Eugene V. Koonin

Orcid: 0000-0003-3943-8299

Affiliations:
  • National Center for Biotechnology Informatio, Bethesda, USA


According to our database1, Eugene V. Koonin authored at least 49 papers between 1992 and 2024.

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Bibliography

2024
On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics.
Proceedings of the Comparative Genomics - 21st International Conference, 2024

2022
ViroidDB: a database of viroids and viroid-like circular RNAs.
Nucleic Acids Res., 2022

2021
COG database update: focus on microbial diversity, model organisms, and widespread pathogens.
Nucleic Acids Res., 2021

Thermodynamics of Evolution and the Origin of Life.
CoRR, 2021

Towards a Theory of Evolution as Multilevel Learning.
CoRR, 2021

2019
Microbial genome analysis: the COG approach.
Briefings Bioinform., 2019

2017
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.
Nucleic Acids Res., 2017

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation.
Nucleic Acids Res., 2017

2015
Expanded microbial genome coverage and improved protein family annotation in the COG database.
Nucleic Acids Res., 2015

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.
BMC Bioinform., 2015

2014
Comparative Genomics Approaches to Identifying Functionally Related Genes.
Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013
The Vast, Conserved Mammalian lincRNome.
PLoS Comput. Biol., 2013

2012
Universal Pacemaker of Genome Evolution.
PLoS Comput. Biol., 2012

Dependencies among Editing Sites in Serotonin 2C Receptor mRNA.
PLoS Comput. Biol., 2012

2011
On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems.
PLoS Comput. Biol., 2011

Predictability of Evolutionary Trajectories in Fitness Landscapes.
PLoS Comput. Biol., 2011

Are There Laws of Genome Evolution?
PLoS Comput. Biol., 2011

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes.
PLoS Comput. Biol., 2011

Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life".
J. Comput. Biol., 2011

Computational methods for Gene Orthology inference.
Briefings Bioinform., 2011

Obituary: Walter Fitch and the orthology paradigm.
Briefings Bioinform., 2011

2010
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.
Bioinform., 2010

EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.
Adv. Bioinformatics, 2010

2009
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.
Nucleic Acids Res., 2009

2007
A Rigorous Analysis of the Pattern of Intron Conservation Supports the <i>Coelomata</i> Clade of Animals.
Proceedings of the Comparative Genomics, RECOMB 2007 International Workshop, 2007

2006
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.
Bioinform., 2006

The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinform., 2006

Biological applications of the theory of birth-and-death processes.
Briefings Bioinform., 2006

2005
Modeling genome evolution with a diffusion approximation of a birth-and-death process.
Bioinform., 2005

Analysis of evolution of exon-intron structure of eukaryotic genes.
Briefings Bioinform., 2005

An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes.
Proceedings of the Comparative Genomics, 2005

2004
Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes.
Briefings Bioinform., 2004

2003
The COG database: an updated version includes eukaryotes.
BMC Bioinform., 2003

Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve?
Bioinform., 2003

2001
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic Acids Res., 2001

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon.
Bioinform., 2001

The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA).
Bioinform., 2001

A top-down method for building genome classification trees with linear binary hierarchies.
Proceedings of the Bioconsensus, 2001

2000
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Nucleic Acids Res., 2000

Winnowing Sequences from a Database Search.
J. Comput. Biol., 2000

1999
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
Bioinform., 1999

1998
Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement, and operon disruption.
Silico Biol., 1998

Genome analysis using clusters of orthologous groups (COGs).
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

1997
SEALS: A System for Easy Analysis of Lots of Sequences.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

A natural taxonomy of gene families from complete genomes.
Proceedings of the German Conference on Bioinformatics, 1997

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

A simple tool to search for sequence motifs that are conserved in BLAST outputs.
Comput. Appl. Biosci., 1994

1992
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria.
Nucleic Acids Res., 1992

Comparative Analysis of Biopolymer Sequences: Reflections on the Validity of the Methodology and the Underlying General Principles.
Proceedings of the Mathematical Methods Of Analysis Of Biopolymer Sequences, 1992


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