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Year Number of Results
1980 1
1983 1
1984 2
1988 6
1989 10
1990 3
1991 14
1992 18
1993 21
1994 24
1995 19
1996 22
1997 19
1998 25
1999 29
2000 40
2001 42
2002 34
2003 33
2004 32
2005 26
2006 33
2007 24
2008 30
2009 39
2010 27
2011 29
2012 36
2013 36
2014 37
2015 40
2016 30
2017 42
2018 40
2019 45
2020 41
2021 45
2022 40
2023 39
2024 21

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Page 1
tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector.
Jain I, Kolesnik M, Kuznedelov K, Minakhin L, Morozova N, Shiriaeva A, Kirillov A, Medvedeva S, Livenskyi A, Kazieva L, Makarova KS, Koonin EV, Borukhov S, Severinov K, Semenova E. Jain I, et al. Among authors: koonin ev. Sci Adv. 2024 Apr 26;10(17):eadl0164. doi: 10.1126/sciadv.adl0164. Epub 2024 Apr 24. Sci Adv. 2024. PMID: 38657076 Free PMC article.
Bacterial defense systems exhibit synergistic anti-phage activity.
Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Wu Y, et al. Among authors: koonin ev. Cell Host Microbe. 2024 Apr 10;32(4):557-572.e6. doi: 10.1016/j.chom.2024.01.015. Epub 2024 Feb 22. Cell Host Microbe. 2024. PMID: 38402614 Free article.
Diversity, origin, and evolution of the ESCRT systems.
Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Makarova KS, et al. Among authors: koonin ev. mBio. 2024 Mar 13;15(3):e0033524. doi: 10.1128/mbio.00335-24. Epub 2024 Feb 21. mBio. 2024. PMID: 38380930 Free PMC article.
Mriyaviruses: Small Relatives of Giant Viruses.
Yutin N, Mutz P, Krupovic M, Koonin EV. Yutin N, et al. Among authors: koonin ev. bioRxiv [Preprint]. 2024 Feb 29:2024.02.29.582850. doi: 10.1101/2024.02.29.582850. bioRxiv. 2024. PMID: 38529486 Free PMC article. Preprint.
Defense systems and horizontal gene transfer in bacteria.
Kogay R, Wolf YI, Koonin EV. Kogay R, et al. Among authors: koonin ev. bioRxiv [Preprint]. 2024 Feb 9:2024.02.09.579689. doi: 10.1101/2024.02.09.579689. bioRxiv. 2024. PMID: 38410456 Free PMC article. Updated. Preprint.
ICTV Virus Taxonomy Profile: Kolmioviridae 2024.
Kuhn JH, Babaian A, Bergner LM, Dény P, Glebe D, Horie M, Koonin EV, Krupovic M, Paraskevopoulou S, de la Peña M, Smura T, Hepojoki J. Kuhn JH, et al. Among authors: koonin ev. J Gen Virol. 2024 Feb;105(2). doi: 10.1099/jgv.0.001963. J Gen Virol. 2024. PMID: 38421275
Addendum: Cellular differentiation into hyphae and spores in halophilic archaea.
Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Tang SK, et al. Among authors: koonin ev. Nat Commun. 2024 Feb 1;15(1):523. doi: 10.1038/s41467-024-44821-2. Nat Commun. 2024. PMID: 38302496 Free PMC article. No abstract available.
Megataxonomy and global ecology of the virosphere.
Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Koonin EV, et al. ISME J. 2024 Jan 8;18(1):wrad042. doi: 10.1093/ismejo/wrad042. ISME J. 2024. PMID: 38365236 Free PMC article. Review.
Microbial transmission in the social microbiome and host health and disease.
Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KV, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Sarkar A, et al. Among authors: koonin ev. Cell. 2024 Jan 4;187(1):17-43. doi: 10.1016/j.cell.2023.12.014. Cell. 2024. PMID: 38181740 Free PMC article. Review.
Unidirectional gene pairs in archaea and bacteria require overlaps or very short intergenic distances for translational coupling via termination-reinitiation and often encode subunits of heteromeric complexes.
Huber M, Vogel N, Borst A, Pfeiffer F, Karamycheva S, Wolf YI, Koonin EV, Soppa J. Huber M, et al. Among authors: koonin ev. Front Microbiol. 2023 Nov 9;14:1291523. doi: 10.3389/fmicb.2023.1291523. eCollection 2023. Front Microbiol. 2023. PMID: 38029211 Free PMC article.
