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ORCIDEugene V. Koonin
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- affiliation: National Center for Biotechnology Informatio, Bethesda, USA
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2020 – today
- 2024
[c10]Sagi Snir, Yuri I. Wolf, Shelly Brezner, Eugene V. Koonin, Mike A. Steel:
On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics. RECOMB-CG 2024: 173-188- 2022
- [j38]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): 432-438 (2022) - 2021
- [j37]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): D274-D281 (2021) - [i2]Vitaly Vanchurin, Yuri I. Wolf, Mikhail I. Katsnelson, Eugene V. Koonin:
Towards a Theory of Evolution as Multilevel Learning. CoRR abs/2110.14602 (2021) - [i1]Vitaly Vanchurin, Yuri I. Wolf, Eugene V. Koonin, Mikhail I. Katsnelson:
Thermodynamics of Evolution and the Origin of Life. CoRR abs/2110.15066 (2021)
2010 – 2019
- 2019
- [j36]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): 1063-1070 (2019) - 2017
- [j35]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): D210-D218 (2017) - [j34]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): D491-D498 (2017) - 2015
- [j33]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: 380:1-380:11 (2015) - [j32]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): 261-269 (2015) - 2014
- [c9]Michael Y. Galperin, Eugene V. Koonin:
Comparative Genomics Approaches to Identifying Functionally Related Genes. AlCoB 2014: 1-24 - 2013
- [j31]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) - 2012
- [j30]Liran Carmel, Eugene V. Koonin, Stella Dracheva:
Dependencies among Editing Sites in Serotonin 2C Receptor mRNA. PLoS Comput. Biol. 8(9) (2012) - [j29]Sagi Snir, Yuri I. Wolf, Eugene V. Koonin:
Universal Pacemaker of Genome Evolution. PLoS Comput. Biol. 8(11) (2012) - 2011
- [j28]Eugene V. Koonin:
Obituary: Walter Fitch and the orthology paradigm. Briefings Bioinform. 12(5): 377-378 (2011) - [j27]David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin:
Computational methods for Gene Orthology inference. Briefings Bioinform. 12(5): 379-391 (2011) - [j26]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): 917-924 (2011) - [j25]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) - [j24]Eugene V. Koonin:
Are There Laws of Genome Evolution? PLoS Comput. Biol. 7(8) (2011) - [j23]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) - [j22]Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin:
Predictability of Evolutionary Trajectories in Fitness Landscapes. PLoS Comput. Biol. 7(12) (2011) - 2010
- [j21]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: 167408:1-167408:4 (2010) - [j20]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): 1481-1487 (2010)
2000 – 2009
- 2009
- [j19]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): 448-454 (2009) - 2007
- [c8]Jie Zheng, Igor B. Rogozin, Eugene V. Koonin, Teresa M. Przytycka:
A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals. RECOMB-CG 2007: 177-191 - 2006
- [j18]Artem S. Novozhilov, Georgy P. Karev, Eugene V. Koonin:
Biological applications of the theory of birth-and-death processes. Briefings Bioinform. 7(1): 70-85 (2006) - [j17]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): 1297-1301 (2006) - [j16]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): 2581-2584 (2006) - 2005
- [j15]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): 118-134 (2005) - [j14]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): 19 (2005) - [c7]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: 35-46 - 2004
- [j13]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): 131-149 (2004) - 2003
- [j12]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): 1889-1900 (2003) - [j11]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: 41 (2003) - 2001
- [j10]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): 859-861 (2001) - [j9]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): 890-900 (2001) - [j8]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): 22-28 (2001) - [c6]Boris G. Mirkin, Eugene V. Koonin:
A top-down method for building genome classification trees with linear binary hierarchies. Bioconsensus 2001: 97-111 - 2000
- [j7]Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller:
Winnowing Sequences from a Database Search. J. Comput. Biol. 7(1-2): 293-302 (2000) - [j6]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): 33-36 (2000)
1990 – 1999
- 1999
- [j5]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): 1000-1011 (1999) - [c5]Piotr Berman, Zheng Zhang, Yuri I. Wolf, Eugene V. Koonin, Webb Miller:
Winnowing sequences from a database search. RECOMB 1999: 50-58 - 1998
- [j4]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): 55-67 (1998) - [c4]Eugene V. Koonin, Roman L. Tatusov, Michael Y. Galperin, Michael N. Rosanov:
Genome analysis using clusters of orthologous groups (COGs). RECOMB 1998: 135-139 - 1997
- [c3]Eugene V. Koonin, Roman L. Tatusov, David J. Lipman:
A natural taxonomy of gene families from complete genomes. German Conference on Bioinformatics 1997: 13-14 - [c2]D. Roland Walker, Eugene V. Koonin:
SEALS: A System for Easy Analysis of Lots of Sequences. ISMB 1997: 333-339 - 1994
- [j3]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): 457-459 (1994) - [j2]Eugene V. Koonin:
Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120. Nucleic Acids Res. 22(13): 2476-2478 (1994) - 1992
- [j1]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): 3279-3285 (1992) - [c1]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: 63-74
Coauthor Index
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