Eugene V Koonin (E Koonin, Eugene Koonin)

ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 167

Top Venues

Proceedings of the National Academy of Sciences of the United States of America

mBio

Nature communications

Science (New York, N.Y.)

NIH

This page only lists publications with an associated author ORCID identifier.

Affiliation History

NIH

United States

Senior Investigator :: National Center for Biotechnology Information

Publications

Han Altae-Tran, Soumya Kannan, Anthony J Suberski, Kepler S Mears, F Esra Demircioglu, Lukas Möller, Selin Kocalar, Rachel Oshiro, Kira S Makarova, Rhiannon K Macrae, Eugene V Koonin, Feng Zhang
Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. Science (New York, N.Y.) 382 (6673) (2023)
Oliver W Bayfield, Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, Jake L R Smith, Dorothy E D P Hawkins, Eugene V Koonin, Colin Hill, Alfred A Antson
Structural atlas of a human gut crassvirus. Nature 617 (7960) (2023)
Sergey A Shmakov, Zachary K Barth, Kira S Makarova, Yuri I Wolf, Vyacheslav Brover, Joseph E Peters, Eugene V Koonin
Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems. Nucleic acids research (2023)
Nash D Rochman, Eugene V Koonin
Learn from the past to predict viral pandemics. Nature (2023)
Eugene V Koonin
Antitoxins within toxins: A new theme in bacterial antivirus defense. Proceedings of the National Academy of Sciences of the United States of America 120 (31) (2023)
Sanasar G Babajanyan, Yuri I Wolf, Andranik Khachatryan, Armen Allahverdyan, Purificacion Lopez-Garcia, Eugene V Koonin
Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes. Proceedings of the National Academy of Sciences of the United States of America 120 (14) (2023)
Dillon S McBride, Sofya K Garushyants, John Franks, Andrew F Magee, Steven H Overend, Devra Huey, Amanda M Williams, Seth A Faith, Ahmed M Kandeil, Sanja Trifkovic, Lance Miller, Trushar Jeevan, Anami Patel, Jacqueline M Nolting, Michael J Tonkovich, J Tyler Genders, Andrew J Montoney, Kevin Kasnyik, Timothy J Linder, Sarah N Bevins, Julianna B Lenoch, Jeffrey C Chandler, Thomas J DeLiberto, Eugene V Koonin, Marc A Suchard, Philippe Lemey, Richard John Webby, Martha I Nelson, Andrew S Bowman
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer. Nature communications 14 (1) (2023)
Sanasar G Babajanyan, Yuri I Wolf, Andranik Khachatryan, Armen Allahverdyan, Purificacion Lopez-Garcia, Eugene V Koonin
Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes. Proceedings of the National Academy of Sciences of the United States of America 120 (14) (2023)
J Thomas Beatty, Eugene V Koonin
Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements. Biomolecules 13 (2) (2023)
Dillon S McBride, Sofya Garushyants, John Franks, Andrew Magee, Steven Overend, Devra Huey, Amanda Williams, Seth Faith, Ahmed M Kandeil, Sanja Trifkovic, Lance Miller, Trushar Jeevan, Anami Patel, Jacqueline M Nolting, Michael Tonkovich, J Tyler Genders, Andrew Montoney, Kevin Kasnyik, Timothy J Linder, Sarah Bevins, Julianna Lenoch, Jeffrey Chandler, Thomas DeLiberto, Eugene V Koonin, Marc A Suchard, Philippe Lemey, Richard John Webby, Martha I Nelson, Andrew S Bowman
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer. Research square (2023)
Oliver W Bayfield, Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, Jake L R Smith, Dorothy E D P Hawkins, Eugene V Koonin, Colin Hill, Alfred A Antson
