BibTeX records: Eugene V. Koonin

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@inproceedings{DBLP:conf/recombcg/SnirWBKS24,
  author       = {Sagi Snir and
                  Yuri I. Wolf and
                  Shelly Brezner and
                  Eugene V. Koonin and
                  Mike Steel},
  editor       = {C{\'{e}}line Scornavacca and
                  Maribel Hern{\'{a}}ndez{-}Rosales},
  title        = {On the Distribution of Synteny Blocks Under a Neutral Model of Genome
                  Dynamics},
  booktitle    = {Comparative Genomics - 21st International Conference, {RECOMB-CG}
                  2024, Boston, MA, USA, April 27-28, 2024, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {14616},
  pages        = {173--188},
  publisher    = {Springer},
  year         = {2024},
  url          = {https://doi.org/10.1007/978-3-031-58072-7\_9},
  doi          = {10.1007/978-3-031-58072-7\_9},
  timestamp    = {Wed, 24 Apr 2024 16:58:28 +0200},
  biburl       = {https://dblp.org/rec/conf/recombcg/SnirWBKS24.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/LeeNOSK22,
  author       = {Benjamin D. Lee and
                  Uri Neri and
                  Caleb J. Oh and
                  Peter Simmonds and
                  Eugene V. Koonin},
  title        = {ViroidDB: a database of viroids and viroid-like circular RNAs},
  journal      = {Nucleic Acids Res.},
  volume       = {50},
  number       = {{D1}},
  pages        = {432--438},
  year         = {2022},
  url          = {https://doi.org/10.1093/nar/gkab974},
  doi          = {10.1093/NAR/GKAB974},
  timestamp    = {Mon, 28 Aug 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/LeeNOSK22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/GalperinWMALK21,
  author       = {Michael Y. Galperin and
                  Yuri I. Wolf and
                  Kira S. Makarova and
                  Roberto Vera Alvarez and
                  David Landsman and
                  Eugene V. Koonin},
  title        = {{COG} database update: focus on microbial diversity, model organisms,
                  and widespread pathogens},
  journal      = {Nucleic Acids Res.},
  volume       = {49},
  number       = {Database-Issue},
  pages        = {D274--D281},
  year         = {2021},
  url          = {https://doi.org/10.1093/nar/gkaa1018},
  doi          = {10.1093/NAR/GKAA1018},
  timestamp    = {Tue, 01 Jun 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/GalperinWMALK21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2110-14602,
  author       = {Vitaly Vanchurin and
                  Yuri I. Wolf and
                  Mikhail I. Katsnelson and
                  Eugene V. Koonin},
  title        = {Towards a Theory of Evolution as Multilevel Learning},
  journal      = {CoRR},
  volume       = {abs/2110.14602},
  year         = {2021},
  url          = {https://arxiv.org/abs/2110.14602},
  eprinttype    = {arXiv},
  eprint       = {2110.14602},
  timestamp    = {Fri, 29 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2110-14602.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-2110-15066,
  author       = {Vitaly Vanchurin and
                  Yuri I. Wolf and
                  Eugene V. Koonin and
                  Mikhail I. Katsnelson},
  title        = {Thermodynamics of Evolution and the Origin of Life},
  journal      = {CoRR},
  volume       = {abs/2110.15066},
  year         = {2021},
  url          = {https://arxiv.org/abs/2110.15066},
  eprinttype    = {arXiv},
  eprint       = {2110.15066},
  timestamp    = {Tue, 02 Nov 2021 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2110-15066.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/GalperinKMWK19,
  author       = {Michael Y. Galperin and
                  David M. Kristensen and
                  Kira S. Makarova and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {Microbial genome analysis: the {COG} approach},
  journal      = {Briefings Bioinform.},
  volume       = {20},
  number       = {4},
  pages        = {1063--1070},
  year         = {2019},
  url          = {https://doi.org/10.1093/bib/bbx117},
  doi          = {10.1093/BIB/BBX117},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/GalperinKMWK19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/KristensenWK17,
  author       = {David M. Kristensen and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {{ATGC} database and ATGC-COGs: an updated resource for micro- and
