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Authors
Eugene V. Koonin

Eugene V. Koonin

National Institutes of Health

ORCID: 0000-0003-3943-8299

Also affiliated with United States National Library of Medicine, National Center for Biotechnology Information

Biochemistry, Genetics and Molecular BiologyEnvironmental ScienceAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

12.9Author DataRank

Indexed papers

15in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 15 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Top data-sharing exemplar

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Nucleic Acids Research(2020)10.1093/nar/gkaa1018

Top 3%

5.9DataRank

Top 3%1021 citations

Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin +1 more

Papers

Driven by 220 papers — median percentile 61. Top paper: “Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs”.

Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs

Proceedings of the National Academy of Sciences(1997)10.1073/pnas.94.11.5831

N/A

14.6DataRank · unranked

235 citations

Douglas E. Bassett, Mark S. Boguski, Peer Bork, Eugene V. Koonin, Arcady R. Mushegian

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

Genome Research(2003)10.1101/gr.1589103

N/A

14.1DataRank · unranked

412 citations

Yuri I. Wolf, Igor B. Rogozin, Eugene V. Koonin, Dmitri M. Krylov

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Nucleic Acids Research(2020)10.1093/nar/gkaa1018

Top 3%

5.9DataRank

Top 3%1021 citations

Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin +1 more

Seeker: alignment-free identification of bacteriophage genomes by deep learning

Nucleic Acids Research(2020)10.1093/nar/gkaa856

N/A

3.8DataRank · unranked

144 citations

Ayal B. Gussow, Sean Benler, Yuri I. Wolf, Eugene V. Koonin, Noam Auslander

RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease

Science(2022)10.1126/science.add7347

N/A

2.4DataRank · unranked

57 citations

Sae Okazaki, Cian Schmitt-Ulms, Kaiyi Jiang, Wenyuan Zhou, Junichiro Ishikawa +9 more

Evidence of Splice Signal Migration from Exon to Intron during Intron Evolution

Current Biology(2003)10.1016/j.cub.2003.12.003

N/A

2.0DataRank · unranked

43 citations

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, Alexander V. Sverdlov

Template switching and duplications in SARS-CoV-2 genomes give rise to insertion variants that merit monitoring

Communications Biology(2021)10.1038/s42003-021-02858-9

N/A

1.9DataRank · unranked

53 citations

Igor B. Rogozin, Eugene V. Koonin, Sofya K. Garushyants

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Archives of Virology(2022)10.1007/s00705-022-05546-z

N/A

1.9DataRank · unranked

90 citations

Scott Adkins, Sergey V. Alkhovsky, Tatjana Avšič‐Županc, Marı́a A. Ayllón, Justin Bahl +95 more

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

bioRxiv (Cold Spring Harbor Laboratory)(2016)10.1101/054742

N/A

1.8DataRank · unranked

46 citations

Jonathan S. Gootenberg, Silvana Konermann, Julia Joung, Ian M. Slaymaker, David B.T. Cox +11 more

COG database update 2024

Nucleic Acids Research(2024)10.1093/nar/gkae983

Top 13%

1.5DataRank

Top 13%128 citations

Roberto Vera Alvarez, Svetlana Karamycheva, Kira S. Makarova, Yuri I. Wolf, David Landsman +2 more

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Journal of General Virology(2023)10.1099/jgv.0.001864

Top 14%

1.5DataRank

Top 14%78 citations

Junya Abe, Scott Adkins, Sergey V. Alkhovsky, Tatjana Avšič‐Županc, Marı́a A. Ayllón +95 more

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

Cell(2015)10.1016/j.cell.2015.09.038

N/A

1.3DataRank · unranked

4816 citations

Jonathan S. Gootenberg, Omar O. Abudayyeh, Ian M. Slaymaker, Kira S. Makarova, Patrick Essletzbichler +7 more

Nucleic acid detection with CRISPR-Cas13a/C2c2

Science(2017)10.1126/science.aam9321

N/A

1.2DataRank · unranked

3722 citations

Omar O. Abudayyeh, Jeong Wook Lee, Patrick Essletzbichler, Aaron J. Dy, Julia Joung +15 more

Nonessential Ribosomal Proteins in Bacteria and Archaea Identified Using Clusters of Orthologous Genes

Journal of Bacteriology(2021)10.1128/jb.00058-21

Top 17%

1.2DataRank

Top 17%44 citations

Yuri I. Wolf, Sofya K. Garushyants, Roberto Vera Alvarez, Eugene V. Koonin, Michael Y. Galperin

Diverse enzymatic activities mediate antiviral immunity in prokaryotes

Science(2020)10.1126/science.aba0372

N/A

0.978DataRank · unranked

676 citations

Han Altae-Tran, Francisca Böhning, Kira S. Makarova, Michael Segel, Jonathan L. Schmid-Burgk +5 more

Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein

Virus Evolution(2023)10.1093/ve/vead035

N/A

0.976DataRank · unranked

46 citations

Simona Kraberger, Zoe E. Smeele, Darren P. Martin, Kara Schmidlin, Rafaela S. Fontenele +9 more

Global Organization and Proposed Megataxonomy of the Virus World

Microbiology and Molecular Biology Reviews(2020)10.1128/mmbr.00061-19

N/A

0.965DataRank · unranked

622 citations

Valerian V. Dolja, Mart Krupovìč, Arvind Varsani, Yuri I. Wolf, Natalya Yutin +3 more

Selection for short introns in highly expressed genes

Nature Genetics(2002)10.1038/ng940

N/A

0.947DataRank · unranked

551 citations

Sergei L. Mekhedov, Daniel L. Hartl, Eugene V. Koonin, Fyodor A. Kondrashov, Cristian I. Castillo-Davis

Expanded diversity of Asgard archaea and their relationships with eukaryotes

Nature(2021)10.1038/s41586-021-03494-3

N/A

0.877DataRank · unranked

346 citations

Kira S. Makarova, Wen-Cong Huang, Yuri I. Wolf, A. N. NIKOL'SKAYA, Xinxu Zhang +8 more

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

Nature Microbiology(2020)10.1038/s41564-020-0755-4

N/A

0.849DataRank · unranked

286 citations

Sukrit Silas, Yongjie Wang, Shuang Wu, M Bocek, Darius Kazlauskas +5 more

Prokaryotic innate immunity through pattern recognition of conserved viral proteins

Science(2022)10.1126/science.abm4096

N/A

0.832DataRank · unranked

255 citations

Max E. Wilkinson, Jonathan Strecker, Kira S. Makarova, Rhiannon K. Macrae, Eugene V. Koonin +2 more

A phylogenomic framework for charting the diversity and evolution of giant viruses

