Publications by authors named "Eugene V Koonin"

100Publications

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

Nucleic Acids Res 2020 Jul 31. Epub 2020 Jul 31.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/nar/gkaa635DOI Listing
July 2020

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

Nat Commun 2020 Jul 29;11(1):3784. Epub 2020 Jul 29.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1038/s41467-020-17652-0DOI Listing
July 2020

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

Nat Microbiol 2020 Jul 20. Epub 2020 Jul 20.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1038/s41564-020-0755-4DOI Listing
July 2020

The LUCA and its complex virome.

Nat Rev Microbiol 2020 Jul 14. Epub 2020 Jul 14.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.

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http://dx.doi.org/10.1038/s41579-020-0408-xDOI Listing
July 2020

Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes.

Commun Biol 2020 Jun 22;3(1):321. Epub 2020 Jun 22.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1038/s42003-020-1014-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7308287PMC
June 2020

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

Proc Natl Acad Sci U S A 2020 06 10;117(26):15193-15199. Epub 2020 Jun 10.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;

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http://dx.doi.org/10.1073/pnas.2008176117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334499PMC
June 2020

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

BMC Biol 2020 Jun 9;18(1):61. Epub 2020 Jun 9.

Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan.

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http://dx.doi.org/10.1186/s12915-020-00800-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281927PMC
June 2020

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

bioRxiv 2020 Apr 9. Epub 2020 Apr 9.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1101/2020.04.05.026450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217234PMC
April 2020

Response to Comment on "RNA-guided DNA insertion with CRISPR-associated transposases".

Science 2020 06;368(6495)

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.abb2920DOI Listing
June 2020

Deep Roots and Splendid Boughs of the Global Plant Virome.

Annu Rev Phytopathol 2020 May 27. Epub 2020 May 27.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1146/annurev-phyto-030320-041346DOI Listing
May 2020

Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea.

mBio 2020 05 19;11(3). Epub 2020 May 19.

Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China

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http://dx.doi.org/10.1128/mBio.00417-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7240154PMC
May 2020

The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome.

Trends Microbiol 2020 May 28;28(5):349-359. Epub 2020 Feb 28.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1016/j.tim.2020.01.010DOI Listing
May 2020

Game-Theoretical Modeling of Interviral Conflicts Mediated by Mini-CRISPR Arrays.

Front Microbiol 2020 20;11:381. Epub 2020 Mar 20.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.

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http://dx.doi.org/10.3389/fmicb.2020.00381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099407PMC
March 2020

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

Nat Commun 2020 03 6;11(1):1234. Epub 2020 Mar 6.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1038/s41467-020-15094-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060240PMC
March 2020

Global Organization and Proposed Megataxonomy of the Virus World.

Microbiol Mol Biol Rev 2020 May 4;84(2). Epub 2020 Mar 4.

Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA

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http://dx.doi.org/10.1128/MMBR.00061-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062200PMC
May 2020

Predator Dormancy is a Stable Adaptive Strategy due to Parrondo's Paradox.

Adv Sci (Weinh) 2020 Feb 12;7(3):1901559. Epub 2019 Dec 12.

Science and Math Cluster Singapore University of Technology and Design (SUTD) Singapore S487372 Singapore.

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http://dx.doi.org/10.1002/advs.201901559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001654PMC
February 2020

A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes.

mBio 2020 01 14;11(1). Epub 2020 Jan 14.

Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA

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http://dx.doi.org/10.1128/mBio.02938-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6960288PMC
January 2020

Phages build anti-defence barriers.

Nat Microbiol 2020 01;5(1):8-9

Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France.

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http://dx.doi.org/10.1038/s41564-019-0635-yDOI Listing
January 2020

Crossing fitness valleys via double substitutions within codons.

BMC Biol 2019 12 16;17(1):105. Epub 2019 Dec 16.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1186/s12915-019-0727-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6916188PMC
December 2019

Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.

Nat Commun 2019 11 26;10(1):5376. Epub 2019 Nov 26.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1038/s41467-019-13429-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879757PMC
November 2019

Virus-borne mini-CRISPR arrays are involved in interviral conflicts.

Nat Commun 2019 11 15;10(1):5204. Epub 2019 Nov 15.

