Academic lineage
Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox
- Eugene V Koonin, Jonathan S Gootenberg, Omar O Abudayyeh, Eugene V Koonin, Jonathan S Gootenberg, Omar O Abudayyeh
- Biochemistry, 10.1021/acs.biochem.3c00159
Structural atlas of a human gut crassvirus
- Andrey N Shkoporov, Natalya Yutin, Ekaterina V Khokhlova, …, Eugene V Koonin, Colin Hill, Alfred A Antson
- Nature, 10.1038/s41586-023-06019-2
The virome of the last eukaryotic common ancestor and eukaryogenesis
- Valerian V Dolja, Valerian V Dolja, Valerian V Dolja, …, Mart Krupovic, Valerian V Dolja, Eugene V Koonin
- Nat Microbiol, 10.1038/s41564-023-01378-y
Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems
- Sergey A Shmakov, Zachary K Barth, Kira S Makarova, …, Vyacheslav Brover, Joseph E Peters, Eugene V Koonin
- None, 10.1101/2023.03.03.530964
Widespread PRC barrel proteins play critical roles in archaeal cell division
- Shan Zhao, Kira S Makarova, Wenchao Zheng, …, Xiangdong Chen, Eugene V Koonin, Shishen Du
- None, 10.1101/2023.03.28.534520
Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling
- Pascal Mutz, Wolfgang Resch, Guilhem Faure, …, Tatiana G Senkevich, Eugene V Koonin, Bernard Moss
- mBio, 10.1128/mbio.00408-23
Cellular differentiation into hyphae and spores in halophilic archaea
- Xiao-Yang Zhi, Yao Zhang, Kira S Makarova, …, Eugene V Koonin, Guo-Ping Zhao, Ping Xu
- Nat Commun, 10.1038/s41467-023-37389-w
Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes
- Sanasar G Babajanyan, Yuri I Wolf, Andranik Khachatryan, …, Armen Allahverdyan, Purificacion Lopez-Garcia, Eugene V Koonin
- Proc Natl Acad Sci U S A, 10.1073/pnas.2301522120
In Silico Approaches for Prediction of Anti-CRISPR Proteins
- Kira S Makarova, Yuri I Wolf, Eugene V Koonin, …, Kira S Makarova, Yuri I Wolf, Eugene V Koonin
- J Mol Biol, 10.1016/j.jmb.2023.168036
Protocol for comparing gene-level selection on coding mutations between two groups of samples with Coselens
- Jaime Iranzo, George Gruenhagen, Jorge Calle-Espinosa, …, George Gruenhagen, Jorge Calle-Espinosa, Eugene V Koonin
- STAR Protoc, 10.1016/j.xpro.2023.102117
Four principles to establish a universal virus taxonomy
- Peter Simmonds, Evelien M Adriaenssens, F Murilo Zerbini, …, Anne-Mieke Vandamme, Arvind Varsani, Nikos Vasilakis
- PLoS Biol, 10.1371/journal.pbio.3001922
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
- Scott Adkins, Sergey V Alkhovsky, Tatjana Avšič-Županc, …, Gongyin Ye, Yong-Zhen Zhang, Arnfinn Lodden Økland
- Arch Virol, 10.1007/s00705-022-05546-z
The miniature CRISPR-Cas12m effector binds DNA to block transcription
- Wen Y Wu, Prarthana Mohanraju, Chunyu Liao, …, Eugene V Koonin, Chase L Beisel, John van der Oost
- Mol Cell, 10.1016/j.molcel.2022.11.003
RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease
- Kazuki Kato, Sae Okazaki, Cian Schmitt-Ulms, …, Omar O Abudayyeh, Jonathan S Gootenberg, Hiroshi Nishimasu
- Science, 10.1126/science.add7347
Host age structure reshapes parasite symbiosis: collaboration begets pathogens, competition begets virulent mutualists
- Carsten O S Portner, Edward G Rong, Jared A Ramirez, …, Angelique P Bosse, Eugene V Koonin, Nash D Rochman
- Biol Direct, 10.1186/s13062-022-00343-9
Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity
- Na Liu, Danping Liu, Kexin Li, …, Kexin Li, Songnian Hu, Zilong He
