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Research | 16 February 2021 | Open
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features
- Eugene V. Koonin
- Natalya Yutin
- , Sean Benler
- , Sergei A. Shmakov
- , Yuri I. Wolf
- , Igor Tolstoy
- , Mike Rayko
- , Dmitry Antipov
- , Pavel A. Pevzner
- & Eugene V. Koonin
Nature Communications 12 , 1–11

Rights & permissionsfor article Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features . Opens in a new window.
Amendments and Corrections | 14 December 2020
Publisher Correction: Mutation–selection balance and compensatory mechanisms in tumour evolution
- Eugene V. Koonin
- Erez Persi
- , Yuri I. Wolf
- , David Horn
- , Eytan Ruppin
- , Francesca Demichelis
- , Robert A. Gatenby
- , Robert J. Gillies
- & Eugene V. Koonin
Nature Reviews Genetics , 1–1

Rights & permissionsfor article Publisher Correction: Mutation–selection balance and compensatory mechanisms in tumour evolution . Opens in a new window.
Reviews | 30 November 2020
Mutation–selection balance and compensatory mechanisms in tumour evolution
- Eugene V. Koonin
- Erez Persi
- , Yuri I. Wolf
- , David Horn
- , Eytan Ruppin
- , Francesca Demichelis
- , Robert A. Gatenby
- , Robert J. Gillies
- & Eugene V. Koonin
Nature Reviews Genetics , 1–12

Rights & permissionsfor article Mutation–selection balance and compensatory mechanisms in tumour evolution . Opens in a new window.
Research | 18 November 2020
Structure and function of virion RNA polymerase of a crAss-like phage
- Eugene V. Koonin
Nature 589 , 306–309

Rights & permissionsfor article Structure and function of virion RNA polymerase of a crAss-like phage . Opens in a new window.
Research | 2 October 2020 | Open
Deep phylogeny of cancer drivers and compensatory mutations
- Eugene V. Koonin
Communications Biology 3 , 1–11

Rights & permissionsfor article Deep phylogeny of cancer drivers and compensatory mutations . Opens in a new window.
Research | 29 July 2020 | Open
Machine-learning approach expands the repertoire of anti-CRISPR protein families
- Eugene V. Koonin
Nature Communications 11 , 1–12

Rights & permissionsfor article Machine-learning approach expands the repertoire of anti-CRISPR protein families . Opens in a new window.
Research | 20 July 2020 | Open
Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome
- Eugene V. Koonin
- Yuri I. Wolf
- , Sukrit Silas
- , Yongjie Wang
- , Shuang Wu
- , Michael Bocek
- , Darius Kazlauskas
- , Mart Krupovic
- , Andrew Fire
- , Valerian V. Dolja
- & Eugene V. Koonin
Nature Microbiology 5 , 1262–1270

Rights & permissionsfor article Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome . Opens in a new window.
Reviews | 14 July 2020
The LUCA and its complex virome
- Eugene V. Koonin
Nature Reviews Microbiology 18 , 661–670

Rights & permissionsfor article The LUCA and its complex virome . Opens in a new window.
Research | 22 June 2020 | Open
Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes
- Eugene V. Koonin
Communications Biology 3 , 1–9

Rights & permissionsfor article Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes . Opens in a new window.
Research | 6 March 2020 | Open
Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability
- Eugene V. Koonin
Nature Communications 11 , 1–11

Rights & permissionsfor article Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability . Opens in a new window.
News & Views | 19 December 2019
Phages build anti-defence barriers
- Eugene V. Koonin
- Eugene V. Koonin
- & Mart Krupovic
Nature Microbiology 5 , 8–9

Rights & permissionsfor article Phages build anti-defence barriers . Opens in a new window.
Reviews | 19 December 2019
Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
- Eugene V. Koonin
- Kira S. Makarova
- , Yuri I. Wolf
- , Jaime Iranzo
- , Sergey A. Shmakov
- , Omer S. Alkhnbashi
- , Stan J. J. Brouns
- , Emmanuelle Charpentier
- , David Cheng
- , Daniel H. Haft
- , Philippe Horvath
- , Sylvain Moineau
- , Francisco J. M. Mojica
- , David Scott
- , Shiraz A. Shah
- , Virginijus Siksnys
- , Michael P. Terns
- , Česlovas Venclovas
- , Malcolm F. White
- , Alexander F. Yakunin
- , Winston Yan
- , Feng Zhang
- , Roger A. Garrett
- , Rolf Backofen
- , John van der Oost
- , Rodolphe Barrangou
- & Eugene V. Koonin
Nature Reviews Microbiology 18 , 67–83

