Comparative Analysis of Biopolymer Sequences: Reflections on the Validity of the Methodology and the Underlying General Principles. - Eugene V. Koonin (Mathematical Methods Of Analysis Of Biopolymer Sequences, 1992)

Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. - Tatyana V. Ilyina; Eugene V. Koonin (Nucleic Acids Res., 1992)

A simple tool to search for sequence motifs that are conserved in BLAST outputs. - Roman L. Tatusov; Eugene V. Koonin (Comput. Appl. Biosci., 1994)

Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120. - Eugene V. Koonin (Nucleic Acids Res., 1994)

A natural taxonomy of gene families from complete genomes. - Eugene V. Koonin; Roman L. Tatusov; David J. Lipman (German Conference on Bioinformatics, 1997)

SEALS: A System for Easy Analysis of Lots of Sequences. - D. Roland Walker; Eugene V. Koonin (ISMB, 1997)

Genome analysis using clusters of orthologous groups (COGs). - Eugene V. Koonin; Roman L. Tatusov; Michael Y. Galperin; Michael N. Rosanov (RECOMB, 1998)

Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption. - Michael Y. Galperin; Eugene V. Koonin (Silico Biol., 1998)

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)

The COG database: a tool for genome-scale analysis of protein functions and evolution. - Roman L. Tatusov; Michael Y. Galperin; Darren A. Natale; Eugene V. Koonin (Nucleic Acids Res., 2000)

A top-down method for building genome classification trees with linear binary hierarchies. - Boris G. Mirkin; Eugene V. Koonin (Bioconsensus, 2001)

The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). - Mark Borodovsky; Eugene V. Koonin; Chris Burge; James W. Fickett; John Logsdon; Andrej Sali; Gary D. Stormo; Igor B. Zhulin (Bioinform., 2001)

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. - Igor B. Rogozin; Alexey V. Kochetov; Fyodor A. Kondrashov; Eugene V. Koonin; Luciano Milanesi (Bioinform., 2001)

The COG database: new developments in phylogenetic classification of proteins from complete genomes. - Roman L. Tatusov; Darren A. Natale; Igor V. Garkavtsev; Tatiana A. Tatusova; Uma T. Shankavaram; Bachoti S. Rao; Boris Kiryutin; Michael Y. Galperin; Natalie D. Fedorova; Eugene V. Koonin (Nucleic Acids Res., 2001)

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)

Analysis of evolution of exon-intron structure of eukaryotic genes. - Igor B. Rogozin; Alexander V. Sverdlov; Vladimir N. Babenko; Eugene V. Koonin (Briefings Bioinform., 2005)

Modeling genome evolution with a diffusion approximation of a birth-and-death process. - Georgy P. Karev; Faina S. Berezovskaya; Eugene V. Koonin (Bioinform., 2005)

Biological applications of the theory of birth-and-death processes. - Artem S. Novozhilov; Georgy P. Karev; Eugene V. Koonin (Briefings Bioinform., 2006)

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)

A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals. - Jie Zheng 002; Igor B. Rogozin; Eugene V. Koonin; Teresa M. Przytycka (RECOMB-CG, 2007)

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)

Obituary: Walter Fitch and the orthology paradigm. - Eugene V. Koonin (Briefings Bioinform., 2011)

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)

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes. - Miklós Csürös; Igor B. Rogozin; Eugene V. Koonin (PLoS Comput. Biol., 2011)

Are There Laws of Genome Evolution? - Eugene V. Koonin (PLoS Comput. Biol., 2011)

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

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems. - Nobuto Takeuchi; Paulien Hogeweg; Eugene V. Koonin (PLoS Comput. Biol., 2011)

Dependencies among Editing Sites in Serotonin 2C Receptor mRNA. - Liran Carmel; Eugene V. Koonin; Stella Dracheva (PLoS Comput. Biol., 2012)

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)

Comparative Genomics Approaches to Identifying Functionally Related Genes. - Michael Y. Galperin; Eugene V. Koonin (AlCoB, 2014)

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. - David M. Kristensen; Usman Saeed; Dmitrij Frishman; Eugene V. Koonin (BMC Bioinform., 2015)

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)

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. - Ana Laura Grazziotin; Eugene V. Koonin; David M. Kristensen (Nucleic Acids Res., 2017)

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)

ViroidDB: a database of viroids and viroid-like circular RNAs. - Benjamin D. Lee; Uri Neri; Caleb J. Oh; Peter Simmonds; Eugene V. Koonin (Nucleic Acids Res., 2022)

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)