                  macro-evolutionary studies of prokaryotic genomes and protein family
                  annotation},
  journal      = {Nucleic Acids Res.},
  volume       = {45},
  number       = {Database-Issue},
  pages        = {D210--D218},
  year         = {2017},
  url          = {https://doi.org/10.1093/nar/gkw934},
  doi          = {10.1093/NAR/GKW934},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/KristensenWK17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/GrazziotinKK17,
  author       = {Ana Laura Grazziotin and
                  Eugene V. Koonin and
                  David M. Kristensen},
  title        = {Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative
                  genomics and protein family annotation},
  journal      = {Nucleic Acids Res.},
  volume       = {45},
  number       = {Database-Issue},
  pages        = {D491--D498},
  year         = {2017},
  url          = {https://doi.org/10.1093/nar/gkw975},
  doi          = {10.1093/NAR/GKW975},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/GrazziotinKK17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/KristensenSFK15,
  author       = {David M. Kristensen and
                  Usman Saeed and
                  Dmitrij Frishman and
                  Eugene V. Koonin},
  title        = {A census of {\(\alpha\)}-helical membrane proteins in double-stranded
                  {DNA} viruses infecting bacteria and archaea},
  journal      = {{BMC} Bioinform.},
  volume       = {16},
  pages        = {380:1--380:11},
  year         = {2015},
  url          = {https://doi.org/10.1186/s12859-015-0817-4},
  doi          = {10.1186/S12859-015-0817-4},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/KristensenSFK15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/GalperinMWK15,
  author       = {Michael Y. Galperin and
                  Kira S. Makarova and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {Expanded microbial genome coverage and improved protein family annotation
                  in the {COG} database},
  journal      = {Nucleic Acids Res.},
  volume       = {43},
  number       = {Database-Issue},
  pages        = {261--269},
  year         = {2015},
  url          = {https://doi.org/10.1093/nar/gku1223},
  doi          = {10.1093/NAR/GKU1223},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/GalperinMWK15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/alcob/GalperinK14,
  author       = {Michael Y. Galperin and
                  Eugene V. Koonin},
  editor       = {Adrian{-}Horia Dediu and
                  Carlos Mart{\'{\i}}n{-}Vide and
                  Bianca Truthe},
  title        = {Comparative Genomics Approaches to Identifying Functionally Related
                  Genes},
  booktitle    = {Algorithms for Computational Biology - First International Conference,
                  AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns},
  series       = {Lecture Notes in Computer Science},
  volume       = {8542},
  pages        = {1--24},
  publisher    = {Springer},
  year         = {2014},
  url          = {https://doi.org/10.1007/978-3-319-07953-0\_1},
  doi          = {10.1007/978-3-319-07953-0\_1},
  timestamp    = {Mon, 16 Sep 2019 15:22:41 +0200},
  biburl       = {https://dblp.org/rec/conf/alcob/GalperinK14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/ManagadzeLWSRK13,
  author       = {David Managadze and
                  Alexander E. Lobkovsky and
                  Yuri I. Wolf and
                  Svetlana A. Shabalina and
                  Igor B. Rogozin and
                  Eugene V. Koonin},
  title        = {The Vast, Conserved Mammalian lincRNome},
  journal      = {PLoS Comput. Biol.},
  volume       = {9},
  number       = {2},
  year         = {2013},
  url          = {https://doi.org/10.1371/journal.pcbi.1002917},
  doi          = {10.1371/JOURNAL.PCBI.1002917},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/ManagadzeLWSRK13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/CarmelKD12,
  author       = {Liran Carmel and
                  Eugene V. Koonin and
                  Stella Dracheva},
  title        = {Dependencies among Editing Sites in Serotonin 2C Receptor mRNA},
  journal      = {PLoS Comput. Biol.},
  volume       = {8},
  number       = {9},
  year         = {2012},
