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Items: 1 to 50 of 195

1.

Escherichia coli ItaT is a type II toxin that inhibits translation by acetylating isoleucyl-tRNAIle.

Wilcox B, Osterman I, Serebryakova M, Lukyanov D, Komarova E, Gollan B, Morozova N, Wolf YI, Makarova KS, Helaine S, Sergiev P, Dubiley S, Borukhov S, Severinov K.

Nucleic Acids Res. 2018 Jun 21. doi: 10.1093/nar/gky560. [Epub ahead of print]

PMID:
29931259
2.

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
3.

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 Apr 21. doi: 10.1007/s00705-018-3843-5. [Epub ahead of print]

PMID:
29680923
4.

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.

5.

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 Apr 11. doi: 10.1007/s00705-018-3814-x. [Epub ahead of print]

PMID:
29637429
6.

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.

7.

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.

8.

Diverse functions of homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence.

Vedula P, Kurosaka S, Leu NA, Wolf YI, Shabalina SA, Wang J, Sterling S, Dong DW, Kashina A.

Elife. 2017 Dec 15;6. pii: e31661. doi: 10.7554/eLife.31661.

9.

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.

10.

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.

11.

Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition.

Yampolsky LY, Wolf YI, Bouzinier MA.

Genome Biol Evol. 2017 Oct 1;9(10):2879-2892. doi: 10.1093/gbe/evx191.

PMID:
28985302
12.

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.

13.

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
14.

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.

15.

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostinčar C, Daly MJ.

Stand Genomic Sci. 2017 Jul 28;12:46. doi: 10.1186/s40793-017-0258-y. eCollection 2017.

16.

'ARMAN' archaea depend on association with euryarchaeal host in culture and in situ.

Golyshina OV, Toshchakov SV, Makarova KS, Gavrilov SN, Korzhenkov AA, La Cono V, Arcadi E, Nechitaylo TY, Ferrer M, Kublanov IV, Wolf YI, Yakimov MM, Golyshin PN.

Nat Commun. 2017 Jul 5;8(1):60. doi: 10.1038/s41467-017-00104-7.

17.

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.

18.

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.

19.

Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport.

Pirkmajer S, Kirchner H, Lundell LS, Zelenin PV, Zierath JR, Makarova KS, Wolf YI, Chibalin AV.

J Physiol. 2017 Jul 15;595(14):4611-4630. doi: 10.1113/JP274254. Epub 2017 May 29.

20.

Reconstruction of the evolution of microbial defense systems.

Puigbò P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV.

BMC Evol Biol. 2017 Apr 4;17(1):94. doi: 10.1186/s12862-017-0942-y.

21.

Diversity and evolution of class 2 CRISPR-Cas systems.

Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV.

Nat Rev Microbiol. 2017 Mar;15(3):169-182. doi: 10.1038/nrmicro.2016.184. Epub 2017 Jan 23.

22.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.

Kristensen DM, Wolf YI, Koonin EV.

Nucleic Acids Res. 2017 Jan 4;45(D1):D210-D218. doi: 10.1093/nar/gkw934. Epub 2016 Oct 18.

23.

Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins.

Persi E, Wolf YI, Koonin EV.

Nat Commun. 2016 Nov 18;7:13570. doi: 10.1038/ncomms13570.

24.

Two fundamentally different classes of microbial genes.

Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV.

Nat Microbiol. 2016 Nov 7;2:16208. doi: 10.1038/nmicrobiol.2016.208.

PMID:
27819663
25.

Theory of prokaryotic genome evolution.

Sela I, Wolf YI, Koonin EV.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11399-11407. Epub 2016 Oct 4.

26.

Inevitability of Genetic Parasites.

Iranzo J, Puigbò P, Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2016 Sep 26;8(9):2856-2869.

27.

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms.

Koonin EV, Wolf YI.

Biol Direct. 2016 Feb 24;11(1):9. doi: 10.1186/s13062-016-0111-z.

28.

Evolvability of an Optimal Recombination Rate.

Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2015 Dec 10;8(1):70-7. doi: 10.1093/gbe/evv249.

29.

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.

Mol Cell. 2015 Nov 5;60(3):385-97. doi: 10.1016/j.molcel.2015.10.008. Epub 2015 Oct 22.

30.

An updated evolutionary classification of CRISPR-Cas systems.

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV.

Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569. Epub 2015 Sep 28. Review.

31.

Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing.

Senkevich TG, Bruno D, Martens C, Porcella SF, Wolf YI, Moss B.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):10908-13. doi: 10.1073/pnas.1514809112. Epub 2015 Aug 18.