Institut Pasteur, Department of Microbiology, 75015, Paris, France.

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http://dx.doi.org/10.1038/s41467-019-13205-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858448PMC
November 2019

Reply to Hedrick and Klitz: High haplotype discovery rate in the HLA locus.

Proc Natl Acad Sci U S A 2019 11 29;116(47):23388-23389. Epub 2019 Oct 29.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;

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http://dx.doi.org/10.1073/pnas.1916124116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876207PMC
November 2019

Key role of recombination in evolutionary processes with migration between two habitats.

Phys Rev E 2019 Sep;100(3-1):030401

Science and Math Cluster, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore.

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http://dx.doi.org/10.1103/PhysRevE.100.030401DOI Listing
September 2019

A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk.

F1000Res 2019 2;8:1000. Epub 2019 Jul 2.

National Center for Biotechnology Information, National Institutes of Health, USA, Bethesda, Maryland, 20814, USA.

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https://f1000research.com/articles/8-1000/v1
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http://dx.doi.org/10.12688/f1000research.19590.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685453PMC
June 2020

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire.

Nat Rev Genet 2020 02 14;21(2):119-131. Epub 2019 Oct 14.

Department of Microbiology, Institut Pasteur, Paris, France.

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http://www.nature.com/articles/s41576-019-0172-9
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http://dx.doi.org/10.1038/s41576-019-0172-9DOI Listing
February 2020

On the feasibility of saltational evolution.

Proc Natl Acad Sci U S A 2019 10 30;116(42):21068-21075. Epub 2019 Sep 30.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894

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http://dx.doi.org/10.1073/pnas.1909031116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800335PMC
October 2019

Systematic prediction of functionally linked genes in bacterial and archaeal genomes.

Nat Protoc 2019 10 13;14(10):3013-3031. Epub 2019 Sep 13.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.

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http://www.nature.com/articles/s41596-019-0211-1
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http://dx.doi.org/10.1038/s41596-019-0211-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6938587PMC
October 2019

Translational coupling via termination-reinitiation in archaea and bacteria.

Nat Commun 2019 09 5;10(1):4006. Epub 2019 Sep 5.

Goethe University, Institute for Molecular Biosciences, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.

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http://dx.doi.org/10.1038/s41467-019-11999-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728339PMC
September 2019

Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids.

Nat Commun 2019 07 31;10(1):3425. Epub 2019 Jul 31.

Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris, 75015, France.

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http://dx.doi.org/10.1038/s41467-019-11433-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668415PMC
July 2019

Identification of Dephospho-Coenzyme A (Dephospho-CoA) Kinase in Thermococcus kodakarensis and Elucidation of the Entire CoA Biosynthesis Pathway in Archaea.

mBio 2019 07 23;10(4). Epub 2019 Jul 23.

Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan

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http://dx.doi.org/10.1128/mBio.01146-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650551PMC
July 2019

Origin of programmed cell death from antiviral defense?

Proc Natl Acad Sci U S A 2019 08 9;116(33):16167-16169. Epub 2019 Jul 9.

Department of Microbiology, Institut Pasteur, 75015 Paris, France

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http://dx.doi.org/10.1073/pnas.1910303116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697789PMC
August 2019

Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.

Methods Mol Biol 2019 ;1910:241-269

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1007/978-1-4939-9074-0_8DOI Listing
January 2020

Multiplicative fitness, rapid haplotype discovery, and fitness decay explain evolution of human MHC.

Proc Natl Acad Sci U S A 2019 07 21;116(28):14098-14104. Epub 2019 Jun 21.

National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894;

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http://dx.doi.org/10.1073/pnas.1714436116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628782PMC
July 2019

RNA-guided DNA insertion with CRISPR-associated transposases.

Science 2019 07 6;365(6448):48-53. Epub 2019 Jun 6.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.aax9181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659118PMC
July 2019

CRISPR-Cas in mobile genetic elements: counter-defence and beyond.

Nat Rev Microbiol 2019 08;17(8):513-525

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://www.nature.com/articles/s41579-019-0204-7
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http://dx.doi.org/10.1038/s41579-019-0204-7DOI Listing
August 2019

Origin of viruses: primordial replicators recruiting capsids from hosts.

