Eugene V. Koonin

发表

Comparative Genomics Approaches to Identifying Functionally Related Genes

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2014, AlCoB.

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

Liran Carmel, Igor B. Rogozin, Eugene V. Koonin, 2010, Adv. Bioinformatics.

Are There Laws of Genome Evolution?

Eugene V. Koonin, E. Koonin, 2011, PLoS Comput. Biol..

Predictability of Evolutionary Trajectories in Fitness Landscapes

Eugene V. Koonin, Yuri I. Wolf, Alexander E. Lobkovsky, 2011, PLoS Comput. Biol..

No waves of intelligent design

Eugene V. Koonin, Yuri I. Wolf, Mikhail I. Katsnelson, 2020, Proceedings of the National Academy of Sciences.

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

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 1998, Silico Biol..

Comparative Analysis of Biopolymer Sequences: Reflections on the Validity of the Methodology and the Underlying General Principles

Eugene V. Koonin, 1992, Mathematical Methods Of Analysis Of Biopolymer Sequences.

Seeker: Alignment-free identification of bacteriophage genomes by deep learning

Eugene V. Koonin, Yuri I. Wolf, Noam Auslander, 2020, bioRxiv.

Computer Analysis of Amino Acid Sequences

Eugene V. Koonin, Arcady Mushegian, Valerian V. Dolja, 1998 .

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

Eugene V. Koonin, Yuri I. Wolf, David M. Kristensen, 2016, Nucleic Acids Res..

Genome analysis using clusters of orthologous groups (COGs)

Michael Y. Galperin, Eugene V. Koonin, Roman L. Tatusov, 1998, RECOMB '98.

Faculty Opinions recommendation of Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.

Eugene V. Koonin, E. Koonin, 2002 .

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

Gary D. Stormo, James W. Fickett, Andrej Sali, 2001, Bioinform..

Universal Pacemaker of Genome Evolution

Sagi Snir, Eugene V. Koonin, Yuri I. Wolf, 2012, PLoS Comput. Biol..

Winnowing sequences from a database search

Piotr Berman, Webb Miller, Eugene V. Koonin, 1999, RECOMB.

The COG database: new developments in phylogenetic classification of proteins from complete genomes

Michael Y. Galperin, Tatiana A. Tatusova, Darren A. Natale, 2001, Nucleic Acids Res..

Expanded microbial genome coverage and improved protein family annotation in the COG database

Michael Y. Galperin, Kira S. Makarova, Eugene V. Koonin, 2014, Nucleic Acids Res..

Obituary: Walter Fitch and the orthology paradigm

Eugene V. Koonin, 2011, Briefings Bioinform..

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

Igor B. Rogozin, Miklós Csürös, Eugene V. Koonin, 2011, PLoS Comput. Biol..

Prediction of an rRNA methyltransferase domain in human tumor-specific nucleolar protein P120

Eugene V. Koonin, E. Koonin, 1994, Nucleic Acids Res..

A top-down method for building genome classification trees with linear binary hierarchies

Eugene V. Koonin, Boris Mirkin, E. Koonin, 2001, Bioconsensus.

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

Dmitrij Frishman, Usman Saeed, Eugene V. Koonin, 2015, BMC Bioinformatics.

The COG database: a tool for genome-scale analysis of protein functions and evolution

Michael Y. Galperin, Darren A. Natale, Eugene V. Koonin, 2000, Nucleic Acids Res..

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

Luciano Milanesi, Igor B. Rogozin, Alexey V. Kochetov, 2001, Bioinform..

Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life"

Eugene V. Koonin, Yuri I. Wolf, Pere Puigbò, 2011, J. Comput. Biol..

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2020, bioRxiv.

Figure 1, [A generalized procedure for constructing...].

Eugene V. Koonin, 2002 .

Faculty Opinions recommendation of Loop fold structure of proteins: resolution of Levinthas paradox.

Eugene V. Koonin, 2002 .

A natural taxonomy of gene families from complete genomes

David J. Lipman, Eugene V. Koonin, Roman L. Tatusov, 1997, German Conference on Bioinformatics.