Structural atlas of a human gut crassvirus. Nature 617 (7960) (2023)
Pascal Mutz, Wolfgang Resch, Guilhem Faure, Tatiana G Senkevich, Eugene V Koonin, Bernard Moss
Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling. mBio (2023)
J Thomas Beatty, Eugene V Koonin
Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements. Biomolecules 13 (2) (2023)
Erez Persi, Yuri I Wolf, Svetlana Karamycheva, Kira S Makarova, Eugene V Koonin
Compensatory relationship between low-complexity regions and gene paralogy in the evolution of prokaryotes. Proceedings of the National Academy of Sciences of the United States of America 120 (16) (2023)
Syun-Ichi Urayama, Akihito Fukudome, Miho Hirai, Tomoyo Okumura, Yosuke Nishimura, Yoshihiro Takaki, Norio Kurosawa, Eugene V Koonin, Mart Krupovic, Takuro Nunoura
Distinct groups of RNA viruses associated with thermoacidophilic bacteria. bioRxiv : the preprint server for biology (2023)
Changhai Duan, Yang Liu, Ying Liu, Lirui Liu, Mingwei Cai, Rui Zhang, Qinglu Zeng, Eugene V Koonin, Mart Krupovic, Meng Li
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components. bioRxiv : the preprint server for biology (2023)
Anamarija Butkovic, Simona Kraberger, Zoe Smeele, Darren P Martin, Kara Schmidlin, Rafaela S Fontenele, Michelle R Shero, Roxanne S Beltran, Amy L Kirkham, Maketalena Aleamotu'a, Jennifer M Burns, Eugene V Koonin, Darren P Martin, Mart Krupovic
Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus evolution 9 (1) (2023)
Dillon S McBride, Sofya Garushyants, John Franks, Andrew Magee, Steven Overend, Devra Huey, Amanda Williams, Seth Faith, Ahmed M Kandeil, Sanja Trifkovic, Lance Miller, Trushar Jeevan, Anami Patel, Jacqueline M Nolting, Michael Tonkovich, J Tyler Genders, Andrew Montoney, Kevin Kasnyik, Timothy J Linder, Sarah Bevins, Julianna Lenoch, Jeffrey Chandler, Thomas DeLiberto, Eugene V Koonin, Marc A Suchard, Philippe Lemey, Richard John Webby, Martha I Nelson, Andrew S Bowman
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer. Research square (2023)
Kaiyi Jiang, Justin Lim, Samantha R Sgrizzi, Michael Trinh, Alisan Kayabolen, Natalya Yutin, Weidong Bao, Kazuki Kato, Eugene V Koonin, Jonathan S Gootenberg, Omar O Abudayyeh
Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses. Science advances 9 (39) (2023)
Dillon S McBride, Sofya Garushyants, John Franks, Andrew Magee, Steven Overend, Devra Huey, Amanda Williams, Seth Faith, Ahmed M Kandeil, Sanja Trifkovic, Lance Miller, Trushar Jeevan, Anami Patel, Jacqueline M Nolting, Michael Tonkovich, J Tyler Genders, Andrew Montoney, Kevin Kasnyik, Timothy J Linder, Sarah Bevins, Julianna Lenoch, Jeffrey Chandler, Thomas DeLiberto, Eugene V Koonin, Marc A Suchard, Philippe Lemey, Richard John Webby, Martha I Nelson, Andrew S Bowman
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer. Research square (2023)
Han Altae-Tran, Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Soumya Kannan, Feng Zhang, Eugene V Koonin
Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12. Proceedings of the National Academy of Sciences of the United States of America 120 (48) (2023)
Harutyun Sahakyan, Kira S Makarova, Eugene V Koonin
Search for Origins of Anti-CRISPR Proteins by Structure Comparison. The CRISPR journal 6 (3) (2023)
J Thomas Beatty, Eugene V Koonin
Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements. Biomolecules 13 (2) (2023)