ICTV Virus Taxonomy Profile: Amnoonviridae 2023.
Koonin EV, Krupovic M, Surachetpong W, Wolf YI, Kuhn JH. Koonin EV, et al. J Gen Virol. 2023 Oct;104(10):001903. doi: 10.1099/jgv.0.001903. J Gen Virol. 2023. PMID: 37873742 Free PMC article.
ICTV Virus Taxonomy Profile: Tosoviridae 2023.
Wolf YI, Krupovic M, Kuhn JH, Koonin EV. Wolf YI, et al. Among authors: koonin ev. J Gen Virol. 2023 Oct;104(10):001908. doi: 10.1099/jgv.0.001908. J Gen Virol. 2023. PMID: 37873739 Free PMC article.
ICTV Virus Taxonomy Profile: Qinviridae 2023.
Wolf YI, Koonin EV, Krupovic M, Kuhn JH. Wolf YI, et al. Among authors: koonin ev. J Gen Virol. 2023 Oct;104(10):001905. doi: 10.1099/jgv.0.001905. J Gen Virol. 2023. PMID: 37823788 Free PMC article.
Learn from the past to predict viral pandemics.
Rochman ND, Koonin EV. Rochman ND, et al. Among authors: koonin ev. Nature. 2023 Oct;622(7984):700-702. doi: 10.1038/d41586-023-02931-9. Nature. 2023. PMID: 37821603 No abstract available.
ICTV Virus Taxonomy Profile: Yueviridae 2023.
Krupovic M, Wolf YI, Koonin EV, Kuhn JH. Krupovic M, et al. Among authors: koonin ev. J Gen Virol. 2023 Oct;104(10):001904. doi: 10.1099/jgv.0.001904. J Gen Virol. 2023. PMID: 37819056 Free PMC article.
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer.
McBride DS, Garushyants SK, Franks J, Magee AF, Overend SH, Huey D, Williams AM, Faith SA, Kandeil A, Trifkovic S, Miller L, Jeevan T, Patel A, Nolting JM, Tonkovich MJ, Genders JT, Montoney AJ, Kasnyik K, Linder TJ, Bevins SN, Lenoch JB, Chandler JC, DeLiberto TJ, Koonin EV, Suchard MA, Lemey P, Webby RJ, Nelson MI, Bowman AS. McBride DS, et al. Among authors: koonin ev. Nat Commun. 2023 Aug 28;14(1):5105. doi: 10.1038/s41467-023-40706-y. Nat Commun. 2023. PMID: 37640694 Free PMC article.
Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems.
Shmakov SA, Barth ZK, Makarova KS, Wolf YI, Brover V, Peters JE, Koonin EV. Shmakov SA, et al. Among authors: koonin ev. Nucleic Acids Res. 2023 Aug 25;51(15):8150-8168. doi: 10.1093/nar/gkad495. Nucleic Acids Res. 2023. PMID: 37283088 Free PMC article.
Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota).
Kuhn JH, Abe J, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Kumar Baranwal V, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Blair CD, Blasdell KR, Blouin AG, Bradfute SB, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Kumar Chaturvedi K, Chooi KM, Crane A, Dal Bó E, Carlos de la Torre J, de Souza WM, de Swart RL, Debat H, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, Laura García M, García-Sastre A, Garrison AR, Gaskin TR, Gong W, Gonzalez JJ, de Bellocq J, Griffiths A, Groschup MH, Günther I, Günther S, Hammond J, Hasegawa Y, Hayashi K, Hepojoki J, Higgins CM, Hongō S, Horie M, Hughes HR, Hume AJ, Hyndman TH, Ikeda K, Jiāng D, Jonson GB, Junglen S, Klempa B, Klingström J, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Lǐ J, Li JM, Liu R, Lukashevich IS, MacDiarmid RM, Maes P, Marklewitz M, Marshall SH, Marzano SL, McCauley JW, Mirazimi A, Mühlberger E, Nabeshi… See abstract for full author list ➔ Kuhn JH, et al. Among authors: koonin ev. J Gen Virol. 2023 Aug;104(8):001864. doi: 10.1099/jgv.0.001864. J Gen Virol. 2023. PMID: 37622664 Free PMC article.