Rights & permissionsfor article Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants . Opens in a new window.
Research | 26 November 2019 | Open
Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence
- Eugene V. Koonin
- Jaime Iranzo
- , Yuri I. Wolf
- , Eugene V. Koonin
- & Itamar Sela
Nature Communications 10 , 1–10

Rights & permissionsfor article Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence . Opens in a new window.
Research | 15 November 2019 | Open
Virus-borne mini-CRISPR arrays are involved in interviral conflicts
- Eugene V. Koonin
Nature Communications 10 , 1–10

Rights & permissionsfor article Virus-borne mini-CRISPR arrays are involved in interviral conflicts . Opens in a new window.
Amendments and Corrections | 14 November 2019
Author Correction: Collaborative networks in gene editing
- NPG Nature Publishing Group US New York Nature Research 41587
- Ying Huang
- , Alan Porter
- , Yi Zhang
- & Rodolphe Barrangou
Nature Biotechnology 37 , 1522–1522

Rights & permissionsfor article Author Correction: Collaborative networks in gene editing . Opens in a new window.
Reviews | 14 October 2019
Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire
- Eugene V. Koonin
Nature Reviews Genetics 21 , 119–131

Rights & permissionsfor article Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire . Opens in a new window.
News | 2 October 2019
Collaborative networks in gene editing
- NPG Nature Publishing Group US New York Nature Research 41587
- Ying Huang
- , Alan Porter
- , Yi Zhang
- & Rodolphe Barrangou
Nature Biotechnology 37 , 1107–1109

Rights & permissionsfor article Collaborative networks in gene editing . Opens in a new window.
Protocols | 13 September 2019
Systematic prediction of functionally linked genes in bacterial and archaeal genomes
- Eugene V. Koonin
Nature Protocols 14 , 3013–3031

Rights & permissionsfor article Systematic prediction of functionally linked genes in bacterial and archaeal genomes . Opens in a new window.
Research | 5 September 2019 | Open
Translational coupling via termination-reinitiation in archaea and bacteria
- Eugene V. Koonin
- Madeleine Huber
- , Guilhem Faure
- , Sebastian Laass
- , Esther Kolbe
- , Kristina Seitz
- , Christina Wehrheim
- , Yuri I. Wolf
- , Eugene V. Koonin
- & Jörg Soppa
Nature Communications 10 , 1–11

Rights & permissionsfor article Translational coupling via termination-reinitiation in archaea and bacteria . Opens in a new window.
Research | 31 July 2019 | Open
Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids
- Eugene V. Koonin
Nature Communications 10 , 1–12

Rights & permissionsfor article Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids . Opens in a new window.
Research | 5 June 2019
CRISPR–Cas in mobile genetic elements: counter-defence and beyond
- Eugene V. Koonin
Nature Reviews Microbiology 17 , 513–525

Rights & permissionsfor article CRISPR–Cas in mobile genetic elements: counter-defence and beyond . Opens in a new window.
Reviews | 29 May 2019
Origin of viruses: primordial replicators recruiting capsids from hosts
- Eugene V. Koonin
Nature Reviews Microbiology 17 , 449–458

Rights & permissionsfor article Origin of viruses: primordial replicators recruiting capsids from hosts . Opens in a new window.
Correspondence | 25 February 2019
Reply to ‘Evolutionary placement of Methanonatronarchaeia’
- Eugene V. Koonin
Nature Microbiology 4 , 560–561

Rights & permissionsfor article Reply to ‘Evolutionary placement of Methanonatronarchaeia’ . Opens in a new window.
Comments & Opinion | 20 February 2019
Classify viruses — the gain is worth the pain
- Eugene V. Koonin is a senior investigator in...
- Jens H. Kuhn
- , Yuri I. Wolf
- , Mart Krupovic
- , Yong-Zhen Zhang
- , Piet Maes
- , Valerian V. Dolja
- & Eugene V. Koonin
Nature 566 , 318–320