Shu-Kun Tang, Xiao-Yang Zhi, Yao Zhang, Kira S Makarova, Bing-Bing Liu, Guo-Song Zheng, Zhen-Peng Zhang, Hua-Jun Zheng, Yuri I Wolf, Yu-Rong Zhao, Song-Hao Jiang, Xi-Ming Chen, En-Yuan Li, Tao Zhang, Pei-Ru Chen, Yu-Zhou Feng, Ming-Xian Xiang, Zhi-Qian Lin, Jia-Hui Shi, Cheng Chang, Xue Zhang, Rui Li, Kai Lou, Yun Wang, Lei Chang, Min Yin, Ling-Ling Yang, Hui-Ying Gao, Zhong-Kai Zhang, Tian-Shen Tao, Tong-Wei Guan, Fu-Chu He, Yin-Hua Lu, Heng-Lin Cui, Eugene V Koonin, Guo-Ping Zhao, Ping Xu
Cellular differentiation into hyphae and spores in halophilic archaea. Nature communications 14 (1) (2023)
Mart Krupovic, Valerian V Dolja, Eugene V Koonin
The virome of the last eukaryotic common ancestor and eukaryogenesis. Nature microbiology (2023)
Oliver W Bayfield, Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, Jake L R Smith, Dorothy E D P Hawkins, Eugene V Koonin, Colin Hill, Alfred A Antson
Structural atlas of a human gut crassvirus. Nature 617 (7960) (2023)
Oliver W Bayfield, Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, Jake L R Smith, Dorothy E D P Hawkins, Eugene V Koonin, Colin Hill, Alfred A Antson
Structural atlas of a human gut crassvirus. Nature 617 (7960) (2023)
J Thomas Beatty, Eugene V Koonin
Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements. Biomolecules 13 (2) (2023)
Oliver W Bayfield, Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, Jake L R Smith, Dorothy E D P Hawkins, Eugene V Koonin, Colin Hill, Alfred A Antson
Structural atlas of a human gut crassvirus. Nature (2023)
Eugene V Koonin, Jonathan S Gootenberg, Omar O Abudayyeh
Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry (2023)
Oliver W Bayfield, Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, Jake L R Smith, Dorothy E D P Hawkins, Eugene V Koonin, Colin Hill, Alfred A Antson
Structural atlas of a human gut crassvirus. Nature 617 (7960) (2023)
Eugene V Koonin, Jonathan S Gootenberg, Omar O Abudayyeh
Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry (2023)
Sanasar G Babajanyan, Yuri I Wolf, Andranik Khachatryan, Armen Allahverdyan, Purificacion Lopez-Garcia, Eugene V Koonin
Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes. Proceedings of the National Academy of Sciences of the United States of America 120 (14) (2023)
Mart Krupovic, Kira S Makarova, Eugene V Koonin
Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom. Proceedings of the National Academy of Sciences of the United States of America 119 (5) (2022)
Vitaly Vanchurin, Yuri I Wolf, Eugene V Koonin, Mikhail I Katsnelson
Thermodynamics of evolution and the origin of life. Proceedings of the National Academy of Sciences of the United States of America 119 (6) (2022)
Natalya Yutin, Mikhail Rayko, Dmitry Antipov, Pascal Mutz, Yuri I Wolf, Mart Krupovic, Eugene V Koonin
Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales . Viruses 14 (9) (2022)
Eugene V Koonin, Mart Krupovic
A life LINE for large viruses. eLife 11 (2022)
Eugene V Koonin, Kira S Makarova
Evolutionary plasticity and functional versatility of CRISPR systems. PLoS biology 20 (1) (2022)
Haolin Zhang, Xuemei Gong, Qianqian Zhao, Takahito Mukai, Oscar Vargas-Rodriguez, Huiming Zhang, Yuxing Zhang, Paul Wassel, Kazuaki Amikura, Julie A Maupin-Furlow, Yan Ren, Xue Liu, Yuri I Wolf, Kira S Makarova, Eugene V Koonin, Yue Shen, Dieter Söll, Xian Fu
The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic acids research 50 (8) (2022)
Sean Benler, Guilhem Faure, Han-Altae Tran, Sergey Shmakov, Feng Zhang, Eugene V Koonin