  url          = {https://doi.org/10.1371/journal.pcbi.1002663},
  doi          = {10.1371/JOURNAL.PCBI.1002663},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/CarmelKD12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/SnirWK12,
  author       = {Sagi Snir and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {Universal Pacemaker of Genome Evolution},
  journal      = {PLoS Comput. Biol.},
  volume       = {8},
  number       = {11},
  year         = {2012},
  url          = {https://doi.org/10.1371/journal.pcbi.1002785},
  doi          = {10.1371/JOURNAL.PCBI.1002785},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/SnirWK12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/Koonin11,
  author       = {Eugene V. Koonin},
  title        = {Obituary: Walter Fitch and the orthology paradigm},
  journal      = {Briefings Bioinform.},
  volume       = {12},
  number       = {5},
  pages        = {377--378},
  year         = {2011},
  url          = {https://doi.org/10.1093/bib/bbr058},
  doi          = {10.1093/BIB/BBR058},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/Koonin11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/KristensenWMK11,
  author       = {David M. Kristensen and
                  Yuri I. Wolf and
                  Arcady R. Mushegian and
                  Eugene V. Koonin},
  title        = {Computational methods for Gene Orthology inference},
  journal      = {Briefings Bioinform.},
  volume       = {12},
  number       = {5},
  pages        = {379--391},
  year         = {2011},
  url          = {https://doi.org/10.1093/bib/bbr030},
  doi          = {10.1093/BIB/BBR030},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/KristensenWMK11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcb/KooninPW11,
  author       = {Eugene V. Koonin and
                  Pere Puigb{\`{o}} and
                  Yuri I. Wolf},
  title        = {Comparison of Phylogenetic Trees and Search for a Central Trend in
                  the "Forest of Life"},
  journal      = {J. Comput. Biol.},
  volume       = {18},
  number       = {7},
  pages        = {917--924},
  year         = {2011},
  url          = {https://doi.org/10.1089/cmb.2010.0185},
  doi          = {10.1089/CMB.2010.0185},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcb/KooninPW11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/TakeuchiHK11,
  author       = {Nobuto Takeuchi and
                  Paulien Hogeweg and
                  Eugene V. Koonin},
  title        = {On the Origin of {DNA} Genomes: Evolution of the Division of Labor
                  between Template and Catalyst in Model Replicator Systems},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {3},
  year         = {2011},
  url          = {https://doi.org/10.1371/journal.pcbi.1002024},
  doi          = {10.1371/JOURNAL.PCBI.1002024},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/TakeuchiHK11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/Koonin11,
  author       = {Eugene V. Koonin},
  title        = {Are There Laws of Genome Evolution?},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {8},
  year         = {2011},
  url          = {https://doi.org/10.1371/journal.pcbi.1002173},
  doi          = {10.1371/JOURNAL.PCBI.1002173},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/Koonin11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/CsurosRK11,
  author       = {Mikl{\'{o}}s Cs{\"{u}}r{\"{o}}s and
                  Igor B. Rogozin and
                  Eugene V. Koonin},
  title        = {A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from
                  a Global Survey of 100 Complete Genomes},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {9},
  year         = {2011},
  url          = {https://doi.org/10.1371/journal.pcbi.1002150},
  doi          = {10.1371/JOURNAL.PCBI.1002150},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/CsurosRK11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/LobkovskyWK11,
  author       = {Alexander E. Lobkovsky and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {Predictability of Evolutionary Trajectories in Fitness Landscapes},
  journal      = {PLoS Comput. Biol.},
  volume       = {7},
  number       = {12},
  year         = {2011},
  url          = {https://doi.org/10.1371/journal.pcbi.1002302},
