Works matching AU Makarova, Kira S.

Results: 93

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

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

High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.

Published in:

Standards in Genomic Sciences, 2017, v. 12, p. 1, doi. 10.1186/s40793-017-0258-y

By:

Matrosova, Vera Y.;
Gaidamakova, Elena K.;
Makarova, Kira S.;
Grichenko, Olga;
Klimenkova, Polina;
Volpe, Robert P.;
Tkavc, Rok;
Ertem, Gözen;
Conze, Isabel H.;
Brambilla, Evelyne;
Huntemann, Marcel;
Clum, Alicia;
Pillay, Manoj;
Palaniappan, Krishnaveni;
Varghese, Neha;
Mikhailova, Natalia;
Stamatis, Dimitrios;
Reddy, T. B. K.;
Daum, Chris;
Shapiro, Nicole

Publication type:

Article

Evolution of plant δµ-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives.

Published in:

Frontiers in Plant Science, 2015, p. 1, doi. 10.3389/fpls.2015.00567

By:

Forlani, Giuseppe;
Bertazzini, Michele;
Makarova, Kira S.;
Ruszkowski, Milosz;
Nocek, Boguslaw

Publication type:

Article

Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity.

Published in:

BMC Biology, 2014, v. 12, n. 1, p. 1, doi. 10.1186/1741-7007-12-36

By:

Krupovic, Mart;
Makarova, Kira S.;
Forterre, Patrick;
Prangishvili, David;
Koonin, Eugene 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

The Structure and Evolution of Penelope in the virilis Species Group of Drosophila: An Ancient Lineage of Retroelements.

Published in:

Journal of Molecular Evolution, 2001, v. 52, n. 5, p. 445, doi. 10.1007/s002390010174

By:

Lyozin, George T.;
Makarova, Kira S.;
Velikodvorskaja, Vera V.;
Zelentsova, Helena S.;
Khechumian, Ruben R.;
Kidwell, Margaret G.;
Koonin, Eugene V.;
Evgen'ev, Michael B.

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

Abundance of type I toxin–antitoxin systems in bacteria: searches for new candidates and discovery of novel families.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 11, p. 3743, doi. 10.1093/nar/gkq054

By:

Fozo, Elizabeth M.;
Makarova, Kira S.;
Shabalina, Svetlana A.;
Yutin, Natalya;
Koonin, Eugene V.;
Storz, Gisela

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

Comparative genomics of the FtsK–HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.

Published in:

Nucleic Acids Research, 2004, v. 32, n. 17, p. 5260, doi. 10.1093/nar/gkh828

By:

Iyer, Lakshminarayan M.;
Makarova, Kira S.;
Koonin, Eugene V.;
Aravind, L.

Publication type:

Article

Identification and functional analysis of ‘hypothetical’ genes expressed in Haemophilus influenzae.

Published in:

Nucleic Acids Research, 2004, v. 32, n. 8, p. 2353, doi. 10.1093/nar/gkh555

By:

Kolker, Eugene;
Makarova, Kira S.;
Shabalina, Svetlana;
Picone, Alex F.;
Purvine, Samuel;
Holzman, Ted;
Cherny, Tim;
Armbruster, David;
Munson, Robert S.;
Kolesov, Grigory;
Frishman, Dmitrij;
Galperin, Michael Y.

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

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 2, p. 482, doi. 10.1093/nar/30.2.482

By:

Makarova, Kira S.;
Aravind, L.;
Grishin, Nick V.;
Rogozin, Igor B.;
Koonin, Eugene V.

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

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

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

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

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

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

Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All theWay There and Back.

Published in:

Genome Biology & Evolution, 2017, v. 9, n. 10, p. 2812, doi. 10.1093/gbe/evx192

By:

Koonin, Eugene V.;
Makarova, Kira S.

Publication type:

Article

Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 2, p. 375, doi. 10.1093/gbe/evw006

By:

Krupovic, Mart;
Shmakov, Sergey;
Makarova, Kira S.;
Forterre, Patrick;
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

Engineering archaeal membrane‐spanning lipid GDGT biosynthesis in bacteria: Implications for early life membrane transformations.

Published in:

mLife, 2025, v. 4, n. 2, p. 193, doi. 10.1002/mlf2.70001

By:

Chen, Huahui;
Zheng, Fengfeng;
Feng, Xi;
Huang, Zijing;
Yang, Wei;
Zhang, Chuanlun;
Du, Wenbin;
Makarova, Kira S.;
Koonin, Eugene V.;
Zeng, Zhirui

Publication type:

Article

GINS, a central nexus in the archaeal DNA replication fork.

Published in:

EMBO Reports, 2006, v. 7, n. 5, p. 539, doi. 10.1038/sj.embor.7400649

By:

Marinsek, Nina;
Barry, Elizabeth R.;
Makarova, Kira S.;
Dionne, Isabelle;
Koonin, Eugene V.;
Bell, Stephen D.

Publication type:

Article

ATGL has a key role in lipid droplet/adiposome degradation in mammalian cells.

