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1

Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

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

Journal:

The CRISPR Journal

Year:

2018

Language:

english

File:

PDF, 4.36 MB

english, 2018

2

Evolution and classification of the CRISPR–Cas systems

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.

Journal:

Nature Reviews Microbiology

Year:

2011

Language:

english

File:

PDF, 726 KB

english, 2011

3

Diversity, classification and evolution of CRISPR-Cas systems

Koonin, Eugene V, Makarova, Kira S, Zhang, Feng

Journal:

Current Opinion in Microbiology

Year:

2017

Language:

english

File:

PDF, 1.96 MB

english, 2017

4

Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes

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

Journal:

Year:

2014

Language:

english

File:

PDF, 2.28 MB

english, 2014

5

How radiation kills cells: Survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress

Debabrota Ghosal, Marina V. Omelchenko, Elena K. Gaidamakova, Vera Y. Matrosova, Alexander Vasilenko, Amudhan Venkateswaran, Min Zhai, Heather M. Kostandarithes, Hassan Brim, Kira S. Makarova, Lawrenc

Journal:

FEMS Microbiology Reviews

Year:

2005

Language:

english

File:

PDF, 990 KB

english, 2005

6

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin

Journal:

Year:

2011

Language:

english

File:

PDF, 2.97 MB

english, 2011

7

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf, Eugene V Koonin

Journal:

Year:

2006

Language:

english

File:

PDF, 884 KB

english, 2006

8

The evolutionary journey of Argonaute proteins

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

Journal:

Nature Structural and Molecular Biology

Year:

2014

Language:

english

File:

PDF, 2.16 MB

english, 2014

9

An updated evolutionary classification of CRISPR–Cas systems

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,

Journal:

Nature Reviews Microbiology

Year:

2015

Language:

english

File:

PDF, 531 KB

english, 2015

10

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Smargon, Aaron A., Cox, David B.T., Pyzocha, Neena K., Zheng, Kaijie, Slaymaker, Ian M., Gootenberg, Jonathan S., Abudayyeh, Omar A., Essletzbichler, Patrick, Shmakov, Sergey, Makarova, Kira S., Kooni

Journal:

Year:

2017

Language:

english

File:

PDF, 4.84 MB

english, 2017

11

SnapShot: Class 2 CRISPR-Cas Systems

Makarova, Kira S., Zhang, Feng, Koonin, Eugene V.

Journal:

Year:

2017

Language:

english

File:

PDF, 385 KB

english, 2017

12

SnapShot: Class 1 CRISPR-Cas Systems

Makarova, Kira S., Zhang, Feng, Koonin, Eugene V.

Journal:

Year:

2017

Language:

english

File:

PDF, 237 KB

english, 2017

13

Recruitment of CRISPR-Cas systems by Tn7-like transposons

Peters, Joseph E., Makarova, Kira S., Shmakov, Sergey, Koonin, Eugene V.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 945 KB

english, 2017

14

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

Yutin, Natalya, Makarova, Kira S., Gussow, Ayal B., Krupovic, Mart, Segall, Anca, Edwards, Robert A., Koonin, Eugene V.

Journal:

Nature Microbiology

Year:

2017

Language:

english

File:

PDF, 1.15 MB

english, 2017

15

DNA-silencing by prokaryotic Argonaute proteins adds a new layer of defence against invading nucleic acids

Willkomm, Sarah, Makarova, Kira, Grohmann, Dina

Journal:

FEMS Microbiology Reviews

Year:

2018

Language:

english

File:

PDF, 684 KB

english, 2018

16

Functionally diverse type V CRISPR-Cas systems

Yan, Winston X., Hunnewell, Pratyusha, Alfonse, Lauren E., Carte, Jason M., Keston-Smith, Elise, Sothiselvam, Shanmugapriya, Garrity, Anthony J., Chong, Shaorong, Makarova, Kira S., Koonin, Eugene V.,

Journal:

Year:

2018

Language:

english

File:

PDF, 1.29 MB

english, 2018

17

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

Faure, Guilhem, Shmakov, Sergey A., Yan, Winston X., Cheng, David R., Scott, David A., Peters, Joseph E., Makarova, Kira S., Koonin, Eugene V.