Erratum for Benler et al., "Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes". mBio 13 (2) (2022)
Pascal Mutz, Nash D Rochman, Yuri I Wolf, Guilhem Faure, Feng Zhang, Eugene V Koonin
Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. Proceedings of the National Academy of Sciences of the United States of America 119 (23) (2022)
Jennifer Dahan, Yuri I Wolf, Gardenia E Orellana, Erik J Wenninger, Eugene V Koonin, Alexander V Karasev
A Novel Flavi-like Virus in Alfalfa ( Medicago sativa L.) Crops along the Snake River Valley. Viruses 14 (6) (2022)
Kang Hao Cheong, Tao Wen, Sean Benler, Jin Ming Koh, Eugene V Koonin
Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's paradox. Proceedings of the National Academy of Sciences of the United States of America 119 (13) (2022)
Kazuki Kato, Sae Okazaki, Soumya Kannan, Han Altae-Tran, F Esra Demircioglu, Yukari Isayama, Junichiro Ishikawa, Masahiro Fukuda, Rhiannon K Macrae, Tomohiro Nishizawa, Kira S Makarova, Eugene V Koonin, Feng Zhang, Hiroshi Nishimasu
Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9. Nature communications 13 (1) (2022)
Irina Sorokina, Arcady R Mushegian, Eugene V Koonin
Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? International journal of molecular sciences 23 (1) (2022)
Nash D Rochman, Guilhem Faure, Yuri I Wolf, Peter L Freddolino, Feng Zhang, Eugene V Koonin
Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape. mBio 13 (2) (2022)
Seiichi Hirano, Kalli Kappel, Han Altae-Tran, Guilhem Faure, Max E Wilkinson, Soumya Kannan, F Esra Demircioglu, Rui Yan, Momoko Shiozaki, Zhiheng Yu, Kira S Makarova, Eugene V Koonin, Rhiannon K Macrae, Feng Zhang
Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Nature 610 (7932) (2022)
Nash D Rochman, Yuri I Wolf, Eugene V Koonin
Molecular adaptations during viral epidemics. EMBO reports 23 (8) (2022)
Michael Y Galperin, Natalya Yutin, Yuri I Wolf, Roberto Vera Alvarez, Eugene V Koonin
Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes . Journal of bacteriology 204 (6) (2022)
Benjamin D Lee, Eugene V Koonin
Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators? Life (Basel, Switzerland) 12 (1) (2022)
Sofia Medvedeva, Jiarui Sun, Natalya Yutin, Eugene V Koonin, Takuro Nunoura, Christian Rinke, Mart Krupovic
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nature microbiology 7 (7) (2022)
Linyi Alex Gao, Max E Wilkinson, Jonathan Strecker, Kira S Makarova, Rhiannon K Macrae, Eugene V Koonin, Feng Zhang
Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science (New York, N.Y.) 377 (6607) (2022)
Kazuki Kato, Sae Okazaki, Cian Schmitt-Ulms, Kaiyi Jiang, Wenyuan Zhou, Junichiro Ishikawa, Yukari Isayama, Shungo Adachi, Tomohiro Nishizawa, Kira S Makarova, Eugene V Koonin, Omar O Abudayyeh, Jonathan S Gootenberg, Hiroshi Nishimasu
RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Science (New York, N.Y.) 378 (6622) (2022)
Vitaly Vanchurin, Yuri I Wolf, Mikhail I Katsnelson, Eugene V Koonin
Toward a theory of evolution as multilevel learning. Proceedings of the National Academy of Sciences of the United States of America 119 (6) (2022)
R Astashkin, Kirill V Kovalev, S Bukhdruker, S Vaganova, Alexander Kuzmin, A Alekseev, T Balandin, Dmitrii V Zabelskii, Ivan Yu Gushchin, A Royant, Dmytro A Volkov, Gleb Bourenkov, Eugene V Koonin, Martin Engelhard, E Bamberg, Valentin I Gordeliy
Structural insights into light-driven anion pumping in cyanobacteria. Nature communications 13 (1) (2022)