PLoS Biology(2021)10.1371/journal.pbio.3001430

N/A

0.811DataRank · unranked

222 citations

Mohammad Moniruzzaman, Anh D. Ha, Eugene V. Koonin, Frank O. Aylward

ViroidDB: a database of viroids and viroid-like circular RNAs

Nucleic Acids Research(2021)10.1093/nar/gkab974

Top 25%

0.797DataRank

Top 25%25 citations

Uri Neri, Caleb J Oh, Peter Simmonds, Eugene V. Koonin, Benjamin D. Lee

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Microbiome(2021)10.1186/s40168-021-01017-w

N/A

0.795DataRank · unranked

199 citations

Natalya Yutin, Dmitry Antipov, Mikhail Rayko, Sergey Shmakov, Ayal B. Gussow +3 more

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

Nature Communications(2021)10.1038/s41467-021-21350-w

N/A

0.788DataRank · unranked

190 citations

Sean Benler, Sergei A. Shmakov, Yuri I. Wolf, Igor Tolstoy, Mikhail Rayko +4 more

Ancient Gene Capture and Recent Gene Loss Shape the Evolution of Orthopoxvirus-Host Interaction Genes

mBio(2021)10.1128/mbio.01495-21

N/A

0.757DataRank · unranked

154 citations

Natalya Yutin, Yuri I. Wolf, Eugene V. Koonin, Bernard Moss, Tatiana G. Senkevich

Microbial transmission in the social microbiome and host health and disease

Cell(2024)10.1016/j.cell.2023.12.014

N/A

0.722DataRank · unranked

122 citations

Cameron J.A. McInroy, Siobhán Harty, Aura Raulo, Neil G.O. Ibata, Mireia Valles‐Colomer +11 more

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer

Cell Reports(2022)10.1016/j.celrep.2022.111272

N/A

0.685DataRank · unranked

22 citations

George W. Gruenhagen, Jorge Calle-Espinosa, Eugene V. Koonin, Jaime Iranzo

Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox

Biochemistry(2023)10.1021/acs.biochem.3c00159

N/A

0.683DataRank · unranked

94 citations

Jonathan S. Gootenberg, Omar O. Abudayyeh, Eugene V. Koonin

A Phylogenomic Framework for Charting the Diversity and Evolution of Giant Viruses

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.05.442809

N/A

0.654DataRank · unranked

21 citations

Mohammad Moniruzzaman, Anh D. Ha, Eugene V. Koonin, Frank O. Aylward

Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century

Trends in Microbiology(2021)10.1016/j.tim.2021.01.005

N/A

0.652DataRank · unranked

76 citations

Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin

An updated evolutionary classification of CRISPR–Cas systems including rare variants

Nature Microbiology(2025)10.1038/s41564-025-02180-8

N/A

0.633DataRank · unranked

67 citations

Sergey Shmakov, Yuri I. Wolf, Pascal Mutz, Han Altae-Tran, Chase L. Beisel +24 more

Megataxonomy and global ecology of the virosphere

The ISME Journal(2024)10.1093/ismejo/wrad042

N/A

0.628DataRank · unranked

65 citations

Jens H. Kuhn, Valerian V. Dolja, Mart Krupovìč, Eugene V. Koonin

The Structure and Evolution of Penelope in the virilis Species Group of Drosophila: An Ancient Lineage of Retroelements

Journal of Molecular Evolution(2001)10.1007/s002390010174

N/A

0.593DataRank · unranked

51 citations

Kira S. Makarova, Vera V. Velikodvorskaja, Helena S. Zelentsova, Ruben R. Khechumian, Margaret G. Kidwell +3 more

Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process?

International Journal of Molecular Sciences(2022)10.3390/ijms23010521

N/A

0.590DataRank · unranked

50 citations

Arcady Mushegian, Eugene V. Koonin, Irina Sorokina

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(2022)10.1073/pnas.2120620119

N/A

0.590DataRank · unranked

50 citations

Kira S. Makarova, Eugene V. Koonin, Mart Krupovìč

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025

Journal of General Virology(2025)10.1099/jgv.0.002111

N/A

0.566DataRank · unranked

28 citations

Evelien M. Adriaenssens, Rudolf Amann, Pavol Bárdy, Nina Bartlau, Jakub Barylski +68 more

Adnaviria : a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes

Journal of Virology(2021)10.1128/jvi.00673-21

N/A

0.553DataRank · unranked

39 citations

Jens H. Kuhn, Fengbin Wang, Diana P. Baquero, Valerian V. Dolja, Edward H. Egelman +3 more

Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability

Nature Communications(2020)10.1038/s41467-020-15094-2

N/A

0.553DataRank · unranked

39 citations

Yuri I. Wolf, Eugene V. Koonin, Noam Auslander

Extending the Lifespan of Multicellular Organisms via Periodic and Stochastic Intercellular Competition

Physical Review Letters(2022)10.1103/physrevlett.128.218101

N/A

0.550DataRank · unranked

38 citations

Kang Hao Cheong, Joel Weijia Lai, Jin Ming Koh, Eugene V. Koonin, Tao Wen

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

Cell(2025)10.1016/j.cell.2025.01.034

N/A

0.546DataRank · unranked

37 citations

Han Altae-Tran, Soumya Kannan, Max E. Wilkinson, Samuel Chau-Duy-Tam Vo, Daniel Strebinger +9 more

Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan

Nature Microbiology(2024)10.1038/s41564-023-01579-5

N/A

0.542DataRank · unranked

36 citations

Akihito Fukudome, Miho Hirai, Tomoyo Okumura, Yosuke Nishimura, Yoshihiro Takaki +5 more

The hidden bacterial microproteome

Molecular Cell(2025)10.1016/j.molcel.2025.01.025

N/A

0.538DataRank · unranked

35 citations

Harutyun Sahakyan, Rajat Dhyani, Svetlana A. Shabalina, Gisela Storz, Eugene V. Koonin +1 more

Modularity and diversity of target selectors in Tn7 transposons

Molecular Cell(2023)10.1016/j.molcel.2023.05.013

N/A

0.533DataRank · unranked

34 citations

Makoto Saito, Sean Benler, Iris Peng, Yuri I. Wolf, Jonathan Strecker +8 more

Evolution of regulatory signatures in primate cortical neurons at cell-type resolution

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2011884117

N/A

0.524DataRank · unranked

32 citations

Marit W. Vermunt, Pasha Apontes, Junhao Li, Ke Hao, Chet C. Sherwood +8 more

Activation of bacterial programmed cell death by phage inhibitors of host immunity

Molecular Cell(2025)10.1016/j.molcel.2025.04.010

N/A

0.521DataRank · unranked

15 citations

Héloïse Carion, Kira S. Makarova, Eric Laderman, Thomas C. Todeschini, Pradeep Kumar +6 more

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(2021)10.1021/jacs.1c02316

N/A

0.520DataRank · unranked

31 citations

Dalibor Košek, Hongbing Liu, Shannon I. Ohlemacher, Brittney Blackburne, A. N. NIKOL'SKAYA +7 more

Phage lysis‐lysogeny switches and programmed cell death: Danse macabre

BioEssays(2020)10.1002/bies.202000114

N/A

0.520DataRank · unranked

31 citations

Eugene V. Koonin, Sean Benler

Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems

Nucleic Acids Research(2023)10.1093/nar/gkad495

N/A

0.510DataRank · unranked

29 citations

Zachary K. Barth, Kira S. Makarova, Yuri I. Wolf, Vyacheslav Brover, Joseph E. Peters +2 more

Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?