Rights & permissionsfor article Classify viruses — the gain is worth the pain . Opens in a new window.
Research | 22 January 2019 | Open
Engineering of CRISPR-Cas12b for human genome editing
- Eugene V. Koonin
- Jonathan Strecker
- , Sara Jones
- , Balwina Koopal
- , Jonathan Schmid-Burgk
- , Bernd Zetsche
- , Linyi Gao
- , Kira S. Makarova
- , Eugene V. Koonin
- & Feng Zhang
Nature Communications 10 , 1–8

Rights & permissionsfor article Engineering of CRISPR-Cas12b for human genome editing . Opens in a new window.
Reviews | 17 December 2018 | Open
Minimum Information about an Uncultivated Virus Genome (MIUViG)
- Eugene V Koonin
- Simon Roux
- , Evelien M Adriaenssens
- , Bas E Dutilh
- , Eugene V Koonin
- , Andrew M Kropinski
- , Mart Krupovic
- , Jens H Kuhn
- , Rob Lavigne
- , J Rodney Brister
- , Arvind Varsani
- , Clara Amid
- , Ramy K Aziz
- , Seth R Bordenstein
- , Peer Bork
- , Mya Breitbart
- , Guy R Cochrane
- , Rebecca A Daly
- , Christelle Desnues
- , Melissa B Duhaime
- , Joanne B Emerson
- , François Enault
- , Jed A Fuhrman
- , Pascal Hingamp
- , Philip Hugenholtz
- , Bonnie L Hurwitz
- , Natalia N Ivanova
- , Jessica M Labonté
- , Kyung-Bum Lee
- , Rex R Malmstrom
- , Manuel Martinez-Garcia
- , Ilene Karsch Mizrachi
- , Hiroyuki Ogata
- , David Páez-Espino
- , Marie-Agnès Petit
- , Catherine Putonti
- , Thomas Rattei
- , Alejandro Reyes
- , Francisco Rodriguez-Valera
- , Karyna Rosario
- , Lynn Schriml
- , Frederik Schulz
- , Grieg F Steward
- , Matthew B Sullivan
- , Shinichi Sunagawa
- , Curtis A Suttle
- , Ben Temperton
- , Susannah G Tringe
- , Rebecca Vega Thurber
- , Nicole S Webster
- , Katrine L Whiteson
- , Steven W Wilhelm
- , K Eric Wommack
- , Tanja Woyke
- , Kelly C Wrighton
- , Pelin Yilmaz
- , Takashi Yoshida
- , Mark J Young
- , Natalya Yutin
- , Lisa Zeigler Allen
- , Nikos C Kyrpides
- & Emiley A Eloe-Fadrosh
Nature Biotechnology 37 , 29–37

Rights & permissionsfor article Minimum Information about an Uncultivated Virus Genome (MIUViG) . Opens in a new window.
Research | 31 July 2018 | Open
Systems analysis of intracellular pH vulnerabilities for cancer therapy
- NPG Nature Publishing Group UK London Nature Research 41467
- Erez Persi
- , Miquel Duran-Frigola
- , Mehdi Damaghi
- , William R. Roush
- , Patrick Aloy
- , John L. Cleveland
- , Robert J. Gillies
- & Eytan Ruppin
Nature Communications 9 , 1–11

Rights & permissionsfor article Systems analysis of intracellular pH vulnerabilities for cancer therapy . Opens in a new window.
Amendments and Corrections | 21 June 2018
Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity
- Eugene V. Koonin
- Fei He
- , Yuvaraj Bhoobalan-Chitty
- , Lan B. Van
- , Anders L. Kjeldsen
- , Matteo Dedola
- , Kira S. Makarova
- , Eugene V. Koonin
- , Ditlev E. Brodersen
- & Xu Peng
Nature Microbiology 3 , 1076–1076

Rights & permissionsfor article Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity . Opens in a new window.
Research | 20 June 2018
A distinct abundant group of microbial rhodopsins discovered using functional metagenomics
- Eugene V. Koonin
- Alina Pushkarev
- , Keiichi Inoue
- , Shirley Larom
- , José Flores-Uribe
- , Manish Singh
- , Masae Konno
- , Sahoko Tomida
- , Shota Ito
- , Ryoko Nakamura
- , Satoshi P. Tsunoda
- , Alon Philosof
- , Itai Sharon
- , Natalya Yutin
- , Eugene V. Koonin
- , Hideki Kandori
- & Oded Béjà
Nature 558 , 595–599