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

Lavanya Kannan, Arcady R. Mushegian, Eugene V. Koonin, 2010, Bioinform..

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

Eugene V. Koonin, Tatyana V. Ilyina, E. Koonin, 1992, Nucleic Acids Res..

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

Eugene V. Koonin, Yuri I. Wolf, Georgy P. Karev, 2003, Bioinform..

The Vast, Conserved Mammalian lincRNome

Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin, 2013, PLoS Comput. Biol..

A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals

Teresa M. Przytycka, Jie Zheng, Igor B. Rogozin, 2007, RECOMB-CG.

Principles and Methods of Sequence Analysis

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2003 .

Epilogue: Peering through the crystal ball

Michael Y. Galperin, Eugene V. Koonin, 2003 .

Winnowing sequences from a database search

Piotr Berman, Webb Miller, Eugene V. Koonin, 1999, J. Comput. Biol..

An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes

Liran Carmel, Igor B. Rogozin, Eugene V. Koonin, 2005, Comparative Genomics.

Table 2, Examples of horizontally transferred operons

L. Aravind, Kira S. Makarova, Eugene V. Koonin, 2002 .

Lamarckian or not, CRISPR-Cas is an elaborate engine of directed evolution

Eugene V. Koonin, E. Koonin, 2019, Biology & Philosophy.

A simple tool to search for sequence motifs that are conserved in BLAST outputs

Eugene V. Koonin, Roman L. Tatusov, E. Koonin, 1994, Comput. Appl. Biosci..

CRISPRidentify: identification of CRISPR arrays using machine learning approach

Rolf Backofen, Kira S. Makarova, Eugene V. Koonin, 2020 .

Modeling genome evolution with a diffusion approximation of a birth-and-death process

Eugene V. Koonin, Georgy P. Karev, Faina S. Berezovskaya, 2005, Bioinform..

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

Michael Y. Galperin, Kira S. Makarova, Eugene V. Koonin, 2006, Bioinform..

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems

Paulien Hogeweg, Eugene V. Koonin, Nobuto Takeuchi, 2011, PLoS Comput. Biol..

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

Eugene V. Koonin, David M. Kristensen, Ana Laura Grazziotin, 2016, Nucleic Acids Res..

SEALS: A System for Easy Analysis of Lots of Sequences

Eugene V. Koonin, D. Roland Walker, E. Koonin, 1997, ISMB.

Dependencies among Editing Sites in Serotonin 2C Receptor mRNA

Liran Carmel, Eugene V. Koonin, Stella Dracheva, 2012, PLoS Comput. Biol..

Analysis of evolution of exon-intron structure of eukaryotic genes

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2005, Briefings Bioinform..

Creation of new order, Ortervirales, for 5 families of reverse-transcribing viruses

Jens H. Kuhn, Hung Fan, Eugene V. Koonin, 2017 .

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

Alejandro A. Schäffer, L. Aravind, Chris P. Ponting, 1999, Bioinform..

Biological applications of the theory of birth-and-death processes

Eugene V. Koonin, Georgy P. Karev, Artem S. Novozhilov, 2005, Briefings Bioinform..

Genome Annotation and Analysis

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2003 .

Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes

Igor B. Rogozin, Kira S. Makarova, Eugene V. Koonin, 2004, Briefings Bioinform..

Bridging the gap between sequence & function : abstracts of papers presented at the 1999 workshop, September 7-September 9, 1999

Michael Q. Zhang, Eugene V. Koonin, Edward Uberbacher, 1999 .

Towards physical principles of biological evolution

Eugene V. Koonin, Yuri I. Wolf, Mikhail I. Katsnelson, 2017, bioRxiv.

Machine-learning approach expands the repertoire of anti-CRISPR protein families

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2020, Nature Communications.

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

Nick V. Grishin, Kira S. Makarova, Eugene V. Koonin, 2006, Bioinform..