  doi          = {10.1371/JOURNAL.PCBI.1002302},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ploscb/LobkovskyWK11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/abi/CarmelWRK10,
  author       = {Liran Carmel and
                  Yuri I. Wolf and
                  Igor B. Rogozin and
                  Eugene V. Koonin},
  title        = {{EREM:} Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization
                  Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution},
  journal      = {Adv. Bioinformatics},
  volume       = {2010},
  pages        = {167408:1--167408:4},
  year         = {2010},
  url          = {https://doi.org/10.1155/2010/167408},
  doi          = {10.1155/2010/167408},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/abi/CarmelWRK10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/KristensenKCWSKM10,
  author       = {David M. Kristensen and
                  Lavanya Kannan and
                  Michael K. Coleman and
                  Yuri I. Wolf and
                  Alexander Sorokin and
                  Eugene V. Koonin and
                  Arcady R. Mushegian},
  title        = {A low-polynomial algorithm for assembling clusters of orthologous
                  groups from intergenomic symmetric best matches},
  journal      = {Bioinform.},
  volume       = {26},
  number       = {12},
  pages        = {1481--1487},
  year         = {2010},
  url          = {https://doi.org/10.1093/bioinformatics/btq229},
  doi          = {10.1093/BIOINFORMATICS/BTQ229},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KristensenKCWSKM10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/NovichkovRWKD09,
  author       = {Pavel S. Novichkov and
                  Igor Ratnere and
                  Yuri I. Wolf and
                  Eugene V. Koonin and
                  Inna Dubchak},
  title        = {{ATGC:} a database of orthologous genes from closely related prokaryotic
                  genomes and a research platform for microevolution of prokaryotes},
  journal      = {Nucleic Acids Res.},
  volume       = {37},
  number       = {Database-Issue},
  pages        = {448--454},
  year         = {2009},
  url          = {https://doi.org/10.1093/nar/gkn684},
  doi          = {10.1093/NAR/GKN684},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/NovichkovRWKD09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/recomb/ZhengRKP07,
  author       = {Jie Zheng and
                  Igor B. Rogozin and
                  Eugene V. Koonin and
                  Teresa M. Przytycka},
  editor       = {Glenn Tesler and
                  Dannie Durand},
  title        = {A Rigorous Analysis of the Pattern of Intron Conservation Supports
                  the \emph{Coelomata} Clade of Animals},
  booktitle    = {Comparative Genomics, {RECOMB} 2007 International Workshop, {RECOMB-CG}
                  2007, San Diego, CA, USA, September 16-18, 2007, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {4751},
  pages        = {177--191},
  publisher    = {Springer},
  year         = {2007},
  url          = {https://doi.org/10.1007/978-3-540-74960-8\_14},
  doi          = {10.1007/978-3-540-74960-8\_14},
  timestamp    = {Mon, 13 May 2019 09:30:09 +0200},
  biburl       = {https://dblp.org/rec/conf/recomb/ZhengRKP07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/NovozhilovKK06,
  author       = {Artem S. Novozhilov and
                  Georgy P. Karev and
                  Eugene V. Koonin},
  title        = {Biological applications of the theory of birth-and-death processes},
  journal      = {Briefings Bioinform.},
  volume       = {7},
  number       = {1},
  pages        = {70--85},
  year         = {2006},
  url          = {https://doi.org/10.1093/bib/bbk006},
  doi          = {10.1093/BIB/BBK006},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/NovozhilovKK06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/MakarovaKHG06,
  author       = {Kira S. Makarova and
                  Eugene V. Koonin and
                  Robert Haselkorn and
                  Michael Y. Galperin},
  title        = {Cyanobacterial response regulator PatA contains a conserved N-terminal
                  domain {(PATAN)} with an alpha-helical insertion},
  journal      = {Bioinform.},
  volume       = {22},
  number       = {11},
  pages        = {1297--1301},
  year         = {2006},
  url          = {https://doi.org/10.1093/bioinformatics/btl096},
