Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 818

1.

Open questions: CRISPR biology.

Koonin EV.

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

PMID:
30244670
2.

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

Koonin EV.

Environ Microbiol. 2018 Sep 9. doi: 10.1111/1462-2920.14403. [Epub ahead of print] No abstract available.

PMID:
30198178
3.

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

Faure G, Makarova KS, Koonin EV.

J Mol Biol. 2018 Sep 5. pii: S0022-2836(18)31013-1. doi: 10.1016/j.jmb.2018.08.030. [Epub ahead of print] Review.

4.

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.

5.

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
6.

The depths of virus exaptation.

Koonin EV, Krupovic M.

Curr Opin Virol. 2018 Jul 30;31:1-8. doi: 10.1016/j.coviro.2018.07.011. [Epub ahead of print] Review.

PMID:
30071360
7.

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 Jun 21. doi: 10.1038/s41564-018-0184-9. [Epub ahead of print]

PMID:
29934592
8.

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
9.

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.

10.

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.

PMID:
29895694
11.

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
12.

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.

PMID:
29784811
13.

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
14.

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.

15.

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
16.

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.

17.

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.

18.

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
19.

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.

20.

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.

PMID:
29618642
21.

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
22.

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 Jun 21;:.

PMID:
29507349
23.

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
24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

PMID:
29175107
30.

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.

31.

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.

32.

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
33.

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.

34.

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.

35.

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.

36.

Microbial genome analysis: the COG approach.

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

Brief Bioinform. 2017 Sep 14. doi: 10.1093/bib/bbx117. [Epub ahead of print]

PMID:
28968633
37.

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions.

Belinky F, Rogozin IB, Koonin EV.

Sci Rep. 2017 Sep 29;7(1):12422. doi: 10.1038/s41598-017-12619-6.

38.

Discovery of Oligonucleotide Signaling Mediated by CRISPR-Associated Polymerases Solves Two Puzzles but Leaves an Enigma.

Koonin EV, Makarova KS.

ACS Chem Biol. 2018 Feb 16;13(2):309-312. doi: 10.1021/acschembio.7b00713. Epub 2017 Sep 27.

PMID:
28937734
39.

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

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

MBio. 2017 Sep 19;8(5). pii: e01397-17. doi: 10.1128/mBio.01397-17.

40.

Origin and Evolution of the Universal Genetic Code.

Koonin EV, Novozhilov AS.

Annu Rev Genet. 2017 Nov 27;51:45-62. doi: 10.1146/annurev-genet-120116-024713. Epub 2017 Aug 30. Review.

PMID:
28853922
41.

Recruitment of CRISPR-Cas systems by Tn7-like transposons.

Peters JE, Makarova KS, Shmakov S, Koonin EV.

Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7358-E7366. doi: 10.1073/pnas.1709035114. Epub 2017 Aug 15.

42.

Adaptation of mRNA structure to control protein folding.

Faure G, Ogurtsov AY, Shabalina SA, Koonin EV.

RNA Biol. 2017 Dec 2;14(12):1649-1654. doi: 10.1080/15476286.2017.1349047. Epub 2017 Aug 29. Review.

43.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ.

MBio. 2017 Jul 11;8(4). pii: e00897-17. doi: 10.1128/mBio.00897-17.

44.
45.

Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity.

Koonin EV, Krupovic M.

Curr Opin Virol. 2017 Aug;25:7-15. doi: 10.1016/j.coviro.2017.06.008. Epub 2017 Jun 30. Review.

46.

Evolutionary Genomics of Defense Systems in Archaea and Bacteria.

Koonin EV, Makarova KS, Wolf YI.

Annu Rev Microbiol. 2017 Sep 8;71:233-261. doi: 10.1146/annurev-micro-090816-093830. Epub 2017 Jun 28. Review.

47.

Disentangling the effects of selection and loss bias on gene dynamics.

Iranzo J, Cuesta JA, Manrubia S, Katsnelson MI, Koonin EV.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):E5616-E5624. doi: 10.1073/pnas.1704925114. Epub 2017 Jun 26.

48.

Diversity, classification and evolution of CRISPR-Cas systems.

Koonin EV, Makarova KS, Zhang F.

Curr Opin Microbiol. 2017 Jun;37:67-78. doi: 10.1016/j.mib.2017.05.008. Epub 2017 Jun 9. Review.

49.

Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis.

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

Nat Microbiol. 2017 May 30;2:17081. doi: 10.1038/nmicrobiol.2017.81.

50.

The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis.

Mekhedov SL, Makarova KS, Koonin EV.

Biol Direct. 2017 May 25;12(1):13. doi: 10.1186/s13062-017-0185-2.

Supplemental Content

Loading ...
Support Center