Life(2022)10.3390/life12010103

N/A

0.505DataRank · unranked

28 citations

Eugene V. Koonin, Benjamin D. Lee

ICTV Virus Taxonomy Profile: Qinviridae 2023

Journal of General Virology(2023)10.1099/jgv.0.001905

Top 39%

0.496DataRank

Top 39%11 citations

Eugene V. Koonin, Mart Krupovìč, Jens H. Kuhn, Yuri I. Wolf

Prediction of the incubation period for COVID-19 and future virus disease outbreaks

BMC Biology(2020)10.1186/s12915-020-00919-9

N/A

0.494DataRank · unranked

26 citations

Noam Auslander, Yuri I. Wolf, Eugene V. Koonin, Ayal B. Gussow

The polinton-like supergroup of viruses: evolution, molecular biology, and taxonomy

Microbiology and Molecular Biology Reviews(2024)10.1128/mmbr.00086-23

N/A

0.489DataRank · unranked

25 citations

Matthias Fischer, Jens H. Kuhn, Mart Krupovìč, Eugene V. Koonin

ICTV Virus Taxonomy Profile: Amnoonviridae 2023

Journal of General Virology(2023)10.1099/jgv.0.001903

Top 40%

0.482DataRank

Top 40%19 citations

Mart Krupovìč, Win Surachetpong, Yuri I. Wolf, Jens H. Kuhn, Eugene V. Koonin

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail

Nature Communications(2024)10.1038/s41467-023-44630-z

N/A

0.479DataRank · unranked

10 citations

Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov +11 more

In Silico Approaches for Prediction of Anti-CRISPR Proteins

Journal of Molecular Biology(2023)10.1016/j.jmb.2023.168036

N/A

0.442DataRank · unranked

18 citations

Yuri I. Wolf, Eugene V. Koonin, Kira S. Makarova

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(2021)10.1073/pnas.2015665118

N/A

0.434DataRank · unranked

17 citations

M. I. Katsnelson, Yuri I. Wolf, Eugene V. Koonin, Yuri Bakhtin

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)10.1093/nar/gkab1065

N/A

0.434DataRank · unranked

17 citations

Ekaterina Savitskaya, Maxim Panov, Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Eugene V. Koonin +2 more

Seeker: Alignment-free identification of bacteriophage genomes by deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.04.025783

N/A

0.425DataRank · unranked

16 citations

Ayal B. Gussow, Sean Benler, Yuri I. Wolf, Eugene V. Koonin, Noam Auslander

Evolution of human respiratory virus epidemics

F1000Research(2021)10.12688/f1000research.53392.2

N/A

0.406DataRank · unranked

14 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman

Evolving concepts of the protein universe

iScience(2025)10.1016/j.isci.2025.112012

N/A

0.396DataRank · unranked

13 citations

Lauren Porter, Tsui‐Fen Chou, Shasha Chong, Fabrizio Chiti, Joseph W. Schafer +10 more

Translon: a single term for translated regions

Nature Methods(2025)10.1038/s41592-025-02810-3

N/A

0.389DataRank · unranked

11 citations

Jack A. S. Tierney, M. Mar Albà, Dmitry E. Andreev, Julie L. Aspden, John F. Atkins +164 more

CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA

eLife(2024)10.7554/elife.94800

N/A

0.385DataRank · unranked

12 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

In silico evolution of globular protein folds from random sequences

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2509015122

N/A

0.385DataRank · unranked

12 citations

S. G. Babajanyan, Yuri I. Wolf, Eugene V. Koonin, Harutyun Sahakyan

Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.26.530102

N/A

0.360DataRank · unranked

10 citations

Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez +10 more

Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

Journal of General Virology(2025)10.1099/jgv.0.002077

Top 52%

0.337DataRank

Top 52%6 citations

Scott Adkins, Sergey V. Alkhovsky, Wenxia An 安雯霞, Tatjana Avšič‐Županc, Marı́a A. Ayllón +95 more

Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity

Nature Communications(2025)10.1038/s41467-025-63056-3

N/A

0.330DataRank · unranked

8 citations

Héloïse Carion, Kira S. Makarova, David Sanchez Godinez, Surabhi Haniyur, Lucy Volino +7 more

Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)

Virus Evolution(2024)10.1093/ve/veae037

N/A

0.330DataRank · unranked

8 citations

Arnau Galan, Donnamae Klocek, Diego H. Macedo, Yuri I. Wolf, Jan Votýpka +8 more

Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea

mBio(2024)10.1128/mbio.03092-23

N/A

0.292DataRank · unranked

6 citations

Changyi Zhang, Yuri I. Wolf, Svetlana Karamycheva, Rachel J. Whitaker, Eugene V. Koonin +1 more

Long range segmentation of prokaryotic genomes by gene age and functionality

Nucleic Acids Research(2024)10.1093/nar/gkae745

N/A

0.292DataRank · unranked

6 citations

Ilya Schurov, Kira S. Makarova, M. I. Katsnelson, Eugene V. Koonin, Yuri I. Wolf

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal dsRNA and ssRNA(−) Viruses Subcommittee, 2025

Journal of General Virology(2025)10.1099/jgv.0.002112

N/A

0.292DataRank · unranked

6 citations

Matthew J. Ballinger, Yīmíng Bào, Nicolás Bejerman, Kim R. Blasdell, Thomas Briese +56 more

Thousands of Previously Unknown Phages Discovered in Whole-community Human Gut Metagenomes

Research Square(2020)10.21203/rs.3.rs-89426/v1

N/A

0.292DataRank · unranked

6 citations

Natalya Yutin, Dmitry Antipov, Mikhail Raykov, Sergey Shmakov, Ayal B. Gussow +3 more

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2502752122

N/A

0.269DataRank · unranked

5 citations

Sofya K. Garushyants, Yuri I. Wolf, Eugene V. Koonin, Sagi Snir, Shelly Brezner

tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.10.468108

N/A

0.269DataRank · unranked

5 citations

Matvey Kolesnik, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov +8 more

Jumping DNA polymerases in bacteriophages

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.26.591309

N/A

0.269DataRank · unranked

5 citations

Igor Tolstoy, Pascal Mutz, Yuri I. Wolf, Mart Krupovìč, Eugene V. Koonin +1 more

ICTV Virus Taxonomy Profile: Yueviridae 2023

Journal of General Virology(2023)10.1099/jgv.0.001904

Top 59%

0.259DataRank

Top 59%4 citations

Yuri I. Wolf, Eugene V. Koonin, Jens H. Kuhn, Mart Krupovìč

Viruses of Asgard archaea

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.29.453957

Top 59%

0.254DataRank

Top 59%3 citations

Jiarui Sun, Natalya Yutin, Eugene V. Koonin, Takuro Nunoura, Christian Rinke +2 more

