Works matching AU Wolf, Yuri I.

Results: 126

An updated evolutionary classification of CRISPR-Cas systems.

Published in:

Nature Reviews Microbiology, 2015, v. 13, n. 11, p. 722, doi. 10.1038/nrmicro3569

By:

Makarova, Kira S.;
Wolf, Yuri I.;
Alkhnbashi, Omer S.;
Costa, Fabrizio;
Shah, Shiraz A.;
Saunders, Sita J.;
Barrangou, Rodolphe;
Brouns, Stan J. J.;
Charpentier, Emmanuelle;
Haft, Daniel H.;
Horvath, Philippe;
Moineau, Sylvain;
Mojica, Francisco J. M.;
Terns, Rebecca M.;
Terns, Michael P.;
White, Malcolm F.;
Yakunin, Alexander F.;
Garrett, Roger A.;
van der Oost, John;
Backofen, Rolf

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

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

Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements.

Published in:

Molecular Biology & Evolution, 2007, v. 24, n. 4, p. 1080, doi. 10.1093/molbev/msm029

By:

Rogozin, Igor B.;
Wolf, Yuri I.;
Carmel, Liran;
Koonin, Eugene V.

Publication type:

Article

Conservation and Coevolution in the Scale-Free Human Gene Coexpression Network.

Published in:

Molecular Biology & Evolution, 2004, v. 21, n. 11, p. 2058, doi. 10.1093/molbev/msh222

By:

Jordan, I. King;
Mariño-Ramírez, Leonardo;
Wolf, Yuri I.;
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

Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales.

Published in:

Viruses (1999-4915), 2022, v. 14, n. 9, p. 1842, doi. 10.3390/v14091842

By:

Yutin, Natalya;
Rayko, Mike;
Antipov, Dmitry;
Mutz, Pascal;
Wolf, Yuri I.;
Krupovic, Mart;
Koonin, Eugene V.

Publication type:

Article

A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley.

Published in:

Viruses (1999-4915), 2022, v. 14, n. 6, p. N.PAG, doi. 10.3390/v14061320

By:

Dahan, Jennifer;
Wolf, Yuri I.;
Orellana, Gardenia E.;
Wenninger, Erik J.;
Koonin, Eugene V.;
Karasev, Alexander 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

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes.

Published in:

BMC Biology, 2014, v. 12, n. 1, p. 1, doi. 10.1186/s12915-014-0066-4

By:

Puigbò, Pere;
Lobkovsky, Alexander E.;
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 novel group of negative-sense RNA viruses associated with epizootics in managed and free-ranging freshwater turtles in Florida, USA.

Published in:

PLoS Pathogens, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.ppat.1010258

By:

Waltzek, Thomas B.;
Stacy, Brian A.;
Ossiboff, Robert J.;
Stacy, Nicole I.;
Fraser, William A.;
Yan, Annie;
Mohan, Shipra;
Koonin, Eugene V.;
Wolf, Yuri I.;
Rodrigues, Thais C. S.;
Viadanna, Pedro H. O.;
Subramaniam, Kuttichantran;
Popov, Vsevolod L.;
Guzman-Vargas, Veronica;
Shender, Lisa A.

Publication type:

Article

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

Corrigendum: A universal trend of amino acid gain and loss in protein evolution.

Published in:

2005

By:

Jordan, I. King;
Kondrashov, Fyodor A.;
Adzhubei, Ivan A.;
Wolf, Yuri I.;
Koonin, Eugene V.;
Kondrashov, Alexey S.;
Sunyaev, Shamil

Publication type:

Correction Notice

A universal trend of amino acid gain and loss in protein evolution.

Published in:

Nature, 2005, v. 433, n. 7026, p. 633, doi. 10.1038/nature03306

By:

Jordan, I. King;
Kondrashov, Fyodor A.;
Adzhubei, Ivan A.;
Wolf, Yuri I.;
Koonin, Eugene V.;
Kondrashov, Alexey S.;
Sunyaev, Shamil

Publication type:

Article

Deep phylogeny of cancer drivers and compensatory mutations.

Published in:

Communications Biology, 2020, v. 3, n. 1, p. N.PAG, doi. 10.1038/s42003-020-01276-7

By:

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

Publication type:

Article

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

Published in:

Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-1014-1

By:

Shmakov, Sergey A.;
Wolf, Yuri I.;
Savitskaya, Ekaterina;
Severinov, Konstantin V.;
Koonin, Eugene V.