Computational methods for Gene Orthology inference

Arcady R. Mushegian, Eugene V. Koonin, Yuri I. Wolf, 2011, Briefings Bioinform..

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

Inna Dubchak, Eugene V. Koonin, Yuri I. Wolf, 2008, Nucleic Acids Res..

The COG database: an updated version includes eukaryotes

Darren A. Natale, Raja Mazumder, Eugene V. Koonin, 2003, BMC Bioinformatics.

Replaying the Tape of Life: Quantification of the Predictability of Evolution

Eugene V. Koonin, Alexander E. Lobkovsky, E. Koonin, 2012, Front. Gene..

Toward a theory of evolution as multilevel learning

Vitaly Vanchurin, Eugene V. Koonin, Yuri I. Wolf, 2021, Proceedings of the National Academy of Sciences.

Thermodynamics of evolution and the origin of life pdf

Vitaly Vanchurin, Eugene V. Koonin, Yuri I. Wolf, 2021, Proceedings of the National Academy of Sciences.

Inventing the dynamo machine: the evolution of the F-type and V-type ATPases

Michael Y. Galperin, Kira S. Makarova, Eugene V. Koonin, 2007, Nature Reviews Microbiology.

Stability along with Extreme Variability in Core Genome Evolution

Sagi Snir, Eugene V. Koonin, Yuri I. Wolf, 2013, Genome biology and evolution.

SnapShot: Class 2 CRISPR-Cas Systems

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2017, Cell.

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

Eugene V. Koonin, Yuri I. Wolf, E. Koonin, 2012, Front. Cell. Inf. Microbio..

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Rolf Backofen, Philippe Horvath, Rodolphe Barrangou, 2019, Nature Reviews Microbiology.

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

Kira S. Makarova, Eugene V. Koonin, Emmanuelle Charpentier, 2013, Nucleic acids research.

Power Laws, Scale-Free Networks and Genome Biology

Eugene V. Koonin, Yuri I. Wolf, Georgy P. Karev, 2006 .

Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central Carbohydrate Metabolism

Martijn A. Huynen, Kira S. Makarova, Eugene V. Koonin, 2004, Journal of bacteriology.

Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers

Subhajyoti De, Anna R. Panchenko, Igor B. Rogozin, 2016, Scientific Reports.

Helicases: amino acid sequence comparisons and structure-function relationships

Eugene V. Koonin, Alexander E. Gorbalenya, E. Koonin, 1993 .

Reconstruction of Ancestral Protosplice Sites

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2004, Current Biology.

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

Eugene V. Koonin, Jaime Iranzo, Mart Krupovic, 2016, Journal of Virology.

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2017, mBio.

TSG101 may be the prototype of a class of dominant negative ubiquitin regulators

Eugene V. Koonin, R. Abagyan, E. Koonin, 1997, Nature Genetics.

Human choroideremia protein contains a FAD-binding domain

Eugene V. Koonin, E. Koonin, 1996, Nature Genetics.

Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2015, Life.

Consensus statement: Virus taxonomy in the age of metagenomics

Andrew J. Davison, Elliot J. Lefkowitz, Jens H. Kuhn, 2017, Nature Reviews Microbiology.

Open questions: CRISPR biology

Eugene V. Koonin, E. Koonin, 2018, BMC Biology.

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

Michael Y. Galperin, Igor B. Rogozin, Patrick Wincker, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

Eugene V. Koonin, Yuri I. Wolf, E. Koonin, 2013, Genome biology and evolution.

De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling

Somasekar Seshagiri, L. Aravind, Eugene V. Koonin, 2004, Nature.

Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell

Boris G. Mirkin, Kira S. Makarova, Eugene V. Koonin, 2005, Nucleic acids research.

The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life

Eugene V. Koonin, E. Koonin, 2015, Journal of Molecular Evolution.

Evolutionary Concept in Genetics and Genomics

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2003 .

Putative papain‐related thiol proteases of positive‐strand RNA viruses Identification of rubi‐ and aphthovirus proteases and delineation of a novel conserved domain associated with proteases of rubi‐, α‐ and coronaviruses

Eugene V. Koonin, Alexander E. Gorbalenya, E. Koonin, 1991, FEBS Letters.