  doi          = {10.1093/BIOINFORMATICS/BTL096},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MakarovaKHG06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/MakarovaGK06,
  author       = {Kira S. Makarova and
                  Nick V. Grishin and
                  Eugene V. Koonin},
  title        = {The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin
                  system in archaea and bacteria},
  journal      = {Bioinform.},
  volume       = {22},
  number       = {21},
  pages        = {2581--2584},
  year         = {2006},
  url          = {https://doi.org/10.1093/bioinformatics/btl418},
  doi          = {10.1093/BIOINFORMATICS/BTL418},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/MakarovaGK06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/RogozinSBK05,
  author       = {Igor B. Rogozin and
                  Alexander V. Sverdlov and
                  Vladimir N. Babenko and
                  Eugene V. Koonin},
  title        = {Analysis of evolution of exon-intron structure of eukaryotic genes},
  journal      = {Briefings Bioinform.},
  volume       = {6},
  number       = {2},
  pages        = {118--134},
  year         = {2005},
  url          = {https://doi.org/10.1093/bib/6.2.118},
  doi          = {10.1093/BIB/6.2.118},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bib/RogozinSBK05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/KarevBK05,
  author       = {Georgy P. Karev and
                  Faina S. Berezovskaya and
                  Eugene V. Koonin},
  title        = {Modeling genome evolution with a diffusion approximation of a birth-and-death
                  process},
  journal      = {Bioinform.},
  volume       = {21},
  number       = {{S3}},
  pages        = {19},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti1202},
  doi          = {10.1093/BIOINFORMATICS/BTI1202},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KarevBK05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/recomb/CarmelRWK05,
  author       = {Liran Carmel and
                  Igor B. Rogozin and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  editor       = {Aoife McLysaght and
                  Daniel H. Huson},
  title        = {An Expectation-Maximization Algorithm for Analysis of Evolution of
                  Exon-Intron Structure of Eukaryotic Genes},
  booktitle    = {Comparative Genomics, {RECOMB} 2005 International Workshop, {RCG}
                  2005, Dublin, Ireland, September 18-20, 2005, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {3678},
  pages        = {35--46},
  publisher    = {Springer},
  year         = {2005},
  url          = {https://doi.org/10.1007/11554714\_4},
  doi          = {10.1007/11554714\_4},
  timestamp    = {Sun, 25 Oct 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/recomb/CarmelRWK05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bib/RogozinMWK04,
  author       = {Igor B. Rogozin and
                  Kira S. Makarova and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {Computational approaches for the analysis of gene neighbourhoods in
                  prokaryotic genomes},
  journal      = {Briefings Bioinform.},
  volume       = {5},
  number       = {2},
  pages        = {131--149},
  year         = {2004},
  url          = {https://doi.org/10.1093/bib/5.2.131},
  doi          = {10.1093/BIB/5.2.131},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bib/RogozinMWK04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/KarevWK03,
  author       = {Georgy P. Karev and
                  Yuri I. Wolf and
                  Eugene V. Koonin},
  title        = {Simple stochastic birth andz death models of genome evolution: was
                  there enough time for us to evolve?},
  journal      = {Bioinform.},
  volume       = {19},
  number       = {15},
  pages        = {1889--1900},
  year         = {2003},
  url          = {https://doi.org/10.1093/bioinformatics/btg351},
  doi          = {10.1093/BIOINFORMATICS/BTG351},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/KarevWK03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/TatusovFJJKKKMMNRSSVWYN03,
  author       = {Roman L. Tatusov and
                  Natalie D. Fedorova and
                  John D. Jackson and
                  Aviva R. Jacobs and
                  Boris Kiryutin and
                  Eugene V. Koonin and
