Eugene V. Koonin

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 8

Top Topics

Protein Families

Comparative Genomics

Top Venues

Nucleic Acids Res.

Publications

Sagi Snir, Yuri I. Wolf, Shelly Brezner, Eugene V. Koonin, Mike Steel
On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics. RECOMB-CG (2024)
Benjamin D. Lee, Uri Neri, Caleb J. Oh, Peter Simmonds, Eugene V. Koonin
ViroidDB: a database of viroids and viroid-like circular RNAs. Nucleic Acids Res. 50 (D1) (2022)
Vitaly Vanchurin, Yuri I. Wolf, Mikhail I. Katsnelson, Eugene V. Koonin
Towards a Theory of Evolution as Multilevel Learning. CoRR (2021)
Vitaly Vanchurin, Yuri I. Wolf, Eugene V. Koonin, Mikhail I. Katsnelson
Thermodynamics of Evolution and the Origin of Life. CoRR (2021)
Michael Y. Galperin, Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 49 (Database-Issue) (2021)
Michael Y. Galperin, David M. Kristensen, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
Microbial genome analysis: the COG approach. Briefings Bioinform. 20 (4) (2019)
Ana Laura Grazziotin, Eugene V. Koonin, David M. Kristensen
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45 (Database-Issue) (2017)
David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. Nucleic Acids Res. 45 (Database-Issue) (2017)
David M. Kristensen, Usman Saeed, Dmitrij Frishman, Eugene V. Koonin
A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. BMC Bioinform. 16 (2015)
Michael Y. Galperin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43 (Database-Issue) (2015)
Michael Y. Galperin, Eugene V. Koonin
Comparative Genomics Approaches to Identifying Functionally Related Genes. AlCoB (2014)
David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin
The Vast, Conserved Mammalian lincRNome. PLoS Comput. Biol. 9 (2) (2013)
Sagi Snir, Yuri I. Wolf, Eugene V. Koonin
Universal Pacemaker of Genome Evolution. PLoS Comput. Biol. 8 (11) (2012)
Liran Carmel, Eugene V. Koonin, Stella Dracheva
Dependencies among Editing Sites in Serotonin 2C Receptor mRNA. PLoS Comput. Biol. 8 (9) (2012)
Eugene V. Koonin
Are There Laws of Genome Evolution? PLoS Comput. Biol. 7 (8) (2011)
Miklós Csürös, Igor B. Rogozin, Eugene V. Koonin
A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes. PLoS Comput. Biol. 7 (9) (2011)
Nobuto Takeuchi, Paulien Hogeweg, Eugene V. Koonin
On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems. PLoS Comput. Biol. 7 (3) (2011)
David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin
Computational methods for Gene Orthology inference. Briefings Bioinform. 12 (5) (2011)
Eugene V. Koonin, Pere Puigbò, Yuri I. Wolf
Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life". J. Comput. Biol. 18 (7) (2011)
Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin
Predictability of Evolutionary Trajectories in Fitness Landscapes. PLoS Comput. Biol. 7 (12) (2011)
Eugene V. Koonin
Obituary: Walter Fitch and the orthology paradigm. Briefings Bioinform. 12 (5) (2011)
Liran Carmel, Yuri I. Wolf, Igor B. Rogozin, Eugene V. Koonin
EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution. Adv. Bioinformatics 2010 (2010)
David M. Kristensen, Lavanya Kannan, Michael K. Coleman, Yuri I. Wolf, Alexander Sorokin, Eugene V. Koonin, Arcady R. Mushegian
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinform. 26 (12) (2010)
Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, Inna Dubchak
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res. 37 (Database-Issue) (2009)
Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka
Clade of Animals. RECOMB-CG (2007)
Artem S. Novozhilov, Georgy P. Karev, Eugene V. Koonin
Biological applications of the theory of birth-and-death processes. Briefings Bioinform. 7 (1) (2006)
Kira S. Makarova, Eugene V. Koonin, Robert Haselkorn, Michael Y. Galperin
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion. Bioinform. 22 (11) (2006)
Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinform. 22 (21) (2006)
Liran Carmel, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin
An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes. Comparative Genomics (2005)
Igor B. Rogozin, Alexander V. Sverdlov, Vladimir N. Babenko, Eugene V. Koonin
Analysis of evolution of exon-intron structure of eukaryotic genes. Briefings Bioinform. 6 (2) (2005)
Georgy P. Karev, Faina S. Berezovskaya, Eugene V. Koonin
Modeling genome evolution with a diffusion approximation of a birth-and-death process. Bioinform. 21 (S3) (2005)
Igor B. Rogozin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes. Briefings Bioinform. 5 (2) (2004)
Georgy P. Karev, Yuri I. Wolf, Eugene V. Koonin
Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve? Bioinform. 19 (15) (2003)
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, Alexander V. Sverdlov, Sona Vasudevan, Yuri I. Wolf, Jodie J. Yin, Darren A. Natale
The COG database: an updated version includes eukaryotes. BMC Bioinform. 4 (2003)
Boris G. Mirkin, Eugene V. Koonin
A top-down method for building genome classification trees with linear binary hierarchies. Bioconsensus (2001)
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinform. 17 (10) (2001)
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
The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29 (1) (2001)
Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinform. 17 (10) (2001)
Roman L. Tatusov, Michael Y. Galperin, Darren A. Natale, Eugene V. Koonin
The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28 (1) (2000)
Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller
Winnowing Sequences from a Database Search. J. Comput. Biol. 7 (1-2) (2000)
Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller
Winnowing sequences from a database search. RECOMB (1999)
Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinform. 15 (12) (1999)
Eugene V. Koonin, Roman L. Tatusov, Michael Y. Galperin, Michael N. Rosanov
Genome analysis using clusters of orthologous groups (COGs). RECOMB (1998)
Michael Y. Galperin, Eugene V. Koonin
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption. Silico Biol. 1 (1) (1998)
D. Roland Walker, Eugene V. Koonin
SEALS: A System for Easy Analysis of Lots of Sequences. ISMB (1997)
Eugene V. Koonin, Roman L. Tatusov, David J. Lipman
A natural taxonomy of gene families from complete genomes. German Conference on Bioinformatics (1997)
Roman L. Tatusov, Eugene V. Koonin
A simple tool to search for sequence motifs that are conserved in BLAST outputs. Comput. Appl. Biosci. 10 (4) (1994)
Eugene V. Koonin
Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120. Nucleic Acids Res. 22 (13) (1994)
Tatyana V. Ilyina, Eugene V. Koonin
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res. 20 (13) (1992)
Eugene V. Koonin
Comparative Analysis of Biopolymer Sequences: Reflections on the Validity of the Methodology and the Underlying General Principles. Mathematical Methods Of Analysis Of Biopolymer Sequences (1992)