Kira S. Makarova

发表

A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization

Victor V. Solovyev, Kira S. Makarova, K. Makarova, 1993, Comput. Appl. Biosci..

Expanded microbial genome coverage and improved protein family annotation in the COG database

Michael Y. Galperin, Kira S. Makarova, Eugene V. Koonin, 2014, Nucleic Acids Res..

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2020, bioRxiv.

DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering

Kira S. Makarova, Yuri I. Wolf, V. V. Soloviev, 1992, Comput. Appl. Biosci..

Table 2, Examples of horizontally transferred operons

L. Aravind, Kira S. Makarova, Eugene V. Koonin, 2002 .

CRISPRidentify: identification of CRISPR arrays using machine learning approach

Rolf Backofen, Kira S. Makarova, Eugene V. Koonin, 2020 .

Kira S. Makarova, Yuri I. Wolf, Igor A. Seledtsov, 1996, German Conference on Bioinformatics.

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

Michael Y. Galperin, Kira S. Makarova, Eugene V. Koonin, 2006, Bioinform..

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes

Igor B. Rogozin, Kira S. Makarova, Eugene V. Koonin, 2004, Briefings Bioinform..

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

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2020, Nature Communications.

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria

Nick V. Grishin, Kira S. Makarova, Eugene V. Koonin, 2006, Bioinform..

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

Michael Y. Galperin, Kira S. Makarova, Eugene V. Koonin, 2007, Nature Reviews Microbiology.

SnapShot: Class 2 CRISPR-Cas Systems

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2017, Cell.

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

Rolf Backofen, Philippe Horvath, Rodolphe Barrangou, 2019, Nature Reviews Microbiology.

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

Kira S. Makarova, Eugene V. Koonin, Emmanuelle Charpentier, 2013, Nucleic acids research.

Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central Carbohydrate Metabolism

Martijn A. Huynen, Kira S. Makarova, Eugene V. Koonin, 2004, Journal of bacteriology.

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2017, mBio.

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

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2015, Life.

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

Michael Y. Galperin, Igor B. Rogozin, Patrick Wincker, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

Boris G. Mirkin, Kira S. Makarova, Eugene V. Koonin, 2005, Nucleic acids research.

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

Sagi Snir, Kira S. Makarova, Eugene V. Koonin, 2011, Journal of bacteriology.

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

Eric S. Lander, Aviv Regev, Kira S. Makarova, 2016, Science.

Classification and evolution of type II CRISPR-Cas systems

Kira S. Makarova, Eugene V. Koonin, Emmanuelle Charpentier, 2014, Nucleic acids research.

Diversity and evolution of class 2 CRISPR–Cas systems

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2017, Nature Reviews Microbiology.

Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL domain-containing accessory protein

Kira S. Makarova, Eugene V. Koonin, David A. Scott, 2018, Molecular cell.

Anti-CRISPRs on the march

Kira S. Makarova, Eugene V. Koonin, E. Koonin, 2018, Science.

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2018, Proceedings of the National Academy of Sciences.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Kira S. Makarova, Eugene V. Koonin, Matthew B. Sullivan, 2017, mBio.

Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2016, bioRxiv.

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2016, Science.

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Mikhail S. Gelfand, Alla Lapidus, Alex Copeland, 2007, PloS one.

Engineering of CRISPR-Cas12b for human genome editing

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2019, Nature Communications.

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

Kira S. Makarova, Eugene V. Koonin, Yinqing Li, 2016, Cell.

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum

George N. Bennett, Lynn Doucette-Stamm, Kira S. Makarova, 2001, Journal of bacteriology.

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

Darren A. Natale, L. Aravind, Igor B. Rogozin, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2011, Journal of bacteriology.

SnapShot: Class 1 CRISPR-Cas Systems

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2017, Cell.

Comparative genomics of defense systems in archaea and bacteria

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2013, Nucleic acids research.