Evolution of regulatory signatures in primate cortical neurons at cell type resolution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.24.219881

N/A

0.241DataRank · unranked

4 citations

Marit W. Vermunt, Pasha Apontes, Junhao Li, Ke Hao, Chet C. Sherwood +8 more

A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.19.500677

N/A

0.241DataRank · unranked

4 citations

Uri Neri, Simon Roux, Yuri I. Wolf, Antônio Pedro Camargo, Mart Krupovìč +6 more

Biochemical plasticity of the Escherichia coliCRISPR Cascade revealed by in vitro reconstitution of Cascade activities from purified Cas proteins

FEBS Journal(2024)10.1111/febs.17295

N/A

0.241DataRank · unranked

4 citations

Greg Brown, Kira S. Makarova, Eugene V. Koonin, Alexander F. Yakunin, Sofia Lemak

Identification of combinations of somatic mutations that predict cancer survival and immunotherapy benefit

NAR Cancer(2021)10.1093/narcan/zcab017

N/A

0.241DataRank · unranked

4 citations

Eugene V. Koonin, Noam Auslander, Ayal B. Gussow

Host age structure reshapes parasite symbiosis: collaboration begets pathogens, competition begets virulent mutualists

Biology Direct(2022)10.1186/s13062-022-00343-9

N/A

0.241DataRank · unranked

4 citations

Edward G. Rong, Jared A. Ramirez, Yuri I. Wolf, Angelique P. Bosse, Eugene V. Koonin +2 more

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.10.475617

N/A

0.210DataRank · unranked

2 citations

George W. Gruenhagen, Jorge Calle-Espinosa, Eugene V. Koonin, Jaime Iranzo

De novo origin of numerous microproteins in enterobacteria

Nucleic Acids Research(2025)10.1093/nar/gkaf1319

N/A

0.208DataRank · unranked

3 citations

Svetlana A. Shabalina, Gisela Storz, Eugene V. Koonin, Igor Fesenko

Genome-level selection in tumors as a universal marker of resistance to therapy

Nature Communications(2025)10.1038/s41467-025-61709-x

N/A

0.208DataRank · unranked

3 citations

Praneeth Sudalagunta, Yuri I. Wolf, Rafael Renatino Canevarolo, Mehdi Damaghi, Kenneth H. Shain +3 more

ICTV Virus Taxonomy Profile: Tosoviridae 2023

Journal of General Virology(2023)10.1099/jgv.0.001908

Top 66%

0.183DataRank

Top 66%2 citations

Mart Krupovìč, Jens H. Kuhn, Eugene V. Koonin, Yuri I. Wolf

Thermodynamics of evolution and the origin of life

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2120042119

N/A

0.165DataRank · unranked

2 citations

Yuri I. Wolf, Eugene V. Koonin, M. I. Katsnelson, Vitaly Vanchurin

Ecological determinants of altruism in prokaryote antivirus defense

Biology Direct(2025)10.1186/s13062-025-00699-8

N/A

0.165DataRank · unranked

2 citations

Kira S. Makarova, Yuri I. Wolf, Levi Waldron, Eugene V. Koonin, Nash D. Rochman +1 more

Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea

mBio(2025)10.1128/mbio.03127-25

N/A

0.165DataRank · unranked

2 citations

Yuri I. Wolf, Eugene V. Koonin, Kira S. Makarova, Svetlana Karamycheva

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.20.432109

N/A

0.104DataRank · unranked

1 citations

Georgy P. Karev, Eugene V. Koonin, Faina Berezovskaya

The protein structurome of Orthornavirae and its dark matter

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.25.615016

N/A

0.104DataRank · unranked

1 citations

Antoni Pedro Camargo, Harutyun Sahakyan, Uri Neri, Anamarija Butković, Yuri I. Wolf +4 more

The key role of cheaters in the persistence of cooperation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.30.621164

N/A

0.104DataRank · unranked

1 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman, S. G. Babajanyan

Diversity and evolution of viroids and viroid-like agents with circular RNA genomes revealed by metatranscriptome mining

Nucleic Acids Research(2024)10.1093/nar/gkae1278

N/A

0DataRank · unranked

16 citations

Benjamin D. Lee, Eugene V. Koonin

The protein structurome of Orthornavirae and its dark matter

mBio(2024)10.1128/mbio.03200-24

N/A

0DataRank · unranked

13 citations

Antônio Pedro Camargo, Harutyun Sahakyan, Uri Neri, Anamarija Butković, Yuri I. Wolf +4 more

Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model

BMC Biology(2024)10.1186/s12915-024-01937-7

N/A

0DataRank · unranked

12 citations

Sofya K. Garushyants, Yuri I. Wolf, Eugene V. Koonin, S. G. Babajanyan

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

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2405771121

N/A

0DataRank · unranked

16 citations

Jens H. Kuhn, Matthias Fischer, Eugene V. Koonin, Mart Krupovìč

Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A

Nature Communications(2024)10.1038/s41467-024-44806-1

N/A

0DataRank · unranked

12 citations

Runyue Xia, Siyu Zhang, Jie Pan, Yang Liu, Yuri I. Wolf +3 more

Novel lineage of anelloviruses with large genomes identified in dolphins

Journal of Virology(2024)10.1128/jvi.01370-24

N/A

0DataRank · unranked

10 citations

Mart Krupovìč, Russell Fielding, Kendal Smith, Kelsie Schiavone, Katharine R. Hall +10 more

DNA polymerase swapping in Caudoviricetes bacteriophages

Virology Journal(2024)10.1186/s12985-024-02482-z

N/A

0DataRank · unranked

7 citations

Igor Tolstoy, Pascal Mutz, Yuri I. Wolf, Mart Krupovìč, Eugene V. Koonin +1 more

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

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2400008121

N/A

0DataRank · unranked

6 citations

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

How flexible parasites can outsmart their hosts for evolutionary dominance

Physical Review Research(2024)10.1103/physrevresearch.6.023104

N/A

0DataRank · unranked

5 citations

Eugene V. Koonin, Kang Hao Cheong, Tao Wen

Circular RNAs from linear viral RNA genomes: A distinct dimension in the virus world

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2401335121

N/A

0DataRank · unranked

3 citations

Eugene V. Koonin

CoCoNuTs are a diverse subclass of Type IV restriction systems predicted to target RNA

eLife(2024)10.7554/elife.94800.3

N/A

0DataRank · unranked

2 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Defense systems and horizontal gene transfer in bacteria

