Works by Makarova, Kira S.

Results: 93

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

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 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

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

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

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

The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota.

Published in:

PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0024222

By:

Siebers, Bettina;
Zaparty, Melanie;
Raddatz, Guenter;
Tjaden, Britta;
Albers, Sonja-Verena;
Bell, Steve D.;
Blombach, Fabian;
Kletzin, Arnulf;
Kyrpides, Nikos;
Lanz, Christa;
Plagens, André;
Rampp, Markus;
Rosinus, Andrea;
Jan, Mathias von;
Makarova, Kira S.;
Klenk, Hans-Peter;
Schuster, Stephan C.;
Hensel, Reinhard

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

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

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

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

The complex domain architecture of SAMD9 family proteins, predicted STANDlike NTPases, suggests new links to inflammation and apoptosis.

Published in:

Biology Direct, 2017, v. 12, p. 1, doi. 10.1186/s13062-017-0185-2

By:

Mekhedov, Sergei L.;
Makarova, Kira S.;
Koonin, Eugene V.

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

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing.

Published in:

Biology Direct, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1745-6150-8-15

By:

Anantharaman, Vivek;
Makarova, Kira S.;
Maxwell Burroughs, A.;
Koonin, Eugene V.;
Aravind, L.

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

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes.

Published in:

Biology Direct, 2012, v. 7, n. 1, p. 40, doi. 10.1186/1745-6150-7-40

By:

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

Publication type:

Article

Two families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.

Published in:

Biology Direct, 2010, v. 5, p. 33, doi. 10.1186/1745-6150-5-33

By:

Makarova, Kira S.;
Koonin, Eugene V.

Publication type:

Article

Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ϵ and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors.

Published in:

Biology Direct, 2009, v. 4, p. 1, doi. 10.1186/1745-6150-4-11

By:

Tahirov, Tahir H.;
Makarova, Kira S.;
Rogozin, Igor B.;
Pavlov, Youri I.;
Koonin, Eugene V.

Publication type:

Article

A highly conserved family of inactivated archaeal B family DNA polymerases.

Published in:

Biology Direct, 2008, v. 3, p. 1, doi. 10.1186/1745-6150-3-32

By:

Rogozin, Igor B.;
Makarova, Kira S.;
Pavlov, Youri 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

The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system.

Published in:

Biology Direct, 2008, v. 3, p. 1, doi. 10.1186/1745-6150-3-2

By:

Podar, Mircea;
Wall, Mark A.;
Makarova, Kira S.;
Koonin, Eugene V.

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

Orthologs of the small RPB8 subunit of the eukaryotic RNApolymerases are conserved in hyperthermophilic Crenarchaeotaand "Korarchaeota".

Published in:

Biology Direct, 2007, v. 2, p. 38, doi. 10.1186/1745-6150-2-38

By:

Koonin, Eugene V.;
Makarova, Kira S.;
Elkins, James G.

Publication type:

Article

CRISPR in mobile genetic elements: counter-defense, inter-element competition and RNA-guided transposition.

Published in:

BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-02090-x

By:

Koonin, Eugene V.;
Makarova, Kira S.

Publication type:

Article

Engineering of CRISPR-Cas12b for human genome editing.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08224-4

By:

Strecker, Jonathan;
Jones, Sara;
Koopal, Balwina;
Schmid-Burgk, Jonathan;
Zetsche, Bernd;
Gao, Linyi;
Makarova, Kira S.;
Koonin, Eugene V.;
Zhang, Feng

Publication type:

Article

Biochemical plasticity of the Escherichia coliCRISPR Cascade revealed by in vitro reconstitution of Cascade activities from purified Cas proteins.

Published in:

FEBS Journal, 2024, v. 291, n. 23, p. 5177, doi. 10.1111/febs.17295

By:

Lemak, Sofia;
Brown, Greg;
Makarova, Kira S.;
Koonin, Eugene V.;
Yakunin, Alexander F.

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

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

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

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

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

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

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

COG database update 2024.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D356, doi. 10.1093/nar/gkae983

By:

Galperin, Michael Y;
Vera Alvarez, Roberto;
Karamycheva, Svetlana;
Makarova, Kira S;
Wolf, Yuri I;
Landsman, David;
Koonin, Eugene V

Publication type:

Article

Long range segmentation of prokaryotic genomes by gene age and functionality.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 18, p. 11045, doi. 10.1093/nar/gkae745

By:

Wolf, Yuri I;
Schurov, Ilya V;
Makarova, Kira S;
Katsnelson, Mikhail I;
Koonin, Eugene V

Publication type:

Article

Widespread CRISPR-derived RNA regulatory elements in CRISPR-Cas systems.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 15, p. 8150, doi. 10.1093/nar/gkad495

By:

Shmakov, Sergey A;
Barth, Zachary K;
Makarova, Kira S;
Wolf, Yuri I;
Brover, Vyacheslav;
Peters, Joseph E;
Koonin, Eugene V

Publication type:

Article

tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 8, p. 4601, doi. 10.1093/nar/gkac271

By:

Zhang, Haolin;
Gong, Xuemei;
Zhao, Qianqian;
Mukai, Takahito;
Vargas-Rodriguez, Oscar;
Zhang, Huiming;
Zhang, Yuxing;
Wassel, Paul;
Amikura, Kazuaki;
Maupin-Furlow, Julie;
Ren, Yan;
Xu, Xun;
Wolf, Yuri I;
Makarova, Kira S;
Koonin, Eugene V;
Shen, Yue;
Söll, Dieter;
Fu, Xian

Publication type:

Article

CRISPRidentify: identification of CRISPR arrays using machine learning approach.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 4, p. e20, doi. 10.1093/nar/gkaa1158

By:

Mitrofanov, Alexander;
Alkhnbashi, Omer S;
Shmakov, Sergey A;
Makarova, Kira S;
Koonin, Eugene V;
Backofen, Rolf

Publication type:

Article

COG database update: focus on microbial diversity, model organisms, and widespread pathogens.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D274, doi. 10.1093/nar/gkaa1018

By:

Galperin, Michael Y;
Wolf, Yuri I;
Makarova, Kira S;
Vera Alvarez, Roberto;
Landsman, David;
Koonin, Eugene V

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2020, v. 48, n. 16, p. 8828, doi. 10.1093/nar/gkaa635

By:

Makarova, Kira S;
Timinskas, Albertas;
Wolf, Yuri I;
Gussow, Ayal B;
Siksnys, Virginijus;
Venclovas, Česlovas;
Koonin, Eugene V

Publication type:

Article