Distinct groups of RNA viruses associated with thermoacidophilic bacteria.
Urayama SI, Fukudome A, Hirai M, Okumura T, Nishimura Y, Takaki Y, Kurosawa N, Koonin EV, Krupovic M, Nunoura T. Urayama SI, et al. Among authors: koonin ev. bioRxiv [Preprint]. 2023 Jul 3:2023.07.02.547447. doi: 10.1101/2023.07.02.547447. bioRxiv. 2023. PMID: 37790367 Free PMC article. Updated. Preprint.
Modularity and diversity of target selectors in Tn7 transposons.
Faure G, Saito M, Benler S, Peng I, Wolf YI, Strecker J, Altae-Tran H, Neumann E, Li D, Makarova KS, Macrae RK, Koonin EV, Zhang F. Faure G, et al. Among authors: koonin ev. Mol Cell. 2023 Jun 15;83(12):2122-2136.e10. doi: 10.1016/j.molcel.2023.05.013. Epub 2023 Jun 1. Mol Cell. 2023. PMID: 37267947 Free PMC article.
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein.
Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu'a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Butkovic A, et al. Among authors: koonin ev. Virus Evol. 2023 May 27;9(1):vead035. doi: 10.1093/ve/vead035. eCollection 2023. Virus Evol. 2023. PMID: 37325085 Free PMC article.
Structural atlas of a human gut crassvirus.
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA. Bayfield OW, et al. Among authors: koonin ev. Nature. 2023 May;617(7960):409-416. doi: 10.1038/s41586-023-06019-2. Epub 2023 May 3. Nature. 2023. PMID: 37138077 Free PMC article.
Cellular differentiation into hyphae and spores in halophilic archaea.
Tang SK, Zhi XY, Zhang Y, Makarova KS, Liu BB, Zheng GS, Zhang ZP, Zheng HJ, Wolf YI, Zhao YR, Jiang SH, Chen XM, Li EY, Zhang T, Chen PR, Feng YZ, Xiang MX, Lin ZQ, Shi JH, Chang C, Zhang X, Li R, Lou K, Wang Y, Chang L, Yin M, Yang LL, Gao HY, Zhang ZK, Tao TS, Guan TW, He FC, Lu YH, Cui HL, Koonin EV, Zhao GP, Xu P. Tang SK, et al. Among authors: koonin ev. Nat Commun. 2023 Apr 1;14(1):1827. doi: 10.1038/s41467-023-37389-w. Nat Commun. 2023. PMID: 37005419 Free PMC article.
In Silico Approaches for Prediction of Anti-CRISPR Proteins.
Makarova KS, Wolf YI, Koonin EV. Makarova KS, et al. Among authors: koonin ev. J Mol Biol. 2023 Apr 1;435(7):168036. doi: 10.1016/j.jmb.2023.168036. Epub 2023 Mar 1. J Mol Biol. 2023. PMID: 36868398 Free PMC article. Review.
Widespread PRC barrel proteins play critical roles in archaeal cell division.
Zhao S, Makarova KS, Zheng W, Liu Y, Zhan L, Wan Q, Gong H, Krupovic M, Lutkenhaus J, Chen X, Koonin EV, Du S. Zhao S, et al. Among authors: koonin ev. bioRxiv [Preprint]. 2023 Mar 28:2023.03.28.534520. doi: 10.1101/2023.03.28.534520. bioRxiv. 2023. PMID: 37090588 Free PMC article. Preprint.
Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems.
Shmakov SA, Barth ZK, Makarova KS, Wolf YI, Brover V, Peters JE, Koonin EV. Shmakov SA, et al. Among authors: koonin ev. bioRxiv [Preprint]. 2023 Mar 3:2023.03.03.530964. doi: 10.1101/2023.03.03.530964. bioRxiv. 2023. PMID: 37090614 Free PMC article. Updated. Preprint.
Four principles to establish a universal virus taxonomy.
Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Simmonds P, et al. Among authors: koonin ev. PLoS Biol. 2023 Feb 13;21(2):e3001922. doi: 10.1371/journal.pbio.3001922. eCollection 2023 Feb. PLoS Biol. 2023. PMID: 36780432 Free PMC article.
Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs.
Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M; RNA Virus Discovery Consortium; Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV. Lee BD, et al. Among authors: koonin ev. Cell. 2023 Feb 2;186(3):646-661.e4. doi: 10.1016/j.cell.2022.12.039. Epub 2023 Jan 24. Cell. 2023. PMID: 36696902 Free PMC article.
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bandte M, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Bigarré L, Blair CD, Blasdell KR, Bradfute SB, Briese T, Brown PA, Bruggmann R, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Candresse T, Carson J, Casas I, Chandran K, Charrel RN, Chiaki Y, Crane A, Crane M, Dacheux L, Bó ED, de la Torre JC, de Lamballerie X, de Souza WM, de Swart RL, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Feuvrier C, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, García ML, García-Sastre A, Garrison AR, Godwin SE, Gonzalez JJ, de Bellocq JG, Griffiths A, Groschup MH, Günther S, Hammond J, Hepojoki J, Hierweger MM, Hongō S, Horie M, Horikawa H, Hughes HR, Hume AJ, Hyndman TH, Jiāng D, Jonson GB, Junglen S, Kadono F, Karlin DG, Klempa B, Klingström J, Koch MC, Kondō H, Koonin EV, Krásová J, Krupovic M, Kubota K, Kuzmin IV, Laenen L, Lambert AJ, Lǐ J, Li JM, Lieffrig F, Lukashevich IS, Luo D, Maes P, Marklewitz M, Marshall SH, Marzano SL, McCauley JW, Mirazimi … See abstract for full author list ➔ Kuhn JH, et al. Among authors: koonin ev. Arch Virol. 2022 Dec;167(12):2857-2906. doi: 10.1007/s00705-022-05546-z. Arch Virol. 2022. PMID: 36437428 Free PMC article.
The miniature CRISPR-Cas12m effector binds DNA to block transcription.
Wu WY, Mohanraju P, Liao C, Adiego-Pérez B, Creutzburg SCA, Makarova KS, Keessen K, Lindeboom TA, Khan TS, Prinsen S, Joosten R, Yan WX, Migur A, Laffeber C, Scott DA, Lebbink JHG, Koonin EV, Beisel CL, van der Oost J. Wu WY, et al. Among authors: koonin ev. Mol Cell. 2022 Dec 1;82(23):4487-4502.e7. doi: 10.1016/j.molcel.2022.11.003. Epub 2022 Nov 24. Mol Cell. 2022. PMID: 36427491 Free article.
Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9.
Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H. Kato K, et al. Among authors: koonin ev. Nat Commun. 2022 Nov 7;13(1):6719. doi: 10.1038/s41467-022-34378-3. Nat Commun. 2022. PMID: 36344504 Free PMC article.
A life LINE for large viruses.
Koonin EV, Krupovic M. Koonin EV, et al. Elife. 2022 Oct 25;11:e83488. doi: 10.7554/eLife.83488. Elife. 2022. PMID: 36282171 Free PMC article.
Expansion of the global RNA virome reveals diverse clades of bacteriophages.
Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Zeigler Allen L, Paez-Espino D, Bryant DA, Bhaya D; RNA Virus Discovery Consortium; Krupovic M, Dolja VV, Kyrpides NC, Koonin EV, Gophna U. Neri U, et al. Among authors: koonin ev. Cell. 2022 Oct 13;185(21):4023-4037.e18. doi: 10.1016/j.cell.2022.08.023. Epub 2022 Sep 28. Cell. 2022. PMID: 36174579 Free article.
Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA.
Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F. Hirano S, et al. Among authors: koonin ev. Nature. 2022 Oct;610(7932):575-581. doi: 10.1038/s41586-022-05324-6. Epub 2022 Oct 12. Nature. 2022. PMID: 36224386 Free PMC article.
Molecular adaptations during viral epidemics.
Rochman ND, Wolf YI, Koonin EV. Rochman ND, et al. Among authors: koonin ev. EMBO Rep. 2022 Aug 3;23(8):e55393. doi: 10.15252/embr.202255393. Epub 2022 Jul 18. EMBO Rep. 2022. PMID: 35848484 Free PMC article. Review.
The logic of virus evolution.
Koonin EV, Dolja VV, Krupovic M. Koonin EV, et al. Cell Host Microbe. 2022 Jul 13;30(7):917-929. doi: 10.1016/j.chom.2022.06.008. Cell Host Microbe. 2022. PMID: 35834963 Free article. Review.
