Eugene V. Koonin

206.4k citations
903 papers · 118.0k indexed · 59 hit papers · h-index 169
Co-authors
Kira S. MakarovaYuri I. WolfL. AravindMichael Y. GalperinRoman L. TatusovFeng ZhangAlexander E. GorbalenyaIgor B. Rogozin
Topics
Genomics and Phylogenetic Studies (259 papers)RNA and protein synthesis mechanisms (250 papers)Bacteriophages and microbial interactions (221 papers)
Cited by
Business and International ManagementEndocrinologyMolecular Biology
Journals
NatureScienceCell
Partner nations
United StatesFranceRussia

In The Last Decade

Eugene V. Koonin

888 papers receiving 115.7k citations

Hit Papers

The COG database: an updated version includes eukaryotes19892026200120132003201519972017201510002.0k3.0k
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. The COG database: an updated version includes eukaryotes
    2003 3.6k citations Eugene V. Koonin, Sergei Mekhedov et al. profile →
  2. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
    2015 3.4k citations Jonathan S. Gootenberg, Omar O. Abudayyeh et al. profile →
  3. A Genomic Perspective on Protein Families
    1997 2.8k citations Eugene V. Koonin et al. Science profile →
  4. Nucleic acid detection with CRISPR-Cas13a/C2c2
    2017 2.7k citations Jonathan S. Gootenberg, Omar O. Abudayyeh et al. Science profile →
  5. In vivo genome editing using Staphylococcus aureus Cas9
    2015 2.0k citations Jonathan S. Gootenberg, Kira S. Makarova et al. profile →
  6. Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
    2008 1.9k citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  7. Evolution and classification of the CRISPR–Cas systems
    2011 1.9k citations Kira S. Makarova, Yuri I. Wolf et al. profile →
  8. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
    2016 1.7k citations Omar O. Abudayyeh, Jonathan S. Gootenberg et al. Science profile →
  9. De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling
    2004 1.5k citations L. Aravind, Eugene V. Koonin et al. profile →
  10. Genome Sequence of an Obligate Intracellular Pathogen of Humans: Chlamydia trachomatis
    1998 1.3k citations L. Aravind, Eugene V. Koonin et al. Science profile →
  11. Expanded microbial genome coverage and improved protein family annotation in the COG database
    2014 1.1k citations Michael Y. Galperin, Kira S. Makarova et al. profile →
  12. Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
    2000 1.1k citations L. Aravind, Eugene V. Koonin et al. Science profile →
  13. Diversity, classification and evolution of CRISPR-Cas systems
    2017 1.0k citations Eugene V. Koonin, Kira S. Makarova et al. profile →
  14. Helicases: amino acid sequence comparisons and structure-function relationships
    1993 977 citations Eugene V. Koonin et al. profile →
  15. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
    2015 919 citations Sergey Shmakov, Omar O. Abudayyeh et al. profile →
  16. Classification and evolution of P-loop GTPases and related ATPases
    2002 901 citations Yuri I. Wolf, Eugene V. Koonin et al. profile →
  17. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
    2006 881 citations Kira S. Makarova, Yuri I. Wolf et al. profile →
  18. Orthologs, Paralogs, and Evolutionary Genomics
    2005 875 citations Eugene V. Koonin profile →
  19. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes
    1989 869 citations Eugene V. Koonin et al. profile →
  20. Horizontal Gene Transfer in Prokaryotes: Quantification and Classification
    2001 825 citations Eugene V. Koonin, Kira S. Makarova et al. profile →
  21. Microbial culturomics: paradigm shift in the human gut microbiome study
    2012 819 citations Isabelle Pagnier, Ghislain Fournous et al. profile →
  22. Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26 S Proteasome
    2002 810 citations Rati Verma, L. Aravind et al. Science profile →
  23. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    2004 794 citations Eugene V. Koonin, Kira S. Makarova et al. profile →
  24. Diversity and evolution of class 2 CRISPR–Cas systems
    2017 761 citations Sergey Shmakov, David Cox et al. profile →
  25. The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses
    1991 732 citations Eugene V. Koonin profile →
  26. Cleavage of Cohesin by the CD Clan Protease Separin Triggers Anaphase in Yeast
    2000 656 citations Eugene V. Koonin et al. profile →
  27. Genome Sequence and Comparative Analysis of the Solvent-Producing BacteriumClostridium acetobutylicum
