DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering. - Kira S. Makarova; A. V. Mazin; Yuri I. Wolf; V. V. Soloviev (Comput. Appl. Biosci., 1992)

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 (Comput. Appl. Biosci., 1993)

Sequence Similarity Significance: Computer Simulations and Analytically obtained Bounds. - Igor A. Seledtsov; Yuri I. Wolf; Dmitry Korshunov; Kira S. Makarova (German Conference on Bioinformatics, 1996)

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. - Igor B. Rogozin; Kira S. Makarova; Yuri I. Wolf; Eugene V. Koonin (Briefings Bioinform., 2004)

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. - Kira S. Makarova; Nick V. Grishin; Eugene V. Koonin (Bioinform., 2006)

Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion. - Kira S. Makarova; Eugene V. Koonin; Robert Haselkorn; Michael Y. Galperin (Bioinform., 2006)

Expanded microbial genome coverage and improved protein family annotation in the COG database. - Michael Y. Galperin; Kira S. Makarova; Yuri I. Wolf; Eugene V. Koonin (Nucleic Acids Res., 2015)

Microbial genome analysis: the COG approach. - Michael Y. Galperin; David M. Kristensen; Kira S. Makarova; Yuri I. Wolf; Eugene V. Koonin (Briefings Bioinform., 2019)

COG database update: focus on microbial diversity, model organisms, and widespread pathogens. - Michael Y. Galperin; Yuri I. Wolf; Kira S. Makarova; Roberto Vera Alvarez; David Landsman; Eugene V. Koonin (Nucleic Acids Res., 2021)