Eugene V Koonin

发表

Defining Life: An Exercise in Semantics or A Route to Biological Insights?

Eugene V Koonin, E. Koonin, 2012, Journal of biomolecular structure & dynamics.

Exceptional error minimization in putative primordial genetic codes

Eugene V Koonin, Artem S Novozhilov, E. Koonin, 2009, Biology Direct.

Malay Kumar Basu, Eugene V Koonin, Emanuel Diego S. Penha, 2019, Proceedings of the National Academy of Sciences.

Reply to Holmes and Duchêne, “Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?”: Deep Phylogenetic Analysis of RNA Viruses Is Highly Challenging but Not Meaningless

Eugene V Koonin, Darius Kazlauskas, Jaime Iranzo, 2019, mBio.

Reply to ‘Evolutionary placement of Methanonatronarchaeia’

Eugene V Koonin, Mark C M van Loosdrecht, Manuel Ferrer, 2019, Nature Microbiology.

Microbial genome analysis: the COG approach

Michael Y. Galperin, Eugene V Koonin, Yuri I Wolf, 2019, Briefings Bioinform..

Origin and evolution of the genetic code: The universal enigma

Eugene V Koonin, Artem S Novozhilov, E. Koonin, 2008, IUBMB life.

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y. Galperin, Eugene V Koonin, David Landsman, 2020, Nucleic Acids Res..

The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes.

Natalya Yutin, Eugene V Koonin, E. Koonin, 2014, Cold Spring Harbor perspectives in biology.

Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution

Natalya Yutin, Eugene V Koonin, Yuri I Wolf, 2009, Virology Journal.

Connected gene neighborhoods in prokaryotic genomes.

Eugene V Koonin, Yuri I Wolf, Roman L Tatusov, 2002, Nucleic acids research.

CRISPR-Cas

Eugene V Koonin, Kira S Makarova, E. Koonin, 2013, RNA biology.

Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus

Cecile Viboud, Eugene V Koonin, Yuri I Wolf, 2006, Biology Direct.

The cyanobacterial genome core and the origin of photosynthesis

Michael Y. Galperin, Denis Kaznadzey, Henry Burd, 2006, Proceedings of the National Academy of Sciences.

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Eugene V Koonin, Dorothea K. Thompson, Kira S Makarova, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Purifying and directional selection in overlapping prokaryotic genes.

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2002, Trends in genetics : TIG.

Classification of the caspase–hemoglobinase fold: Detection of new families and implications for the origin of the eukaryotic separins

Eugene V Koonin, E. Koonin, L. Aravind, 2002, Proteins.

The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases

Eugene V Koonin, E. Koonin, L. Aravind, 2001, Genome Biology.

A Non-Adaptationist Perspective on Evolution of Genomic Complexity or the Continued Dethroning of Man

Eugene V Koonin, E. Koonin, 2004, Cell cycle.

Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

Eugene V Koonin, Yuri I Wolf, Kira S Makarova, 2018, The CRISPR journal.

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies

Natalya Yutin, Eugene V Koonin, Didier Raoult, 2013, Virology Journal.

Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion.

Eugene V Koonin, E. Koonin, I. Rogozin, 2004, Gene.

Horizontal gene transfer: the path to maturity

Eugene V Koonin, E. Koonin, 2003, Molecular microbiology.

Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach.

Eugene V Koonin, E. Koonin, I. Rogozin, 2008, Molecular biology and evolution.

Mathematical modeling of tumor therapy with oncolytic viruses: Regimes with complete tumor elimination within the framework of deterministic models

Eugene V Koonin, Artem S Novozhilov, Faina S Berezovskaya, 2006, Biology Direct.

Systemic determinants of gene evolution and function

Eugene V Koonin, E. Koonin, 2005, Molecular systems biology.

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

Liran Carmel, Miklós Csürös, Eugene V Koonin, 2008, Biology Direct.

Classification and quantification of bacteriophage taxa in human gut metagenomes

Peer Bork, Shinichi Sunagawa, Eugene V Koonin, 2014, The ISME Journal.

Paralogs and mutational robustness linked through transcriptional reprogramming.

Eugene V Koonin, E. Koonin, 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation

Eugene V Koonin, Fyodor A Kondrashov, E. Koonin, 2006, Biology Direct.