Journal:

Nature Reviews Microbiology

Year:

2019

Language:

english

File:

PDF, 1.30 MB

english, 2019

18

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Makarova, Kira S., Wolf, Yuri I., Iranzo, Jaime, Shmakov, Sergey A., Alkhnbashi, Omer S., Brouns, Stan J. J., Charpentier, Emmanuelle, Cheng, David, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvai

Journal:

Nature Reviews Microbiology

Year:

2019

File:

PDF, 2.42 MB

2019

19

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

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

Journal:

Nature Communications

Year:

2020

File:

PDF, 843 KB

2020

20

Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking

David A. Mills, Helen Rawsthorne, Courtney Parker, Dafna Tamir, Kira Makarova

Journal:

FEMS Microbiology Reviews

Year:

2005

Language:

english

File:

PDF, 349 KB

english, 2005

21

Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis

Kira S. Makarova, Eugene V. Koonin

Journal:

FEMS Microbiology Letters

Year:

2003

Language:

english

File:

PDF, 728 KB

english, 2003

22

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

Kira S Makarova, Eugene V Koonin

Journal:

Year:

2010

Language:

english

File:

PDF, 642 KB

english, 2010

23

The Structure and Evolution ofPenelopein thevirilisSpecies Group ofDrosophila:An Ancient Lineage of Retroelements

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

Journal:

Journal of Molecular Evolution

Year:

2001

Language:

english

File:

PDF, 2.67 MB

english, 2001

24

Functional curation of theSulfolobus solfataricusP2 andS. acidocaldarius98-3 complete genome sequences

Domink Esser, Theresa Kouril, Melanie Zaparty, Pawel Sierocinski, Patricia P. Chan, Todd Lowe, John Van der Oost, Sonja-Verena Albers, Dietmar Schomburg, Kira S. Makarova, Bettina Siebers

Journal:

Year:

2011

Language:

english

File:

PDF, 1.53 MB

english, 2011

25

Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain

Marina V. Omelchenko, Kira S. Makarova, Eugene V. Koonin

Journal:

FEMS Microbiology Letters

Year:

2002

Language:

english

File:

PDF, 491 KB

english, 2002

26

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

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

Journal:

Nature Reviews Microbiology

Year:

2007

Language:

english

File:

PDF, 522 KB

english, 2007

27

Evolution of diverse cell division and vesicle formation systems in Archaea

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

Journal:

Nature Reviews Microbiology

Year:

2010

Language:

english

File:

PDF, 629 KB

english, 2010

28

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

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

Journal:

Year:

2006

Language:

english

File:

PDF, 464 KB

english, 2006

29

GINS, a central nexus in the archaeal DNA replication fork

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

Journal:

Year:

2006

Language:

english

File:

PDF, 197 KB

english, 2006

30

Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases

Rai, Reena, Mushegian, Arcady, Makarova, Kira, Kashina, Anna

Journal:

Year:

2006

Language:

english

File:

PDF, 1.37 MB

english, 2006

31

Specific Expansion of Protein Families in the Radioresistant Bacterium Deinococcus Radiodurans

Kira S. Makarova, L. Aravind, Michael J. Daly, Eugene V. Koonin

Journal:

Year:

2000

Language:

english

File:

PDF, 182 KB

english, 2000

32

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

Nick V. Grishin, Kira S. Makarova

Journal:

Protein Science

Year:

1999

Language:

english

File:

PDF, 1.60 MB

english, 1999

33

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

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

Journal:

Protein Science

Year:

1999

Language:

english

File:

PDF, 2.92 MB

english, 1999

34

HORIZONTAL GENE TRANSFER IN PROKARYOTES: Quantification and Classification1

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

Journal:

Annual Review of Microbiology

Year:

2001

Language:

english

File:

PDF, 429 KB

english, 2001

35

Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking

David A. Mills, Helen Rawsthorne, Courtney Parker, Dafna Tamir, Kira Makarova

Journal:

FEMS Microbiology Reviews

Year:

2005

Language:

english

File:

PDF, 349 KB

english, 2005

36

How radiation kills cells: Survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress

