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)

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)

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. - Alejandro A. Schäffer; Yuri I. Wolf; Chris P. Ponting; Eugene V. Koonin; L. Aravind; Stephen F. Altschul (Bioinform., 1999)

Winnowing Sequences from a Database Search. - Piotr Berman; Zheng Zhang 004; Yuri I. Wolf; Eugene V. Koonin; Webb Miller (J. Comput. Biol., 2000)

Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve? - Georgy P. Karev; Yuri I. Wolf; Eugene V. Koonin (Bioinform., 2003)

The COG database: an updated version includes eukaryotes. - Roman L. Tatusov; Natalie D. Fedorova; John D. Jackson; Aviva R. Jacobs; Boris Kiryutin; Eugene V. Koonin; Dmitri M. Krylov; Raja Mazumder; Sergei L. Mekhedov; Anastasia N. Nikolskaya; B. Sridhar Rao; Sergei Smirnov; et al. (BMC Bioinform., 2003)

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)

An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes. - Liran Carmel; Igor B. Rogozin; Yuri I. Wolf; Eugene V. Koonin (Comparative Genomics, 2005)

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. - Pavel S. Novichkov; Igor Ratnere; Yuri I. Wolf; Eugene V. Koonin; Inna Dubchak (Nucleic Acids Res., 2009)

EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution. - Liran Carmel; Yuri I. Wolf; Igor B. Rogozin; Eugene V. Koonin (Adv. Bioinformatics, 2010)

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. - David M. Kristensen; Lavanya Kannan; Michael K. Coleman; Yuri I. Wolf; Alexander Sorokin; Eugene V. Koonin; Arcady R. Mushegian (Bioinform., 2010)

Computational methods for Gene Orthology inference. - David M. Kristensen; Yuri I. Wolf; Arcady R. Mushegian; Eugene V. Koonin (Briefings Bioinform., 2011)

Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life". - Eugene V. Koonin; Pere Puigbò; Yuri I. Wolf (J. Comput. Biol., 2011)

Predictability of Evolutionary Trajectories in Fitness Landscapes. - Alexander E. Lobkovsky; Yuri I. Wolf; Eugene V. Koonin (PLoS Comput. Biol., 2011)

Universal Pacemaker of Genome Evolution. - Sagi Snir; Yuri I. Wolf; Eugene V. Koonin (PLoS Comput. Biol., 2012)

The Vast, Conserved Mammalian lincRNome. - David Managadze; Alexander E. Lobkovsky; Yuri I. Wolf; Svetlana A. Shabalina; Igor B. Rogozin; Eugene V. Koonin (PLoS Comput. Biol., 2013)

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)

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. - David M. Kristensen; Yuri I. Wolf; Eugene V. Koonin (Nucleic Acids Res., 2017)

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

Towards a Theory of Evolution as Multilevel Learning. - Vitaly Vanchurin; Yuri I. Wolf; Mikhail I. Katsnelson; Eugene V. Koonin (CoRR, 2021)

Thermodynamics of Evolution and the Origin of Life. - Vitaly Vanchurin; Yuri I. Wolf; Eugene V. Koonin; Mikhail I. Katsnelson (CoRR, 2021)

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)

On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics. - Sagi Snir; Yuri I. Wolf; Shelly Brezner; Eugene V. Koonin; Mike A. Steel (RECOMB-CG, 2024)