Nat Rev Microbiol 2019 07;17(7):449-458

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.

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http://dx.doi.org/10.1038/s41579-019-0205-6DOI Listing
July 2019

Unexpected connections between type VI-B CRISPR-Cas systems, bacterial natural competence, ubiquitin signaling network and DNA modification through a distinct family of membrane proteins.

FEMS Microbiol Lett 2019 04;366(8)

National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/femsle/fnz088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700684PMC
April 2019

Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

CRISPR J 2018 10;1(5):325-336

National Center for Biotechnology Information , National Library of Medicine, Bethesda, Maryland.

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https://www.liebertpub.com/doi/10.1089/crispr.2018.0033
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http://dx.doi.org/10.1089/crispr.2018.0033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636873PMC
October 2018

In silico learning of tumor evolution through mutational time series.

Proc Natl Acad Sci U S A 2019 05 23;116(19):9501-9510. Epub 2019 Apr 23.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

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http://dx.doi.org/10.1073/pnas.1901695116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510994PMC
May 2019

Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array.

FEMS Microbiol Lett 2019 04;366(7)

National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/femsle/fnz079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6702361PMC
April 2019

Allele fixation probability in a Moran model with fluctuating fitness landscapes.

Phys Rev E 2019 Feb;99(2-1):022407

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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https://link.aps.org/doi/10.1103/PhysRevE.99.022407
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http://dx.doi.org/10.1103/PhysRevE.99.022407DOI Listing
February 2019

CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology.

Authors:
Eugene V Koonin

Biol Philos 2019 19;34(1). Epub 2019 Jan 19.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 USA.

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http://link.springer.com/10.1007/s10539-018-9658-7
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http://dx.doi.org/10.1007/s10539-018-9658-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404382PMC
January 2019

Origins and evolution of CRISPR-Cas systems.

Philos Trans R Soc Lond B Biol Sci 2019 05;374(1772):20180087

National Center for Biotechnology Information, National Library of Medicine , Bethesda, MD 20894 , USA.

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http://dx.doi.org/10.1098/rstb.2018.0087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6452270PMC
May 2019

Reply to 'Evolutionary placement of Methanonatronarchaeia'.

Nat Microbiol 2019 04;4(4):560-561

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1038/s41564-019-0358-0DOI Listing
April 2019

Integrated mobile genetic elements in Thaumarchaeota.

Environ Microbiol 2019 06 18;21(6):2056-2078. Epub 2019 Mar 18.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1111/1462-2920.14564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563490PMC
June 2019

Grammar of protein domain architectures.

Proc Natl Acad Sci U S A 2019 02 7;116(9):3636-3645. Epub 2019 Feb 7.

Department of Pathology, University of Alabama, Birmingham, AL 35249;

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http://dx.doi.org/10.1073/pnas.1814684116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397568PMC
February 2019

Towards functional characterization of archaeal genomic dark matter.

Biochem Soc Trans 2019 02 1;47(1):389-398. Epub 2019 Feb 1.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, U.S.A.

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http://dx.doi.org/10.1042/BST20180560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393860PMC
February 2019

Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism.

Adv Virus Res 2019 10;103:167-202. Epub 2018 Nov 10.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States.

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http://dx.doi.org/10.1016/bs.aivir.2018.09.002DOI Listing
April 2019

Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve.

Biol Direct 2018 12 14;13(1):27. Epub 2018 Dec 14.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1186/s13062-018-0230-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822691PMC
December 2018

Multiple evolutionary origins of giant viruses.

F1000Res 2018 22;7. Epub 2018 Nov 22.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.12688/f1000research.16248.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6259494PMC
March 2019

Origins and Evolution of the Global RNA Virome.

mBio 2018 11 27;9(6). Epub 2018 Nov 27.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://mbio.asm.org/lookup/doi/10.1128/mBio.02329-18
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http://dx.doi.org/10.1128/mBio.02329-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282212PMC
November 2018

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures.

Environ Microbiol 2019 06 8;21(6):2002-2014. Epub 2019 Jan 8.

Department of Microbiology, BMGE, Institut Pasteur, Paris, 75015, France.

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http://doi.wiley.com/10.1111/1462-2920.14479
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http://dx.doi.org/10.1111/1462-2920.14479DOI Listing
June 2019

Criticality in tumor evolution and clinical outcome.