Gene-influx-driven evolution.
Saakian DB, Koonin EV. Saakian DB, et al. Among authors: koonin ev. Phys Rev E. 2022 Jul;106(1-1):014403. doi: 10.1103/PhysRevE.106.014403. Phys Rev E. 2022. PMID: 35974500
The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism.
Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova KS, Koonin EV, Shen Y, Söll D, Fu X. Zhang H, et al. Among authors: koonin ev. Nucleic Acids Res. 2022 May 6;50(8):4601-4615. doi: 10.1093/nar/gkac271. Nucleic Acids Res. 2022. PMID: 35466371 Free PMC article.
Thermodynamic selection: mechanisms and scenarios.
Babajanyan SG, Koonin EV, Allahverdyan AE. Babajanyan SG, et al. Among authors: koonin ev. New J Phys. 2022 May;24(5):053006. doi: 10.1088/1367-2630/ac6531. Epub 2022 May 5. New J Phys. 2022. PMID: 36776225 Free PMC article.
A novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA.
Waltzek TB, Stacy BA, Ossiboff RJ, Stacy NI, Fraser WA, Yan A, Mohan S, Koonin EV, Wolf YI, Rodrigues TCS, Viadanna PHO, Subramaniam K, Popov VL, Guzman-Vargas V, Shender LA. Waltzek TB, et al. Among authors: koonin ev. PLoS Pathog. 2022 Mar 11;18(3):e1010258. doi: 10.1371/journal.ppat.1010258. eCollection 2022 Mar. PLoS Pathog. 2022. PMID: 35275967 Free PMC article.
Thermodynamics of evolution and the origin of life.
Vanchurin V, Wolf YI, Koonin EV, Katsnelson MI. Vanchurin V, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2022 Feb 8;119(6):e2120042119. doi: 10.1073/pnas.2120042119. Proc Natl Acad Sci U S A. 2022. PMID: 35131858 Free PMC article.
Toward a theory of evolution as multilevel learning.
Vanchurin V, Wolf YI, Katsnelson MI, Koonin EV. Vanchurin V, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2022 Feb 8;119(6):e2120037119. doi: 10.1073/pnas.2120037119. Proc Natl Acad Sci U S A. 2022. PMID: 35121666 Free PMC article.
Compact RNA editors with small Cas13 proteins.
Kannan S, Altae-Tran H, Jin X, Madigan VJ, Oshiro R, Makarova KS, Koonin EV, Zhang F. Kannan S, et al. Among authors: koonin ev. Nat Biotechnol. 2022 Feb;40(2):194-197. doi: 10.1038/s41587-021-01030-2. Epub 2021 Aug 30. Nat Biotechnol. 2022. PMID: 34462587 Free PMC article.
ViroidDB: a database of viroids and viroid-like circular RNAs.
Lee BD, Neri U, Oh CJ, Simmonds P, Koonin EV. Lee BD, et al. Among authors: koonin ev. Nucleic Acids Res. 2022 Jan 7;50(D1):D432-D438. doi: 10.1093/nar/gkab974. Nucleic Acids Res. 2022. PMID: 34751403 Free PMC article.
Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Ka… See abstract for full author list ➔ Kuhn JH, et al. Among authors: koonin ev. Arch Virol. 2021 Dec;166(12):3567-3579. doi: 10.1007/s00705-021-05266-w. Arch Virol. 2021. PMID: 34786611 Free PMC article. No abstract available.
2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Ka… See abstract for full author list ➔ Kuhn JH, et al. Among authors: koonin ev. Arch Virol. 2021 Dec;166(12):3513-3566. doi: 10.1007/s00705-021-05143-6. Arch Virol. 2021. PMID: 34463877 Free PMC article.
A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants.
Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. Fesenko I, et al. Among authors: koonin ev. Nucleic Acids Res. 2021 Oct 11;49(18):10328-10346. doi: 10.1093/nar/gkab816. Nucleic Acids Res. 2021. PMID: 34570232 Free PMC article.
CRISPRclassify: Repeat-Based Classification of CRISPR Loci.
Nethery MA, Korvink M, Makarova KS, Wolf YI, Koonin EV, Barrangou R. Nethery MA, et al. Among authors: koonin ev. CRISPR J. 2021 Aug;4(4):558-574. doi: 10.1089/crispr.2021.0021. CRISPR J. 2021. PMID: 34406047 Free PMC article.