Publication type:

Article

Comparative genomics of defense systems in archaea and bacteria.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 8, p. 4360, doi. 10.1093/nar/gkt157

By:

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

Publication type:

Article

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D448, doi. 10.1093/nar/gkn684

By:

Novichkov, Pavel S.;
Ratnere, Igor;
Wolf, Yuri I.;
Koonin, Eugene V.;
Dubchak, Inna

Publication type:

Article

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 21, p. 6688, doi. 10.1093/nar/gkn668

By:

Koonin, Eugene V.;
Wolf, Yuri I.

Publication type:

Article

Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 14, p. 4626, doi. 10.1093/nar/gki775

By:

Makarova, Kira S.;
Wolf, Yuri I.;
Mekhedov, Sergey L.;
Mirkin, Boris G.;
Koonin, Eugene V.

Publication type:

Article

Congruent evolution of different classes of non‐coding DNA in prokaryotic genomes.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 19, p. 4264, doi. 10.1093/nar/gkf549

By:

Rogozin, Igor B.;
Makarova, Kira S.;
Natale, Darren A.;
Spiridonov, Alexey N.;
Tatusov, Roman L.;
Wolf, Yuri I.;
Yin, Jodie;
Koonin, Eugene V.

Publication type:

Article

Connected gene neighborhoods in prokaryotic genomes.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 10, p. 2212, doi. 10.1093/nar/30.10.2212

By:

Rogozin, Igor B.;
Makarova, Kira S.;
Murvai, Janos;
Czabarka, Eva;
Wolf, Yuri I.;
Tatusov, Roman L.;
Szekely, Laszlo A.;
Koonin, Eugene V.

Publication type:

Article

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.

Published in:

Nucleic Acids Research, 2001, v. 29, n. 14, p. 2994, doi. 10.1093/nar/29.14.2994

By:

Schäffer, Alejandro A.;
Aravind, L.;
Madden, Thomas L.;
Shavirin, Sergei;
Spouge, John L.;
Wolf, Yuri I.;
Koonin, Eugene V.;
Altschul, Stephen F.

Publication type:

Article

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

Published in:

RNA Biology, 2019, v. 16, n. 4, p. 435, doi. 10.1080/15476286.2018.1493331

By:

Faure, Guilhem;
Shmakov, Sergey A.;
Makarova, Kira S.;
Wolf, Yuri I.;
Crawley, Alexandra B.;
Barrangou, Rodolphe;
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

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

Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales.

Published in:

Life (2075-1729), 2015, v. 5, n. 1, p. 818, doi. 10.3390/life5010818

By:

Makarova, Kira S.;
Wolf, Yuri I.;
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

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

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

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

Horizontal Transfer of Bacterial Operons into Eukaryote Genomes.

Published in:

Genome Biology & Evolution, 2025, v. 17, n. 4, p. 1, doi. 10.1093/gbe/evaf055

By:

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

Publication type:

Article

Extreme Deviations from Expected Evolutionary Rates in Archaeal Protein Families.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 10, p. 2791, doi. 10.1093/gbe/evx189

By:

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

Publication type:

Article

Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 10, p. 2879, doi. 10.1093/gbe/evx191

By:

Yampolsky, Lev Y.;
Wolf, Yuri I.;
Bouzinier, Michael A.

Publication type:

Article

Inevitability of Genetic Parasites.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 9, p. 2867, doi. 10.1093/gbe/evw193

By:

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

Publication type:

Article

Evolvability of an Optimal Recombination Rate.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 1, p. 70, doi. 10.1093/gbe/evv249

By:

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

Publication type:

Article

Universal Pacemaker of Genome Evolution in Animals and Fungi and Variation of Evolutionary Rates in Diverse Organisms.

Published in:

Genome Biology & Evolution, 2014, v. 6, n. 6, p. 1268, doi. 10.1093/gbe/evu091

By:

Snir, Sagi;
Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

Stability along with Extreme Variability in Core Genome Evolution.

Published in:

Genome Biology & Evolution, 2013, v. 5, n. 7, p. 1393, doi. 10.1093/gbe/evt098

By:

Wolf, Yuri I.;
Snir, Sagi;
Koonin, Eugene V.

Publication type:

Article

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution.

Published in:

Genome Biology & Evolution, 2013, v. 5, n. 1, p. 233, doi. 10.1093/gbe/evt002

By:

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

Publication type:

Article

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes.

Published in:

Genome Biology & Evolution, 2012, v. 4, n. 12, p. 1286, doi. 10.1093/gbe/evs100

By:

Wolf, Yuri I.;
Koonin, Eugene V.

Publication type:

Article

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes.

Published in:

Genome Biology & Evolution, 2012, v. 4, n. 9, p. 1286, doi. 10.1093/gbe/evs100

By:

Wolf, Yuri I.;
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

Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems.

Published in:

BMC Evolutionary Biology, 2015, v. 15, n. 1, p. 1, doi. 10.1186/s12862-015-0324-2

By:

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

Publication type:

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