Rights & permissionsfor article A distinct abundant group of microbial rhodopsins discovered using functional metagenomics . Opens in a new window.
Research | 18 June 2018 | Open
Purifying and positive selection in the evolution of stop codons
- Eugene V. Koonin
Scientific Reports 8 , 1–11

Rights & permissionsfor article Purifying and positive selection in the evolution of stop codons . Opens in a new window.
Research | 5 March 2018
Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity
- Eugene V. Koonin
- Fei He
- , Yuvaraj Bhoobalan-Chitty
- , Lan B. Van
- , Anders L. Kjeldsen
- , Matteo Dedola
- , Kira S. Makarova
- , Eugene V. Koonin
- , Ditlev E. Brodersen
- & Xu Peng
Nature Microbiology 3 , 461–469

Rights & permissionsfor article Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity . Opens in a new window.
Research | 13 November 2017
Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut
- Eugene V. Koonin
- Natalya Yutin
- , Kira S. Makarova
- , Ayal B. Gussow
- , Mart Krupovic
- , Anca Segall
- , Robert A. Edwards
- & Eugene V. Koonin
Nature Microbiology 3 , 38–46

Rights & permissionsfor article Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut . Opens in a new window.
Reviews | 10 November 2017
The enigmatic archaeal virosphere
- Eugene V. Koonin is the leader of the...
Nature Reviews Microbiology 15 , 724–739

Rights & permissionsfor article The enigmatic archaeal virosphere . Opens in a new window.
Research | 29 September 2017 | Open
Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions
- Eugene V. Koonin
Scientific Reports 7 , 1–10

Rights & permissionsfor article Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions . Opens in a new window.
Research | 30 May 2017
Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis
- Eugene V. Koonin
Nature Microbiology 2 , 1–11

Rights & permissionsfor article Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis . Opens in a new window.
Research | 23 January 2017
Diversity and evolution of class 2 CRISPR–Cas systems
- Eugene V. Koonin is the leader of the...
- Sergey Shmakov
- , Aaron Smargon
- , David Scott
- , David Cox
- , Neena Pyzocha
- , Winston Yan
- , Omar O. Abudayyeh
- , Jonathan S. Gootenberg
- , Kira S. Makarova
- , Yuri I. Wolf
- , Konstantin Severinov
- , Feng Zhang
- & Eugene V. Koonin
Nature Reviews Microbiology 15 , 169–182

Rights & permissionsfor article Diversity and evolution of class 2 CRISPR–Cas systems . Opens in a new window.
Reviews | 3 January 2017 | Open
Virus taxonomy in the age of metagenomics
- Eugene V. Koonin is the leader of the...
- Peter Simmonds
- , Mike J. Adams
- , Mária Benkő
- , Mya Breitbart
- , J. Rodney Brister
- , Eric B. Carstens
- , Andrew J. Davison
- , Eric Delwart
- , Alexander E. Gorbalenya
- , Balázs Harrach
- , Roger Hull
- , Andrew M.Q. King
- , Eugene V. Koonin
- , Mart Krupovic
- , Jens H. Kuhn
- , Elliot J. Lefkowitz
- , Max L. Nibert
- , Richard Orton
- , Marilyn J. Roossinck
- , Sead Sabanadzovic
- , Matthew B. Sullivan
- , Curtis A. Suttle
- , Robert B. Tesh
- , René A. van der Vlugt
- , Arvind Varsani
- & F. Murilo Zerbini
Nature Reviews Microbiology 15 , 161–168

Rights & permissionsfor article Virus taxonomy in the age of metagenomics . Opens in a new window.
News & Views | 7 December 2016
A parasite's parasite saves host's neighbours
- Eugene V. Koonin is at the National Center...
- Eugene V. Koonin
- & Mart Krupovic
Nature 540 , 204–205

Rights & permissionsfor article A parasite's parasite saves host's neighbours . Opens in a new window.
Research | 7 December 2016 | Open
Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers
- Eugene V. Koonin
Scientific Reports 6 , 1–9