Proc Natl Acad Sci U S A 2018 11 7;115(47):E11101-E11110. Epub 2018 Nov 7.

Center for Bioinformatics and Computational Biology, Institute of Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742;

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http://dx.doi.org/10.1073/pnas.1807256115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255199PMC
November 2018

A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition.

Mol Cell 2018 11 18;72(4):700-714.e8. Epub 2018 Oct 18.

Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765183078
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http://dx.doi.org/10.1016/j.molcel.2018.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242336PMC
November 2018

Anti-CRISPRs on the march.

Science 2018 10;362(6411):156-157

National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA.

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http://www.sciencemag.org/lookup/doi/10.1126/science.aav2440
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http://dx.doi.org/10.1126/science.aav2440DOI Listing
October 2018

Open questions: CRISPR biology.

Authors:
Eugene V Koonin

BMC Biol 2018 09 24;16(1):95. Epub 2018 Sep 24.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1186/s12915-018-0565-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151929PMC
September 2018

Environmental microbiology and metagenomics: the Brave New World is here, what's next?

Authors:
Eugene V Koonin

Environ Microbiol 2018 12 15;20(12):4210-4212. Epub 2018 Oct 15.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1111/1462-2920.14403DOI Listing
December 2018

CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity.

J Mol Biol 2019 01 5;431(1):3-20. Epub 2018 Sep 5.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836183101
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http://dx.doi.org/10.1016/j.jmb.2018.08.030DOI Listing
January 2019

Physical foundations of biological complexity.

Proc Natl Acad Sci U S A 2018 09 27;115(37):E8678-E8687. Epub 2018 Aug 27.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1807890115
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http://dx.doi.org/10.1073/pnas.1807890115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140470PMC
September 2018

Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems.

RNA Biol 2019 04 14;16(4):435-448. Epub 2018 Aug 14.

a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA.

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https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1
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http://dx.doi.org/10.1080/15476286.2018.1493331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546382PMC
April 2019

The depths of virus exaptation.

Curr Opin Virol 2018 08 30;31:1-8. Epub 2018 Jul 30.

Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France. Electronic address:

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http://dx.doi.org/10.1016/j.coviro.2018.07.011DOI Listing
August 2018

Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

Nat Microbiol 2018 Sep;3(9):1076

Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41564-018-0184-9DOI Listing
September 2018

Purifying and positive selection in the evolution of stop codons.

Sci Rep 2018 06 18;8(1):9260. Epub 2018 Jun 18.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1038/s41598-018-27570-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006363PMC
June 2018

Cancer-mutation network and the number and specificity of driver mutations.

Proc Natl Acad Sci U S A 2018 06 12;115(26):E6010-E6019. Epub 2018 Jun 12.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;

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http://dx.doi.org/10.1073/pnas.1803155115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042135PMC
June 2018

Hunting for Treasure Chests in Microbial Defense Islands.

Authors:
Eugene V Koonin

Mol Cell 2018 06 7;70(5):761-762. Epub 2018 Jun 7.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.05.025DOI Listing
June 2018

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis.

Proc Natl Acad Sci U S A 2018 06 21;115(23):E5307-E5316. Epub 2018 May 21.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;

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http://dx.doi.org/10.1073/pnas.1803440115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003329PMC
June 2018

Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.