                  Dmitri M. Krylov and
                  Raja Mazumder and
                  Sergei L. Mekhedov and
                  Anastasia N. Nikolskaya and
                  B. Sridhar Rao and
                  Sergei Smirnov and
                  Alexander V. Sverdlov and
                  Sona Vasudevan and
                  Yuri I. Wolf and
                  Jodie J. Yin and
                  Darren A. Natale},
  title        = {The {COG} database: an updated version includes eukaryotes},
  journal      = {{BMC} Bioinform.},
  volume       = {4},
  pages        = {41},
  year         = {2003},
  url          = {https://doi.org/10.1186/1471-2105-4-41},
  doi          = {10.1186/1471-2105-4-41},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/TatusovFJJKKKMMNRSSVWYN03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/BorodovskyKBFLSSZ01,
  author       = {Mark Borodovsky and
                  Eugene V. Koonin and
                  Chris Burge and
                  James W. Fickett and
                  John Logsdon and
                  Andrej Sali and
                  Gary D. Stormo and
                  Igor B. Zhulin},
  title        = {The Third Georgia Tech-Emory International Conference on Bioinformatics:
                  In Silico Biology; Bioinformatics After Human Genome (November 15-18,
                  2001, Atlanta, Georgia, {USA)}},
  journal      = {Bioinform.},
  volume       = {17},
  number       = {10},
  pages        = {859--861},
  year         = {2001},
  url          = {https://doi.org/10.1093/bioinformatics/17.10.859},
  doi          = {10.1093/BIOINFORMATICS/17.10.859},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BorodovskyKBFLSSZ01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/RogozinKKKM01,
  author       = {Igor B. Rogozin and
                  Alexey V. Kochetov and
                  Fyodor A. Kondrashov and
                  Eugene V. Koonin and
                  Luciano Milanesi},
  title        = {Presence of {ATG} triplets in 5' untranslated regions of eukaryotic
                  cDNAs correlates with a 'weak' context of the start codon},
  journal      = {Bioinform.},
  volume       = {17},
  number       = {10},
  pages        = {890--900},
  year         = {2001},
  url          = {https://doi.org/10.1093/bioinformatics/17.10.890},
  doi          = {10.1093/BIOINFORMATICS/17.10.890},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/RogozinKKKM01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/TatusovNGTSRKGFK01,
  author       = {Roman L. Tatusov and
                  Darren A. Natale and
                  Igor V. Garkavtsev and
                  Tatiana A. Tatusova and
                  Uma T. Shankavaram and
                  Bachoti S. Rao and
                  Boris Kiryutin and
                  Michael Y. Galperin and
                  Natalie D. Fedorova and
                  Eugene V. Koonin},
  title        = {The {COG} database: new developments in phylogenetic classification
                  of proteins from complete genomes},
  journal      = {Nucleic Acids Res.},
  volume       = {29},
  number       = {1},
  pages        = {22--28},
  year         = {2001},
  url          = {https://doi.org/10.1093/nar/29.1.22},
  doi          = {10.1093/NAR/29.1.22},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/TatusovNGTSRKGFK01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/dimacs/MirkinK01,
  author       = {Boris G. Mirkin and
                  Eugene V. Koonin},
  editor       = {Melvin F. Janowitz and
                  Fran{\c{c}}ois{-}Joseph Lapointe and
                  Fred R. McMorris and
                  Boris G. Mirkin and
                  Fred S. Roberts},
  title        = {A top-down method for building genome classification trees with linear
                  binary hierarchies},
  booktitle    = {Bioconsensus, Proceedings of a {DIMACS} Workshop, New Brunswick, New
                  Jersey, USA, 2001},
  series       = {{DIMACS} Series in Discrete Mathematics and Theoretical Computer Science},
  volume       = {61},
  pages        = {97--111},
  publisher    = {{DIMACS/AMS}},
  year         = {2001},
  url          = {https://doi.org/10.1090/dimacs/061/07},
  doi          = {10.1090/DIMACS/061/07},
  timestamp    = {Mon, 22 May 2023 16:07:34 +0200},
  biburl       = {https://dblp.org/rec/conf/dimacs/MirkinK01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcb/BermanZWKM00,