Eugene V Koonin, Valerian V Dolja, Mart Krupovic, J Thomas Beatty
Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiology and molecular biology reviews : MMBR (2021)
Ahsen Özcan, Rohan Krajeski, Eleonora Ioannidi, Brennan Lee, Apolonia Gardner, Kira S Makarova, Eugene V Koonin, Omar O Abudayyeh, Jonathan S Gootenberg
Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. Nature 597 (7878) (2021)
Han Altae-Tran, Soumya Kannan, F Esra Demircioglu, Rachel Oshiro, Suchita P Nety, Luke J McKay, Mensur Dlakić, William P Inskeep, Kira S Makarova, Rhiannon K Macrae, Eugene V Koonin, Feng Zhang
The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science (New York, N.Y.) 374 (6563) (2021)
Nash D Rochman, Yuri I Wolf, Guilhem Faure, Pascal Mutz, Feng Zhang, Eugene V Koonin
Ongoing global and regional adaptive evolution of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 118 (29) (2021)
Noam Auslander, Ayal B Gussow, Eugene V Koonin
Incorporating Machine Learning into Established Bioinformatics Frameworks. International journal of molecular sciences 22 (6) (2021)
Benjamin D Lee, Uri Neri, Caleb J Oh, Peter Simmonds, Eugene V Koonin
ViroidDB: a database of viroids and viroid-like circular RNAs. Nucleic acids research (2021)
Natalya Yutin, Sean Benler, Sergei A Shmakov, Yuri I Wolf, Igor Tolstoy, Mikhail Rayko, Dmitry Antipov, Pavel A Pevzner, Eugene V Koonin
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nature communications 12 (1) (2021)
Dmitrii V Zabelskii, Natalia Dmitrieva, Oleksandr Volkov, Vitaly Shevchenko, Kirill Kovalev, Taras Balandin, Dmytro V Soloviov, Roman Astashkin, Egor Zinovev, Alexey Alekseev, Ekaterina Round, Vitaly Polovinkin, Igor Chizhov, Andrey Rogachev, Ivan Okhrimenko, Valentin I Borshchevskiy, Vladimir Chupin, Georg Büldt, Natalya Yutin, Ernst Bamberg, Eugene V Koonin, Valentin I Gordeliy
Structure-based insights into evolution of rhodopsins. Communications biology 4 (1) (2021)
Nash D Rochman, Yuri Wolf, Eugene V Koonin
Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics. F1000Research 10 (2021)
Bogdan Kirillov, Ekaterina Savitskaya, Maxim Panov, Aleksey Y Ogurtsov, Svetlana A Shabalina, Eugene V Koonin, Konstantin V Severinov
Uncertainty-aware and interpretable evaluation of Cas9-gRNA and Cas12a-gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning. Nucleic acids research (2021)
Nash D Rochman, Yuri Wolf, Eugene V Koonin
Evolution of human respiratory virus epidemics. F1000Research 10 (2021)
Igor A Fesenko, Svetlana A Shabalina, Anna Mamaeva, Andrey Knyazev, Anna Glushkevich, Irina Lyapina, Rustam Ziganshin, Sergey Kovalchuk, Daria Kharlampieva, Vassili Lazarev, Michael Taliansky, Eugene V Koonin
A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic acids research 49 (18) (2021)
Nash D Rochman, Yuri Wolf, Eugene V Koonin
Evolution of human respiratory virus epidemics. F1000Research 10 (2021)
Soumya Kannan, Han Altae-Tran, Xin Jin, Victoria J Madigan, Rachel Oshiro, Kira S Makarova, Eugene V Koonin, Feng Zhang
Compact RNA editors with small Cas13 proteins. Nature biotechnology (2021)
Sean Benler, Guilhem Faure, Han Altae-Tran, Sergey Shmakov, Feng Zheng, Eugene V Koonin
Cargo Genes of Tn7-Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes. mBio (2021)
Sofya K Garushyants, Igor B Rogozin, Eugene V Koonin
Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring. Communications biology 4 (1) (2021)