32.

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF.

J Biol Chem. 2015 Jul 24;290(30):18678-98. doi: 10.1074/jbc.M115.657916. Epub 2015 Jun 12.

33.

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae.

Pagnier I, Yutin N, Croce O, Makarova KS, Wolf YI, Benamar S, Raoult D, Koonin EV, La Scola B.

Biol Direct. 2015 Mar 31;10:13. doi: 10.1186/s13062-015-0043-z.

34.

Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems.

Iranzo J, Lobkovsky AE, Wolf YI, Koonin EV.

BMC Evol Biol. 2015 Mar 13;15:43. doi: 10.1186/s12862-015-0324-2.

36.

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.

Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV.

ISME J. 2015 Sep;9(9):2021-7. doi: 10.1038/ismej.2015.20. Epub 2015 Feb 24.

37.

Estimation of prokaryotic supergenome size and composition from gene frequency distributions.

Lobkovsky AE, Wolf YI, Koonin EV.

BMC Genomics. 2014;15 Suppl 6:S14. doi: 10.1186/1471-2164-15-S6-S14. Epub 2014 Oct 17.

38.

Virus-host arms race at the joint origin of multicellularity and programmed cell death.

Iranzo J, Lobkovsky AE, Wolf YI, Koonin EV.

Cell Cycle. 2014;13(19):3083-8. doi: 10.4161/15384101.2014.949496.

39.

Expanded microbial genome coverage and improved protein family annotation in the COG database.

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

Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9. doi: 10.1093/nar/gku1223. Epub 2014 Nov 26.

40.

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution.

Koonin EV, Wolf YI.

Mol Biosyst. 2015 Jan;11(1):20-7. doi: 10.1039/c4mb00438h. Epub 2014 Sep 19. Review.

41.

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

Puigbò P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV.

BMC Biol. 2014 Aug 21;12:66. doi: 10.1186/s12915-014-0066-4.

42.

Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes.

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

Extremophiles. 2014 Sep;18(5):877-93. doi: 10.1007/s00792-014-0672-7. Epub 2014 Aug 12.

43.

Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life.

Yutin N, Wolf YI, Koonin EV.

Virology. 2014 Oct;466-467:38-52. doi: 10.1016/j.virol.2014.06.032. Epub 2014 Jul 17.

44.

Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis.

Berezovskaya FS, Wolf YI, Koonin EV, Karev GP.

Biol Direct. 2014 Jul 2;9:13. doi: 10.1186/1745-6150-9-13.

45.

Universal pacemaker of genome evolution in animals and fungi and variation of evolutionary rates in diverse organisms.

Snir S, Wolf YI, Koonin EV.

Genome Biol Evol. 2014 May 7;6(6):1268-78. doi: 10.1093/gbe/evu091.

46.

Small proteins can no longer be ignored.

Storz G, Wolf YI, Ramamurthi KS.

Annu Rev Biochem. 2014;83:753-77. doi: 10.1146/annurev-biochem-070611-102400. Epub 2014 Mar 3. Review.

47.

Drastic neofunctionalization associated with evolution of the timezyme AANAT 500 Mya.

Falcón J, Coon SL, Besseau L, Cazaméa-Catalan D, Fuentès M, Magnanou E, Paulin CH, Boeuf G, Sauzet S, Jørgensen EH, Mazan S, Wolf YI, Koonin EV, Steinbach PJ, Hyodo S, Klein DC.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):314-9. doi: 10.1073/pnas.1312634110. Epub 2013 Dec 18.

48.

The basic building blocks and evolution of CRISPR-CAS systems.

Makarova KS, Wolf YI, Koonin EV.

Biochem Soc Trans. 2013 Dec;41(6):1392-400. doi: 10.1042/BST20130038. Review.

49.

Differential translation tunes uneven production of operon-encoded proteins.

Quax TE, Wolf YI, Koehorst JJ, Wurtzel O, van der Oost R, Ran W, Blombach F, Makarova KS, Brouns SJ, Forster AC, Wagner EG, Sorek R, Koonin EV, van der Oost J.

Cell Rep. 2013 Sep 12;4(5):938-44. doi: 10.1016/j.celrep.2013.07.049. Epub 2013 Sep 5.

50.

Stability along with extreme variability in core genome evolution.

Wolf YI, Snir S, Koonin EV.

Genome Biol Evol. 2013;5(7):1393-402. doi: 10.1093/gbe/evt098.

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