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.09.579689

N/A

0DataRank · unranked

2 citations

Yuri I. Wolf, Eugene V. Koonin, Roman Kogay

Diversity, Origin and Evolution of the ESCRT Systems

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.06.579148

N/A

0DataRank · unranked

1 citations

Victor Tobiasson, Yuri I. Wolf, Zhongyi Lu, Yang Liu, Siyu Zhang +4 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.18.585575

N/A

0DataRank · unranked

1 citations

Jens H. Kuhn, Matthias Fischer, Eugene V. Koonin, Mart Krupovìč

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

eLife(2024)10.7554/elife.94800.1

N/A

0DataRank · unranked

0 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Reviewer #1 (Public Review): CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

(2024)10.7554/elife.94800.1.sa1

N/A

0DataRank · unranked

0 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Mriyaviruses: Small Relatives of Giant Viruses

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.29.582850

N/A

0DataRank · unranked

0 citations

Pascal Mutz, Mart Krupovìč, Eugene V. Koonin, Natalya Yutin

Reviewer #2 (Public Review): CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

(2024)10.7554/elife.94800.2.sa0

N/A

0DataRank · unranked

0 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Author response: CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

(2024)10.7554/elife.94800.2.sa3

N/A

0DataRank · unranked

0 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Reviewer #1 (Public Review): CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

(2024)10.7554/elife.94800.2.sa1

N/A

0DataRank · unranked

0 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

eLife(2024)10.7554/elife.94800.2

N/A

0DataRank · unranked

0 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Long range segmentation of prokaryotic genomes by gene age and functionality

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.26.591304

N/A

0DataRank · unranked

0 citations

Ilya Schurov, Kira S. Makarova, M. I. Katsnelson, Eugene V. Koonin, Yuri I. Wolf

Ecological Determinants of Altruism in Prokaryote Antivirus Defense

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.05.622165

N/A

0DataRank · unranked

0 citations

Kira S. Makarova, Yuri I. Wolf, Levi Waldron, Eugene V. Koonin, Nash D. Rochman +1 more

Jumbo phage killer immune system targets early infection of nucleus-forming phages

Cell(2025)10.1016/j.cell.2025.02.016

N/A

0DataRank · unranked

23 citations

Linlin Guan, Isabelle Becher, Kira S. Makarova, Xueli Cao, Surabhi Hareendranath +13 more

Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites

Cell(2025)10.1016/j.cell.2025.07.002

N/A

0DataRank · unranked

19 citations

Thomas C. Todeschini, Yi Wu, Roman Kogay, Ameena Naji, Joaquin Cardenas Rodriguez +10 more

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal DNA Viruses and Retroviruses Subcommittee, 2025

Journal of General Virology(2025)10.1099/jgv.0.002113

N/A

0DataRank · unranked

13 citations

Adly M. M. Abd‐Alla, Niklas Arnberg, Kelly S. Bateman, Mária Benkő, Annie Bézier +46 more

Evolution of antivirus defense in prokaryotes, depending on the environmental virus prevalence and virome dynamics

mBio(2025)10.1128/mbio.02409-25

N/A

0DataRank · unranked

3 citations

Sofya K. Garushyants, Yuri I. Wolf, Eugene V. Koonin, S. G. Babajanyan

“Paraxenoviridae”, a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes

The ISME Journal(2025)10.1093/ismejo/wraf139

N/A

0DataRank · unranked

2 citations

Sofia Medvedeva, Akihito Fukudome, Yuri I. Wolf, Syun‐ichi Urayama, Yosuke Nishimura +5 more

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Archaeal Viruses Subcommittee, 2025

Journal of General Virology(2025)10.1099/jgv.0.002117

N/A

0DataRank · unranked

1 citations

Diana P. Baquero, Eduardo A. Bignon, Ariane Bize, Guillaume Borrel, Mingwei Cai +18 more

Identification of Obelisk-like covalently closed circular RNA replicon in hot springs by double-stranded RNA sequencing and expansion of the diversity of the Obelisk superfamily

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.03.673927

N/A

0DataRank · unranked

4 citations

Akihito Fukudome, Pascal Mutz, Yosuke Matsushita, Yoshihiro Takaki, Yosuke Nishimura +5 more

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.03.647019

N/A

0DataRank · unranked

1 citations

Sofya K. Garushyants, Yuri I. Wolf, Eugene V. Koonin, Sagi Snir, Shelly Brezner

The key role of cheaters in the persistence of cooperation

Research Square(2025)10.21203/rs.3.rs-6280939/v1

N/A

0DataRank · unranked

0 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman, S. G. Babajanyan

Evolution of antivirus defense in prokaryotes depending on the environmental virus prevalence and virome dynamics

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.27.656525

N/A

0DataRank · unranked

0 citations

Sofya K. Garushyants, Yuri I. Wolf, Eugene V. Koonin, S. G. Babajanyan

Ecological determinants of altruism in prokaryote antivirus defense

Research Square(2025)10.21203/rs.3.rs-7165116/v1

N/A

0DataRank · unranked

0 citations

Kira S. Makarova, Yuri I. Wolf, Levi Waldron, Eugene V. Koonin, Nash D. Rochman +1 more

A prevalent huge phage clade in human and animal gut microbiomes

Research Square(2025)10.21203/rs.3.rs-7356405/v1

N/A

0DataRank · unranked

0 citations

Antônio Pedro Camargo, Yiting Qin, Haoyu Wang, Yuanqiang Zou, Yi Duan +3 more

The heterogeneous selection landscape of genome evolution in prokaryotes

Research Square(2025)10.21203/rs.3.rs-8216272/v1

N/A

0DataRank · unranked

0 citations

Sofiya Garushyants, Svetlana Karamycheva, Nash D. Rochman, Yuri I. Wolf, Eugene V. Koonin

Antitoxins within toxins: A new theme in bacterial antivirus defense

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2311001120

N/A

0DataRank · unranked

1 citations

Eugene V. Koonin

Functional Long Non-coding RNAs Evolve from Junk Transcripts

Cell(2020)10.1016/j.cell.2020.09.047

N/A

0DataRank · unranked

271 citations

Eugene V. Koonin, Alexander F. Palazzo

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2008176117

N/A

0DataRank · unranked

250 citations

Noam Auslander, Guilhem Faure, Yuri I. Wolf, Feng Zhang, Eugene V. Koonin +1 more

The replication machinery of LUCA: common origin of DNA replication and transcription

BMC Biology(2020)10.1186/s12915-020-00800-9

N/A

0DataRank · unranked

119 citations

Mart Krupovìč, Sonoko Ishino, Yoshizumi Ishino, Eugene V. Koonin

Evolutionary and functional classification of the CARF domain superfamily, key sensors in prokaryotic antivirus defense

Nucleic Acids Research(2020)10.1093/nar/gkaa635

N/A

0DataRank · unranked

115 citations

Albertas Timinskas, Yuri I. Wolf, Ayal B. Gussow, Virginijus Šikšnys, Česlovas Venclovas +2 more