Getting positive about selection

Eugene V Koonin, E. Koonin, I. Rogozin, 2003, Genome Biology.

Evolution of genome architecture.

Eugene V Koonin, E. Koonin, 2009, The international journal of biochemistry & cell biology.

The Biological Big Bang model for the major transitions in evolution

Eugene V Koonin, E. Koonin, 2007, Biology Direct.

Universal distribution of protein evolution rates as a consequence of protein folding physics

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2010, Proceedings of the National Academy of Sciences.

Interkingdom gene fusions

Eugene V Koonin, Yuri I Wolf, Alexey S Kondrashov, 2000, Genome Biology.

Estimation of prokaryotic supergenome size and composition from gene frequency distributions

Eugene V Koonin, Yuri I Wolf, Alexander E Lobkovsky, 2014, BMC Genomics.

Classification and quantification of bacteriophage taxa in human gut metagenomes

Peer Bork, Shinichi Sunagawa, Eugene V Koonin, 2014, The ISME Journal.

Evolution and classification of P-loop kinases and related proteins.

Detlef D. Leipe, Eugene V Koonin, E. Koonin, 2003, Journal of molecular biology.

Phylogenomics of Prokaryotic Ribosomal Proteins

Natalya Yutin, Eugene V Koonin, Yuri I Wolf, 2012, Genome Biology.

Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation.

Jie Zheng, Eugene V Koonin, Teresa M Przytycka, 2007, Molecular biology and evolution.

A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications.

Eugene V Koonin, Fyodor A Kondrashov, E. Koonin, 2004, Trends in genetics : TIG.

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

Eugene V Koonin, E. Koonin, V. Kapitonov, 2015, Biology Direct.

Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging.

Eugene V Koonin, Kira S Makarova, E. Koonin, 2004, Nucleic acids research.

Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions.

Michael Y. Galperin, Keith S Wilson, Eugene V Koonin, 2005, Journal of molecular biology.

Prevalence of intron gain over intron loss in the evolution of paralogous gene families.

Eugene V Koonin, E. Koonin, I. Rogozin, 2004, Nucleic acids research.

RNA-guided DNA insertion with CRISPR-associated transposases

Eugene V Koonin, Alim Ladha, Kira S Makarova, 2019, Science.

Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases

Eugene V Koonin, E. Koonin, 2006, Biology Direct.

On the Origin of Cells and Viruses

Eugene V Koonin, E. Koonin, 2009, Annals of the New York Academy of Sciences.

Cleavage of Cohesin by the CD Clan Protease Separin Triggers Anaphase in Yeast

Kim Nasmyth, Eugene V Koonin, Frank Uhlmann, 2000, Cell.

Evolutionary systems biology: links between gene evolution and function.

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2006, Current opinion in biotechnology.

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions

Eugene V Koonin, E. Koonin, I. Rogozin, 2017, Scientific Reports.

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

Robert A Edwards, Natalya Yutin, Eugene V Koonin, 2017, Nature Microbiology.

Multiple origins of viral capsid proteins from cellular ancestors

Eugene V Koonin, Mart Krupovic, E. Koonin, 2017, Proceedings of the National Academy of Sciences.

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales

Eugene V Koonin, Yuri I Wolf, David M Kristensen, 2015, The ISME Journal.

Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family*

Liran Carmel, Eugene V Koonin, Hirotada Mori, 2006, Journal of Biological Chemistry.

Origin and Evolution of the Universal Genetic Code.

Eugene V Koonin, Artem S Novozhilov, E. Koonin, 2017, Annual review of genetics.

A glimpse of a putative pre-intron phase of eukaryotic evolution.

Eugene V Koonin, Miklos Csuros, E. Koonin, 2007, Trends in genetics : TIG.

CRISPR-Cas: an adaptive immunity system in prokaryotes

Eugene V Koonin, Kira S Makarova, E. Koonin, 2009, F1000 biology reports.

Olivier Bodenreider, Panayiotis Tsaparas, Eugene V Koonin, 2006, BMC Evolutionary Biology.

Differential translation tunes uneven production of operon-encoded proteins.

Rotem Sorek, Eugene V Koonin, Stan J. J. Brouns, 2013, Cell reports.