Published in:

EMBO Reports, 2006, v. 7, n. 1, p. 106, doi. 10.1038/sj.embor.7400559

By:

Smirnova, Elena;
Goldberg, Elysa B.;
Makarova, Kira S.;
Lin, Lin;
Brown, William J.;
Jackson, Catherine L.

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

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 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

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

Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-34378-3

By:

Kato, Kazuki;
Okazaki, Sae;
Kannan, Soumya;
Altae-Tran, Han;
Esra Demircioglu, F.;
Isayama, Yukari;
Ishikawa, Junichiro;
Fukuda, Masahiro;
Macrae, Rhiannon K.;
Nishizawa, Tomohiro;
Makarova, Kira S.;
Koonin, Eugene V.;
Zhang, Feng;
Nishimasu, Hiroshi

Publication type:

Article

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

Published in:

Nature Protocols, 2019, v. 14, n. 10, p. 3013, doi. 10.1038/s41596-019-0211-1

By:

Shmakov, Sergey A.;
Faure, Guilhem;
Makarova, Kira S.;
Wolf, Yuri I.;
Severinov, Konstantin V.;
Koonin, Eugene V.

Publication type:

Article

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.

Published in:

BMC Evolutionary Biology, 2005, v. 5, p. 1, doi. 10.1186/1471-2148-5-57

By:

Omelchenko, Marina V;
Wolf, Yuri I;
Gaidamakova, Elena K;
Matrosova, Vera Y;
Vasilenko, Alexander;
Min Zhai;
Daly, Michael J;
Koonin, Eugene V;
Makarova, Kira S

Publication type:

Article

Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 8, p. 1855, doi. 10.1093/molbev/msy075

By:

Ausiannikava, Darya;
Mitchell, Laura;
Marriott, Hannah;
Smith, Victoria;
Hawkins, Michelle;
Makarova, Kira S;
Koonin, Eugene V;
Nieduszynski, Conrad A;
Allers, Thorsten

Publication type:

Article

The Deep Archaeal Roots of Eukaryotes.

Published in:

Molecular Biology & Evolution, 2008, v. 25, n. 8, p. 1619, doi. 10.1093/molbev/msn108

By:

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

Publication type:

Article

Diversity and Evolution of Type IV pili Systems in Archaea.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00667

By:

Makarova, Kira S.;
Koonin, Eugene V.;
Albers, Sonja-Verena

Publication type:

Article

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.

Published in:

Frontiers in Microbiology, 2014, v. 5, p. 1, doi. 10.3389/fmicb.2014.00354

By:

Makarova, Kira S.;
Krupovic, Mart;
Koonin, Eugene V.

Publication type:

Article

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery.

Published in:

Frontiers in Microbiology, 2014, v. 5, p. 1, doi. 10.3389/fmicb.2014.00354

By:

Makarova, Kira S.;
Krupovic, Mart;
Koonin, Eugene V.

Publication type:

Article

SURVEY AND SUMMARY.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 18, p. 3417, doi. 10.1093/nar/28.18.3417

By:

Aravind, L.;
Makarova, Kira S.;
Koonin, Eugene V.

Publication type:

Article

Regulatory sequence-based discovery of anti-defense genes in archaeal viruses.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-48074-x

By:

Bhoobalan-Chitty, Yuvaraj;
Xu, Shuanshuan;
Martinez-Alvarez, Laura;
Karamycheva, Svetlana;
Makarova, Kira S.;
Koonin, Eugene V.;
Peng, Xu

Publication type:

Article

Addendum: Cellular differentiation into hyphae and spores in halophilic archaea.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-44821-2

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

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44630-z

By:

Chaban, Anastasiia;
Minakhin, Leonid;
Goldobina, Ekaterina;
Bae, Brain;
Hao, Yue;
Borukhov, Sergei;
Putzeys, Leena;
Boon, Maarten;
Kabinger, Florian;
Lavigne, Rob;
Makarova, Kira S.;
Koonin, Eugene V.;
Nair, Satish K.;
Tagami, Shunsuke;
Severinov, Konstantin;
Sokolova, Maria L.

Publication type:

Article

Thermolysin and mitochondrial processing peptidase: How far structure-functional convergence goes.

Published in:

Protein Science: A Publication of the Protein Society, 1999, v. 8, n. 11, p. 2537, doi. 10.1110/ps.8.11.2537

By:

Grishin, Nick V.;
Makarova, Kira S.

Publication type:

Article

A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.

Published in:

Protein Science: A Publication of the Protein Society, 1999, v. 8, n. 8, p. 1714

By:

MAKAROVA, KIRA S.;
ARAVIND, L.;
KOONIN, EUGENE V.

Publication type:

Article

Evolutionary plasticity and functional versatility of CRISPR systems.

Published in:

PLoS Biology, 2022, v. 20, n. 1, p. 1, doi. 10.1371/journal.pbio.3001481

By:

Koonin, Eugene V.;
Makarova, Kira S.

Publication type:

Article