- Microbiol Spectr, 10.1128/spectrum.03117-22
Structural insights into light-driven anion pumping in cyanobacteria
- R Astashkin, K Kovalev, S Bukhdruker, …, M Engelhard, E Bamberg, V Gordeliy
- Nat Commun, 10.1038/s41467-022-34019-9
Expansion of the global RNA virome reveals diverse clades of bacteriophages
- Uri Neri, Yuri I Wolf, Simon Roux, …, Nikos C Kyrpides, Eugene V Koonin, Uri Gophna
- Cell, 10.1016/j.cell.2022.08.023
Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales
- Natalya Yutin, Mike Rayko, Dmitry Antipov, …, Yuri I Wolf, Mart Krupovic, Eugene V Koonin
- Viruses, 10.3390/v14091842
Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions
- Svetlana Karamycheva, Yuri I Wolf, Erez Persi, Eugene V Koonin, Kira S Makarova
- Biol Direct, 10.1186/s13062-022-00337-7
Pervasive conditional selection of driver mutations and modular epistasis networks in cancer
- Jaime Iranzo, George Gruenhagen, Jorge Calle-Espinosa, Eugene V Koonin
- Cell Rep, 10.1016/j.celrep.2022.111272
Author Correction: Programmable RNA targeting with the single-protein CRISPR effector Cas7-11
- Ahsen Özcan, Rohan Krajeski, Eleonora Ioannidi, …, Eugene V Koonin, Omar O Abudayyeh, Jonathan S Gootenberg
- Nature, 10.1038/s41586-022-05003-6
Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?
- Benjamin D Lee, Eugene V Koonin
- None, 10.3390/life12010103
Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?
- Irina Sorokina, Arcady R Mushegian, Eugene V Koonin
- Int J Mol Sci, 10.3390/ijms23010521
Evolutionary plasticity and functional versatility of CRISPR systems
- Eugene V Koonin, Kira S Makarova
- PLoS Biol, 10.1371/journal.pbio.3001481
Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring
- Sofya K Garushyants, Igor B Rogozin, Eugene V Koonin, Sofya K Garushyants, Igor B Rogozin, Eugene V Koonin
- Commun Biol, 10.1038/s42003-021-02858-9
Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
- Jens H Kuhn, Scott Adkins, Bernard R Agwanda, …, Jinguo Zhang, Zhe Zhang, Xueping Zhou
- Arch Virol, 10.1007/s00705-021-05266-w
ViroidDB: a database of viroids and viroid-like circular RNAs
- Benjamin D Lee, Uri Neri, Caleb J Oh, Peter Simmonds, Eugene V Koonin
- Nucleic Acids Res, 10.1093/nar/gkab974
A three-organelle complex made by wrappER contacts with peroxisomes and mitochondria responds to liver lipid flux changes
- Nicolò Ilacqua, Irene Anastasia, Andrea Raimondi, …, Katalin Toth, Eugene V Koonin, Luca Pellegrini
- J Cell Sci, 10.1242/jcs.259091
Thousands of previously unknown phages discovered in whole-community human gut metagenomes
- Sean Benler, Natalya Yutin, Dmitry Antipov, …, Ayal B Gussow, Pavel Pevzner, Eugene V Koonin
- Microbiome, 10.1186/s40168-021-01017-w
Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase
- Mart Krupovic, Natalya Yutin, Eugene Koonin
- None, 10.1093/ve/veaa059
Unprecedented Diversity of Unique CRISPR-Cas-Related Systems and Cas1 Homologs in Asgard Archaea
- Kira S Makarova, Yuri I Wolf, Sergey A Shmakov, Yang Liu, Meng Li, Eugene V Koonin
- CRISPR J, 10.1089/crispr.2020.0012
Evolution in the weak-mutation limit: Stasis periods punctuated by fast transitions between saddle points on the fitness landscape
- Yuri Bakhtin, Mikhail I Katsnelson, Yuri I Wolf, Eugene V Koonin
- Proc Natl Acad Sci U S A, 10.1073/pnas.2015665118