Phylogenomics of Prokaryotic Ribosomal Proteins

Eugene V. Koonin, Yuri I. Wolf, Natalya Yutin, 2012, PloS one.

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

Sagi Snir, Kira S. Makarova, Eugene V. Koonin, 2011, Journal of bacteriology.

Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea

Eugene V. Koonin, David M. Kristensen, E. Koonin, 2014, mBio.

A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes

Eugene V. Koonin, Yuri I. Wolf, E. Koonin, 2012, Genome biology and evolution.

Comparative Genome Analysis of the Pathogenic Spirochetes Borrelia burgdorferi and Treponema pallidum

L. Aravind, Eugene V. Koonin, E. Koonin, 2000, Infection and Immunity.

Sequence — Evolution — Function

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2003, Springer US.

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms

Eugene V. Koonin, Yuri I. Wolf, E. Koonin, 2016, Biology Direct.

Gene Family Level Comparative Analysis of Gene Expression in Mammals Validates the Ortholog Conjecture

Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin, 2014, Genome biology and evolution.

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

Eric S. Lander, Aviv Regev, Kira S. Makarova, 2016, Science.

Classification and evolution of type II CRISPR-Cas systems

Kira S. Makarova, Eugene V. Koonin, Emmanuelle Charpentier, 2014, Nucleic acids research.

A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes

Liran Carmel, Eugene V. Koonin, E. Koonin, 2009, Genome biology and evolution.

Comparing Microbial Genomes: How the Gene Set Determines the Lifestyle

Michael Y. Galperin, Eugene V. Koonin, Roman L. Tatusov, 1999 .

Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms

Eugene V. Koonin, Natalya Yutin, Michael G. Rossmann, 2009, Proceedings of the National Academy of Sciences.

Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution

Mikhail S. Gelfand, Eugene V. Koonin, Yuri I. Wolf, 2004, Journal of bacteriology.

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

Peer Bork, Arcady R. Mushegian, Eugene V. Koonin, 2012, Journal of bacteriology.

Diversity and evolution of class 2 CRISPR–Cas systems

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2017, Nature Reviews Microbiology.

The meaning of biological information

Eugene V. Koonin, E. Koonin, 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL domain-containing accessory protein

Kira S. Makarova, Eugene V. Koonin, David A. Scott, 2018, Molecular cell.

Anti-CRISPRs on the march

Kira S. Makarova, Eugene V. Koonin, E. Koonin, 2018, Science.

Evidence of Splice Signal Migration from Exon to Intron during Intron Evolution

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2003, Current Biology.

Splendor and misery of adaptation, or the importance of neutral null for understanding evolution

Eugene V. Koonin, E. Koonin, 2016, BMC Biology.

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members

Detlef D. Leipe, L. Aravind, Eugene V. Koonin, 2005, Nucleic acids research.

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2018, Proceedings of the National Academy of Sciences.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Kira S. Makarova, Eugene V. Koonin, Matthew B. Sullivan, 2017, mBio.

Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2016, bioRxiv.

Comparative genomics, minimal gene-sets and the last universal common ancestor

Eugene V. Koonin, E. Koonin, 2003, Nature Reviews Microbiology.

Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes

Inna Dubchak, Eugene V. Koonin, Yuri I. Wolf, 2008, Journal of bacteriology.

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2016, Science.

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Mikhail S. Gelfand, Alla Lapidus, Alex Copeland, 2007, PloS one.

Novel Predicted RNA-Binding Domains Associated with the Translation Machinery

L. Aravind, Eugene V. Koonin, E. Koonin, 1999, Journal of Molecular Evolution.

Who's your neighbor? New computational approaches for functional genomics

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2000, Nature Biotechnology.

Role of mRNA structure in the control of protein folding

Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Eugene V. Koonin, 2016, Nucleic acids research.