Machine-learning approach expands the repertoire of anti-CRISPR protein families

Nature Communications(2020)10.1038/s41467-020-17652-0

N/A

0DataRank · unranked

111 citations

Allyson E. Park, Adair L. Borges, Sergey Shmakov, Kira S. Makarova, Yuri I. Wolf +3 more

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes

Communications Biology(2020)10.1038/s42003-020-1014-1

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0DataRank · unranked

62 citations

Yuri I. Wolf, Ekaterina Savitskaya, Konstantin Severinov, Eugene V. Koonin, Sergey Shmakov

Can Environmental Manipulation Help Suppress Cancer? Non‐Linear Competition Among Tumor Cells in Periodically Changing Conditions

Advanced Science(2020)10.1002/advs.202000340

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14 citations

Eugene V. Koonin, Kang Hao Cheong, S. G. Babajanyan

Deep phylogeny of cancer drivers and compensatory mutations

Communications Biology(2020)10.1038/s42003-020-01276-7

N/A

0DataRank · unranked

28 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.05.026450

N/A

0DataRank · unranked

55 citations

Noam Auslander, Guilhem Faure, Yuri I. Wolf, Feng Zhang, Eugene V. Koonin +1 more

Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.12.336644

N/A

0DataRank · unranked

36 citations

Yuri I. Wolf, Guilhem Faure, Pascal Mutz, Feng Zhang, Eugene V. Koonin +1 more

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.07.330464

N/A

0DataRank · unranked

17 citations

Natalya Yutin, Dmitry Antipov, Mikhail Raykov, Sergey Shmakov, Ayal B. Gussow +3 more

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.23.916767

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0DataRank · unranked

12 citations

Sergey Shmakov, Kira S. Makarova, Yuri I. Wolf, Joseph Bondy‐Denomy, Eugene V. Koonin +1 more

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.19.343400

N/A

0DataRank · unranked

7 citations

Kira S. Makarova, Wen-Cong Huang, Yuri I. Wolf, Anastasia Nikolskaya, Xinxu Zhang +8 more

Substantial Impact of Post Vaccination Contacts on Cumulative Infections during Viral Epidemics

medRxiv(2020)10.1101/2020.12.19.20248554

N/A

0DataRank · unranked

5 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman

Punctuated equilibrium as the default mode of evolution of large populations on fitness landscapes dominated by saddle points in the weak-mutation limit

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.20.212241

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3 citations

M. I. Katsnelson, Yuri I. Wolf, Eugene V. Koonin, Yuri Bakhtin

Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.14.041392

N/A

0DataRank · unranked

0 citations

Yuri I. Wolf, Eugene V. Koonin, Itamar Sela

Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery

Science(2021)10.1126/science.abg6155

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0DataRank · unranked

428 citations

Blake Lash, Jingwei Song, Alim Ladha, Catherine C. Liu, Xin Jin +5 more

Ongoing global and regional adaptive evolution of SARS-CoV-2

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2104241118

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262 citations

Yuri I. Wolf, Guilhem Faure, Pascal Mutz, Feng Zhang, Eugene V. Koonin +1 more

Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis

Cell Reports(2021)10.1016/j.celrep.2021.108873

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0DataRank · unranked

146 citations

Nicolò Ilacqua, Andrea Raimondi, Philippe Lemieux, Rana Ghandehari‐Alavijeh, Guilhem Faure +14 more

The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution?

Microbiology and Molecular Biology Reviews(2021)10.1128/mmbr.00053-21

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123 citations

Mart Krupovìč, Vadim I. Agol, Eugene V. Koonin

Viruses Defined by the Position of the Virosphere within the Replicator Space

Microbiology and Molecular Biology Reviews(2021)10.1128/mmbr.00193-20

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98 citations

Valerian V. Dolja, Mart Krupovìč, Jens H. Kuhn, Eugene V. Koonin

The healthy human virome: from virus–host symbiosis to disease

Current Opinion in Virology(2021)10.1016/j.coviro.2021.02.002

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93 citations

Valerian V. Dolja, Mart Krupovìč, Eugene V. Koonin

Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

mBio(2021)10.1128/mbio.02938-21

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59 citations

Guilhem Faure, Han Altae-Tran, Sergey Shmakov, Feng Zhang, Eugene V. Koonin +1 more

A three-organelle complex made by wrappER contacts with peroxisomes and mitochondria responds to liver lipid flux changes

Journal of Cell Science(2021)10.1242/jcs.259091

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44 citations

Irene Anastasia, Andrea Raimondi, Philippe Lemieux, Thomas Q. de Aguiar Vallim, Katalin Tóth +3 more

Assessment of assumptions underlying models of prokaryotic pangenome evolution

BMC Biology(2021)10.1186/s12915-021-00960-2

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25 citations

Yuri I. Wolf, Eugene V. Koonin, Itamar Sela

An alternating active-dormitive strategy enables disadvantaged prey to outcompete the perennially active prey through Parrondo’s paradox

BMC Biology(2021)10.1186/s12915-021-01097-y

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13 citations

Eugene V. Koonin, Kang Hao Cheong, Tao Wen

A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains

Frontiers in Microbiology(2021)10.3389/fmicb.2021.721392

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10 citations

Yuri I. Wolf, Svetlana Karamycheva, Eugene V. Koonin, Kira S. Makarova

Fishing for phages in metagenomes: what do we catch, what do we miss?

Current Opinion in Virology(2021)10.1016/j.coviro.2021.05.008

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20 citations

Eugene V. Koonin, Sean Benler

Evolution of human respiratory virus epidemics

F1000Research(2021)10.12688/f1000research.53392.1

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0DataRank · unranked

16 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman

Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics

F1000Research(2021)10.12688/f1000research.52341.2

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0DataRank · unranked

10 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman

Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics

F1000Research(2021)10.12688/f1000research.52341.1

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9 citations

Yuri I. Wolf, Eugene V. Koonin, Nash D. Rochman

Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.30.458225

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10 citations

Guilhem Faure, Yuri I. Wolf, Peter L. Freddolino, Feng Zhang, Eugene V. Koonin +1 more

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.23.441209

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9 citations

Igor B. Rogozin, Eugene V. Koonin, Sofya K. Garushyants

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

Research Square(2021)10.21203/rs.3.rs-89426/v2

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7 citations

Natalya Yutin, Dmitry Antipov, Mikhail Raykov, Sergey Shmakov, Ayal B. Gussow +3 more

Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo’s Paradox

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.07.434273

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6 citations

Tao Wen, Sean Benler, Eugene V. Koonin, Kang Hao Cheong

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern

Research Square(2021)10.21203/rs.3.rs-456574/v1

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5 citations

Igor B. Rogozin, Eugene V. Koonin, Sofiya Garushyants

Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.24.428004

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5 citations

Vladimir Svetlov, Yuri I. Wolf, Eugene V. Koonin, Evgeny Nudler, Irina Artsimovitch +1 more