Ongoing global and regional adaptive evolution of SARS-CoV-2.
Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Rochman ND, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2104241118. doi: 10.1073/pnas.2104241118. Epub 2021 Jul 2. Proc Natl Acad Sci U S A. 2021. PMID: 34292871 Free PMC article.
Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product.
Zhao G, Kosek D, Liu HB, Ohlemacher SI, Blackburne B, Nikolskaya A, Makarova KS, Sun J, Barry Iii CE, Koonin EV, Dyda F, Bewley CA. Zhao G, et al. Among authors: koonin ev. J Am Chem Soc. 2021 Jun 2;143(21):8056-8068. doi: 10.1021/jacs.1c02316. Epub 2021 May 24. J Am Chem Soc. 2021. PMID: 34028251 Free PMC article.
Expanded diversity of Asgard archaea and their relationships with eukaryotes.
Liu Y, Makarova KS, Huang WC, Wolf YI, Nikolskaya AN, Zhang X, Cai M, Zhang CJ, Xu W, Luo Z, Cheng L, Koonin EV, Li M. Liu Y, et al. Among authors: koonin ev. Nature. 2021 May;593(7860):553-557. doi: 10.1038/s41586-021-03494-3. Epub 2021 Apr 28. Nature. 2021. PMID: 33911286
Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems.
Li M, Gong L, Cheng F, Yu H, Zhao D, Wang R, Wang T, Zhang S, Zhou J, Shmakov SA, Koonin EV, Xiang H. Li M, et al. Among authors: koonin ev. Science. 2021 Apr 30;372(6541):eabe5601. doi: 10.1126/science.abe5601. Science. 2021. PMID: 33926924
Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis.
Anastasia I, Ilacqua N, Raimondi A, Lemieux P, Ghandehari-Alavijeh R, Faure G, Mekhedov SL, Williams KJ, Caicci F, Valle G, Giacomello M, Quiroga AD, Lehner R, Miksis MJ, Toth K, de Aguiar Vallim TQ, Koonin EV, Scorrano L, Pellegrini L. Anastasia I, et al. Among authors: koonin ev. Cell Rep. 2021 Mar 16;34(11):108873. doi: 10.1016/j.celrep.2021.108873. Cell Rep. 2021. PMID: 33730569 Free article.
Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2.
Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Rochman ND, et al. Among authors: koonin ev. bioRxiv [Preprint]. 2021 Mar 2:2020.10.12.336644. doi: 10.1101/2020.10.12.336644. bioRxiv. 2021. PMID: 33083804 Free PMC article. Updated. Preprint.
Evolution of DNA packaging in gene transfer agents.
Esterman ES, Wolf YI, Kogay R, Koonin EV, Zhaxybayeva O. Esterman ES, et al. Among authors: koonin ev. Virus Evol. 2021 Feb 19;7(1):veab015. doi: 10.1093/ve/veab015. eCollection 2021 Jan. Virus Evol. 2021. PMID: 33732503 Free PMC article.
Structure and function of virion RNA polymerase of a crAss-like phage.
Drobysheva AV, Panafidina SA, Kolesnik MV, Klimuk EI, Minakhin L, Yakunina MV, Borukhov S, Nilsson E, Holmfeldt K, Yutin N, Makarova KS, Koonin EV, Severinov KV, Leiman PG, Sokolova ML. Drobysheva AV, et al. Among authors: koonin ev. Nature. 2021 Jan;589(7841):306-309. doi: 10.1038/s41586-020-2921-5. Epub 2020 Nov 18. Nature. 2021. PMID: 33208949
CRISPR Arrays Away from cas Genes.
Shmakov SA, Utkina I, Wolf YI, Makarova KS, Severinov KV, Koonin EV. Shmakov SA, et al. Among authors: koonin ev. CRISPR J. 2020 Dec;3(6):535-549. doi: 10.1089/crispr.2020.0062. CRISPR J. 2020. PMID: 33346707 Free PMC article.