Michael Y Galperin, Yuri I Wolf, Sofya K Garushyants, Roberto Vera Alvarez, Eugene V Koonin
Non-essential ribosomal proteins in bacteria and archaea identified using COGs. Journal of bacteriology (2021)
Yuri Bakhtin, Mikhail I Katsnelson, Yuri I Wolf, Eugene V Koonin
Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape. Proceedings of the National Academy of Sciences of the United States of America 118 (4) (2021)
Nash D Rochman, Yuri Wolf, Eugene V Koonin
Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics. F1000Research 10 (2021)
Sean Benler, Natalya Yutin, Dmitry Antipov, Mikhail Rayko, Sergey Shmakov, Ayal B Gussow, Pavel Pevzner, Eugene V Koonin
Thousands of previously unknown phages discovered in whole-community human gut metagenomes. Microbiome 9 (1) (2021)
Ming Li, Luyao Gong, Feiyue Cheng, Haiying Yu, Dahe Zhao, Rui Wang, Tian Wang, Shengjie Zhang, Jian Zhou, Sergey A Shmakov, Eugene V Koonin, Hua Xiang
Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems. Science (New York, N.Y.) 372 (6541) (2021)
Emma S Esterman, Yuri I Wolf, Roman Kogay, Eugene V Koonin, Olga Zhaxybayeva
Evolution of DNA packaging in gene transfer agents. Virus evolution 7 (1) (2021)
Ayal B Gussow, Eugene V Koonin, Noam Auslander
Identification of combinations of somatic mutations that predict cancer survival and immunotherapy benefit. NAR cancer 3 (2) (2021)
Gengxiang Zhao, Dalibor Kosek, Hong-Bing Liu, Shannon I Ohlemacher, Brittney Blackburne, Anastasia Nikolskaya, Kira S Makarova, Jiadong Sun, Clifton E Barry Iii, Eugene V Koonin, Fred Dyda, Carole A Bewley
Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product. Journal of the American Chemical Society 143 (21) (2021)
Yang Liu, Kira S Makarova, Wen-Cong Huang, Yuri I Wolf, Anastasia N Nikolskaya, Xinxu Zhang, Mingwei Cai, Cui-Jing Zhang, Wei Xu, Zhu-Hua Luo, Lei Cheng, Eugene V Koonin, Meng Li
Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593 (7860) (2021)
Michael Segel, Blake Lash, Jingwei Song, Alim Ladha, Catherine C Liu, Xin Jin, Sergei L Mekhedov, Rhiannon K Macrae, Eugene V Koonin, Feng Zhang
Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery. Science (New York, N.Y.) 373 (6557) (2021)
Eugene V Koonin, Mart Krupovic, Sonoko Ishino, Yoshizumi Ishino
The replication machinery of LUCA: common origin of DNA replication and transcription. BMC biology 18 (1) (2020)
Sean Benler, Eugene V Koonin
Phage lysis-lysogeny switches and programmed cell death: Danse macabre. BioEssays : news and reviews in molecular, cellular and developmental biology 42 (12) (2020)
Mart Krupovic, Natalya Yutin, Eugene V Koonin
Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase. Virus evolution 6 (2) (2020)
Guilhem Faure, Sergey A Shmakov, Winston X Yan, David R Cheng, David A Scott, Joseph E Peters, Kira S Makarova, Eugene V Koonin
CRISPR-Cas in mobile genetic elements: counter-defence and beyond. Nature reviews. Microbiology 17 (8) (2020)
Ayal B Gussow, Noam Auslander, Guilhem Faure, Yuri I Wolf, Feng Zhang, Eugene V Koonin
Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proceedings of the National Academy of Sciences of the United States of America 117 (26) (2020)
Ayal B Gussow, Noam Auslander, Yuri I Wolf, Eugene V Koonin
Prediction of the incubation period for COVID-19 and future virus disease outbreaks. BMC biology 18 (1) (2020)