Towards a Theory of Evolution as Multilevel Learning

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.03.466494

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0DataRank · unranked

5 citations

Yuri I. Wolf, M. I. Katsnelson, Eugene V. Koonin, Vitaly Vanchurin

tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

Research Square(2021)10.21203/rs.3.rs-1068910/v1

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0DataRank · unranked

3 citations

Ishita Jain, Matvey Kolesnik, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva +8 more

Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.10.472150

N/A

0DataRank · unranked

1 citations

Nash D. Rochman, Yuri I. Wolf, Guilhem Faure, Feng Zhang, Eugene V. Koonin +1 more

Non-essential ribosomal proteins in bacteria and archaea identified using COGs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.31.429008

N/A

0DataRank · unranked

0 citations

Yuri I. Wolf, Sofya K. Garushyants, Roberto Vera Alvarez, Eugene V. Koonin, Michael Y. Galperin

Toward a theory of evolution as multilevel learning

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2120037119

N/A

0DataRank · unranked

118 citations

Yuri I. Wolf, M. I. Katsnelson, Eugene V. Koonin, Vitaly Vanchurin

Evolutionary plasticity and functional versatility of CRISPR systems

PLoS Biology(2022)10.1371/journal.pbio.3001481

N/A

0DataRank · unranked

91 citations

Kira S. Makarova, Eugene V. Koonin

The global virome: How much diversity and how many independent origins?

Environmental Microbiology(2022)10.1111/1462-2920.16207

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0DataRank · unranked

73 citations

Mart Krupovìč, Valerian V. Dolja, Eugene V. Koonin

Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape

mBio(2022)10.1128/mbio.00135-22

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0DataRank · unranked

64 citations

Guilhem Faure, Yuri I. Wolf, Lydia Freddolino, Feng Zhang, Eugene V. Koonin +1 more

Alternating lysis and lysogeny is a winning strategy in bacteriophages due to Parrondo's paradox

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2115145119

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0DataRank · unranked

53 citations

Tao Wen, Sean Benler, Jin Ming Koh, Eugene V. Koonin, Kang Hao Cheong

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Nature Microbiology(2022)10.1038/s41564-022-01144-6

N/A

0DataRank · unranked

52 citations

Jiarui Sun, Natalya Yutin, Eugene V. Koonin, Takuro Nunoura, Christian Rinke +2 more

Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9

Nature Communications(2022)10.1038/s41467-022-34378-3

N/A

0DataRank · unranked

46 citations

Sae Okazaki, Soumya Kannan, Han Altae-Tran, F. Esra Demircioglu, Yukari Isayama +9 more

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

Nature(2022)10.1038/s41586-022-05324-6

N/A

0DataRank · unranked

42 citations

Kalli Kappel, Han Altae-Tran, Guilhem Faure, Max E. Wilkinson, Soumya Kannan +9 more

Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes

Frontiers in Molecular Biosciences(2022)10.3389/fmolb.2022.821197

N/A

0DataRank · unranked

29 citations

Eugene V. Koonin, Sean Benler

A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley

Viruses(2022)10.3390/v14061320

N/A

0DataRank · unranked

27 citations

Yuri I. Wolf, Gardenia E. Orellana, Erik J. Wenninger, Eugene V. Koonin, Alexander V. Karasev +1 more

A novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA

PLoS Pathogens(2022)10.1371/journal.ppat.1010258

N/A

0DataRank · unranked

15 citations

Brian A. Stacy, Robert J. Ossiboff, Nicole I. Stacy, William Fraser, Annie Yan +10 more

Phylogenomic analysis of the diversity of graspetides and proteins involved in their biosynthesis

Biology Direct(2022)10.1186/s13062-022-00320-2

N/A

0DataRank · unranked

13 citations

Brittney Blackburne, Yuri I. Wolf, A. N. NIKOL'SKAYA, Svetlana Karamycheva, Marlene Espinoza‐Moraga +4 more

Thermodynamic selection: mechanisms and scenarios

New Journal of Physics(2022)10.1088/1367-2630/ac6531

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0DataRank · unranked

9 citations

Eugene V. Koonin, A. E. Allahverdyan, S. G. Babajanyan

Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales

Viruses(2022)10.3390/v14091842

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0DataRank · unranked

9 citations

Mikhail Rayko, Dmitry Antipov, Pascal Mutz, Yuri I. Wolf, Mart Krupovìč +2 more

A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.15.480533

N/A

0DataRank · unranked

26 citations

Yuri I. Wolf, Simon Roux, Antônio Pedro Camargo, Benjamin D. Lee, Darius Kazlauskas +12 more

A family of novel immune systems targets early infection of nucleus-forming jumbo phages

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.17.508391

N/A

0DataRank · unranked

23 citations

Jingwen Guan, Surabhi Hareendranath, Emily Crawford, David A. Agard, Kira S. Makarova +3 more

Conservation and evolution of the sporulation gene set in diverse members of the Firmicutes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.25.481979

N/A

0DataRank · unranked

5 citations

Natalya Yutin, Yuri I. Wolf, Roberto Vera Alvarez, Eugene V. Koonin, Michael Y. Galperin

RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.17.504292

N/A

0DataRank · unranked

5 citations

Sae Okazaki, Cian Schmitt-Ulms, Kaiyi Jiang, Wenyuan Zhou, Junichiro Ishikawa +9 more

Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.22.517515

N/A

0DataRank · unranked

2 citations

Wolfgang Resch, Guilhem Faure, Tatiana G. Senkevich, Eugene V. Koonin, Bernard Moss +1 more

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail

The Medicine Forum(2022)10.1101/2022.12.01.518664

N/A

0DataRank · unranked

1 citations

Leonid Minakhin, Ekaterina Goldobina, Brain Bae, Yue Hao, Sergei Borukhov +10 more

Host Age Structure Defines Interactions with Pathogens: Grandparent Effect under Collaboration and Virulent Mutualism under Competition

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.16.504183

N/A

0DataRank · unranked

0 citations

Edward G. Rong, Jared A. Ramirez, Yuri I. Wolf, Angelique P. Bosse, Eugene V. Koonin +2 more

Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.22.509036

N/A

0DataRank · unranked

0 citations

Yuri I. Wolf, Andranik Khachatryan, A. E. Allahverdyan, Purificación López‐García, Eugene V. Koonin +1 more

Four principles to establish a universal virus taxonomy

PLoS Biology(2023)10.1371/journal.pbio.3001922

N/A

0DataRank · unranked

139 citations

Evelien M. Adriaenssens, F. Murilo Zerbini, Nicola G. A. Abrescia, Pakorn Aiewsakun, Poliane Alfenas‐Zerbini +38 more

