Works by Wolf, Yuri I.

Results: 126

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

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

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

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

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

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

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

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

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

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

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.

Published in:

Environmental Microbiology, 2012, v. 14, n. 11, p. 2870, doi. 10.1111/j.1462-2920.2012.02841.x

By:

Galperin, Michael Y.;
Mekhedov, Sergei L.;
Puigbo, Pere;
Smirnov, Sergey;
Wolf, Yuri I.;
Rigden, Daniel J.

Publication type:

Article

Cellular differentiation into hyphae and spores in halophilic archaea.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37389-w

By:

Tang, Shu-Kun;
Zhi, Xiao-Yang;
Zhang, Yao;
Makarova, Kira S.;
Liu, Bing-Bing;
Zheng, Guo-Song;
Zhang, Zhen-Peng;
Zheng, Hua-Jun;
Wolf, Yuri I.;
Zhao, Yu-Rong;
Jiang, Song-Hao;
Chen, Xi-Ming;
Li, En-Yuan;
Zhang, Tao;
Chen, Pei-Ru;
Feng, Yu-Zhou;
Xiang, Ming-Xian;
Lin, Zhi-Qian;
Shi, Jia-Hui;
Chang, Cheng

Publication type:

Article

No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 9, p. 2021, doi. 10.1038/ismej.2015.20

By:

Gophna, Uri;
Kristensen, David M;
Wolf, Yuri I;
Popa, Ovidiu;
Drevet, Christine;
Koonin, Eugene V

Publication type:

Article

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

Published in:

Biology Direct, 2018, v. 13, n. 1, p. N.PAG, doi. 10.1186/s13062-018-0230-9

By:

Berezovskaya, Faina;
Karev, Georgy P.;
Katsnelson, Mikhail I.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

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

Published in:

Biology Direct, 2017, v. 12, p. 1, doi. 10.1186/s13062-017-0202-5

By:

Koonin, Eugene V.;
Wolf, Yuri I.;
Katsnelson, Mikhail I.

Publication type:

Article

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms.

Published in:

Biology Direct, 2016, v. 11, p. 1, doi. 10.1186/s13062-016-0111-z

By:

Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

Article

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae.

Published in:

Biology Direct, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s13062-015-0043-z

By:

Pagnier, Isabelle;
Yutin, Natalya;
Croce, Olivier;
Makarova, Kira S.;
Wolf, Yuri I.;
Benamar, Samia;
Raoult, Didier;
Koonin, Eugene V.;
La Scola, Bernard

Publication type:

Article

Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis.

Published in:

Biology Direct, 2014, v. 9, n. 1, p. 1, doi. 10.1186/1745-6150-9-13

By:

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

Publication type:

Article

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.

Published in:

Biology Direct, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1745-6150-8-9

By:

Podar, Mircea;
Makarova, Kira S.;
Graham, David E.;
Wolf, Yuri I.;
Koonin, Eugene V.;
Reysenbach, Anna-Louise

Publication type:

Article

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

Published in:

Biology Direct, 2012, v. 7, n. 1, p. 46, doi. 10.1186/1745-6150-7-46

By:

Wolf, Yuri I.;
Makarova, Kira S.;
Yutin, Natalya;
Koonin, Eugene V.

Publication type:

Article

The common ancestry of life.

Published in:

Biology Direct, 2010, v. 5, p. 64, doi. 10.1186/1745-6150-5-64

By:

Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

Article

Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution.

Published in:

Biology Direct, 2010, v. 5, p. 31, doi. 10.1186/1745-6150-5-31

By:

Omelchenko, Marina V.;
Galperin, Michael Y.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

The origins of phagocytosis and eukaryogenesis.

Published in:

Biology Direct, 2009, v. 4, p. 1, doi. 10.1186/1745-6150-4-9

By:

Yutin, Natalya;
Wolf, Maxim Y.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia.

Published in:

Biology Direct, 2008, v. 3, p. 1, doi. 10.1186/1745-6150-3-26

By:

Hou, Shaobin;
Makarova, Kira S.;
Saw, Jimmy H. W.;
Senin, Pavel;
Ly, Benjamin V.;
Zhemin Zhou;
Yan Ren;
Jianmei Wang;
Galperin, Michael Y.;
Omelchenko, Marina V.;
Wolf, Yuri I.;
Yutin, Natalya;
Koonin, Eugene V.;
Stott, Matthew B.;
Mountain, Bruce W.;
Crowe, Michelle A.;
Smirnova, Angela V.;
Dunfield, Peter F.;
Lu Feng;
Lei Wang

Publication type:

Article

Evolutionary primacy of sodium bioenergetics.

