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Items: 1 to 50 of 213

1.

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.

PMID:
31278667
2.

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.

PMID:
31227609
3.

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.

4.

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
5.

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.

6.

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.

7.

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.

8.

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
9.

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
10.

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.

11.

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.

12.

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.

13.

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.

14.

Antibody-Mediated Protective Mechanisms Induced by a Trivalent Parainfluenza Virus-Vectored Ebolavirus Vaccine.

Kimble JB, Malherbe DC, Meyer M, Gunn BM, Karim MM, Ilinykh PA, Iampietro M, Mohamed KS, Negi S, Gilchuk P, Huang K, Wolf YI, Braun W, Crowe JE, Alter G, Bukreyev A.

J Virol. 2019 Feb 5;93(4). pii: e01845-18. doi: 10.1128/JVI.01845-18. Print 2019 Feb 15.

PMID:
30518655
15.

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.

16.

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.

17.

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.

18.

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.

19.

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 Sep 6;46(15):7873-7885. doi: 10.1093/nar/gky560.

20.

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.

21.

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
22.

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.

23.

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
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.

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.

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.

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.

30.

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.

31.

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
32.

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.

33.

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.

34.

'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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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
43.

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.

44.

Inevitability of Genetic Parasites.

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

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

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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