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1.

Microbial transmission in the social microbiome and host health and disease.

Sarkar, Amar; McInroy, Cameron J A; Harty, Siobhán; Raulo, Aura; Ibata, Neil G O; Valles-Colomer, Mireia; Johnson, Katerina V-A; Brito, Ilana L; Henrich, Joseph; Archie, Elizabeth A; Barreiro, Luis B; Gazzaniga, Francesca S; Finlay, B Brett; Koonin, Eugene V; Carmody, Rachel N; Moeller, Andrew H.

Cell ; 187(1): 17-43, 2024 01 04.

Article in English | MEDLINE | ID: mdl-38181740

2.

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs.

Lee, Benjamin D; Neri, Uri; Roux, Simon; Wolf, Yuri I; Camargo, Antonio Pedro; Krupovic, Mart; Simmonds, Peter; Kyrpides, Nikos; Gophna, Uri; Dolja, Valerian V; Koonin, Eugene V.

Cell ; 186(3): 646-661.e4, 2023 02 02.

Article in English | MEDLINE | ID: mdl-36696902

3.

Expansion of the global RNA virome reveals diverse clades of bacteriophages.

Neri, Uri; Wolf, Yuri I; Roux, Simon; Camargo, Antonio Pedro; Lee, Benjamin; Kazlauskas, Darius; Chen, I Min; Ivanova, Natalia; Zeigler Allen, Lisa; Paez-Espino, David; Bryant, Donald A; Bhaya, Devaki; Krupovic, Mart; Dolja, Valerian V; Kyrpides, Nikos C; Koonin, Eugene V; Gophna, Uri.

Cell ; 185(21): 4023-4037.e18, 2022 10 13.

Article in English | MEDLINE | ID: mdl-36174579

4.

Functional Long Non-coding RNAs Evolve from Junk Transcripts.

Palazzo, Alexander F; Koonin, Eugene V.

Cell ; 183(5): 1151-1161, 2020 11 25.

Article in English | MEDLINE | ID: mdl-33068526

5.

SnapShot: Class 1 CRISPR-Cas Systems.

Makarova, Kira S; Zhang, Feng; Koonin, Eugene V.

Cell ; 168(5): 946-946.e1, 2017 02 23.

Article in English | MEDLINE | ID: mdl-28235204

6.

SnapShot: Class 2 CRISPR-Cas Systems.

Makarova, Kira S; Zhang, Feng; Koonin, Eugene V.

Cell ; 168(1-2): 328-328.e1, 2017 Jan 12.

Article in English | MEDLINE | ID: mdl-28086097

7.

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA.

Yamano, Takashi; Nishimasu, Hiroshi; Zetsche, Bernd; Hirano, Hisato; Slaymaker, Ian M; Li, Yinqing; Fedorova, Iana; Nakane, Takanori; Makarova, Kira S; Koonin, Eugene V; Ishitani, Ryuichiro; Zhang, Feng; Nureki, Osamu.

Cell ; 165(4): 949-62, 2016 May 05.

Article in English | MEDLINE | ID: mdl-27114038

8.

Modularity and diversity of target selectors in Tn7 transposons.

Faure, Guilhem; Saito, Makoto; Benler, Sean; Peng, Iris; Wolf, Yuri I; Strecker, Jonathan; Altae-Tran, Han; Neumann, Edwin; Li, David; Makarova, Kira S; Macrae, Rhiannon K; Koonin, Eugene V; Zhang, Feng.

Mol Cell ; 83(12): 2122-2136.e10, 2023 Jun 15.

Article in English | MEDLINE | ID: mdl-37267947

9.

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system.

Zetsche, Bernd; Gootenberg, Jonathan S; Abudayyeh, Omar O; Slaymaker, Ian M; Makarova, Kira S; Essletzbichler, Patrick; Volz, Sara E; Joung, Julia; van der Oost, John; Regev, Aviv; Koonin, Eugene V; Zhang, Feng.

Cell ; 163(3): 759-71, 2015 Oct 22.

Article in English | MEDLINE | ID: mdl-26422227

10.

The miniature CRISPR-Cas12m effector binds DNA to block transcription.

Wu, Wen Y; Mohanraju, Prarthana; Liao, Chunyu; Adiego-Pérez, Belén; Creutzburg, Sjoerd C A; Makarova, Kira S; Keessen, Karlijn; Lindeboom, Timon A; Khan, Tahseen S; Prinsen, Stijn; Joosten, Rob; Yan, Winston X; Migur, Anzhela; Laffeber, Charlie; Scott, David A; Lebbink, Joyce H G; Koonin, Eugene V; Beisel, Chase L; van der Oost, John.