Role of Predicted Metalloprotease Motif of Jab1/Csn5 in Cleavage of Nedd8 from Cul1

L. Aravind, Eugene V. Koonin, S. Lawrence Zipursky, 2002, Science.

Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2005, Nucleic acids research.

Provirophages and transpovirons as the diverse mobilome of giant viruses

Eugene V. Koonin, Natalya Yutin, Didier Raoult, 2012, Proceedings of the National Academy of Sciences.

Nucleic acid detection with CRISPR-Cas 13 a / C 2 c 2 Citation

Aviv Regev, James J. Collins, Catherine A. Freije, 2017 .

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

Eugene V. Koonin, Yuri I. Wolf, Feng Zhang, 2020, Proceedings of the National Academy of Sciences.

Engineering of CRISPR-Cas12b for human genome editing

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2019, Nature Communications.

Why the Central Dogma: on the nature of the great biological exclusion principle

Eugene V. Koonin, 2015, Biology Direct.

Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin

Igor B. Rogozin, Eugene V. Koonin, E. Koonin, 2005, Nature.

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

Kira S. Makarova, Eugene V. Koonin, Yinqing Li, 2016, Cell.

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum

George N. Bennett, Lynn Doucette-Stamm, Kira S. Makarova, 2001, Journal of bacteriology.

Universal Pacemaker of Genome Evolution in Animals and Fungi and Variation of Evolutionary Rates in Diverse Organisms

Sagi Snir, Eugene V. Koonin, Yuri I. Wolf, 2014, Genome biology and evolution.

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Eugene V. Koonin, Valerian V. Dolja, E. Koonin, 2014, Microbiology and Molecular Reviews.

Constraints and plasticity in genome and molecular-phenome evolution

Eugene V. Koonin, Yuri I. Wolf, E. Koonin, 2010, Nature Reviews Genetics.

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

Eugene V. Koonin, Yuri I. Wolf, Feng Zhang, 2020, bioRxiv.

Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome

L. Aravind, W. Hayes McDonald, Rati Verma, 2002, Science.

Dollo parsimony and the reconstruction of genome evolution

Igor B. Rogozin, Vladimir N. Babenko, Eugene V. Koonin, 2006 .

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

Darren A. Natale, L. Aravind, Igor B. Rogozin, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2011, Journal of bacteriology.

Sequence ― Evolution ― Function: Computational Approaches in Comparative Genomics

Michael Y. Galperin, Eugene V. Koonin, E. Koonin, 2010 .

Photosystem I gene cassettes are present in marine virus genomes

Ron Y. Pinter, Forest Rohwer, Fabian Glaser, 2009, Nature.

Reviving a culture of scientific debate

Eugene V. Koonin, E. Koonin, 2006 .

Theory of prokaryotic genome evolution

Eugene V. Koonin, Yuri I. Wolf, Itamar Sela, 2016, Proceedings of the National Academy of Sciences.

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin, 2011, Genome biology and evolution.

SnapShot: Class 1 CRISPR-Cas Systems

Kira S. Makarova, Eugene V. Koonin, Feng Zhang, 2017, Cell.

Sequencing and analysis of bacterial genomes

Arcady R. Mushegian, Eugene V. Koonin, Kenneth E. Rudd, 1996, Current Biology.

Introns and the origin of nucleus–cytosol compartmentalization

Eugene V. Koonin, E. Koonin, W. Martin, 2006, Nature.

[18] Protein sequence comparison at genome scale

Eugene V. Koonin, Kenneth E. Rudd, Roman L. Tatusov, 1996 .

Comparative genomics of defense systems in archaea and bacteria

Kira S. Makarova, Eugene V. Koonin, Yuri I. Wolf, 2013, Nucleic acids research.

Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces

L. Aravind, Eugene V. Koonin, Edward F. DeLong, 2002, Applied and Environmental Microbiology.

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

Eugene V. Koonin, Jaime Iranzo, Mart Krupovic, 2016, mBio.

Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context

Eugene V. Koonin, Yuri I. Wolf, Jaime Iranzo, 2013, Journal of bacteriology.