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonička T, Basler C, Bavari S, Beer M, Bente DA, Bergeron É, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao M, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi IR, Clegg JCS, Crozier I, da Graça JV, Dal Bó E, Dávila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Dürrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astúa J, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JJ, Griffiths A, Groschup MH, Günther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Höper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiāng D, Jin Q, Jonson GB, Junglen S, Karadağ S, Keller KE, Klempa B, Klin… See abstract for full author list ➔ Kuhn JH, et al. Among authors: koonin ev. Arch Virol. 2020 Dec;165(12):3023-3072. doi: 10.1007/s00705-020-04731-2. Epub 2020 Sep 4. Arch Virol. 2020. PMID: 32888050 Free PMC article.
Evolution of Human Respiratory Virus Epidemics.
Rochman ND, Wolf YI, Koonin EV. Rochman ND, et al. Among authors: koonin ev. medRxiv [Preprint]. 2020 Nov 24:2020.11.23.20237503. doi: 10.1101/2020.11.23.20237503. medRxiv. 2020. PMID: 33269367 Free PMC article. Updated. Preprint.
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution.
Kozlenkov A, Vermunt MW, Apontes P, Li J, Hao K, Sherwood CC, Hof PR, Ely JJ, Wegner M, Mukamel EA, Creyghton MP, Koonin EV, Dracheva S. Kozlenkov A, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28422-28432. doi: 10.1073/pnas.2011884117. Epub 2020 Oct 27. Proc Natl Acad Sci U S A. 2020. PMID: 33109720 Free PMC article.
The LUCA and its complex virome.
Krupovic M, Dolja VV, Koonin EV. Krupovic M, et al. Among authors: koonin ev. Nat Rev Microbiol. 2020 Nov;18(11):661-670. doi: 10.1038/s41579-020-0408-x. Epub 2020 Jul 14. Nat Rev Microbiol. 2020. PMID: 32665595 Free article. Review.
Diverse enzymatic activities mediate antiviral immunity in prokaryotes.
Gao L, Altae-Tran H, Böhning F, Makarova KS, Segel M, Schmid-Burgk JL, Koob J, Wolf YI, Koonin EV, Zhang F. Gao L, et al. Among authors: koonin ev. Science. 2020 Aug 28;369(6507):1077-1084. doi: 10.1126/science.aba0372. Science. 2020. PMID: 32855333 Free PMC article.
Deep Roots and Splendid Boughs of the Global Plant Virome.
Dolja VV, Krupovic M, Koonin EV. Dolja VV, et al. Among authors: koonin ev. Annu Rev Phytopathol. 2020 Aug 25;58:23-53. doi: 10.1146/annurev-phyto-030320-041346. Epub 2020 May 27. Annu Rev Phytopathol. 2020. PMID: 32459570 Free article.
No waves of intelligent design.
Koonin EV, Wolf YI, Katsnelson MI. Koonin EV, et al. Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):19639-19640. doi: 10.1073/pnas.2011220117. Proc Natl Acad Sci U S A. 2020. PMID: 32817478 Free PMC article. No abstract available.
Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes.
Krupovic M, Varsani A, Kazlauskas D, Breitbart M, Delwart E, Rosario K, Yutin N, Wolf YI, Harrach B, Zerbini FM, Dolja VV, Kuhn JH, Koonin EV. Krupovic M, et al. Among authors: koonin ev. J Virol. 2020 Jun 1;94(12):e00582-20. doi: 10.1128/JVI.00582-20. Print 2020 Jun 1. J Virol. 2020. PMID: 32269128 Free PMC article. No abstract available.
Global Organization and Proposed Megataxonomy of the Virus World.
Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Koonin EV, et al. Microbiol Mol Biol Rev. 2020 Mar 4;84(2):e00061-19. doi: 10.1128/MMBR.00061-19. Print 2020 May 20. Microbiol Mol Biol Rev. 2020. PMID: 32132243 Free PMC article. Review.
Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases.
Minina EA, Staal J, Alvarez VE, Berges JA, Berman-Frank I, Beyaert R, Bidle KD, Bornancin F, Casanova M, Cazzulo JJ, Choi CJ, Coll NS, Dixit VM, Dolinar M, Fasel N, Funk C, Gallois P, Gevaert K, Gutierrez-Beltran E, Hailfinger S, Klemenčič M, Koonin EV, Krappmann D, Linusson A, Machado MFM, Madeo F, Megeney LA, Moschou PN, Mottram JC, Nyström T, Osiewacz HD, Overall CM, Pandey KC, Ruland J, Salvesen GS, Shi Y, Smertenko A, Stael S, Ståhlberg J, Suárez MF, Thome M, Tuominen H, Van Breusegem F, van der Hoorn RAL, Vardi A, Zhivotovsky B, Lam E, Bozhkov PV. Minina EA, et al. Among authors: koonin ev. Mol Cell. 2020 Mar 5;77(5):927-929. doi: 10.1016/j.molcel.2019.12.020. Mol Cell. 2020. PMID: 32142688 Free PMC article.
Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.
Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. Makarova KS, et al. Among authors: koonin ev. Nat Rev Microbiol. 2020 Feb;18(2):67-83. doi: 10.1038/s41579-019-0299-x. Epub 2019 Dec 19. Nat Rev Microbiol. 2020. PMID: 31857715 Free PMC article. Review.
Phages build anti-defence barriers.
Koonin EV, Krupovic M. Koonin EV, et al. Nat Microbiol. 2020 Jan;5(1):8-9. doi: 10.1038/s41564-019-0635-y. Nat Microbiol. 2020. PMID: 31857728 Free article. No abstract available.
Reply to Hedrick and Klitz: High haplotype discovery rate in the HLA locus.
Louzoun Y, Lobkovsky AE, Levi L, Wolf YI, Maiers M, Gragert L, Alter I, Koonin EV. Louzoun Y, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23388-23389. doi: 10.1073/pnas.1916124116. Epub 2019 Oct 29. Proc Natl Acad Sci U S A. 2019. PMID: 31662470 Free PMC article. No abstract available.
Virus-borne mini-CRISPR arrays are involved in interviral conflicts.
Medvedeva S, Liu Y, Koonin EV, Severinov K, Prangishvili D, Krupovic M. Medvedeva S, et al. Among authors: koonin ev. Nat Commun. 2019 Nov 15;10(1):5204. doi: 10.1038/s41467-019-13205-2. Nat Commun. 2019. PMID: 31729390 Free PMC article.
On the feasibility of saltational evolution.
Katsnelson MI, Wolf YI, Koonin EV. Katsnelson MI, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21068-21075. doi: 10.1073/pnas.1909031116. Epub 2019 Sep 30. Proc Natl Acad Sci U S A. 2019. PMID: 31570621 Free PMC article.
Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues.
Persi E, Prandi D, Wolf YI, Pozniak Y, Barnabas GD, Levanon K, Barshack I, Barbieri C, Gasperini P, Beltran H, Faltas BM, Rubin MA, Geiger T, Koonin EV, Demichelis F, Horn D. Persi E, et al. Among authors: koonin ev. Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):16987-16996. doi: 10.1073/pnas.1908790116. Epub 2019 Aug 6. Proc Natl Acad Sci U S A. 2019. PMID: 31387980 Free PMC article.
Origin of programmed cell death from antiviral defense?
Koonin EV, Krupovic M. Koonin EV, et al. Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16167-16169. doi: 10.1073/pnas.1910303116. Epub 2019 Jul 9. Proc Natl Acad Sci U S A. 2019. PMID: 31289224 Free PMC article. No abstract available.
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. Faure G, et al. Among authors: koonin ev. Nat Rev Microbiol. 2019 Aug;17(8):513-525. doi: 10.1038/s41579-019-0204-7. Nat Rev Microbiol. 2019. PMID: 31165781
Microbial genome analysis: the COG approach.
Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Galperin MY, et al. Among authors: koonin ev. Brief Bioinform. 2019 Jul 19;20(4):1063-1070. doi: 10.1093/bib/bbx117. Brief Bioinform. 2019. PMID: 28968633 Free PMC article. Review.
RNA-guided DNA insertion with CRISPR-associated transposases.
Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F. Strecker J, et al. Among authors: koonin ev. Science. 2019 Jul 5;365(6448):48-53. doi: 10.1126/science.aax9181. Epub 2019 Jun 6. Science. 2019. PMID: 31171706 Free PMC article.
Integrated mobile genetic elements in Thaumarchaeota.
Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV. Krupovic M, et al. Among authors: koonin ev. Environ Microbiol. 2019 Jun;21(6):2056-2078. doi: 10.1111/1462-2920.14564. Epub 2019 Mar 18. Environ Microbiol. 2019. PMID: 30773816 Free PMC article.
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