Mol Cell ; 82(23): 4487-4502.e7, 2022 12 01.

Article in English | MEDLINE | ID: mdl-36427491

11.

Calorie restriction à Lamarck.

Koonin, Eugene V.

Cell ; 158(2): 237-238, 2014 Jul 17.

Article in English | MEDLINE | ID: mdl-25036622

12.

Structural atlas of a human gut crassvirus.

Bayfield, Oliver W; Shkoporov, Andrey N; Yutin, Natalya; Khokhlova, Ekaterina V; Smith, Jake L R; Hawkins, Dorothy E D P; Koonin, Eugene V; Hill, Colin; Antson, Alfred A.

Nature ; 617(7960): 409-416, 2023 05.

Article in English | MEDLINE | ID: mdl-37138077

13.

Evolution of cell division: from shear mechanics to complex molecular machineries.

Koonin, Eugene V; Mulkidjanian, Armen Y.

Cell ; 152(5): 942-4, 2013 Feb 28.

Article in English | MEDLINE | ID: mdl-23452845

14.

Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA.

Hirano, Seiichi; Kappel, Kalli; Altae-Tran, Han; Faure, Guilhem; Wilkinson, Max E; Kannan, Soumya; Demircioglu, F Esra; Yan, Rui; Shiozaki, Momoko; Yu, Zhiheng; Makarova, Kira S; Koonin, Eugene V; Macrae, Rhiannon K; Zhang, Feng.

Nature ; 610(7932): 575-581, 2022 10.

Article in English | MEDLINE | ID: mdl-36224386

15.

Mutation-selection balance and compensatory mechanisms in tumour evolution.

Persi, Erez; Wolf, Yuri I; Horn, David; Ruppin, Eytan; Demichelis, Francesca; Gatenby, Robert A; Gillies, Robert J; Koonin, Eugene V.

Nat Rev Genet ; 22(4): 251-262, 2021 04.

Article in English | MEDLINE | ID: mdl-33257848

16.

Programmable RNA targeting with the single-protein CRISPR effector Cas7-11.

Özcan, Ahsen; Krajeski, Rohan; Ioannidi, Eleonora; Lee, Brennan; Gardner, Apolonia; Makarova, Kira S; Koonin, Eugene V; Abudayyeh, Omar O; Gootenberg, Jonathan S.

Nature ; 597(7878): 720-725, 2021 09.

Article in English | MEDLINE | ID: mdl-34489594

17.

Expanded diversity of Asgard archaea and their relationships with eukaryotes.

Liu, Yang; Makarova, Kira S; Huang, Wen-Cong; Wolf, Yuri I; Nikolskaya, Anastasia N; Zhang, Xinxu; Cai, Mingwei; Zhang, Cui-Jing; Xu, Wei; Luo, Zhuhua; Cheng, Lei; Koonin, Eugene V; Li, Meng.

Nature ; 593(7860): 553-557, 2021 05.

Article in English | MEDLINE | ID: mdl-33911286

18.

Structure and function of virion RNA polymerase of a crAss-like phage.

Drobysheva, Arina V; Panafidina, Sofia A; Kolesnik, Matvei V; Klimuk, Evgeny I; Minakhin, Leonid; Yakunina, Maria V; Borukhov, Sergei; Nilsson, Emelie; Holmfeldt, Karin; Yutin, Natalya; Makarova, Kira S; Koonin, Eugene V; Severinov, Konstantin V; Leiman, Petr G; Sokolova, Maria L.

Nature ; 589(7841): 306-309, 2021 01.

Article in English | MEDLINE | ID: mdl-33208949

19.

Balance between asymmetric allocation and repair of somatic damage in unicellular life forms as an ancient form of r/K selection.

Biba, Dmitry A; Wolf, Yuri I; Koonin, Eugene V; Rochman, Nash D.

Proc Natl Acad Sci U S A ; 121(22): e2400008121, 2024 May 28.

Article in English | MEDLINE | ID: mdl-38787879

20.

Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins.

Krupovic, Mart; Kuhn, Jens H; Fischer, Matthias G; Koonin, Eugene V.

Proc Natl Acad Sci U S A ; 121(23): e2405771121, 2024 Jun 04.

Article in English | MEDLINE | ID: mdl-38805295

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