Works by Koonin, Eugene V.

Results: 376

Megataxonomy and global ecology of the virosphere.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrad042

By:

Koonin, Eugene V;
Kuhn, Jens H;
Dolja, Valerian V;
Krupovic, Mart

Publication type:

Article

The evolutionary journey of Argonaute proteins.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 9, p. 743, doi. 10.1038/nsmb.2879

By:

Swarts, Daan C;
Makarova, Kira;
Wang, Yanli;
Nakanishi, Kotaro;
Ketting, René F;
Koonin, Eugene V;
Patel, Dinshaw J;
van der Oost, John

Publication type:

Article

Evolution and classification of the CRISPR-Cas systems.

Published in:

2011

By:

Makarova, Kira S.;
Haft, Daniel H.;
Barrangou, Rodolphe;
Brouns, Stan J. J.;
Charpentier, Emmanuelle;
Horvath, Philippe;
Moineau, Sylvain;
Mojica, Francisco J. M.;
Wolf, Yuri I.;
Yakunin, Alexander F.;
van der Oost, John;
Koonin, Eugene V.

Publication type:

Opinion

Evolution of diverse cell division and vesicle formation systems in Archaea.

Published in:

Nature Reviews Microbiology, 2010, v. 8, n. 10, p. 731, doi. 10.1038/nrmicro2406

By:

Makarova, Kira S.;
Yutin, Natalya;
Bell, Stephen D.;
Koonin, Eugene V.

Publication type:

Article

Compelling reasons why viruses are relevant for the origin of cells.

Published in:

2009

By:

Koonin, Eugene V.;
Senkevich, Tatiana G.;
Dolja, Valerian V.

Publication type:

Letter

The complexity of the virus world.

Published in:

2009

By:

Koonin, Eugene V.;
Wolf, Yuri I.;
Nagasaki, Keizo;
Dolja, Valerian V.

Publication type:

Letter

The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.

Published in:

Nature Reviews Microbiology, 2008, v. 6, n. 12, p. 925, doi. 10.1038/nrmicro2030

By:

Koonin, Eugene V.;
Wolf, Yuri I.;
Nagasaki, Keizo;
Dolja, Valerian V.

Publication type:

Article

Inventing the dynamo machine: the evolution of the F-type and V-type ATPases.

Published in:

Nature Reviews Microbiology, 2007, v. 5, n. 11, p. 892, doi. 10.1038/nrmicro1767

By:

Mulkidjanian, Armen Y.;
Makarova, Kira S.;
Galperin, Michael Y.;
Koonin, Eugene V.

Publication type:

Article

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.

Published in:

Bioinformatics, 2010, v. 26, n. 12, p. 1481, doi. 10.1093/bioinformatics/btq229

By:

Kristensen, David M.;
Kannan, Lavanya;
Coleman, Michael K.;
Wolf, Yuri I.;
Sorokin, Alexander;
Koonin, Eugene V.;
Mushegian, Arcady

Publication type:

Article

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.

Published in:

Bioinformatics, 2006, v. 22, n. 21, p. 2581, doi. 10.1093/bioinformatics/btl418

By:

Kira S. Makarova;
Nick V. Grishin;
Eugene V. Koonin

Publication type:

Article

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.

Published in:

Bioinformatics, 2006, v. 22, n. 11, p. 1297, doi. 10.1093/bioinformatics/btl096

By:

Kira S. Makarova;
Eugene V. Koonin;
Robert Haselkorn;
Michael Y. Galperin

Publication type:

Article

Modeling genome evolution with a diffusion approximation of a birth-and-death process.

Published in:

Bioinformatics, 2005, v. 21, p. iii12, doi. 10.1093/bioinformatics/bti1202

By:

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

Publication type:

Article

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

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02858-9

By:

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

Publication type:

Article

Evolution of adaptive immunity from transposable elements combined with innate immune systems.

Published in:

Nature Reviews Genetics, 2015, v. 16, n. 3, p. 184, doi. 10.1038/nrg3859

By:

Koonin, Eugene V.;
Krupovic, Mart

Publication type:

Article

Identification of Myosin XI Receptors in Arabidopsis Defines a Distinct Class of Transport Vesicles.

Published in:

Plant Cell, 2013, v. 25, n. 8, p. 3022, doi. 10.1105/tpc.113.113704

By:

Peremyslov, Valera V.;
Morgun, Eva A.;
Kurth, Elizabeth G.;
Makarova, Kira S.;
Koonin, Eugene V.;
Dolja, Valerian V.

Publication type:

Article

Defence systems and horizontal gene transfer in bacteria.