Dmitrii V Zabelskii, Alexey Alekseev, Kirill Kovalev, Vladan Rankovic, Taras Balandin, Dmytro V Soloviov, Dmitry Bratanov, Ekaterina Savelyeva, Elizaveta Podolyak, Dmytro A Volkov, Svetlana Vaganova, Roman Astashkin, Igor Chizhov, Natalia Yutin, Maksim Rulev, Alexander Popov, Ana-Sofia Eria-Oliveira, Tatyana I Rokitskaya, Thomas Mager, Yuri Antonenko, Riccardo Rosselli, Grigoriy Armeev, Konstantin V Shaitan, Michel Vivaudou, Georg Büldt, Andrey Rogachev, Francisco Rodriguez-Valera, Mikhail Kirpichnikov, Tobias Moser, Andreas Offenha Usser, Dieter Willbold, Eugene V Koonin, Ernst Bamberg, Valentin I Gordeliy
Viral rhodopsins 1 are an unique family of light-gated cation channels. Nature communications 11 (1) (2020)
Yuri I Wolf, Sukrit Silas, Yongjie Wang PhD, Shuang Wu, Michael Bocek, Darius Kazlauskas, Mart Krupovic, Andrew Z Fire, Valerian V Dolja, Eugene V Koonin
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. Nature microbiology 5 (10) (2020)
Nash D Rochman, Yuri I Wolf, Eugene V Koonin
Deep phylogeny of cancer drivers and compensatory mutations. Communications biology 3 (1) (2020)
Eugene V Koonin, Yuri I Wolf, Mikhail I Katsnelson
No waves of intelligent design. Proceedings of the National Academy of Sciences of the United States of America 117 (33) (2020)
Roman Kogay, Yuri I Wolf, Eugene V Koonin, Olga Zhaxybayeva
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. mBio 11 (4) (2020)
Erez Persi, Yuri I Wolf, David Horn, Eytan Ruppin, Francesca Demichelis, Robert A Gatenby, Robert J Gillies, Eugene V Koonin
Mutation-selection balance and compensatory mechanisms in tumour evolution. Nature reviews. Genetics 22 (4) (2020)
Jonathan Strecker, Alim Ladha, Kira S Makarova, Eugene V Koonin, Feng Zhang
Response to Comment on "RNA-guided DNA insertion with CRISPR-associated transposases". Science (New York, N.Y.) 368 (6495) (2020)
Mart Krupovic, Darren P Martin, Darius Kazlauskas, Mya Breitbart, Eric L Delwart, Karyna Rosario, Natalya Yutin, Yuri I Wolf, Balázs Harrach, Francisco Murilo Zerbini, Valerian V Dolja, J Thomas Beatty, Eugene V Koonin
Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes. Journal of virology 94 (12) (2020)
Kuttichantran Subramaniam, Donald C Behringer, Jamie Bojko, Natalya Yutin, Abigail S Clark, Kelly S Bateman, Ronny van Aerle, David Bass, Rose C Kerr, Eugene V Koonin, Grant D Stentiford, Thomas B Waltzek
A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes. mBio 11 (1) (2020)
Arina V Drobysheva, Sofia A Panafidina, Matvei V Kolesnik, Evgeniy I Klimuk, Leonid Minakhin, Maria V Yakunina, Sergei Borukhov, Emelie Nilsson, Karin Holmfeldt, Natalya Yutin, Kira S Makarova, Eugene V Koonin, Konstantin V Severinov, Petr G Leiman, Maria L Sokolova
Structure and function of virion RNA polymerase of a crAss-like phage. Nature 589 (7841) (2020)
Mart Krupovic, Valerian V Dolja, Eugene V Koonin
The LUCA and its complex virome. Nature reviews. Microbiology 18 (11) (2020)
Ayal B Gussow, Allyson E Park, Adair L Borges, Sergey A Shmakov, Kira S Makarova, Yuri I Wolf, Joseph Bondy-Denomy, Eugene V Koonin
Machine-learning approach expands the repertoire of anti-CRISPR protein families. Nature communications 11 (1) (2020)
Roman Kogay, Yuri I Wolf, Eugene V Koonin, Olga Zhaxybayeva
Erratum for Kogay et al., "Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents". mBio 11 (6) (2020)

Eugene V Koonin.css-eqlu8i{font-size:small;padding-left:4px;} (E Koonin, Eugene Koonin)

Publication Activity (10 Years)

Top Topics

Top Venues

Eugene V Koonin (E Koonin, Eugene Koonin)