    2001 634 citations Kira S. Makarova, Yuri I. Wolf et al. Journal of Bacteriology profile →
  28. Evolutionary history and higher order classification of AAA+ ATPases
    2003 626 citations Eugene V. Koonin, L. Aravind et al. profile →
  29. Regeneration of Peroxiredoxins by p53-Regulated Sestrins, Homologs of Bacterial AhpD
    2004 622 citations Eugene V. Koonin et al. Science profile →
  30. A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins
    1997 617 citations Eugene V. Koonin et al. profile →
  31. Selection in the evolution of gene duplications
    2002 586 citations Yuri I. Wolf, Eugene V. Koonin et al. profile →
  32. Iterated profile searches with PSI-BLAST—a tool for discovery in protein databases
    1998 575 citations Eugene V. Koonin et al. profile →
  33. Role of Predicted Metalloprotease Motif of Jab1/Csn5 in Cleavage of Nedd8 from Cul1
    2002 571 citations Gregory A. Cope, Greg S. B. Suh et al. Science profile →
  34. Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics
    2001 558 citations Kira S. Makarova, L. Aravind et al. profile →
  35. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA
    2016 552 citations Ian M. Slaymaker, Kira S. Makarova et al. profile →
  36. COG database update: focus on microbial diversity, model organisms, and widespread pathogens
    2020 530 citations Michael Y. Galperin, Yuri I. Wolf et al. profile →
  37. Novel domains of the prokaryotic two-component signal transduction systems
    2001 513 citations Michael Y. Galperin, Eugene V. Koonin et al. profile →
  38. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
    2006 478 citations Eugene V. Koonin, L. Aravind et al. profile →
  39. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems
    2016 476 citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  40. RNA-guided DNA insertion with CRISPR-associated transposases
    2019 455 citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  41. Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28
    2017 434 citations David Cox, Ian M. Slaymaker et al. profile →
  42. Functional and evolutionary implications of gene orthology
    2013 409 citations Eugene V. Koonin et al. profile →
  43. Viral proteins containing the purine NTP-binding sequence pattern
    1989 384 citations Eugene V. Koonin et al. profile →
  44. Global Organization and Proposed Megataxonomy of the Virus World
    2020 381 citations Eugene V. Koonin, Valerian V. Dolja et al. profile →
  45. The evolutionary journey of Argonaute proteins
    2014 381 citations Kira S. Makarova, Eugene V. Koonin et al. profile →
  46. Functionally diverse type V CRISPR-Cas systems
    2018 373 citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  47. Origins and evolution of viruses of eukaryotes: The ultimate modularity
    2015 365 citations Eugene V. Koonin, Valerian V. Dolja et al. profile →
  48. Classification and evolution of type II CRISPR-Cas systems
    2014 362 citations Kira S. Makarova, Eugene V. Koonin et al. profile →
  49. Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein
    2018 350 citations Kira S. Makarova, Eugene V. Koonin et al. profile →
  50. Diverse enzymatic activities mediate antiviral immunity in prokaryotes
    2020 342 citations Kira S. Makarova, Yuri I. Wolf et al. Science profile →
  51. Origins and Evolution of the Global RNA Virome
    2018 330 citations Yuri I. Wolf, Jaime Iranzo et al. profile →
  52. Origins and evolution of CRISPR-Cas systems
    2019 305 citations Eugene V. Koonin, Kira S. Makarova profile →
  53. Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery
    2021 289 citations Sergei Mekhedov, Eugene V. Koonin et al. Science profile →
  54. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems
    2013 256 citations Kira S. Makarova, Eugene V. Koonin et al. profile →
  55. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases
    2021 239 citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  56. Prokaryotic innate immunity through pattern recognition of conserved viral proteins
    2022 138 citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  57. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering
    2023 81 citations Kira S. Makarova, Eugene V. Koonin et al. Science profile →
  58. Microbial transmission in the social microbiome and host health and disease
    2024 50 citations Eugene V. Koonin et al. profile →
  59. Bacterial defense systems exhibit synergistic anti-phage activity
    2024 48 citations Eugene V. Koonin et al. profile →