Published in:

Environmental Microbiology, 2024, v. 26, n. 4, p. 1, doi. 10.1111/1462-2920.16630

By:

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

Publication type:

Article

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

Published in:

Environmental Microbiology, 2023, v. 25, n. 1, p. 40, doi. 10.1111/1462-2920.16207

By:

Koonin, Eugene V.;
Krupovic, Mart;
Dolja, Valerian V.

Publication type:

Article

Integrated mobile genetic elements in Thaumarchaeota.

Published in:

Environmental Microbiology, 2019, v. 21, n. 6, p. 2056, doi. 10.1111/1462-2920.14564

By:

Krupovic, Mart;
Makarova, Kira S.;
Wolf, Yuri I.;
Medvedeva, Sofia;
Prangishvili, David;
Forterre, Patrick;
Koonin, Eugene V.

Publication type:

Article

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

Published in:

Environmental Microbiology, 2019, v. 21, n. 6, p. 2002, doi. 10.1111/1462-2920.14479

By:

Liu, Ying;
Brandt, David;
Ishino, Sonoko;
Ishino, Yoshizumi;
Koonin, Eugene V.;
Kalinowski, Jörn;
Krupovic, Mart;
Prangishvili, David

Publication type:

Article

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

Published in:

2018

By:

Koonin, Eugene V.

Publication type:

Editorial

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

Published in:

Genes, 2018, v. 9, n. 2, p. 28, doi. 10.3390/genes9020028

By:

Ferrer, Manuel;
Sorokin, Dimitry Y.;
Wolf, Yuri I.;
Ciordia, Sergio;
Mena, María C.;
Bargiela, Rafael;
Koonin, Eugene V.;
Makarova, Kira S.

Publication type:

Article

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

Published in:

PLoS ONE, 2018, v. 13, n. 4, p. 1, doi. 10.1371/journal.pone.0195571

By:

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

Publication type:

Article

Selection for short introns in highly expressed genes.

Published in:

Nature Genetics, 2002, v. 31, n. 4, p. 415, doi. 10.1038/ng940

By:

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

Publication type:

Article

Evolution of alternative and constitutive regions of mammalian 5′UTRs.

Published in:

BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-162

By:

Resch, Alissa M.;
Ogurtsov, Aleksey Y.;
Rogozin, Igor B.;
Shabalina, Svetlana A.;
Koonin, Eugene V.

Publication type:

Article

Classification and evolutionary history of the single-strand annealing proteins, RecT, Redβ, ERF and RAD52.

Published in:

BMC Genomics, 2002, v. 3, p. 8, doi. 10.1186/1471-2164-3-8

By:

Iyer, Lakshminarayan M.;
Koonin, Eugene V.;
Aravind, L.

Publication type:

Article

Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ‘weak’ context of the start codon.

Published in:

Bioinformatics, 2001, v. 17, n. 10, p. 890, doi. 10.1093/bioinformatics/17.10.890

By:

Rogozin, Igor B.;
Kochetov, Alexey V.;
Kondrashov, Fyodor A.;
Koonin, Eugene V.;
Milanesi, Luciano

Publication type:

Article

THE EMERGING PARADIGM AND OPEN PROBLEMS IN COMPARATIVE GENOMICS.

Published in:

Bioinformatics, 1999, v. 15, n. 4, p. 265, doi. 10.1093/bioinformatics/15.4.265

By:

Koonin, Eugene V.

Publication type:

Article

Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses.

Published in:

Intervirology, 2010, v. 53, n. 5, p. 284, doi. 10.1159/000312913

By:

Koonin, Eugene V.;
Yutin, Natalya

Publication type:

Article

Planctomycetes and eukaryotes: A case of analogy not homology.

Published in:

BioEssays, 2011, v. 33, n. 11, p. 810, doi. 10.1002/bies.201100045

By:

McInerney, James O.;
Martin, William F.;
Koonin, Eugene V.;
Allen, John F.;
Galperin, Michael Y.;
Lane, Nick;
Archibald, John M.;
Embley, T. Martin

Publication type:

Article

Paralogs and mutational robustness linked through transcriptional reprogramming.

Published in:

BioEssays, 2005, v. 27, n. 9, p. 865, doi. 10.1002/bies.20296

By:

Koonin, Eugene V.

Publication type:

Article

Scale-free networks in biology: new insights into the fundamentals of evolution?

Published in:

BioEssays, 2002, v. 24, n. 2, p. 105, doi. 10.1002/bies.10059

By:

Wolf, Yuri I.;
Karev, Georgy;
Koonin, Eugene V.

Publication type:

Article

Origin and evolution of the genetic code: The universal enigma.

Published in:

IUBMB Life, 2009, v. 61, n. 2, p. 99, doi. 10.1002/iub.146

By:

Koonin, Eugene V.;
Novozhilov, Artem S.

