28;17(1):232. doi: 10.1186/s12862-017-1081-1.

44.

Viruses of archaea: Structural, functional, environmental and evolutionary genomics.

Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV.

Virus Res. 2018 Jan 15;244:181-193. doi: 10.1016/j.virusres.2017.11.025. Epub 2017 Nov 22. Review.

45.

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.

Yutin N, Makarova KS, Gussow AB, Krupovic M, Segall A, Edwards RA, Koonin EV.

Nat Microbiol. 2018 Jan;3(1):38-46. doi: 10.1038/s41564-017-0053-y. Epub 2017 Nov 13.

46.

Cellular origin of the viral capsid-like bacterial microcompartments.

Krupovic M, Koonin EV.

Biol Direct. 2017 Nov 13;12(1):25. doi: 10.1186/s13062-017-0197-y.

47.

The enigmatic archaeal virosphere.

Prangishvili D, Bamford DH, Forterre P, Iranzo J, Koonin EV, Krupovic M.

Nat Rev Microbiol. 2017 Nov 10;15(12):724-739. doi: 10.1038/nrmicro.2017.125. Review.

PMID:
29123227
48.

Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer.

Dolja VV, Koonin EV.

Virus Res. 2018 Jan 15;244:36-52. doi: 10.1016/j.virusres.2017.10.020. Epub 2017 Nov 8. Review.

49.

Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.

Petitjean C, Makarova KS, Wolf YI, Koonin EV.

Genome Biol Evol. 2017 Oct 1;9(10):2791-2811. doi: 10.1093/gbe/evx189.

50.

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back.

Koonin EV, Makarova KS.

Genome Biol Evol. 2017 Oct 1;9(10):2812-2825. doi: 10.1093/gbe/evx192. Review.

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