Published in:

Biology Direct, 2008, v. 3, p. 1, doi. 10.1186/1745-6150-3-13

By:

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

Publication type:

Article

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

Published in:

Biology Direct, 2007, v. 2, p. 33, doi. 10.1186/1745-6150-2-33

By:

Makarova, Kira S.;
Sorokin, Alexander V.;
Novichkov, Pavel S.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.

Published in:

Biology Direct, 2007, v. 2, p. 24, doi. 10.1186/1745-6150-2-24

By:

Novozhilov, Artem S.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus.

Published in:

Biology Direct, 2006, v. 1, p. 34, doi. 10.1186/1745-6150-1-34

By:

Wolf, Yuri I.;
Viboud, Cecile;
Holmes, Edward C.;
Koonin, Eugene V.;
Lipman, David J.

Publication type:

Article

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

Published in:

BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-01937-7

By:

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

Publication type:

Article

Evolutionary plasticity of protein families: Coupling between sequence and structure variation.

Published in:

Proteins, 2005, v. 61, n. 3, p. 535, doi. 10.1002/prot.20644

By:

Panchenko, Anna R.;
Wolf, Yuri I.;
Panchenko, Larisa A.;
Madej, Thomas

Publication type:

Article

Global Analysis of Posttranslational Protein Arginylation.

Published in:

PLoS Biology, 2007, v. 5, n. 10, p. e258, doi. 10.1371/journal.pbio.0050258

By:

Wong, Catherine C. L.;
Tao Xu;
Rai, Reena;
Bailey, Aaron O.;
Yates 3rd, John R.;
Wolf, Yuri I.;
Zebroski, Henry;
Kashina, Anna

Publication type:

Article

Molecular adaptations during viral epidemics.

Published in:

EMBO Reports, 2022, v. 23, n. 8, p. 1, doi. 10.15252/embr.202255393

By:

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

Publication type:

Article

Constraints and plasticity in genome and molecular-phenome evolution.

Published in:

2010

By:

Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

journal article

Microbial genome analysis: the COG approach.

Published in:

Briefings in Bioinformatics, 2019, p. 1063, doi. 10.1093/bib/bbx117

By:

Galperin, Michael Y;
Kristensen, David M;
Makarova, Kira S;
Wolf, Yuri I;
Koonin, Eugene V

Publication type:

Article

Computational methods for Gene Orthology inference.

Published in:

Briefings in Bioinformatics, 2011, v. 12, n. 5, p. 379, doi. 10.1093/bib/bbr030

By:

Kristensen, David M.;
Wolf, Yuri I.;
Mushegian, Arcady R.;
Koonin, Eugene V.

Publication type:

Article

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.

Published in:

Briefings in Bioinformatics, 2004, v. 5, n. 2, p. 131, doi. 10.1093/bib/5.2.131

By:

Rogozin, Igor B.;
Makarova, Kira S.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

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

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21350-w

By:

Yutin, Natalya;
Benler, Sean;
Shmakov, Sergei A.;
Wolf, Yuri I.;
Tolstoy, Igor;
Rayko, Mike;
Antipov, Dmitry;
Pevzner, Pavel A.;
Koonin, Eugene V.

Publication type:

Article

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

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17652-0

By:

Gussow, Ayal B.;
Park, Allyson E.;
Borges, Adair L.;
Shmakov, Sergey A.;
Makarova, Kira S.;
Wolf, Yuri I.;
Bondy-Denomy, Joseph;
Koonin, Eugene V.

Publication type:

Article

Genome reduction as the dominant mode of evolution.

Published in:

BioEssays, 2013, v. 35, n. 9, p. 829, doi. 10.1002/bies.201300037

By:

Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Virus-host arms race at the joint origin of multicellularity and programmed cell death.

Published in:

Cell Cycle, 2014, v. 13, n. 19, p. 3083, doi. 10.4161/15384101.2014.949496

By:

Iranzo, Jaime;
Lobkovsky, Alexander E;
Wolf, Yuri I;
Koonin, Eugene V

Publication type:

Article

The basic building blocks and evolution of CRISPR-Cas systems.

Published in:

Biochemical Society Transactions, 2013, v. 41, n. 6, p. 1392, doi. 10.1042/BST20130038

By:

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

Publication type:

Article

Estimation of prokaryotic supergenome size and composition from gene frequency distributions.

Published in:

BMC Genomics, 2014, v. 15, p. 1, doi. 10.1186/1471-2164-15-S6-S14

By:

Lobkovsky, Alexander E.;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Assessment of assumptions underlying models of prokaryotic pangenome evolution.

Published in:

BMC Biology, 2021, v. 19, n. 1, p. 1, doi. 10.1186/s12915-021-00960-2

By:

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

Publication type:

Article

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

Published in:

BMC Biology, 2020, v. 18, n. 1, p. 1, doi. 10.1186/s12915-020-00919-9

By:

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

Publication type:

Article