Publication type:

Article

Origin and evolution of the genetic code: The universal enigma.

Published in:

IUBMB Life, 2009, v. 61, n. 2, p. spcone, doi. 10.1002/iub.190

By:

Koonin, Eugene V.;
Novozhilov, Artem S.

Publication type:

Article

A network perspective on the virus world.

Published in:

Communicative & Integrative Biology, 2017, v. 10, n. 2, p. N.PAG, doi. 10.1080/19420889.2017.1296614

By:

Iranzo, Jaime;
Krupovic, Mart;
Koonin, Eugene V.

Publication type:

Article

Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0040683

By:

Swanson, Maud M.;
Reavy, Brian;
Makarova, Kira S.;
Cock, Peter J.;
Hopkins, David W.;
Torrance, Lesley;
Koonin, Eugene V.;
Taliansky, Michael

Publication type:

Article

Phylogenomics of Prokaryotic Ribosomal Proteins.

Published in:

PLoS ONE, 2012, v. 7, n. 5, p. 1, doi. 10.1371/journal.pone.0036972

By:

Yutin, Natalya;
Puigbò, Pere;
Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

Article

Phylogenomics of Cas4 family nucleases.

Published in:

BMC Evolutionary Biology, 2017, v. 17, p. 1, doi. 10.1186/s12862-017-1081-1

By:

Hudaiberdiev, Sanjarbek;
Shmakov, Sergey;
Wolf, Yuri I.;
Terns, Michael P.;
Makarova, Kira S.;
Koonin, Eugene V.

Publication type:

Article

Reconstruction of the evolution of microbial defense systems.

Published in:

BMC Evolutionary Biology, 2017, v. 17, p. 1, doi. 10.1186/s12862-017-0942-y

By:

Puigbò, Pere;
Makarova, Kira S.;
Kristensen, David M.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Seeing the Tree of Life behind the phylogenetic forest.

Published in:

2013

By:

Puigbò, Pere;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Letter

Taming of the shrewd: novel eukaryotic genes from RNA viruses.

Published in:

BMC Biology, 2010, v. 8, p. 1, doi. 10.1186/1741-7007-8-2

By:

Koonin, Eugene V.

Publication type:

Article

Chance and necessity in cellular response to challenge.

Published in:

Molecular Systems Biology, 2007, v. 3, n. 1, p. 107, doi. 10.1038/msb4100152

By:

Koonin, Eugene V

Publication type:

Article

Systemic determinants of gene evolution and function.

Published in:

Molecular Systems Biology, 2005, v. 1, n. 1, p. E1, doi. 10.1038/msb4100029

By:

Koonin, Eugene V

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.721392

By:

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

Publication type:

Article

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

Published in:

Frontiers in Cellular & Infection Microbiology, 2012, v. 2, p. 1, doi. 10.3389/fcimb.2012.00119

By:

Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

Article

Microbial genomics challenge Darwin.

Published in:

Frontiers in Cellular & Infection Microbiology, 2012, v. 2, p. 1, doi. 10.3389/fcimb.2012.00127

By:

Raoult, Didier;
Koonin, Eugene V.

Publication type:

Article

Microbial genomics challenge Darwin.

Published in:

Frontiers in Cellular & Infection Microbiology, 2012, v. 2, p. 1, doi. 10.3389/fcimb.2012.00127

By:

Raoult, Didier;
Koonin, Eugene V.

Publication type:

Article

Evolution of microbes and viruses: A paradigm shift in evolutionary biology?

Published in:

Frontiers in Cellular & Infection Microbiology, 2012, v. 2, p. 1, doi. 10.3389/fcimb.2012.00119

By:

Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

Article

Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens.

Published in:

Environmental Microbiology, 2013, v. 15, n. 2, p. 307, doi. 10.1111/j.1462-2920.2012.02886.x

By:

Busby, Ben;
Kristensen, David M.;
Koonin, Eugene V.

Publication type:

Article

TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus.

Published in:

Environmental Microbiology, 2012, v. 14, n. 2, p. 503, doi. 10.1111/j.1462-2920.2011.02662.x

By:

Gorlas, Aurore;
Koonin, Eugene V.;
Bienvenu, Nadège;
Prieur, Daniel;
Geslin, Claire

Publication type:

Article

Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.

Published in:

Environmental Microbiology, 2000, v. 2, n. 5, p. 516

By:

Béjà, Oded;
Suzuki, Marcelino T.;
Koonin, Eugene V.;
Aravind, L.;
Hadd, Andrew;
Nguyen, Linh P.;
Villacorta, Rachel;
Amjadi, Mojgan;
Garrigues, Corey;
Jovanovich, Stevan B.;
Feldman, Robert A.;
DeLong, Edward F.

Publication type:

Article