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

Cell(2023)10.1016/j.cell.2022.12.039

N/A

0DataRank · unranked

94 citations

Uri Neri, Simon Roux, Yuri I. Wolf, Antônio Pedro Camargo, Mart Krupovìč +6 more

Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2308224120

N/A

0DataRank · unranked

72 citations

Sergey Shmakov, Kira S. Makarova, Yuri I. Wolf, Soumya Kannan, Feng Zhang +2 more

Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

Nature Communications(2023)10.1038/s41467-023-40706-y

N/A

0DataRank · unranked

69 citations

Sofya K. Garushyants, John Franks, Andrew F. Magee, Steven H. Overend, Devra Huey +24 more

The virome of the last eukaryotic common ancestor and eukaryogenesis

Nature Microbiology(2023)10.1038/s41564-023-01378-y

N/A

0DataRank · unranked

56 citations

Valerian V. Dolja, Eugene V. Koonin, Mart Krupovìč

Structural atlas of a human gut crassvirus

Nature(2023)10.1038/s41586-023-06019-2

N/A

0DataRank · unranked

52 citations

Andrey Shkoporov, Natalya Yutin, Ekaterina V. Khokhlova, Jake L. R. Smith, Dorothy E. D. P. Hawkins +4 more

Plant virus movement proteins originated from jelly-roll capsid proteins

PLoS Biology(2023)10.1371/journal.pbio.3002157

N/A

0DataRank · unranked

34 citations

Valerian V. Dolja, Eugene V. Koonin, Mart Krupovìč, Anamarija Butković

Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling

mBio(2023)10.1128/mbio.00408-23

N/A

0DataRank · unranked

29 citations

Wolfgang Resch, Guilhem Faure, Tatiana G. Senkevich, Eugene V. Koonin, Bernard Moss +1 more

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(2023)10.1073/pnas.2301522120

N/A

0DataRank · unranked

22 citations

Yuri I. Wolf, Andranik Khachatryan, A. E. Allahverdyan, Purificación López‐García, Eugene V. Koonin +1 more

Viriforms—A New Category of Classifiable Virus-Derived Genetic Elements

Biomolecules(2023)10.3390/biom13020289

N/A

0DataRank · unranked

18 citations

Eugene V. Koonin, Jens H. Kuhn

Cellular differentiation into hyphae and spores in halophilic archaea

Nature Communications(2023)10.1038/s41467-023-37389-w

N/A

0DataRank · unranked

16 citations

Xiao‐Yang Zhi, Yao Zhang, Kira S. Makarova, Bing-Bing Liu, Guosong Zheng +32 more

Compensatory relationship between low-complexity regions and gene paralogy in the evolution of prokaryotes

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2300154120

N/A

0DataRank · unranked

14 citations

Yuri I. Wolf, Svetlana Karamycheva, Kira S. Makarova, Eugene V. Koonin, Erez Persi

New faces of prokaryotic mobile genetic elements: Guide RNAs link transposition with host defense mechanisms

Current Opinion in Systems Biology(2023)10.1016/j.coisb.2023.100473

N/A

0DataRank · unranked

12 citations

Mart Krupovìč, Eugene V. Koonin

DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution

Molecular Biology and Evolution(2023)10.1093/molbev/msad274

N/A

0DataRank · unranked

12 citations

Sameer Sundrani, Richard Nelson Hall, Mart Krupovìč, Eugene V. Koonin, Andrew Fire +1 more

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

Frontiers in Microbiology(2023)10.3389/fmicb.2023.1291523

N/A

0DataRank · unranked

8 citations

N. de Vogel, Andreas Borst, Friedhelm Pfeiffer, Svetlana Karamycheva, Yuri I. Wolf +3 more

Protocol for comparing gene-level selection on coding mutations between two groups of samples with Coselens

STAR Protocols(2023)10.1016/j.xpro.2023.102117

N/A

0DataRank · unranked

1 citations

George W. Gruenhagen, Jorge Calle-Espinosa, Eugene V. Koonin, Jaime Iranzo

Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

Research Square(2023)10.21203/rs.3.rs-2574993/v1

N/A

0DataRank · unranked

19 citations

Sofya K. Garushyants, John Franks, Andrew F. Magee, Steven H. Overend, Devra Huey +24 more

Activation of programmed cell death and counter-defense functions of phage accessory genes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.06.535777

N/A

0DataRank · unranked

11 citations

Héloïse Carion, Kira S. Makarova, Eric Laderman, David Sanchez Godinez, Matthew C. Johnson +6 more

Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.03.530964

N/A

0DataRank · unranked

5 citations

Zachary K. Barth, Kira S. Makarova, Yuri I. Wolf, Vyacheslav Brover, Joseph E. Peters +2 more

DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.22.554363

N/A

0DataRank · unranked

2 citations

Sameer Sundrani, Richard Nelson Hall, Mart Krupovìč, Eugene V. Koonin, Andrew Fire +1 more

Diversity, Origin and Evolution of the ESCRT Systems

Research Square(2023)10.21203/rs.3.rs-2989530/v1

N/A

0DataRank · unranked

1 citations

Victor Tobiasson, Yuri I. Wolf, Zhongyi Lu, Yang Liu, Siyu Zhang +4 more

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.31.551357

N/A

0DataRank · unranked

1 citations

Harutyun Sahakyan, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, Ryan T. Bell

Distinct groups of RNA viruses associated with thermoacidophilic bacteria

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.02.547447

N/A

0DataRank · unranked

0 citations

Akihito Fukudome, Miho Hirai, Tomoyo Okumura, Yosuke Nishimura, Yoshihiro Takaki +5 more

Unicellular life balances asymmetric allocation and repair of somatic damage representing the origin of r/K selection

Educational leadership(2023)10.1101/2023.11.21.568103

N/A

0DataRank · unranked

0 citations

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

Bacterial defense systems exhibit synergistic anti-phage activity

Cell Host & Microbe(2024)10.1016/j.chom.2024.01.015

N/A

0DataRank · unranked

131 citations

Sofya K. Garushyants, Anne van den Hurk, Cristian Aparicio-Maldonado, Simran Krishnakant Kushwaha, Claire King +8 more

Defence systems and horizontal gene transfer in bacteria

Environmental Microbiology(2024)10.1111/1462-2920.16630

N/A

0DataRank · unranked

44 citations

Yuri I. Wolf, Eugene V. Koonin, Roman Kogay

Diversity, origin, and evolution of the ESCRT systems

mBio(2024)10.1128/mbio.00335-24

N/A

0DataRank · unranked

28 citations

Victor Tobiasson, Yuri I. Wolf, Zhongyi Lu, Yang Liu, Siyu Zhang +4 more

Mriyaviruses: small relatives of giant viruses

mBio(2024)10.1128/mbio.01035-24

N/A

0DataRank · unranked

17 citations

Pascal Mutz, Mart Krupovìč, Eugene V. Koonin, Natalya Yutin