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Eugene V Koonin, Yuri I Wolf, David J Lipman, 2009, Proceedings of the National Academy of Sciences.

Nucleic acid detection with CRISPR-Cas13a/C2c2

Aviv Regev, Cameron Myhrvold, James J Collins, 2017, Science.

Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection

Eugene V Koonin, Galina V Glazko, Igor B Rogozin, 2006, Biology Direct.

A community experiment with fully open and published peer review

Eugene V Koonin, David J Lipman, D. Lipman, 2006, Biology Direct.

Evolutionary significance of gene expression divergence.

Eugene V Koonin, I King Jordan, Leonardo Mariño-Ramírez, 2005, Gene.

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.

Nick V Grishin, Eugene V Koonin, Kira S Makarova, 2002, Nucleic acids research.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

Natalya Yutin, Eugene V Koonin, Yuri I Wolf, 2012, Biology Direct.

Microevolutionary genomics of bacteria.

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2002, Theoretical population biology.

Correction: No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2003, BMC Evolutionary Biology.

A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair

Andrew Emili, Mohan Babu, Eugene V Koonin, 2011, Molecular microbiology.

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.

Eugene V Koonin, Feng Zhang, Konstantin Severinov, 2015, Molecular cell.

Origins and impact of constraints in evolution of gene families.

Eugene V Koonin, Boris E. Shakhnovich, Boris E Shakhnovich, 2006, Genome research.

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

Eugene V Koonin, Yuri I Wolf, Kira S Makarova, 2005, BMC Evolutionary Biology.

Widespread positive selection in synonymous sites of mammalian genes.

Liran Carmel, Eugene V Koonin, Aleksey Y Ogurtsov, 2007, Molecular biology and evolution.

YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics.

Eugene V Koonin, Eric D Brown, E. Koonin, 2002, Biochemistry.

Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.

Eugene V Koonin, Aleksey Y Ogurtsov, David J Lipman, 2004, Nucleic acids research.

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.

Eugene V Koonin, Vivek Anantharaman, E. Koonin, 2002, Journal of molecular microbiology and biotechnology.

Evolution of alternative and constitutive regions of mammalian 5'UTRs

Eugene V Koonin, Aleksey Y Ogurtsov, Alissa M. Resch, 2009, BMC Genomics.

Unifying measures of gene function and evolution

Liran Carmel, Eugene V Koonin, Yuri I Wolf, 2006, Proceedings of the Royal Society B: Biological Sciences.

Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics

Eugene V Koonin, Artem S Novozhilov, E. Koonin, 2006, Biology Direct.

Phylogenomics of prokaryotic ribosomal proteins

Natalya Yutin, Eugene V Koonin, Yuri I Wolf, 2011, Genome Biology.

Mathematical modeling of evolution of horizontally transferred genes.

Eugene V Koonin, Artem S Novozhilov, E. Koonin, 2005, Molecular biology and evolution.

Genome reduction as the dominant mode of evolution

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements.

Liran Carmel, Eugene V Koonin, Yuri I Wolf, 2007, Molecular biology and evolution.

Duplicated genes evolve slower than singletons despite the initial rate increase

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2004, BMC Evolutionary Biology.

Evolutionary history and higher order classification of AAA+ ATPases.

Detlef D. Leipe, Eugene V Koonin, E. Koonin, 2004, Journal of structural biology.

Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP‐ATPase nucleotide‐binding domains: implications for protein evolution in the RNA world

Eugene V Koonin, Vivek Anantharaman, E. Koonin, 2002, Proteins.

Comparative genomics and evolution of proteins involved in RNA metabolism.

Eugene V Koonin, Vivek Anantharaman, E. Koonin, 2002, Nucleic acids research.

Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors

Eugene V Koonin, Kira S Makarova, E. Koonin, 2009, Biology Direct.

Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis

Eugene V Koonin, Fyodor A Kondrashov, E. Koonin, 2006, BMC Cancer.

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

Eugene V Koonin, Yuri I Wolf, Kira S Makarova, 2011, Biology Direct.

'Conserved hypothetical' proteins: prioritization of targets for experimental study.

Michael Y. Galperin, Eugene V Koonin, Michael Y Galperin, 2004, Nucleic acids research.

The common ancestry of life

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2010, Biology Direct.

Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2004, BMC Evolutionary Biology.

Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens.

Eugene V Koonin, David M Kristensen, Ben Busby, 2013, Environmental microbiology.

Biology direct: celebrating 7 years of open, published peer review

Eugene V Koonin, David J Lipman, Laura F Landweber, 2013, Biology Direct.

Evolvability of an Optimal Recombination Rate

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2015, Genome biology and evolution.

Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.

Eugene V Koonin, E. Koonin, L. Aravind, 2006, Virus research.

Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity

Xu Peng, Eugene V Koonin, Fei He, 2018, Nature Microbiology.

No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2003, BMC Evolutionary Biology.

Origin and evolution of spliceosomal introns

Liran Carmel, Eugene V Koonin, Miklos Csuros, 2012, Biology Direct.

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2009, Biology Direct.

Co-evolution of primordial membranes and membrane proteins.

Michael Y. Galperin, Eugene V Koonin, Michael Y Galperin, 2009, Trends in biochemical sciences.

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

Eugene V Koonin, Yuri I Wolf, E. Koonin, 2008, Biology Direct.

Implications for proteasome nuclear localization revealed by the structure of the nuclear proteasome tether protein Cut8

Eugene V Koonin, Mitsuhiro Yanagida, E. Koonin, 2011, Proceedings of the National Academy of Sciences.

The basic building blocks and evolution of CRISPR-CAS systems.

Eugene V Koonin, Yuri I Wolf, Kira S Makarova, 2013, Biochemical Society transactions.

Diversity, classification and evolution of CRISPR-Cas systems.

Eugene V Koonin, Feng Zhang, Kira S Makarova, 2017, Current opinion in microbiology.

Predator Dormancy is a Stable Adaptive Strategy due to Parrondo's Paradox

Kang Hao Cheong, Jin Ming Koh, Eugene V Koonin, 2019, Advanced science.

An apology for orthologs - or brave new memes

Eugene V Koonin, E. Koonin, 2001, Genome Biology.

The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes

Eugene V Koonin, Kira S Makarova, E. Koonin, 2012, Biology Direct.

Complex selection on 5' splice sites in intron-rich organisms.

Eugene V Koonin, Josep F Abril, Manuel Irimia, 2009, Genome research.

On the origin of genomes and cells within inorganic compartments

Eugene V Koonin, E. Koonin, W. Martin, 2005, Trends in Genetics.

Classification and evolution of P-loop GTPases and related ATPases.

Detlef D. Leipe, Eugene V Koonin, Yuri I Wolf, 2002, Journal of molecular biology.

Comparative genomics and structural biology of the molecular innovations of eukaryotes.

Eugene V Koonin, E. Koonin, L. Aravind, 2006, Current opinion in structural biology.

New dimensions of the virus world discovered through metagenomics.

Eugene V Koonin, David M Kristensen, Valerian V Dolja, 2010, Trends in microbiology.

Annotation and Classification of CRISPR-Cas Systems.

Eugene V Koonin, Kira S Makarova, E. Koonin, 2015, Methods in molecular biology.

Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins

Eugene V Koonin, I King Jordan, Yuri I Wolf, 2001, Genome Biology.

Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis.

Eugene V Koonin, Kira S Makarova, E. Koonin, 2003, FEMS microbiology letters.

Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences.

Eugene V Koonin, Fyodor A Kondrashov, E. Koonin, 2003, Trends in genetics : TIG.

The relationship of protein conservation and sequence length

Alexander Souvorov, Eugene V Koonin, Anna R Panchenko, 2002, BMC Evolutionary Biology.

Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors

Eugene V Koonin, E. Koonin, L. Aravind, 2002, Genome Biology.

Hedgehog Patterning Activity: Role of a Lipophilic Modification Mediated by the Carboxy-Terminal Autoprocessing Domain

Eugene V Koonin, Philip A Beachy, Amina S Woods, 1996, Cell.

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection

Kunihiko Kaneko, Nobuto Takeuchi, Eugene V Koonin, 2015, BMC Biology.

Does the central dogma still stand?

Eugene V Koonin, E. Koonin, 2012, Biology Direct.

A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions.

Eugene V Koonin, G. Glazko, E. Koonin, 2003, Trends in genetics : TIG.