  author       = {Piotr Berman and
                  Zheng Zhang and
                  Yuri I. Wolf and
                  Eugene V. Koonin and
                  Webb Miller},
  title        = {Winnowing Sequences from a Database Search},
  journal      = {J. Comput. Biol.},
  volume       = {7},
  number       = {1-2},
  pages        = {293--302},
  year         = {2000},
  url          = {https://doi.org/10.1089/10665270050081531},
  doi          = {10.1089/10665270050081531},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcb/BermanZWKM00.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/TatusovGNK00,
  author       = {Roman L. Tatusov and
                  Michael Y. Galperin and
                  Darren A. Natale and
                  Eugene V. Koonin},
  title        = {The {COG} database: a tool for genome-scale analysis of protein functions
                  and evolution},
  journal      = {Nucleic Acids Res.},
  volume       = {28},
  number       = {1},
  pages        = {33--36},
  year         = {2000},
  url          = {https://doi.org/10.1093/nar/28.1.33},
  doi          = {10.1093/NAR/28.1.33},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/TatusovGNK00.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/SchafferWPKAA99,
  author       = {Alejandro A. Sch{\"{a}}ffer and
                  Yuri I. Wolf and
                  Chris P. Ponting and
                  Eugene V. Koonin and
                  L. Aravind and
                  Stephen F. Altschul},
  title        = {{IMPALA:} matching a protein sequence against a collection of PSI-BLAST-constructed
                  position-specific score matrices},
  journal      = {Bioinform.},
  volume       = {15},
  number       = {12},
  pages        = {1000--1011},
  year         = {1999},
  url          = {https://doi.org/10.1093/bioinformatics/15.12.1000},
  doi          = {10.1093/BIOINFORMATICS/15.12.1000},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/SchafferWPKAA99.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/recomb/BermanZWKM99,
  author       = {Piotr Berman and
                  Zheng Zhang and
                  Yuri I. Wolf and
                  Eugene V. Koonin and
                  Webb Miller},
  editor       = {Sorin Istrail and
                  Pavel A. Pevzner and
                  Michael S. Waterman},
  title        = {Winnowing sequences from a database search},
  booktitle    = {Proceedings of the Third Annual International Conference on Research
                  in Computational Molecular Biology, {RECOMB} 1999, Lyon, France, April
                  11-14, 1999},
  pages        = {50--58},
  publisher    = {{ACM}},
  year         = {1999},
  url          = {https://doi.org/10.1145/299432.299451},
  doi          = {10.1145/299432.299451},
  timestamp    = {Mon, 13 May 2019 09:30:09 +0200},
  biburl       = {https://dblp.org/rec/conf/recomb/BermanZWKM99.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/isb/GalperinK98,
  author       = {Michael Y. Galperin and
                  Eugene V. Koonin},
  title        = {Sources of systematic error in functional annotation of genomes: domain
                  rearrangement, non-orthologous gene displacement, and operon disruption},
  journal      = {Silico Biol.},
  volume       = {1},
  number       = {1},
  pages        = {55--67},
  year         = {1998},
  url          = {http://content.iospress.com/articles/in-silico-biology/isb00007},
  timestamp    = {Thu, 20 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/isb/GalperinK98.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/recomb/KooninTGR98,
  author       = {Eugene V. Koonin and
                  Roman L. Tatusov and
                  Michael Y. Galperin and
                  Michael N. Rosanov},
  editor       = {Sorin Istrail and
                  Pavel A. Pevzner and
                  Michael S. Waterman},
  title        = {Genome analysis using clusters of orthologous groups (COGs)},
  booktitle    = {Proceedings of the Second Annual International Conference on Research
                  in Computational Molecular Biology, {RECOMB} 1998, New York, NY, USA,
                  March 22-25, 1998},
  pages        = {135--139},
  publisher    = {{ACM}},
  year         = {1998},
  url          = {https://doi.org/10.1145/279069.279106},
  doi          = {10.1145/279069.279106},