Authors:
Piet Maes Sergey V Alkhovsky Yīmíng Bào Martin Beer Monica Birkhead Thomas Briese Michael J Buchmeier Charles H Calisher Rémi N Charrel Il Ryong Choi Christopher S Clegg Juan Carlos de la Torre Eric Delwart Joseph L DeRisi Patrick L Di Bello Francesco Di Serio Michele Digiaro Valerian V Dolja Christian Drosten Tobiasz Z Druciarek Jiang Du Hideki Ebihara Toufic Elbeaino Rose C Gergerich Amethyst N Gillis Jean-Paul J Gonzalez Anne-Lise Haenni Jussi Hepojoki Udo Hetzel Thiện Hồ Ní Hóng Rakesh K Jain Petrus Jansen van Vuren Qi Jin Miranda Gilda Jonson Sandra Junglen Karen E Keller Alan Kemp Anja Kipar Nikola O Kondov Eugene V Koonin Richard Kormelink Yegor Korzyukov Mart Krupovic Amy J Lambert Alma G Laney Matthew LeBreton Igor S Lukashevich Marco Marklewitz Wanda Markotter Giovanni P Martelli Robert R Martin Nicole Mielke-Ehret Hans-Peter Mühlbach Beatriz Navarro Terry Fei Fan Ng Márcio Roberto Teixeira Nunes Gustavo Palacios Janusz T Pawęska Clarence J Peters Alexander Plyusnin Sheli R Radoshitzky Víctor Romanowski Pertteli Salmenperä Maria S Salvato Hélène Sanfaçon Takahide Sasaya Connie Schmaljohn Bradley S Schneider Yukio Shirako Stuart Siddell Tarja A Sironen Mark D Stenglein Nadia Storm Harikishan Sudini Robert B Tesh Ioannis E Tzanetakis Mangala Uppala Olli Vapalahti Nikos Vasilakis Peter J Walker Guópíng Wáng Lìpíng Wáng Yànxiăng Wáng Tàiyún Wèi Michael R Wiley Yuri I Wolf Nathan D Wolfe Zhìqiáng Wú Wénxìng Xú Li Yang Zuòkūn Yāng Shyi-Dong Yeh Yǒng-Zhèn Zhāng Yàzhōu Zhèng Xueping Zhou Chénxī Zhū Florian Zirkel Jens H Kuhn

Arch Virol 2018 Aug 21;163(8):2295-2310. Epub 2018 Apr 21.

Division of Clinical Research (DCR), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.

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http://dx.doi.org/10.1007/s00705-018-3843-5DOI Listing
August 2018

Estimation of universal and taxon-specific parameters of prokaryotic genome evolution.

PLoS One 2018 13;13(4):e0195571. Epub 2018 Apr 13.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195571PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898727PMC
July 2018

Taxonomy of the order Mononegavirales: update 2018.

Arch Virol 2018 Aug 11;163(8):2283-2294. Epub 2018 Apr 11.

Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.

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http://dx.doi.org/10.1007/s00705-018-3814-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076851PMC
August 2018

Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis.

Virol J 2018 04 10;15(1):67. Epub 2018 Apr 10.

National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA.

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http://dx.doi.org/10.1186/s12985-018-0974-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894146PMC
April 2018

Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

Nat Microbiol 2018 04 5;3(4):461-469. Epub 2018 Mar 5.

Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41564-018-0120-zDOI Listing
April 2018

Metaviromics: a tectonic shift in understanding virus evolution.

Virus Res 2018 02;246:A1-A3

Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331. Electronic address:

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http://dx.doi.org/10.1016/j.virusres.2018.02.001DOI Listing
February 2018

Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia".

Genes (Basel) 2018 Jan 23;9(2). Epub 2018 Jan 23.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.3390/genes9020028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852551PMC
January 2018

Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.

J Bacteriol 2018 04 12;200(7). Epub 2018 Mar 12.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1128/JB.00681-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5847659PMC
April 2018

Proposed Role for KaiC-Like ATPases as Major Signal Transduction Hubs in Archaea.

mBio 2017 Dec 5;8(6). Epub 2017 Dec 5.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1128/mBio.01959-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717392PMC
December 2017

Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.

Biol Direct 2017 Dec 4;12(1):31. Epub 2017 Dec 4.

Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands.

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http://dx.doi.org/10.1186/s13062-017-0202-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5715634PMC
December 2017

Phylogenomics of Cas4 family nucleases.

BMC Evol Biol 2017 11 28;17(1):232. Epub 2017 Nov 28.

National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.

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https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12862-017-1081-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704561PMC
November 2017

Viruses of archaea: Structural, functional, environmental and evolutionary genomics.

Virus Res 2018 01 22;244:181-193. Epub 2017 Nov 22.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.

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http://dx.doi.org/10.1016/j.virusres.2017.11.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801132PMC
January 2018

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.

Nat Microbiol 2018 Jan 13;3(1):38-46. Epub 2017 Nov 13.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.

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http://dx.doi.org/10.1038/s41564-017-0053-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736458PMC
January 2018