Debabrota Ghosal, Marina V. Omelchenko, Elena K. Gaidamakova, Vera Y. Matrosova, Alexander Vasilenko, Amudhan Venkateswaran, Min Zhai, Heather M. Kostandarithes, Hassan Brim, Kira S. Makarova, Lawrenc

Journal:

FEMS Microbiology Reviews

Year:

2005

Language:

english

File:

PDF, 990 KB

english, 2005

37

Multiple antimutagenesis mechanisms affect mutagenic activity and specificity of the base analog 6-N-hydroxylaminopurine in bacteria and yeast

Stanislav G. Kozmin, Roel M. Schaaper, Polina V. Shcherbakova, Vladimir N. Kulikov, Vladimir N. Noskov, Maria L. Guetsova, Vladimir V. Alenin, Igor B. Rogozin, Kira S. Makarova, Youri I. Pavlov

Journal:

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis

Year:

1998

Language:

english

File:

PDF, 346 KB

english, 1998

38

Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae

I.King Jordan, Kira S Makarova, Yuri I Wolf, Eugene V Koonin

Journal:

Trends in Genetics

Year:

2001

Language:

english

File:

PDF, 46 KB

english, 2001

39

Potential genomic determinants of hyperthermophily

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

Journal:

Trends in Genetics

Year:

2003

Language:

english

File:

PDF, 105 KB

english, 2003

40

SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes

Kira S Makarova, L Aravind, Eugene V Koonin

Journal:

Trends in Biochemical Sciences

Year:

2002

Language:

english

File:

PDF, 46 KB

english, 2002

41

A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae

Kira S Makarova, L Aravind, Eugene V Koonin

Journal:

Trends in Biochemical Sciences

Year:

2000

Language:

english

File:

PDF, 938 KB

english, 2000

42

Comparative genomics ofThermus thermophilusandDeinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

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

Journal:

BMC Evolutionary Biology

Year:

2005

Language:

english

File:

PDF, 504 KB

english, 2005

43

FrancisellaRNA polymerase contains a heterodimer of non-identical α subunits

Damir Mukhamedyarov, Kira S Makarova, Konstantin Severinov, Konstantin Kuznedelov

Journal:

BMC Molecular Biology

Year:

2011

Language:

english

File:

PDF, 2.10 MB

english, 2011

44

The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes

Kira S Makarova, Eugene V Koonin, Zvi Kelman

Journal:

Year:

2012

Language:

english

File:

PDF, 383 KB

english, 2012

45

The Zn-peptidase superfamily: functional convergence after evolutionary divergence

Kira S. Makarova, Nick V. Grishin

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 577 KB

english, 1999

46

Dimeric dUTPases, HisE, and MazG belong to a New Superfamily of all-α NTP Pyrophosphohydrolases with Potential “House-cleaning” Functions

Olga V. Moroz, Alexey G. Murzin, Kira S. Makarova, Eugene V. Koonin, Keith S. Wilson, Michael Y. Galperin

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 2.29 MB

english, 2005

47

Structural and Functional Characterization of Microcin C Resistance Peptidase MccF from Bacillus anthracis

Boguslaw Nocek, Anton Tikhonov, Gyorgy Babnigg, Minyi Gu, Min Zhou, Kira S. Makarova, Gaston Vondenhoff, Arthur Van Aerschot, Keehwan Kwon, Wayne F. Anderson, Konstantin Severinov, Andrzej Joachimiak

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 2.69 MB

english, 2012

48

Evolutionary and functional genomics of the Archaea

Kira S Makarova, Eugene V Koonin

Journal:

Current Opinion in Microbiology

Year:

2005

Language:

english

File:

PDF, 354 KB

english, 2005

49

Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain

Marina V. Omelchenko, Kira S. Makarova, Eugene V. Koonin

Journal:

FEMS Microbiology Letters

Year:

2002

Language:

english

File:

PDF, 494 KB

english, 2002

50

Short repeats and IS elements in the extremely radiation-resistant bacterium Deinococcus radiodurans and comparison to other bacterial species

Kira S Makarova, Yuri I Wolf, Owen White, Ken Minton, Michael J Daly

Journal:

Research in Microbiology

Year:

1999

Language:

english

File:

PDF, 1.09 MB

english, 1999