Eugene V. Koonin

51 papers A 1B 2Journal 41Unranked 7
YearRankTypeTitle / Venue / Authors
2024 — conf
On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics.
RECOMB-CG
Sagi Snir, Yuri I. Wolf, Shelly Brezner, Eugene V. Koonin, Mike A. Steel
2022 J jnl
ViroidDB: a database of viroids and viroid-like circular RNAs.
Nucleic Acids Res.
Benjamin D. Lee, Uri Neri, Caleb J. Oh, Peter Simmonds, Eugene V. Koonin
2021 J jnl
COG database update: focus on microbial diversity, model organisms, and widespread pathogens.
Nucleic Acids Res.
Michael Y. Galperin, Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin
2021 J jnl
Thermodynamics of Evolution and the Origin of Life.
CoRR
Vitaly Vanchurin, Yuri I. Wolf, Eugene V. Koonin, Mikhail I. Katsnelson
2021 J jnl
Towards a Theory of Evolution as Multilevel Learning.
CoRR
Vitaly Vanchurin, Yuri I. Wolf, Mikhail I. Katsnelson, Eugene V. Koonin
2019 J jnl
Microbial genome analysis: the COG approach.
Briefings Bioinform.
Michael Y. Galperin, David M. Kristensen, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
2017 J jnl
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.
Nucleic Acids Res.
David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin
2017 J jnl
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation.
Nucleic Acids Res.
Ana Laura Grazziotin, Eugene V. Koonin, David M. Kristensen
2015 J jnl
A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.
BMC Bioinform.
David M. Kristensen, Usman Saeed, Dmitrij Frishman, Eugene V. Koonin
2015 J jnl
Expanded microbial genome coverage and improved protein family annotation in the COG database.
Nucleic Acids Res.
Michael Y. Galperin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
2014 — conf
Comparative Genomics Approaches to Identifying Functionally Related Genes.
AlCoB
Michael Y. Galperin, Eugene V. Koonin
2013 J jnl
The Vast, Conserved Mammalian lincRNome.
PLoS Comput. Biol.
David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin
2012 J jnl
Dependencies among Editing Sites in Serotonin 2C Receptor mRNA.
PLoS Comput. Biol.
Liran Carmel, Eugene V. Koonin, Stella Dracheva
2012 J jnl
Universal Pacemaker of Genome Evolution.
PLoS Comput. Biol.
Sagi Snir, Yuri I. Wolf, Eugene V. Koonin
2011 J jnl
A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes.
PLoS Comput. Biol.
Miklós Csürös, Igor B. Rogozin, Eugene V. Koonin
2011 J jnl
Are There Laws of Genome Evolution?
PLoS Comput. Biol.
Eugene V. Koonin
2011 J jnl
Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life".
J. Comput. Biol.
Eugene V. Koonin, Pere Puigbò, Yuri I. Wolf
2011 J jnl
Computational methods for Gene Orthology inference.
Briefings Bioinform.
David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin
2011 J jnl
Obituary: Walter Fitch and the orthology paradigm.
Briefings Bioinform.
Eugene V. Koonin
2011 J jnl
On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems.
PLoS Comput. Biol.
Nobuto Takeuchi, Paulien Hogeweg, Eugene V. Koonin
2011 J jnl
Predictability of Evolutionary Trajectories in Fitness Landscapes.
PLoS Comput. Biol.
Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin
2010 J jnl
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.
Bioinform.
David M. Kristensen, Lavanya Kannan, Michael K. Coleman, Yuri I. Wolf, Alexander Sorokin, Eugene V. Koonin, Arcady R. Mushegian
2010 J jnl
EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.
Adv. Bioinformatics
Liran Carmel, Yuri I. Wolf, Igor B. Rogozin, Eugene V. Koonin
2009 J jnl
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.
Nucleic Acids Res.
Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, Inna Dubchak
2007 — conf
A Rigorous Analysis of the Pattern of Intron Conservation Supports the
RECOMB-CG
Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka
2006 J jnl
Biological applications of the theory of birth-and-death processes.
Briefings Bioinform.
Artem S. Novozhilov, Georgy P. Karev, Eugene V. Koonin
2006 J jnl
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.
Bioinform.
Kira S. Makarova, Eugene V. Koonin, Robert Haselkorn, Michael Y. Galperin
2006 J jnl
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinform.
Kira S. Makarova, Nick V. Grishin, Eugene V. Koonin
2005 — conf
An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes.
Comparative Genomics
Liran Carmel, Igor B. Rogozin, Yuri I. Wolf, Eugene V. Koonin
2005 J jnl
Analysis of evolution of exon-intron structure of eukaryotic genes.
Briefings Bioinform.
Igor B. Rogozin, Alexander V. Sverdlov, Vladimir N. Babenko, Eugene V. Koonin
2005 J jnl
Modeling genome evolution with a diffusion approximation of a birth-and-death process.
Bioinform.
Georgy P. Karev, Faina S. Berezovskaya, Eugene V. Koonin
2004 J jnl
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.
Briefings Bioinform.
Igor B. Rogozin, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin
2003 J jnl
Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve?
Bioinform.
Georgy P. Karev, Yuri I. Wolf, Eugene V. Koonin
2003 J jnl
The COG database: an updated version includes eukaryotes.
BMC Bioinform.
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
2001 — conf
A top-down method for building genome classification trees with linear binary hierarchies.
Bioconsensus
Boris G. Mirkin, Eugene V. Koonin
2001 J jnl
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon.
Bioinform.
Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi
2001 J jnl
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic Acids Res.
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
2001 J jnl
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA).
Bioinform.
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
2000 J jnl
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Nucleic Acids Res.
Roman L. Tatusov, Michael Y. Galperin, Darren A. Natale, Eugene V. Koonin
2000 J jnl
Winnowing Sequences from a Database Search.
J. Comput. Biol.
Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller
1999 J jnl
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
Bioinform.
Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul
1999 J jnl
The emerging paradigm and open problems in comparative genomics.
Bioinform.
Eugene V. Koonin
1999 B conf
Winnowing sequences from a database search.
RECOMB
Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller
1998 B conf
Genome analysis using clusters of orthologous groups (COGs).
RECOMB
Eugene V. Koonin, Roman L. Tatusov, Michael Y. Galperin, Michael N. Rosanov
1998 J jnl
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption.
Silico Biol.
Michael Y. Galperin, Eugene V. Koonin
1997 — conf
A natural taxonomy of gene families from complete genomes.
German Conference on Bioinformatics
Eugene V. Koonin, Roman L. Tatusov, David J. Lipman
1997 A conf
SEALS: A System for Easy Analysis of Lots of Sequences.
ISMB
D. Roland Walker, Eugene V. Koonin
1994 J jnl
A simple tool to search for sequence motifs that are conserved in BLAST outputs.
Comput. Appl. Biosci.
Roman L. Tatusov, Eugene V. Koonin
1994 J jnl
Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120.
Nucleic Acids Res.
Eugene V. Koonin
1992 — conf
Comparative Analysis of Biopolymer Sequences: Reflections on the Validity of the Methodology and the Underlying General Principles.
Mathematical Methods Of Analysis Of Biopolymer Sequences
Eugene V. Koonin
1992 J jnl
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria.
Nucleic Acids Res.
Tatyana V. Ilyina, Eugene V. Koonin