Peers

Eugene V. Koonin
Comparison fields: 5 of 218
  • Molecular Biology 86.6k
  • Ecology 24.0k
  • Plant Science 23.3k
  • Genetics 21.4k
  • Endocrinology 7.8k
Replace Kira S. Makarova with:
Kira S. Makarova United States
George M. Church United States
Jennifer A. Doudna United States
Eric S. Lander United States
Yuri I. Wolf United States
Feng Zhang United States
James J. Collins United States
Adam P. Arkin United States
Jonathan S. Weissman United States
Steven L. Salzberg United States
Eugene V. Koonin relative to Kira S. Makarova United States Kira S. Makarova's profile →
Citations per field
00.5×2×3×4.4×
Kira S. Makarova · 1×
Citations per year

Countries citing papers authored by Eugene V. Koonin

Since Specialization
Citations

This map shows the geographic impact of Eugene V. Koonin's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Eugene V. Koonin with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Eugene V. Koonin more than expected).

Fields of papers citing papers by Eugene V. Koonin

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Eugene V. Koonin. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Eugene V. Koonin. The network helps show where Eugene V. Koonin may publish in the future.

Co-authorship network of co-authors of Eugene V. Koonin

This figure shows the co-authorship network connecting the top 25 collaborators of Eugene V. Koonin. A scholar is included among the top collaborators of Eugene V. Koonin based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Eugene V. Koonin. Eugene V. Koonin is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
#WorkIndexed citations
1
Toward a theory of evolution as multilevel learning
2022 ·Proceedings of the National Academy of Sciences ·Vitaly Vanchurin,Yuri I. Wolf,M. I. Katsnelson,Eugene V. Koonin
54
2
Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems
2021 ·Science ·Ming Li,(unknown),Feiyue Cheng,Haiying Yu,Dahe Zhao,Rui Wang,Tian Wang,Shengjie Zhang,Jian Zhou,Sergey Shmakov,Eugene V. Koonin,Hua Xiang
73
3
Ongoing global and regional adaptive evolution of SARS-CoV-2
2021 ·Proceedings of the National Academy of Sciences ·Nash D. Rochman,Yuri I. Wolf,Guilhem Faure,Pascal Mutz,Feng Zhang,Eugene V. Koonin
157
4
In silico learning of tumor evolution through mutational time series
2019 ·Proceedings of the National Academy of Sciences ·Noam Auslander,Yuri I. Wolf,Eugene V. Koonin
18
5
Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism
2018 ·Advances in virus research ·Eugene V. Koonin,Natalya Yutin
119
6
Cancer-mutation network and the number and specificity of driver mutations
2018 ·Proceedings of the National Academy of Sciences ·Jaime Iranzo,Iñigo Martincorena,Eugene V. Koonin
90
7
Criticality in tumor evolution and clinical outcome
2018 ·Proceedings of the National Academy of Sciences ·Erez Persi,Yuri I. Wolf,Mark D.M. Leiserson,Eugene V. Koonin,Eytan Ruppin
19
8
Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis
2018 ·Proceedings of the National Academy of Sciences ·Sergey Shmakov,Kira S. Makarova,Yuri I. Wolf,Konstantin Severinov,Eugene V. Koonin
104
9
Microbial genome analysis: the COG approach
2017 ·Briefings in Bioinformatics ·Michael Y. Galperin,David M. Kristensen,Kira S. Makarova,Yuri I. Wolf,Eugene V. Koonin
198
10
Disentangling the effects of selection and loss bias on gene dynamics
2017 ·Proceedings of the National Academy of Sciences ·Jaime Iranzo,José A. Cuesta,Susanna C. Manrubia,M. I. Katsnelson,Eugene V. Koonin
43
11
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems
2017 ·Journal of Bacteriology ·Michael Y. Galperin,Kira S. Makarova,Yuri I. Wolf,Eugene V. Koonin
40
12
Recruitment of CRISPR-Cas systems by Tn7-like transposons
2017 ·Proceedings of the National Academy of Sciences ·Joseph E. Peters,Kira S. Makarova,Sergey Shmakov,Eugene V. Koonin
186
13
Myosin-driven transport network in plants
2017 ·Proceedings of the National Academy of Sciences ·Elizabeth G. Kurth,Valera V. Peremyslov,Hannah L. Turner,Kira S. Makarova,Jaime Iranzo,Sergei Mekhedov,Eugene V. Koonin,Valerian V. Dolja
50
14
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effectorbreakdown →
2016 ·Science ·Omar O. Abudayyeh,Jonathan S. Gootenberg,Silvana Konermann,Julia Joung,Ian M. Slaymaker,David Cox,Sergey Shmakov,Kira S. Makarova,Ekaterina Semenova,Leonid Minakhin,Konstantin Severinov,Aviv Regev,Eric S. Lander,Eugene V. Koonin,Feng Zhang
1689
15
Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms
2009 ·Proceedings of the National Academy of Sciences ·Mickaël Boyer,Natalya Yutin,Isabelle Pagnier,Lina Barrassi,Ghislain Fournous,Léon Espinosa,Catherine Robert,Saı̈d Azza,Siyang Sun,Michael G. Rossmann,Marie Suzan‐Monti,Bernard La Scola,Eugene V. Koonin,Didier Raoult
304
16
Myosin XI-K Is Required for Rapid Trafficking of Golgi Stacks, Peroxisomes, and Mitochondria in Leaf Cells of Nicotiana benthamiana    
2008 ·PLANT PHYSIOLOGY ·Dror Avisar,Alexey I. Prokhnevsky,Kira S. Makarova,Eugene V. Koonin,Valerian V. Dolja
180
17
Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes
2008 ·Journal of Bacteriology ·Pavel S. Novichkov,Yuri I. Wolf,Inna Dubchak,Eugene V. Koonin
104
18
A korarchaeal genome reveals insights into the evolution of the Archaea
2008 ·Proceedings of the National Academy of Sciences ·James G. Elkins,Mircea Podar,David E. Graham,Kira S. Makarova,Yuri I. Wolf,Lennart Randau,Brian P. Hedlund,Céline Brochier‐Armanet,Victor Kunin,Iain Anderson,Alla Lapidus,Eugene Goltsman,Kerrie Barry,Eugene V. Koonin,Philip Hugenholtz,Nikos C. Kyrpides,Gerhard Wanner,Paul Richardson,Martin Keller,Karl O. Stetter
199
19
Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26 S Proteasomebreakdown →
2002 ·Science ·Rati Verma,L. Aravind,Robert Oania,W. Hayes McDonald,John R. Yates,Eugene V. Koonin,Raymond J. Deshaies
810
20
Role of Predicted Metalloprotease Motif of Jab1/Csn5 in Cleavage of Nedd8 from Cul1breakdown →
2002 ·Science ·Gregory A. Cope,Greg S. B. Suh,L. Aravind,Sylvia E. Schwarz,S Lawrence Zipursky,Eugene V. Koonin,Raymond J. Deshaies
571

About Eugene V. Koonin

Eugene V. Koonin is a scholar working on Endocrinology, Ecology and Molecular Biology, having authored 903 papers that have together received 118.0k indexed citations. Recurring topics across this work include Genomics and Phylogenetic Studies (259 papers), RNA and protein synthesis mechanisms (250 papers) and Bacteriophages and microbial interactions (221 papers). The work is most often cited by research in Business and International Management (3.0k citations), Endocrinology (7.8k citations) and Molecular Biology (86.6k citations). Eugene V. Koonin has collaborated with scholars based in United States, France and Russia. Frequent co-authors include Kira S. Makarova, Yuri I. Wolf, L. Aravind, Michael Y. Galperin, Roman L. Tatusov, Feng Zhang, Alexander E. Gorbalenya, Igor B. Rogozin, Valerian V. Dolja and Mart Krupovìč. Their work appears in journals such as Nature, Science and Cell.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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