  timestamp    = {Mon, 13 May 2019 09:30:09 +0200},
  biburl       = {https://dblp.org/rec/conf/recomb/KooninTGR98.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/gcb/KooninTL97,
  author       = {Eugene V. Koonin and
                  Roman L. Tatusov and
                  David J. Lipman},
  title        = {A natural taxonomy of gene families from complete genomes},
  booktitle    = {Proceedings of the German Conference on Bioinformatics, {GCB} 1997,
                  Kloster Irsee, Bavaria, Germany, September 1997},
  pages        = {13--14},
  publisher    = {Oxford University Press},
  year         = {1997},
  timestamp    = {Fri, 02 Aug 2019 15:48:15 +0200},
  biburl       = {https://dblp.org/rec/conf/gcb/KooninTL97.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/ismb/WalkerK97,
  author       = {D. Roland Walker and
                  Eugene V. Koonin},
  editor       = {Terry Gaasterland and
                  Peter D. Karp and
                  Kevin Karplus and
                  Christos A. Ouzounis and
                  Chris Sander and
                  Alfonso Valencia},
  title        = {{SEALS:} {A} System for Easy Analysis of Lots of Sequences},
  booktitle    = {Proceedings of the 5th International Conference on Intelligent Systems
                  for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
  pages        = {333--339},
  publisher    = {{AAAI}},
  year         = {1997},
  url          = {http://www.aaai.org/Library/ISMB/1997/ismb97-051.php},
  timestamp    = {Thu, 13 Dec 2012 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/ismb/WalkerK97.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/TatusovK94,
  author       = {Roman L. Tatusov and
                  Eugene V. Koonin},
  title        = {A simple tool to search for sequence motifs that are conserved in
                  {BLAST} outputs},
  journal      = {Comput. Appl. Biosci.},
  volume       = {10},
  number       = {4},
  pages        = {457--459},
  year         = {1994},
  url          = {https://doi.org/10.1093/bioinformatics/10.4.457},
  doi          = {10.1093/BIOINFORMATICS/10.4.457},
  timestamp    = {Fri, 15 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/TatusovK94.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/Koonin94,
  author       = {Eugene V. Koonin},
  title        = {Prediction of an rRNA methyltransferase domain in human tumor-specific
                  nucleolar protein {P120}},
  journal      = {Nucleic Acids Res.},
  volume       = {22},
  number       = {13},
  pages        = {2476--2478},
  year         = {1994},
  url          = {https://doi.org/10.1093/nar/22.13.2476},
  doi          = {10.1093/NAR/22.13.2476},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/Koonin94.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/IlyinaK92,
  author       = {Tatyana V. Ilyina and
                  Eugene V. Koonin},
  title        = {Conserved sequence motifs in the initiator proteins for rolling circle
                  {DNA} replication encoded by diverse replicons from eubacteria, eucaryotes
                  and archaebacteria},
  journal      = {Nucleic Acids Res.},
  volume       = {20},
  number       = {13},
  pages        = {3279--3285},
  year         = {1992},
  url          = {https://doi.org/10.1093/nar/20.13.3279},
  doi          = {10.1093/NAR/20.13.3279},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/IlyinaK92.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/dimacs/Koonin92,
  author       = {Eugene V. Koonin},
  editor       = {Simon Gindikin},
  title        = {Comparative Analysis of Biopolymer Sequences: Reflections on the Validity
                  of the Methodology and the Underlying General Principles},
  booktitle    = {Mathematical Methods Of Analysis Of Biopolymer Sequences, Proceedings
                  of a {DIMACS} Workshop},
  series       = {{DIMACS} Series in Discrete Mathematics and Theoretical Computer Science},
  volume       = {8},
  pages        = {63--74},
  publisher    = {{DIMACS/AMS}},
  year         = {1992},
  url          = {https://doi.org/10.1090/dimacs/008/04},
  doi          = {10.1090/DIMACS/008/04},
  timestamp    = {Mon, 22 May 2023 16:07:35 +0200},
  biburl       = {https://dblp.org/rec/conf/dimacs/Koonin92.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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