Rights & permissionsfor article Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers . Opens in a new window.
Research | 18 November 2016 | Open
Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins
- Eugene V Koonin
Nature Communications 7 , 1–11

Rights & permissionsfor article Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins . Opens in a new window.
Research | 7 November 2016
Two fundamentally different classes of microbial genes
- Eugene V. Koonin
Nature Microbiology 2 , 1–6

Rights & permissionsfor article Two fundamentally different classes of microbial genes . Opens in a new window.
Research | 5 July 2016 | Open
Germline viral “fossils” guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus
- Eugene V. Koonin
Scientific Reports 6 , 1–17

Rights & permissionsfor article Germline viral “fossils” guide <i>in silico</i> reconstruction of a mid-Cenozoic era marsupial adeno-associated virus . Opens in a new window.
Research | 28 September 2015
An updated evolutionary classification of CRISPR–Cas systems
- Eugene V. Koonin
Nature Reviews Microbiology 13 , 722–736

Rights & permissionsfor article An updated evolutionary classification of CRISPR–Cas systems . Opens in a new window.
Research | 30 July 2015 | Open
Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response
- Eugene V Koonin
- Antonio Fabio Di Narzo
- , Alexey Kozlenkov
- , Yongchao Ge
- , Bin Zhang
- , Leo Sanelli
- , Zacnicte May
- , Yanqing Li
- , Karim Fouad
- , Christopher Cardozo
- , Eugene V Koonin
- , David J Bennett
- & Stella Dracheva
Scientific Reports 5 , 1–15

Rights & permissionsfor article Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response . Opens in a new window.
Research | 22 June 2015
A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase
- Eugene V. Koonin
- Bing Liu
- , Songying Ouyang
- , Kira S. Makarova
- , Qiu Xia
- , Yanping Zhu
- , Zhimeng Li
- , Li Guo
- , Eugene V. Koonin
- , Zhi-Jie Liu
- & Li Huang
Nature Communications 6 , 1–11

Rights & permissionsfor article A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase . Opens in a new window.
Research | 1 April 2015
In vivo genome editing using Staphylococcus aureus Cas9
- Eugene V. Koonin
- F. Ann Ran
- , Le Cong
- , Winston X. Yan
- , David A. Scott
- , Jonathan S. Gootenberg
- , Andrea J. Kriz
- , Bernd Zetsche
- , Ophir Shalem
- , Xuebing Wu
- , Kira S. Makarova
- , Eugene V. Koonin
- , Phillip A. Sharp
- & Feng Zhang
Nature 520 , 186–191

Rights & permissionsfor article <i>In vivo</i> genome editing using <i>Staphylococcus aureus</i> Cas9 . Opens in a new window.
Research | 24 February 2015 | Open
No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales
- Eugene V Koonin
- Uri Gophna
- , David M Kristensen
- , Yuri I Wolf
- , Ovidiu Popa
- , Christine Drevet
- & Eugene V Koonin
The ISME Journal 9 , 2021–2027

Rights & permissionsfor article No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales . Opens in a new window.
Reviews | 22 December 2014
Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution
- Eugene V. Koonin is the leader of the...
- Mart Krupovic
- & Eugene V. Koonin
Nature Reviews Microbiology 13 , 105–115

Rights & permissionsfor article Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution . Opens in a new window.
Reviews | 9 December 2014
Evolution of adaptive immunity from transposable elements combined with innate immune systems
- Eugene V. Koonin is the leader of the...
- Eugene V. Koonin
- & Mart Krupovic
Nature Reviews Genetics 16 , 184–192

Rights & permissionsfor article Evolution of adaptive immunity from transposable elements combined with innate immune systems . Opens in a new window.
Reviews | 5 September 2014
The evolutionary journey of Argonaute proteins
- Eugene V Koonin
- Daan C Swarts
- , Kira Makarova
- , Yanli Wang
- , Kotaro Nakanishi
- , René F Ketting
- , Eugene V Koonin
- , Dinshaw J Patel
- & John van der Oost
Nature Structural & Molecular Biology 21 , 743–753

Rights & permissionsfor article The evolutionary journey of Argonaute proteins . Opens in a new window.

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